Applied Microbiology

Research

18 pages, 3198 KiB

Open AccessArticle

Moderate Phosphorus Addition to Field-Grown Bananas Enhanced Soil Microbial Enzyme Activities but Had Negligible Impacts on Bacterial, Fungal, and Nematode Diversity

by Anna-Belle C. Clarke, Hazel R. Lapis-Gaza, Stuart Irvine-Brown, Rebecca Lyons, Jiarui Sun, Anthony B. Pattison and Paul G. Dennis

Appl. Microbiol. 2024, 4(4), 1582-1599; https://doi.org/10.3390/applmicrobiol4040108 - 29 Nov 2024

Viewed by 340

Abstract

On commercial banana (Musa spp.) plantations, soils are often supplemented with phosphorus (P) fertiliser to optimise production. Such additions may influence the diversity and function of soil microbial communities, which play important roles in P cycling and affect plant fitness. Here, we [...] Read more.

On commercial banana (Musa spp.) plantations, soils are often supplemented with phosphorus (P) fertiliser to optimise production. Such additions may influence the diversity and function of soil microbial communities, which play important roles in P cycling and affect plant fitness. Here, we characterised the effects of P addition on the diversity and function of banana-associated microbial communities. P addition was associated with significant increases in soil P and the activities of alpha-glucosidase, chitinase, arylsulphatase, and acid phosphatase, but not beta-glucosidase or xylosidase. P addition also expedited bunch emergence and harvest, but did not influence fruit yield, plant height, or foliar P. There were no significant effects of P addition on the alpha or beta diversity of bacterial, fungal, and nematode communities, including members of the core microbiome. The only exceptions to this was an increase in the relative abundance of a Fusarium population in roots. These results indicate that phosphorus application to banana soils may stimulate microbial enzyme activities with minor or negligible effects on microbial diversity. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 467 KiB

Open AccessArticle

Molecular Typing of Somatic Coliphage Groups and Their Occurrence and Survival in Sewage

by Heesuk Lee, Jeremy Chemla, Thomas A. Randall, Emily S. Bailey and Mark D. Sobsey

Appl. Microbiol. 2024, 4(4), 1464-1475; https://doi.org/10.3390/applmicrobiol4040101 - 19 Oct 2024

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Abstract

A conventional, group-specific PCR method was developed to identify each of the four previously defined major taxa (Myoviridae, Siphoviridae, Podoviridae and Microviridae) of somatic coliphages and used to classify isolates from sewage. Somatic coliphage infectivity detection, occurrence and survival [...] Read more.

A conventional, group-specific PCR method was developed to identify each of the four previously defined major taxa (Myoviridae, Siphoviridae, Podoviridae and Microviridae) of somatic coliphages and used to classify isolates from sewage. Somatic coliphage infectivity detection, occurrence and survival in primary human sewage effluent was observed over time to further understand the presence and behavior of the groups of somatic coliphages at two environmental temperatures (4 and 25 °C). Over time, the taxonomic composition of the somatic coliphage population in sewage changed, with the Microviridae family becoming the most prevalent family in the sewage population after several weeks. Based on their persistence and prevalence in environmental waters, phages belonging to the Microviridae family provide supporting information on sewage contamination and possibly of human enteric viruses in sewage-contaminated water. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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11 pages, 2337 KiB

Open AccessArticle

Integration of Whole-Genome Sequencing with ddPCR Kit for Detection of Omicron Subvariants in Wastewater in the Upper Peninsula of Michigan

by Michelle M. Jarvie, Thu N. T. Nguyen, Benjamin Southwell and Derek Wright

Appl. Microbiol. 2024, 4(4), 1453-1463; https://doi.org/10.3390/applmicrobiol4040100 - 13 Oct 2024

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Abstract

This study explores the integration of genome sequencing and digital droplet polymerase chain reaction (ddPCR)-based methods for tracking the diversity of COVID-19 variants in wastewater. The research focuses on monitoring various Omicron subvariants during a period of significant viral evolution. Genome sequencing, particularly [...] Read more.

This study explores the integration of genome sequencing and digital droplet polymerase chain reaction (ddPCR)-based methods for tracking the diversity of COVID-19 variants in wastewater. The research focuses on monitoring various Omicron subvariants during a period of significant viral evolution. Genome sequencing, particularly using Oxford Nanopore Technology (ONT), provides a detailed view of emerging variants, surpassing the limitations of PCR-based detection kits that rely on known sequences. Of the 43 samples analyzed, 39.5% showed matching results between the GT Molecular ddPCR kits and sequencing, though only 4% were exact matches. Some mismatches occurred due to newer subvariants like XBB and BQ.1, which the ddPCR kits could not detect. This emphasized the limitations of ddPCR kits, which rely on known variant sequences, while sequencing provides real-time data on emerging variants, offering a more comprehensive view of circulating strains. This study highlights the effectiveness of combining these methodologies to enhance early detection and inform public health strategies, especially in regions with limited clinical sequencing capabilities. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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19 pages, 2313 KiB

Open AccessArticle

Recovery of Pasteurization-Resistant Vagococcus lutrae from Raw Seafoods Using a Two-Step Enrichment, Its Presumptive Prevalence, and Novel Classification Phenotypes

by Elizabeth F. Scruggs, Zaria Gulley, Guadalupe Steele, Mohammed Alahmadi, Asim Barnawi, Hussain Majrshi and Hung King Tiong

Appl. Microbiol. 2024, 4(4), 1434-1452; https://doi.org/10.3390/applmicrobiol4040099 - 4 Oct 2024

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Abstract

V. lutrae is an emerging human pathogen attributed to increasing hospitalization cases in humans; however, its biology and epidemiology are under-explored. The present study explored V. lutrae recovery, prevalence, and biology. A two-step enrichment method (i.e., step 1, nourishment; step 2, heat, 80 [...] Read more.

V. lutrae is an emerging human pathogen attributed to increasing hospitalization cases in humans; however, its biology and epidemiology are under-explored. The present study explored V. lutrae recovery, prevalence, and biology. A two-step enrichment method (i.e., step 1, nourishment; step 2, heat, 80 °C, 20 min) and thiosulfate–citrate–bile salts–sucrose (TCBS) agar were employed for recovering V. lutrae in raw seafood. Bacterial colonies were streaked for purification before 16S rRNA bacterial identification. Confirmed V. lutrae isolates were analyzed for their culture-challenged turbidity and virulence. Of 41 bacterial isolates, 9 confirmed V. lutrae, including regular (33%; nourished 24 h) and heat-resistant (67%; nourished 48 h plus heating) isolates, were exclusively from yellow colonies (i.e., TCBS) and were exclusively recovered from nourished shrimp (78%) and crab (22%) only. The culture and virulence biology revealed that they could diversely tolerate salinity (i.e., 0–17.5% additional NaCl), pasteurization (63 °C, 8 h), oxygen availability, and antibiotic sensitivity (i.e., erythromycin, gentamicin, and vancomycin). Further, this pathogen exhibited no visible hemolytic and alkalization activities. Emerging foodborne pathogens could readily evade the established food safety regime. The present study reveals systematic investigation and diverse phenotypes of V. lutrae to enhance its detection and contribute to public health initiatives. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 2494 KiB

Open AccessArticle

Investigation of SARS-CoV-2 Contamination of Indoor Air and Highly Touched Surfaces On-Campus Buildings

by Nita Khanal, Lauren Roppolo Brazell, Md Ariful Islam Juel, Cynthia Gibas, Jessica Schlueter and Mariya Munir

Appl. Microbiol. 2024, 4(3), 1384-1395; https://doi.org/10.3390/applmicrobiol4030095 - 22 Sep 2024

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Abstract

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spreads primarily through respiratory droplets, aerosols, and contaminated surfaces. While high-traffic locations like hospitals and airports have been studied extensively, detecting significant virus levels in aerosols and on environmental surfaces, campus settings remain underexplored. This study focused [...] Read more.

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spreads primarily through respiratory droplets, aerosols, and contaminated surfaces. While high-traffic locations like hospitals and airports have been studied extensively, detecting significant virus levels in aerosols and on environmental surfaces, campus settings remain underexplored. This study focused on two crowded buildings at the University of North Carolina at Charlotte (UNCC). From December 2021 to March 2022, we collected 16 indoor air samples and 201 samples from high-touch surfaces. During the sampling timeframe, 44.82% of surface samples from the Student Union and 28% from the University Recreational Center (UREC) tested positive for the presence of SARS-CoV-2 RNA. Median and average viral RNA copies per swab were higher in UREC (273 and 475) than in Student Union (92 and 269). However, all air samples tested negative. Surface positivity in these high-traffic campus locations was directly correlated with COVID-19 clinical cases in Mecklenburg County. The campus COVID-19 cases, driven by the Omicron wave, peaked a week before the peak detection of surface contamination. These findings underscore the importance of surface hygiene measures and highlight environmental conditions as potential contributors to COVID-19 spread on campuses. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 2027 KiB

Open AccessArticle

Escherichia coli Reporter Strains Allow for the In Vivo Evaluation of Recombinant Elongation Factor Protein (EF-P)

by Natalia Trachtmann, Aydar Bikmullin, Shamil Validov and Georg A. Sprenger

Appl. Microbiol. 2024, 4(3), 1335-1347; https://doi.org/10.3390/applmicrobiol4030092 - 18 Sep 2024

Viewed by 653

Abstract

Background: Elongation factor protein (EF-P) in bacteria helps ribosomes to incorporate contiguous proline residues (xPro) into proteins. In this way, EF-P rescues ribosomes from stalling at these xPro motifs. Whereas EF-P deficiency is lethal for some species, others show reduced virulence or generally [...] Read more.

Background: Elongation factor protein (EF-P) in bacteria helps ribosomes to incorporate contiguous proline residues (xPro) into proteins. In this way, EF-P rescues ribosomes from stalling at these xPro motifs. Whereas EF-P deficiency is lethal for some species, others show reduced virulence or generally lower growth rates, such as Escherichia coli (E. coli). EF-P needs to be post-translationally modified to gain full functionality. Methods: We constructed E. coli K-12 mutant strains with deletion of the serA gene leading to an auxotrophy for L-serine. Then, we engineered a 6xPro motif in the recombinant serA gene, which was then chromosomally inserted under its native promoter. Furthermore, mutant strains which were deleted for efp and/or epmA (encoding the EF-P modification protein EpmA) were engineered. Results: Δefp, ΔepmA, and Δefp/ΔepmA double mutants showed already significantly reduced growth rates in minimal media. ΔserA derivatives of these strains were complemented by the wt serA gene but not by 6xPro-serA. ΔserA mutants with intact efp were complemented by all serA-constructs. Chromosomal expression of the recombinant efp gene from E. coli or from the pathogen, Staphylococcus aureus (S. aureus), restored growth, even without epmA expression. Conclusions: We provide a novel synthetic reporter system for in vivo evaluation of EF-P deficiency. In addition, we demonstrated that both EF-P-E. coli and EF-P-S. aureus restored the growth of a 6xPro-serA: Δefp, ΔepmA strain, which is evidence that modification of EF-P might be dispensable for rescuing of ribosomes stalled during translation of proline repeats. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 2922 KiB

Open AccessArticle

Specific Synbiotic Sugars Stimulate Streptococcus salivarius BLIS K12 and BLIS M18 Lantibiotic Production to Expand Bacterial Inhibition Range and Potency

by Liam K. Harold, Nicola C. Jones, Sarah L. Barber, Abigail L. Voss, Rohit Jain, John R. Tagg and John D. F. Hale

Appl. Microbiol. 2024, 4(3), 1320-1334; https://doi.org/10.3390/applmicrobiol4030091 - 16 Sep 2024

Viewed by 925

Abstract

Synbiotics are mixtures of prebiotics and probiotics that enhance the activity of probiotic bacteria when co-administered to provide greater benefits to the host. Traditionally, the synbiotics that have been discovered enhance gut probiotic strains and are nutritionally complex molecules that survive digestive breakdown [...] Read more.

Synbiotics are mixtures of prebiotics and probiotics that enhance the activity of probiotic bacteria when co-administered to provide greater benefits to the host. Traditionally, the synbiotics that have been discovered enhance gut probiotic strains and are nutritionally complex molecules that survive digestive breakdown until they reach the later stages of the intestinal tract. Here, we screened and identified sugars or sugar substitutes as synbiotics for the oral probiotic strains Streptococcus salivarius BLIS K12 and BLIS M18. Using a modified deferred antagonism assay, we found that 0.5% (w/v) galactose and 2.5% (w/v) raffinose were the best candidates for use as synbiotics with BLIS K12 and M18, as they trigger enhanced antimicrobial activity against a range of bacteria representing species from the mouth, gut, and skin. Using reverse transcriptase quantitative PCR, we found that this enhanced antimicrobial activity was caused by the upregulation of the lantibiotic genes salA, salB, and sal9 in either K12 or M18. This led to the conclusion that either 2.5% (w/v) raffinose or 0.5% (w/v) galactose, respectively, are suitable synbiotics for use in conjunction with BLIS K12 and M18 to enhance probiotic performance. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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10 pages, 1461 KiB

Open AccessArticle

Inter-Species Competition of Mono- or Dual Species Biofilms- of MDR-Staphylococcus aureus and Pseudomonas aeruginosa Promotes the Killing Efficacy of Phage or Phage Cocktail

by Pallavali RojaRani, Guda Dinneswara Reddy, Degati Vijayalakshmi, Durbaka Vijaya Raghava Prasad and Jeong Dong Choi

Appl. Microbiol. 2024, 4(3), 1247-1256; https://doi.org/10.3390/applmicrobiol4030085 - 20 Aug 2024

Viewed by 1049

Abstract

Pseudomonas aeruginosa and Staphylococcus aureus are opportunistic bacteria frequently linked to burn wound infections. These bacteria can grow as biofilms, which increases their level of drug resistance to current antibiotics. The purpose of the present study is to analyze the effect of biofilm [...] Read more.

Pseudomonas aeruginosa and Staphylococcus aureus are opportunistic bacteria frequently linked to burn wound infections. These bacteria can grow as biofilms, which increases their level of drug resistance to current antibiotics. The purpose of the present study is to analyze the effect of biofilm formation, phage and phage cocktail action on single species and dual species biofilms I, e the coexistence of Gram positive (S. aureus) and Gram negative (P. aeruginosa). To this scenario, we employed multi-drug resistant bacteria (P. aeruginosa and S. aureus at 10⁹ CFU/µL) biofilm as single and in combination of both Gram-positive and Gram-negative bacterial biofilms of 24 h grown with respective phage (10⁹ PFU/µL) and phage cocktail (10⁹ PFU/µL) at 4 h of incubation under static conditions. The bacteriolytic activity of phages vB_SAnS_SADP1 and vB_PAnP_PADP4 on 24-h-old biofilms of P. aeruginosa (0.761 ± 0.031) and S. aureus (0.856 ± 0.055), both alone and in combination (0.67 ± 0.02), was the focus of this investigation. The structural organization of biofilms in single- or dual-species combinations under in vitro conditions was validated by scanning and confocal laser scanning microscopy investigations. After 24 h of incubation, single-species biofilms are denser and more resilient whereas dual species biofilms are more loosely associated. Loose association of dual-species biofilm under scanning electron microscopic images at the same conditions, indicated the interspecies -competition of the Gram-positive and Gram-negative bacteria and dual-species biofilms (0.67 ± 0.02) have weak associations and are readily impacted by phage and a phage cocktail (0.16 ± 0.02). Dual-species biofilms were more readily impacted in in vitro settings. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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16 pages, 1614 KiB

Open AccessArticle

Phosphate Solubilization and Plant Growth Promotion by Enterobacter sp. Isolate

by Jean Louise Cocson Damo, Mannix Pedro and Maria Lourdes Sison

Appl. Microbiol. 2024, 4(3), 1177-1192; https://doi.org/10.3390/applmicrobiol4030080 - 31 Jul 2024

Viewed by 1137

Abstract

Phosphorus (P) solubilization is one of the major traits for plant growth-promoting rhizobacteria since P is easily rendered insoluble in soil. Phosphate-solubilizing microorganisms can be harnessed as an environment-friendly strategy to enhance the mobilization and acquisition of P by crops. Utilization of such [...] Read more.

Phosphorus (P) solubilization is one of the major traits for plant growth-promoting rhizobacteria since P is easily rendered insoluble in soil. Phosphate-solubilizing microorganisms can be harnessed as an environment-friendly strategy to enhance the mobilization and acquisition of P by crops. Utilization of such microorganisms as microbial inoculants in agriculture serves as an alternative to chemical fertilizers and an approach for more efficient P fertilization. Hence, this study aims to characterize a phosphate-solubilizing isolate and evaluate its potential as a microbial inoculant. Morphological, biochemical, and genetic characterization of the isolate were performed. Then, the mineral phosphate solubilization ability of the isolate was evaluated. Lastly, this study evaluated the plant growth promotion of the isolate as a single inoculant in rice or as a co-inoculant with rhizobia in peanuts. On the basis of biochemical and 16S rRNA analysis, the isolate was identified as Enterobacter sp. Also, it can solubilize P from tricalcium phosphate or aluminum phosphate. Simultaneous with P solubilization, medium acidification, and gluconic acid secretion were observed. Lastly, the Enterobacter sp. isolate could potentially be developed as a biofertilizer in reducing P resource input or to enhance the performance of a rhizobia inoculant. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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16 pages, 2541 KiB

Open AccessArticle

Metatranscriptomic Analysis of Argentinian Kefirs Varying in Apparent Viscosity

by Diego Lisboa Rios, Ana Agustina Bengoa, Patrícia Costa Lima da Silva, César Silva Santana Moura, Graciela Liliana Garrote, Analía Graciela Abraham, Gabriel da Rocha Fernandes, Jacques Robert Nicoli, Elisabeth Neumann and Álvaro Cantini Nunes

Appl. Microbiol. 2024, 4(3), 1150-1164; https://doi.org/10.3390/applmicrobiol4030078 - 24 Jul 2024

Viewed by 825

Abstract

Comparative metatranscriptomics of the bacterial and yeast communities of two milk kefir beverages (MKAA1 and MKAA2) was carried out. They were obtained by fermentation with two different frozen stocks of the kefir grain CIDCA AGK1, differing in rheological features and production of organic [...] Read more.

Comparative metatranscriptomics of the bacterial and yeast communities of two milk kefir beverages (MKAA1 and MKAA2) was carried out. They were obtained by fermentation with two different frozen stocks of the kefir grain CIDCA AGK1, differing in rheological features and production of organic acids. We hypothesised that the differences in their physicochemical and rheological properties might be due to the microbial activity in each product. The dominance of lactic acid bacteria, yeast, and a marginal amount of acetic acid bacteria characterised the microbiome. The bacterial families Lactobacillaceae and Streptococcaceae accounted for almost all of the bacterial gene transcripts, with Lactobacillus helveticus, L. kefiranofaciens, L. gallinarum, and Lactococcus lactis being most frequent in the microbiome of the MKAA1 beverage and L. kefiranofaciens, Lc. Lactis, and Leuconostoc mesenteroides being the most prevalent in MKAA2. Dipodascaceae and Saccharomycetaceae were the leading yeast families, represented by Yarrowia lipolytica, Saccharomyces unisporus, and Kluyveromyces marxianus. MKAA1 and MKAA2 shared >75% KEGG Ortologs (KOs) in their bacteria and yeast libraries. The considerable decreases in total expressed genes (KEGG Ortologs) assigned to Lactobacillus helveticus and L. gallinarum might be related to the variations in the rheological features of the beverages, probably by compromising the interrelations with L. kefiranofaciens, which might explain the variations in the rheological features of the beverages. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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8 pages, 493 KiB

Open AccessArticle

Genomic Characterization of Selected Escherichia coli Strains from Catfish (Clarias gariepinus) in Nigeria

by Chibuzo Linda Ekwuazi, Frank C. Ogbo, Anna Stöger, Werner Ruppitsch and Adriana Cabal Rosel

Appl. Microbiol. 2024, 4(3), 1142-1149; https://doi.org/10.3390/applmicrobiol4030077 - 24 Jul 2024

Viewed by 819

Abstract

According to a report by the World Health Organization (WHO), each year, over 550 million individuals worldwide suffer from and 230,000 die from diarrheal illnesses, which accounts for more than half of the global foodborne disease burden. Among them, children face a heightened [...] Read more.

According to a report by the World Health Organization (WHO), each year, over 550 million individuals worldwide suffer from and 230,000 die from diarrheal illnesses, which accounts for more than half of the global foodborne disease burden. Among them, children face a heightened vulnerability, with approximately 220 million falling ill and 96,000 succumbing to these diseases annually. This work aimed to study the genomic characterization of selected E. coli strains from catfish (Clarias (C.) gariepinus) caught from the Onitsha North axis of the River Niger in Anambra state, Nigeria. A total of 50 fish were randomly purchased from different fishermen over a period of four months. Samples that comprised six different organs (skin, flesh, gills, gonads, guts, and liver) were screened for E. coli strains using cultural and biochemical methods. Multilocus sequence typing (MLST) and core genome (cg)MLST were performed using Ridom SeqSphere+ software. The aerobic plate count (APC) and coliform count ranged from 0.5 × 10⁴ to 3.7 × 10⁴ cfu/g and 0 to 3.0 × 10⁴ cfu/g, respectively. Whole-genome sequencing (WGS) confirmed the presence of E. coli and Klebsiella quasipneumoniae isolates in our samples. We could identify only two serotypes (O102:H7 and O40:H4) of E. coli. Antimicrobial resistance genes (ARGs) and point mutations that conferred antibiotic resistance were extracted from the genome assemblies. Good hygiene is recommended to avoid the cross-contamination of raw C. gariepinus with ready-to-eat food. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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19 pages, 3225 KiB

Open AccessArticle

Assessing the Microbial Impact on the Performance of Bentonite Clay at Different Thermo-Hydro-Geochemical Conditions

by Julia Mitzscherling, Anja M. Schleicher, Steffi Genderjahn, Marie Bonitz and Dirk Wagner

Appl. Microbiol. 2024, 4(3), 1091-1109; https://doi.org/10.3390/applmicrobiol4030074 - 20 Jul 2024

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Abstract

Because of its swelling capacity, compacted bentonite clay is a suitable buffer material in deep geological repositories for high-level nuclear waste. However, this only applies if the swelling capacity is maintained. Accordingly, bentonites have to be stable to changing temperature, humidity, infiltrating fluids [...] Read more.

Because of its swelling capacity, compacted bentonite clay is a suitable buffer material in deep geological repositories for high-level nuclear waste. However, this only applies if the swelling capacity is maintained. Accordingly, bentonites have to be stable to changing temperature, humidity, infiltrating fluids or microbial activity. In batch experiments, we investigated combined microbial and thermo-hydro-geochemical effects on the swelling capacity of uncompacted bentonite MX-80. Bentonite was exposed to fluids of different ionic strength and the bacterium Stenotrophomonas bentonitica. Bacterial growth was monitored by counting colony-forming units while the swelling capacity of bentonite was evaluated using in situ XRD at varied temperatures and humidity. The presence of bentonite prolonged the survival of S. bentonitica. However, electron microscopy, XRD and ICP-OES analyses showed neither an interaction of S. bentonitica with bentonite, nor significant changes in the swelling capacity or element composition. The swelling capacity and diffraction peak intensity were, however, strongly reduced by the ionic strength of the fluid and the exposure time. The study highlights that bentonite is affected by thermo-hydro-geochemical and microbial processes to different degrees and that the complexity of different co-occurring factors in potential nuclear waste repositories is important to consider in safety assessments. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 1955 KiB

Open AccessArticle

The Development of Novel Edible Films from Single-Cell Protein Produced by the Biotechnological Valorization of Cheese Whey

by Danai Ioanna Koukoumaki, Seraphim Papanikolaou, Zacharias Ioannou, Konstantinos Gkatzionis and Dimitris Sarris

Appl. Microbiol. 2024, 4(3), 1030-1041; https://doi.org/10.3390/applmicrobiol4030070 - 3 Jul 2024

Cited by 1 | Viewed by 1798

Abstract

The production of value-added products from microorganisms, such as single-cell protein (SCP), through the valorization of agricultural byproducts enhances circular economy while offering alternative solutions for waste treatment. In this study, SCP was obtained through the biotechnological treatment and valorization of cheese whey, [...] Read more.

The production of value-added products from microorganisms, such as single-cell protein (SCP), through the valorization of agricultural byproducts enhances circular economy while offering alternative solutions for waste treatment. In this study, SCP was obtained through the biotechnological treatment and valorization of cheese whey, the main byproduct of the dairy industry, for the development of novel edible films. To the best of the authors’ knowledge, this is the first report examining SCP as a biopolymer for edible film production. Specifically, Kluyveromyces marxianus, which has gained QPS and GRAS status, strain EXF-5288 cultivated in deproteinized cheese whey (DCW) lactose (10.0 g/L) in a 3 L fed-batch bioreactor, resulting in a SCP_max of 2.63 g/L with a protein content of up to 49.1% w/w. The addition of increased glycerol concentrations (30, 40, and 50% w/w of dry cells) as plasticizers was examined to develop SCP-based edible films. Regarding physicochemical characterization, increased glycerol concentration significantly increased moisture content (MC%) and solubility (S%), but there was not a significant difference in other parameters. Regarding wettability, SCP-based films could be described as oleophilic surfaces since the degree of oil contact angle (OCA) ranged between 46.7° ± 1.3 and 54.0° ± 0.5. The proposed holistic approach could contribute to the development of sustainable packaging materials through waste treatment. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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14 pages, 3154 KiB

Open AccessArticle

Evaluation of qPCR for the Selective Detection of Enteric Adenovirus Followed by Sequence-Based Genetic Characterization of F Strains Circulating in Brazil

by Lilian Gonçalves do Nascimento, Sylvia Kahwage Sarmento, Reinaldo Röpke Junior and Tulio Machado Fumian

Appl. Microbiol. 2024, 4(3), 1016-1029; https://doi.org/10.3390/applmicrobiol4030069 - 27 Jun 2024

Viewed by 848

Abstract

Human adenovirus (HAdV) F40/41 is an important pathogen in pediatric acute gastroenteritis cases. However, the diversity of study designs and diagnostic methods often leads to misinterpretations of their impact. Our study explored the genetic diversity of HAdV-F40/41 in Brazil using a specific qPCR [...] Read more.

Human adenovirus (HAdV) F40/41 is an important pathogen in pediatric acute gastroenteritis cases. However, the diversity of study designs and diagnostic methods often leads to misinterpretations of their impact. Our study explored the genetic diversity of HAdV-F40/41 in Brazil using a specific qPCR assay for HAdV species F, combined with a phylogenetic analysis of the partial hexon and fiber genes. Our results demonstrated that HAdV-F41 strains predominated and exhibited higher diversity than HAdV-F40 strains. Based on the hexon gene, Brazilian HAdV-F41 strains were grouped into two genome type clusters (GTC), further divided into subclusters, with most strains clusteringto GTC2. The partial shaft region of the fiber gene exhibited higher conservation among HAdV-F41. The specific qPCR assay for HAdV species F identified HAdV-F in an additional 31.5% (34/108) of previously uncharacterized HAdV-positive samples detected using a non-specific HAdV qPCR assay. Both assays strongly correlated in detecting HAdV-F, and the specific qPCR assay for enteric types can enhance HAdV surveillance, especially when sequencing is not possible. Our study provides novel insights regarding the genetic diversity of HAdV-F species in Brazil. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 1679 KiB

Open AccessArticle

Valorisation of Spent Yeast Fermentation Media through Compositional-Analysis-Directed Supplementation

by Laura Murphy, Ciara D. Lynch and David J. O’Connell

Appl. Microbiol. 2024, 4(2), 959-971; https://doi.org/10.3390/applmicrobiol4020065 - 12 Jun 2024

Cited by 1 | Viewed by 1481

Abstract

Spent fermentation media from bioprocessing represent a significant waste stream, and interest in recycling them as part of the developing circular bioeconomy is growing. The potential to reuse yeast spent culture media (YSM) to feed secondary bacterial fermentations producing recombinant protein was investigated [...] Read more.

Spent fermentation media from bioprocessing represent a significant waste stream, and interest in recycling them as part of the developing circular bioeconomy is growing. The potential to reuse yeast spent culture media (YSM) to feed secondary bacterial fermentations producing recombinant protein was investigated in this study. Elemental and amino acid compositional analysis using inductively coupled plasma mass spectrometry (ICP-MS) and LC-MS/MS identified significant differences in the concentrations of 6 elements and 18/20 amino acids in YSM compared with rich microbiological media (LB). Restoration of levels of magnesium and sodium through addition of their salts and amino acids from tryptone supplementation led to the expression of equivalent titres of recombinant proteins by E. coli (0.275 g/L), compared to that in LB media (0.296 g/L) and BMMY media (0.294 g/L) in shake flask culture. When this supplementation strategy was employed in a bioreactor system, we observed a significant increase in recombinant protein titre using the supplemented YSM (2.29 (±0.02) g/L) over that produced using LB media (1.29 (±0.09) g/L). This study demonstrates through highly sensitive compositional analysis and identification of supplementation strategies the potential to valorise spent media from yeast fermentations that underpin industrial processes of significant scale, creating a circular approach to waste stream management. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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19 pages, 1725 KiB

Open AccessArticle

Trichoderma: Population Structure and Genetic Diversity of Species with High Potential for Biocontrol and Biofertilizer Applications

by Adnan Ismaiel, Dilip K. Lakshman, Prashant P. Jambhulkar and Daniel P. Roberts

Appl. Microbiol. 2024, 4(2), 875-893; https://doi.org/10.3390/applmicrobiol4020060 - 27 May 2024

Viewed by 1233

Abstract

Certain Trichoderma isolates provide biofertilizer, biocontrol, and other plant-beneficial activities while inhabiting the soil or internal plant tissue, and their use in agricultural systems can contribute to sustainable food production. It is thought that colonization of soil or internal plant tissue is fundamental [...] Read more.

Certain Trichoderma isolates provide biofertilizer, biocontrol, and other plant-beneficial activities while inhabiting the soil or internal plant tissue, and their use in agricultural systems can contribute to sustainable food production. It is thought that colonization of soil or internal plant tissue is fundamental for biocontrol and biofertilizer applications. Our collective analyses of prior surveys, where the tef1α sequence was almost exclusively used to identify Trichoderma species, showed that isolates from the Harzianum complex clade, the T. asperellum/T. asperelloides group, T. virens, T. hamatum, and T. atroviride were prevalent in soil and/or as endophytes. Population structure and genetic diversity based on the genetic markers tef1α, rpb2, and ITS were investigated, and new lineages with statistical bootstrap support within T. atroviride, T. asperellum, T. hamatum, and T. virens populations were found. The nearest relatives of some of these species were also revealed. Choosing isolates from among more than 500 known Trichoderma species for use in non-targeted evaluation screens for biocontrol or biofertilizer applications is time-consuming and expensive. Preferentially selecting isolates from T. atroviride, T. asperellum/T. asperelloides, T. hamatum, the T. harzianum complex clade, T. virens, and possibly nearest relatives may speed the identification of candidates for commercialization due to the demonstrated ability of these species to successfully inhabit the soil and internal plant tissue. To our knowledge, this is the first report where dominant soil and endophytic Trichoderma species were identified from past survey data and population structure and genetic diversity analyses conducted. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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17 pages, 4080 KiB

Open AccessArticle

TRI14 Is Critical for Fusarium graminearum Infection and Spread in Wheat

by Guixia Hao, Robert H. Proctor, Daren W. Brown, Nicholas A. Rhoades, Todd A. Naumann, HyeSeon Kim, Santiago Gutiėrrez and Susan P. McCormick

Appl. Microbiol. 2024, 4(2), 839-855; https://doi.org/10.3390/applmicrobiol4020058 - 23 May 2024

Cited by 1 | Viewed by 1559

Abstract

Trichothecenes are sesquiterpenoid toxins produced by diverse ascomycetes, including Fusarium. The trichothecene analog deoxynivalenol (DON) produced by the Fusarium head blight (FHB) pathogen Fusarium graminearum is a virulence factor on wheat and a major food and feed safety concern. In Fusarium, [...] Read more.

Trichothecenes are sesquiterpenoid toxins produced by diverse ascomycetes, including Fusarium. The trichothecene analog deoxynivalenol (DON) produced by the Fusarium head blight (FHB) pathogen Fusarium graminearum is a virulence factor on wheat and a major food and feed safety concern. In Fusarium, the trichothecene biosynthetic gene (TRI) cluster consists of 7–14 genes. Most TRI cluster genes are conserved and their specific roles in trichothecene biosynthesis have been determined. An exception is TRI14, which is not required for DON synthesis in vitro but is required for spread of F. graminearum in wheat heads. In the current study, gene expression analyses revealed that TRI14 was highly induced in infected wheat heads. We demonstrated that TRI14 was not only required for F. graminearum spread but also important for initial infection in wheat. Although a prior study did not detect DON in infected seeds, our analyses showed significantly less DON and fungal biomass in TRI14-mutant (designated ∆tri14)-inoculated heads than wild-type-inoculated heads. Gene expression comparison showed that the level of expression of TRI genes was similar in the wheat tissues infected with ∆tri14 or the wild type, indicating the reduced toxin levels caused by ∆tri14 may be due to less fungal growth. ∆tri14 also caused less lesion and grew less in wheat coleoptiles than the wild type. The growth of ∆tri14 in carboxymethylcellulose medium was more sensitive to hydrogen peroxide than the wild type. The data suggest that TRI14 plays a critical role in F. graminearum growth, and potentially protects the fungus from plant defense compounds. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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8 pages, 608 KiB

Open AccessArticle

A Sublethal Concentration of Chlorine Induces Antibiotic Resistance in Salmonella via Production of Reactive Oxygen Species

by Mohammed Aljuwayd, Israa Abdullah Malli, Steven C. Ricke and Young Min Kwon

Appl. Microbiol. 2024, 4(2), 745-752; https://doi.org/10.3390/applmicrobiol4020051 - 30 Apr 2024

Viewed by 1215

Abstract

Studies have shown that the production of reactive oxygen species (ROS) is triggered by bactericidal antibiotics, which contributes significantly to the killing of bacterial cells and increasing mutations in surviving cells. In this study, we hypothesized that exposure of Salmonella to sublethal concentrations [...] Read more.

Studies have shown that the production of reactive oxygen species (ROS) is triggered by bactericidal antibiotics, which contributes significantly to the killing of bacterial cells and increasing mutations in surviving cells. In this study, we hypothesized that exposure of Salmonella to sublethal concentrations of hypochlorite (NaOCl), a commonly used sanitizer in household and food industries increases mutation rates, leading to the development of antibiotic resistance. We found that a sublethal concentration (20 ppm) of NaOCl increased the mutation rates of S. typhimurium 14028s significantly (p < 0.05), which was prevented by the ROS scavenger thiourea, supporting that the increased mutation was due to NaOCl-triggered ROS production. We further found that the exposure of S. typhimurium 14028s to the same sublethal concentration of NaOCl increases resistance to kanamycin among the 3 antibiotics evaluated. The results of this study suggest that when NaOCl applied as a sanitizer fails to kill Salmonella due to diluted local concentrations or presence of organic materials, it can cause an adverse outcome of developing antibiotic resistance of the pathogen. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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22 pages, 4109 KiB

Open AccessArticle

Diversity of Microbial Communities in Trade Wastes—Implications for Treatments and Operations

by Jake A. K. Elliott, Christian Krohn and Andrew S. Ball

Appl. Microbiol. 2024, 4(2), 682-703; https://doi.org/10.3390/applmicrobiol4020047 - 19 Apr 2024

Viewed by 1752

Abstract

Industrial wastewaters display a complex and diverse range of physicochemical properties that are measured, studied, and treated by businesses and water service providers. Less frequently measured are the microbial communities in these wastes, despite possible implications for health, equipment maintenance, and the environment. [...] Read more.

Industrial wastewaters display a complex and diverse range of physicochemical properties that are measured, studied, and treated by businesses and water service providers. Less frequently measured are the microbial communities in these wastes, despite possible implications for health, equipment maintenance, and the environment. This study aimed to assess the microbial communities of eighteen raw and discharge-ready wastewaters across eleven industrial sites to compare the microbial compositions of these wastewaters across different industry sectors, on-site treatment levels, and other wastewater components. The potential for variance in the biomethane yield, depending on microbial communities, was also measured. Using targeted sequencing, a unique taxonomy was identified, including genera linked to animals (Acetitomaculum, Lactobacillus, NK4A214, Prevotella, and Shuttleworthia), cooling water (Bosea, Legionella, Methyloversatilis, and Reyranella), and extreme conditions (Alkalibacillus, Geobacillus, Halorubrum, and Pyrobaculum). However, the compositions of the microbial communities were not found to be directly correlated to industry sector or on-site treatment levels, nor were they found to have a direct effect on the biomethane potential. However, the presence of certain individual taxa is linked to the methane yield and treatment status and may be explained in the context of physicochemical properties while serving as potential markers for identifying, improving, or developing on-site processes. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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17 pages, 2631 KiB

Open AccessArticle

Bioprospection of Bacterial Strains from Chromite Process Industry Residues from Mexico for Potential Remediation

by Paola Abigail Martínez-Aldape, Mario Enrique Sandoval-Vergara, Reyna Edith Padilla-Hernández, César Augusto Caretta, Julio César Valerdi-Negreros, Pablo Casanova, Magna Maria Monteiro, Claire Gassie, Marisol Goñi-Urriza, Elcia Margareth Souza Brito and Remy Guyoneaud

Appl. Microbiol. 2024, 4(2), 665-681; https://doi.org/10.3390/applmicrobiol4020046 - 18 Apr 2024

Viewed by 1322

Abstract

Industrial residues with high concentrations of hexavalent chromium [Cr(VI)], characterized by an alkaline pH (between 9 and 13) and high salinity (around 100 psu), were used as a source for extremophilic chromium-resistant and -reducing microorganisms. An investigation of biodiversity through MiSeq showed the [...] Read more.

Industrial residues with high concentrations of hexavalent chromium [Cr(VI)], characterized by an alkaline pH (between 9 and 13) and high salinity (around 100 psu), were used as a source for extremophilic chromium-resistant and -reducing microorganisms. An investigation of biodiversity through MiSeq showed the presence of 20 bacterial classes, with Bacilli (47%), Negativicutes (15%), Bacteriodia (8%), Gammaproteobacteria (7%) and Clostridia (5%) being the most abundant. The bioprospection allowed the cultivation of 87 heterotrophic bacterial colonies and 17 bacterial isolates at the end of the isolation, and screening procedures were obtained. The isolates were related to Cellulosimicrobium aquatile, C. funkei, Acinetobacter radioresistens, Staphylococcus equorum, S. epidermis, Brachybacterium paraconglometratum, Glutamicibacter creatinolyticus, Pseudomonas songnenensis, Microbacterium algeriense and Pantoea eucalypti, most of them being resistant to Cr(VI). Resistances of up to 400

{m g . L}^{- 1}

of chromate were obtained for four related strains (QReMLB55A, QRePRA55, QReMLB33A and QReMLB44C). The C. aquatile strain QReMLB55A and the P. songnenensis strain QReMLB33A were exposed to

K_{2} {C r}_{2} O_{7}

(200

{m g . L}^{- 1}

) under optimal conditions, diminishing 94% and 24% of the Cr(VI) in 6 days, respectively. These strains exhibited a high potential for chromium remediation biotechnologies. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 1066 KiB

Open AccessArticle

Molecular Characterization of the Gorgonzola Cheese Mycobiota and Selection of a Putative Probiotic Saccharomyces cerevisiae var. boulardii for Evaluation as a Veterinary Feed Additive

by Samuele Voyron, Francesca Bietto, Mauro Fontana, Elisa Martello, Natascia Bruni and Enrica Pessione

Appl. Microbiol. 2024, 4(2), 650-664; https://doi.org/10.3390/applmicrobiol4020045 - 3 Apr 2024

Viewed by 1400

Abstract

Gorgonzola is an Italian “erborinato” blue cheese from cow’s milk, bearing blue-green “parsley-like” spots due to the spread of Penicillium roqueforti mycelium. Due to its pH, water activity, and high nutrient content, as well as the environmental conditions required for its maturation, Gorgonzola [...] Read more.

Gorgonzola is an Italian “erborinato” blue cheese from cow’s milk, bearing blue-green “parsley-like” spots due to the spread of Penicillium roqueforti mycelium. Due to its pH, water activity, and high nutrient content, as well as the environmental conditions required for its maturation, Gorgonzola constitutes an optimal ecological niche supporting the growth of both yeasts and filamentous fungi. Therefore, exploring the abundant mycobiota present in this peculiar habitat is of great interest regarding the search for new probiotic strains. The present investigation aimed to characterize the Gorgonzola mycobiota using both phenotypic (macroscopic and microscopic morphological analyses) and genotypic (DNA barcoding) analyses to find possible putative probiotic strains to be used in veterinary medicine in feed supplements. Among the different isolated filamentous fungi (Mucor and Penicillium) and yeasts (Yarrowia, Debaryomyces, Saccharomyces, and Sporobolomyces), we selected a strain of Saccharomyces cerevisiae var. boulardii. We tested its adaptation to thermal stress and its stability in feed matrices. The overall results highlight that the selected strain is stable for three months and can be considered as a possible candidate for use as a probiotic in veterinary feed supplements. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 2891 KiB

Open AccessArticle

Longitudinal Sequencing and Variant Detection of SARS-CoV-2 across Southern California Wastewater

by Jason A. Rothman, Andrew Saghir, Amity G. Zimmer-Faust, Kylie Langlois, Kayla Raygoza, Joshua A. Steele, John F. Griffith and Katrine L. Whiteson

Appl. Microbiol. 2024, 4(2), 635-649; https://doi.org/10.3390/applmicrobiol4020044 - 29 Mar 2024

Cited by 1 | Viewed by 1387

Abstract

Wastewater-based epidemiology (WBE) is useful for detecting pathogen prevalence and may serve to effectively monitor diseases across broad scales. WBE has been used throughout the COVID-19 pandemic to track disease burden through quantifying SARS-CoV-2 RNA present in wastewater. Aside from case load estimation, [...] Read more.

Wastewater-based epidemiology (WBE) is useful for detecting pathogen prevalence and may serve to effectively monitor diseases across broad scales. WBE has been used throughout the COVID-19 pandemic to track disease burden through quantifying SARS-CoV-2 RNA present in wastewater. Aside from case load estimation, WBE is being used to assay viral genomic diversity and emerging potential SARS-CoV-2 variants. Here, we present a study in which we sequenced RNA extracted from sewage influent obtained from eight wastewater treatment plants representing 16 million people in Southern California from April 2020 to August 2021. We sequenced SARS-CoV-2 with two methods: Illumina Respiratory Virus-Enriched metatranscriptomic sequencing (N = 269), and QIAseq SARS-CoV-2-tiled amplicon sequencing (N = 95). We classified SARS-CoV-2 reads into lineages and sublineages that approximated named variants and identified single nucleotide variants (SNVs), of which many are putatively novel SNVs and SNVs of unknown potential function and prevalence. Through our retrospective study, we also show that several SARS-CoV-2 sublineages were detected in wastewater before clinical detection, which may assist in the prediction of future variants of concern. Lastly, we show that sublineage diversity was similar across Southern California and that diversity changed over time, indicating that WBE is effective across megaregions. As the COVID-19 pandemic moves to new phases, and SARS-CoV-2 variants emerge, monitoring wastewater is important to understand local- and population-level dynamics of the virus. These results will aid in our ability to monitor the evolutionary potential of SARS-CoV-2 and help understand circulating SNVs to further combat COVID-19. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 1208 KiB

Open AccessArticle

Breaking the Mold: Towards Rapid and Cost-Effective Microbial Contamination Detection in Paints and Cosmetics Using ATP-Bioluminescence

by Mira Mutschlechner, Daniela Chisté and Harald Schöbel

Appl. Microbiol. 2024, 4(2), 582-593; https://doi.org/10.3390/applmicrobiol4020040 - 22 Mar 2024

Cited by 1 | Viewed by 1531

Abstract

Traditional culture-based methods, though a “gold standard” for bacterial detection in various industrial sectors, do often not fulfill today’s high requirements regarding rapidity, on-site applicability, and cost-efficiency both during operation and evaluation. Here, the feasibility of using an adenosine triphosphate (ATP)-based assay for [...] Read more.

Traditional culture-based methods, though a “gold standard” for bacterial detection in various industrial sectors, do often not fulfill today’s high requirements regarding rapidity, on-site applicability, and cost-efficiency both during operation and evaluation. Here, the feasibility of using an adenosine triphosphate (ATP)-based assay for determining microbial contaminations in paints and cosmetics was investigated and compared with standard plate count techniques and dipslides. Therefore, we initially determined the level of sensitivity and assessed the accuracy and concordance among the different methods via spiking tests using a mix of frequently abundant bacterial species to simulate microbial contamination. Bioluminescence intensity was linearly proportional to log colony counts over five orders of magnitude (R² = 0.99), indicating a high level of sensitivity. Overall, the accuracy varied depending on the test specimen, most probably due to matrix-related quenching effects. Although the degree of conformity was consistently higher at target concentrations ≥ 10⁵ CFU·mL⁻¹, microbial contaminations were detectable down to 10³ CFU·mL⁻¹, thus meeting the high requirements of various industries. ATP-based results tended to be within an order of magnitude lower than the reference. However, bearing that in mind, the developed assay serves as a rapid, real-time alternative for routine quality control and hygiene monitoring. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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19 pages, 2624 KiB

Open AccessArticle

Green Macroalgae Hydrolysate for Biofuel Production: Potential of Ulva rigida

by Walaa Sayed, Audrey Cabrol, Alaa Salma, Abdeltif Amrane, Maud Benoit, Ronan Pierre and Hayet Djelal

Appl. Microbiol. 2024, 4(2), 563-581; https://doi.org/10.3390/applmicrobiol4020039 - 22 Mar 2024

Cited by 1 | Viewed by 1325

Abstract

In this study, the green macroalgae Ulva rigida, which contains 34.9% carbohydrates, underwent treatment with commercial hydrolytic enzymes. This treatment yielded a hydrolysate that contained 23 ± 0.6 g·L⁻¹ of glucose, which was subsequently fermented with Saccharomyces cerevisiae. The fermentation process [...] Read more.

In this study, the green macroalgae Ulva rigida, which contains 34.9% carbohydrates, underwent treatment with commercial hydrolytic enzymes. This treatment yielded a hydrolysate that contained 23 ± 0.6 g·L⁻¹ of glucose, which was subsequently fermented with Saccharomyces cerevisiae. The fermentation process resulted in an ethanol concentration of 9.55 ± 0.20 g·L⁻¹. The optimal conditions for ethanol production by S. cerevisiae were identified as follows: non-sterilized conditions, an absence of enrichment, and using an inoculum size of 118 mg·L⁻¹. Under these conditions, the fermentation of the green macroalgal hydrolysate achieved a remarkable conversion efficiency of 80.78%. The ethanol o/t ratio, namely the ratios of the experimental to theoretical ethanol produced, for Scheffersomyces stipitis, Candida guilliermondii, Kluyveromyces marxianus, and S. cerevisiae after 48 h of fermentation were 52.25, 63.20, 70.49, and 82.87%, respectively. Furthermore, S. cerevisiae exhibited the best outcomes in terms of ethanol production (9.35 g·L⁻¹) and conversion efficiency (80.78%) after 24 h (optimal time) of fermentation. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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16 pages, 14072 KiB

Open AccessArticle

PluMu—A Mu-like Bacteriophage Infecting Actinobacillus pleuropneumoniae

by Lee Julia Bartsch, Roberto Fernandez Crespo, Yunfei Wang, Michael A. Skinner, Andrew N. Rycroft, William Cooley, David J. Everest, Yanwen Li, Janine T. Bossé and Paul R. Langford

Appl. Microbiol. 2024, 4(1), 520-535; https://doi.org/10.3390/applmicrobiol4010037 - 17 Mar 2024

Viewed by 1227

Abstract

Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia, an economically important lung disease in pigs. In draft genomes of two Cypriot clinical A. pleuropneumoniae isolates (MIDG3457 and MIDG3459), we previously identified single genomic regions with homology to Mu-like bacteriophage and presented preliminary evidence [...] Read more.

Actinobacillus pleuropneumoniae is the causative agent of pleuropneumonia, an economically important lung disease in pigs. In draft genomes of two Cypriot clinical A. pleuropneumoniae isolates (MIDG3457 and MIDG3459), we previously identified single genomic regions with homology to Mu-like bacteriophage and presented preliminary evidence of active phage. Here, updated Phastest genomic analysis identified two loci in both MIDG3457 and MIDG3459 that were predicted to encode proteins with high homology to, and whose organisation was characteristic of, Mu-like phages. Phylogenetically, the closest matches were with Mannheimia Vb and Glaesserella SuMu phages. Phastest scored the loci as “complete”, indicating they produced active phage. PCR amplification of the Mu-like phage c and tail genes from DNase-treated polyethylene glycol 8000 (PEG)-precipitated supernatants of MIDG3457 and MIDG3459 (grown in either Brain Heart Infusion-NAD or Grace’s Insect Medium-NAD broth) indicated the presence of intact virions. The phages from MIDG3457 and MIDG3459 were named PluMu 3457-1, 3457-2, and PluMu 3459-1 and PluMu 3459-2, respectively. Transmission electron microscopy (TEM) of the PEG-precipitated supernatants of broth-grown MIDG3459 identified virions with icosahedral heads and tails, consistent with other Mu-like phages. We conclude that MIDG3459 produces an active Mu-like phage. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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10 pages, 727 KiB

Open AccessArticle

Thermal Inactivation of the Heat-Resistant Pathogens Salmonella Senftenberg 775W and Escherichia coli AW1.7 in Whey Concentrate

by Gregor Fiedler, Stefan Nöbel, Sönke Matzen, Meike Samtlebe and Charles M. A. P. Franz

Appl. Microbiol. 2024, 4(1), 510-519; https://doi.org/10.3390/applmicrobiol4010036 - 15 Mar 2024

Viewed by 1608

Abstract

Pasteurized whey concentrate is used as a base for the production of ingredients for various food products. Whey concentrate (30% dry matter) was used to assess the thermal inactivation of Salmonella (S.) enterica serovar Senftenberg 775W (DSM 10062) and Escherichia ( [...] Read more.

Pasteurized whey concentrate is used as a base for the production of ingredients for various food products. Whey concentrate (30% dry matter) was used to assess the thermal inactivation of Salmonella (S.) enterica serovar Senftenberg 775W (DSM 10062) and Escherichia (E.) coli AW1.7 (DSM 108612) strains in a pilot-scale pasteurizer mimicking industrial heat processing. These strains, chosen for their exceptional heat resistance, represent the most challenging scenario for pasteurization within the context of S. enterica and E. coli. Heat resistance was tested at temperatures of 56, 60, 64, 68, and 72 °C at an average holding time of 17.5 s. These exceptionally heat-resistant strains showed a relatively low reduction in numbers of between 0 and 4.2 log₁₀ CFU/mL at lower inactivation temperatures of ≤68 °C. A reduction of at least 5 log₁₀ CFU/mL, as required for adequate heat processing, was achieved for both species after heating at 72 °C for 17.5 s. This study shows that whey concentrate should not lead to contamination of food ingredients and can be considered safe after pasteurization at 72 °C for at least 17.5 s with respect to the pathogens tested. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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14 pages, 1423 KiB

Open AccessArticle

The Tale of Staphylococcus aureus Isolated from Mastitis Infections: The Effect of Antimicrobials and Bacterial Relatedness

by Angela Perdomo, Maria Salazar, Rasmi Janardhanan and Alexandra Calle

Appl. Microbiol. 2024, 4(1), 496-509; https://doi.org/10.3390/applmicrobiol4010035 - 9 Mar 2024

Viewed by 1617

Abstract

Staphylococcus aureus is a common causative agent of mastitis in dairy cattle, posing a substantial threat to animal health and resulting in significant economic losses. Preventive measures are usually in place to control the spread of the organism between animals and around the [...] Read more.

Staphylococcus aureus is a common causative agent of mastitis in dairy cattle, posing a substantial threat to animal health and resulting in significant economic losses. Preventive measures are usually in place to control the spread of the organism between animals and around the dairy environment; however, mastitis outbreaks can still be recurrent. During this investigation, a total of 30 S. aureus isolates were obtained from six deceased cows, all diagnosed with chronic mastitis during an outbreak in West Texas. The aim of this study was to evaluate the response of the S. aureus isolates causing severe mastitis infections to iodine treatments and their antibiotic susceptibility, planktonic growth, and biofilm formation. Udder skin was inoculated with S. aureus and subjected to various iodine concentrations of 0.25%, 0.38%, 0.50%, 0.75%, and 1.00%, with exposure times of 15 s, 10 s, and 60 s. The same concentrations were tested on S. aureus’s biofilm formation. The results of the antimicrobial susceptibility test indicate that the exposure time did not influence the treatment. Lower iodine concentrations were compared with 1.00%, as the standard treatment used by the dairy for teat disinfection, and statistical difference (p < 0.001) was evident in the 0.00% iodine treatment compared to the other iodine concentrations. Moreover, a significant difference (p < 0.001) emerged when comparing the 0.25% and 0.38% iodine concentrations with 1.00%. No difference (p > 0.161) was detected between 0.50%, 0.75%, and 1.00%. These results suggest that, under the conditions investigated, iodine can be lowered to around 50% of the currently used dose without negatively impacting microbial control. On the other hand, S. aureus strains were susceptible to the tested antibiotics, demonstrating that antimicrobial resistance does not always play a role in the persistent mastitis infections caused by S. aureus. Further microbial phenotypic typing conducted on S. aureus strains indicated a possible common source of the infections, demonstrating the potential of there being resident S. aureus strains at this dairy farm. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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11 pages, 1235 KiB

Open AccessArticle

Complementation of an Escherichia coli K-12 Mutant Strain Deficient in KDO Synthesis by Forming D-Arabinose 5-Phosphate from Glycolaldehyde with Fructose 6-Phosphate Aldolase (FSA)

by Emma Guitart Font and Georg A. Sprenger

Appl. Microbiol. 2024, 4(1), 470-480; https://doi.org/10.3390/applmicrobiol4010032 - 3 Mar 2024

Viewed by 1193

Abstract

KDO (2-keto-3-deoxy-D-manno-octulosonate) is a landmark molecule of the Gram-negative outer membrane. Mutants without KDO formation are known to be barely viable. Arabinose 5-phosphate (A5P) is a precursor of KDO biosynthesis and is normally derived from ribulose 5-phosphate by A5P isomerases, encoded [...] Read more.

KDO (2-keto-3-deoxy-D-manno-octulosonate) is a landmark molecule of the Gram-negative outer membrane. Mutants without KDO formation are known to be barely viable. Arabinose 5-phosphate (A5P) is a precursor of KDO biosynthesis and is normally derived from ribulose 5-phosphate by A5P isomerases, encoded by kdsD and gutQ genes in E. coli K-12. We created a kdsD gutQ-deficient double mutant of strain BW25113 and confirmed that these cells are A5P auxotrophs. Fructose 6-phosphate aldolase (FSA) is known to utilize (among other donors such as dihydroxyacetone or hydroxyacetone) glycolaldehyde (GoA) as a donor compound and to provide A5P in vitro when glyceraldehyde 3-phosphate is the acceptor. We show here that this FSA function in vivo fully reverses the growth defect and the A5P deficiency in kdsD gutQ double mutants. Expression of both plasmid-encoded fsaA, fsaA^A129S, or fsaB genes as well as a chromosomally integrated form of fsaA^A129S led to maximal OD₆₀₀ values of >2.2 when GoA was added exogenously (together with glucose as a C source) at a concentration of 100 µM (K_s values in the range of 4–10 µM). Thus, a novel bio-orthogonal bypass to overcome an A5P deficiency was opened. Lower GoA concentrations led to lower growth yields. Interestingly, mutant strains with recombinant fsa genes showed considerable growth yields even without exogenous GoA addition, pointing to yet unknown endogenous GoA sources in E. coli metabolism. This is a further example of the usefulness of FSA in rewiring central metabolic pathways in E. coli. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 1281 KiB

Open AccessArticle

A Major Facilitator Superfamily Transporter Contributes to Ergot Alkaloid Accumulation but Not Secretion in Aspergillus leporis

by Abigail M. Jones, Kyle A. Davis and Daniel G. Panaccione

Appl. Microbiol. 2024, 4(1), 406-417; https://doi.org/10.3390/applmicrobiol4010028 - 20 Feb 2024

Viewed by 980

Abstract

Ergot alkaloids are fungal natural products with important roles in agriculture and medicine. We used heterologous expression and gene knockout approaches to investigate potential roles for the product of a major facilitator superfamily transporter gene (easT) recently found in an ergot [...] Read more.

Ergot alkaloids are fungal natural products with important roles in agriculture and medicine. We used heterologous expression and gene knockout approaches to investigate potential roles for the product of a major facilitator superfamily transporter gene (easT) recently found in an ergot alkaloid biosynthetic gene cluster in Aspergillus leporis. A strain of Aspergillus fumigatus previously engineered to accumulate lysergic acid, but which did not convert the precursor agroclavine to lysergic acid efficiently or secrete lysergic acid well, was chosen as an expression host for easT. Expression of easT in this strain resulted in accumulation of significantly more pathway intermediates but no detectable lysergic acid. Secretion of ergot alkaloids was reduced in the easT-expressing strain. EasT localized to discrete vesicle-like structures in the cytosol of A. fumigatus, with no localization detected in the plasma membrane. When easT was knocked out in A. leporis, accumulation of lysergic acid amides was reduced relative to the wild type. There was no negative effect on secretion of ergot alkaloids in the knockout mutant. The data indicate that easT encodes a product that contributes to accumulation of ergot alkaloids, perhaps by transporting intermediates between cellular compartments, but does not have a significant role in secreting ergot alkaloids. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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16 pages, 6769 KiB

Open AccessArticle

Transcriptional Response of Salmonella enterica to Bacteriophage Treatments with Differential Multiplicities of Infection

by Catherine W. Y. Wong and Siyun Wang

Appl. Microbiol. 2024, 4(1), 390-405; https://doi.org/10.3390/applmicrobiol4010027 - 16 Feb 2024

Viewed by 1468

Abstract

Salmonella enterica (S. enterica) is a causative agent of numerous foodborne outbreaks, as current industrial measures may be <90% effective. Therefore, bacteriophages have been suggested as an antimicrobial treatment against S. enterica, but it is currently unclear if there is [...] Read more.

Salmonella enterica (S. enterica) is a causative agent of numerous foodborne outbreaks, as current industrial measures may be <90% effective. Therefore, bacteriophages have been suggested as an antimicrobial treatment against S. enterica, but it is currently unclear if there is an optimal bacteriophage multiplicity of infection (MOI) against S. enterica. Two bacteriophage cocktails at MOIs 1, 10, 100, 1000 and 10,000 were co-inoculated against four S. enterica strains (S. Enteritidis, S. Newport, S. Muenchen and S. Typhimurium), and populations were estimated on days 0–3. The transcriptional profiles of 20 genes previously indicated to be differentially expressed after bacteriophage treatment were studied by extracting RNA from all four S. enterica strains after bacteriophage SE14, SF5 and SF6 treatment on days 0, 1 and 3, and RT-qPCR was conducted to determine the expression of the 20 selected genes. The results showed that an MOI of 1000 was the most optimal in reducing S. Enteritidis populations to undetectable levels from day 0 to 3. The cas1 (SOS response) and mod (DNA modification and recombination) genes were highly upregulated between 2.5- and 5-fold on day 0 for S. Enteritidis S5-483 and S. Typhimurium S5-536 at MOIs of 1000 and 10,000. On day 3, hsdS (DNA modification and recombination) was upregulated by ~1-fold for S. enteritidis S5-483 after an MOI of 1000. Understanding an optimal bacteriophage MOI can be beneficial to implementing effective and optimal bacteriophage treatments in the industry. Knowledge of S. enterica’s transcriptional response after bacteriophage treatment provides further insight into how S. enterica can survive bacteriophage infection. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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14 pages, 3969 KiB

Open AccessArticle

Utilizing a Metagenome Assembled Genome Approach Revealed Further Insights into Microbially Mediated Heavy-Metal Resistance in Soils from a Former Nuclear Materials Production Facility

by Navya Kommu, Paul Stothard, Christian Chukwujindu, Ashish Pathak and Ashvini Chauhan

Appl. Microbiol. 2024, 4(1), 376-389; https://doi.org/10.3390/applmicrobiol4010026 - 13 Feb 2024

Cited by 1 | Viewed by 1826

Abstract

Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat, [...] Read more.

Soils and sediments from the Savannah River Site (SRS), located in the USA are known to have a long history of co-contamination with radionuclides (mainly uranium) and heavy metals. To better understand the bacterial taxonomic and genomic characteristic of the SRS soil habitat, shotgun metagenomes were obtained from three different levels of contaminated soil—high, medium, and low. Sequences were then assembled and annotated to generate metagenome-assembled genomes (MAGs) using toolkits within the nf-core/mag. The initial analysis resulted in a total of 254 MAGs. After bin refinement and de-replication, 55 MAGs which met the quality standard with a completeness > 75% and contamination < 25%, accounting for 21.67% of all the MAGs, were reconstructed. Further refinement with completeness > 90% and contamination < 10% yielded 24 MAGs (18 from the winter season and 6 from the summer season) spanning 6 bacterial phyla, predominantly Actinomycetota, Proteobacteriota, Bacteroidota, and Cyanobacteria. Overall, the Arthrobacter MAG was found to be robust for further analysis, with over 1749 genes putatively involved in the crucial metabolism of elements viz. nitrogen, phosphorous, and sulfur, and 598 genes encoding enzymes for the resistance of metals including cadmium, zinc, chromium, arsenic, and copper. In summary, this project enhances our understanding of genes conferring resistance to heavy metals in uranium-contaminated soils. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 316 KiB

Open AccessArticle

Antibiotic-Resistant Bacteria across a Wastewater Treatment Plant

by Ofélia Godinho, Olga Maria Lage and Sandra Quinteira

Appl. Microbiol. 2024, 4(1), 364-375; https://doi.org/10.3390/applmicrobiol4010025 - 12 Feb 2024

Cited by 2 | Viewed by 3656

Abstract

Antimicrobial resistance is presently one of the leading causes of death worldwide. The surveillance of different environments, namely, wastewater treatment plants (WWTPs), as hotspots of antibiotic-resistant bacteria, has become crucial under the One Health approach. This study aimed to characterize, phenotypically and genotypically, [...] Read more.

Antimicrobial resistance is presently one of the leading causes of death worldwide. The surveillance of different environments, namely, wastewater treatment plants (WWTPs), as hotspots of antibiotic-resistant bacteria, has become crucial under the One Health approach. This study aimed to characterize, phenotypically and genotypically, antibiotic-resistant bacteria along a WWTP receiving domestic and industrial sewage. Four sampling sites, representing distinct treatment points of the WWTP, were selected for sampling bacterial isolation in selective media supplemented, or not, with antibiotics, and subsequent antimicrobial susceptibility testing. Antibiotic resistance encoding genes were screened by molecular methods. A total of 50 bacterial isolates were obtained, 50% of which were affiliated with the genus Enterococcus. The antimicrobial susceptibility testing revealed antibiotic phenotypic resistance in isolates obtained from all the four treatment points of the wastewater samples, with resistance to tetracycline (32.5%) and ampicillin (25%) being the most common. Three isolates were found to be multidrug resistant and were affiliated with the genera Citrobacter, Shigella and Klebsiella. Molecular screening revealed the presence of tet(M), bla_TEM, bla_SHV and bla_CTX-M, as well as class 1 integrons carrying dfrA25, ANT(3″)-IIa and aadA6 genes. This study highlights the relevance of bacterial isolation and their antimicrobial susceptibility evaluation in WWTP systems since antibiotic-resistant strains were found from the raw influent to the final effluent discharged into the environment, denoting the need for surveillance and containment measures. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

10 pages, 1822 KiB

Open AccessArticle

Inhibitory Effects of Bacillus subtilis Isolated from Meju (Fermented Soybean Brick) on the Growth of Aspergillus parasiticus

by Jong-Gyu Kim and Jeong-Yeong Park

Appl. Microbiol. 2024, 4(1), 354-363; https://doi.org/10.3390/applmicrobiol4010024 - 12 Feb 2024

Viewed by 1370

Abstract

Background: Meju is a base material for making soy sauce, soybean paste, and red chili pepper paste, which are representative ingredients of Korean cuisine. Objectives: This study aimed to isolate a predominant bacterial strain of B. subtilis from meju and to observe its inhibitory [...] Read more.

Background: Meju is a base material for making soy sauce, soybean paste, and red chili pepper paste, which are representative ingredients of Korean cuisine. Objectives: This study aimed to isolate a predominant bacterial strain of B. subtilis from meju and to observe its inhibitory effects on an aflatoxigenic mold. Methods: We used yellow soybeans (Glycine max (L.) Merr.) grown in South Korea, and meju was produced according to the recommended methods of the Korea Food Research Institute. The identification of the strain was conducted based on its morphological and biochemical characteristics and 16S rDNA sequence. Evaluation of the bacterial effect against A. parasiticus ATCC 15517 was done in yeast extract–sucrose broth at 28 °C. Its inhibitory effect was evaluated using two approaches: mycelial weight and aflatoxin production. Aflatoxins were determined using high-performance liquid chromatography. Results: In the meju samples fermented for three months, a B. subtilis strain, K-0924 was identified. At the end of the incubation period of A. parasiticus, dry mycelial weight was significantly reduced by more than 80% (p < 0.01) and total aflatoxin production was inhibited by more than 63% (p < 0.05) in the presence of B. subtilis. Conclusions: These results indicate that B. subtilis K-0924 inhibits the growth and aflatoxin production of toxigenic Aspergillus, which can be contaminated with meju. We could expect more inhibition by other bacteria related to fermentation of meju, and further examination is necessary on species other than B. subtilis. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 477 KiB

Open AccessArticle

Detecting Closer to Care: Combining Phage and LAMP to Detect Tuberculosis, Bovine TB and Johne’s Disease

by Christopher G. Shield, Alexandra E. M. Bartlett, Pranabashis Haldar and Benjamin M. C. Swift

Appl. Microbiol. 2024, 4(1), 341-353; https://doi.org/10.3390/applmicrobiol4010023 - 1 Feb 2024

Viewed by 1526

Abstract

Mycobacterial diseases impact millions in the human and veterinary fields each year. Their diagnosis is long and laborious, often only sensitive in the late stages of disease. This has created an unmet need for new diagnostics that are effective in the earlier stages [...] Read more.

Mycobacterial diseases impact millions in the human and veterinary fields each year. Their diagnosis is long and laborious, often only sensitive in the late stages of disease. This has created an unmet need for new diagnostics that are effective in the earlier stages of infection and are quick and easy to perform. This study details the optimization of LAMP assays for the detection of M. tuberculosis, M. bovis and M. avium subsp. paratuberculosis combined with phage-mediated lysis to meet the needs of a novel diagnostic—termed phage-LAMP. The optimized phage-LAMP assay had a limit of detection of less than 10 mycobacteria per ml and no cross-reaction was seen between assays. The phage-LAMP method was then tested on a small number of clinical blood samples from suspected TB patients and herds suspected of Johne’s disease. The phage-LAMP assay could detect viable Mycobacterium tuberculosis and M. avium subsp. paratuberculosis in these samples. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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17 pages, 4108 KiB

Open AccessArticle

Mapping Selected Emergent Marine Toxin-Producing Organisms Using Historical Samples with Two Methods (Biosensors and Real-Time PCR): A Comparison of Resolution

by Gerado Mengs, Rowena F. Stern, Jessica L. Clarke, Matthew Faith and Linda K. Medlin

Appl. Microbiol. 2024, 4(1), 312-328; https://doi.org/10.3390/applmicrobiol4010021 - 30 Jan 2024

Viewed by 1437

Abstract

The Continuous Plankton Recorder (CPR) survey is a valuable resource for mapping changes in plankton distribution and understanding harmful algal ecology because of its breadth and longevity. Preservation methods with formalin degrade DNA, making it difficult to use as a molecular tool for [...] Read more.

The Continuous Plankton Recorder (CPR) survey is a valuable resource for mapping changes in plankton distribution and understanding harmful algal ecology because of its breadth and longevity. Preservation methods with formalin degrade DNA, making it difficult to use as a molecular tool for archived marine samples. DNA was extracted from CPR samples immediately after collection, seven months later and after nine years of storage from a cruise track along the Iberian Peninsula. PCR reactions performed from the nine-year timepoint were hybridized to probes in an electrochemical biosensor and compared to results obtained from RT-PCR performed at two earlier time points. The successful identification of Pseudo-nitzschia spp., Prorocentrum lima, Alexandrium minutum, Alexandrium ostenfeldii, Gambierdiscus spp. and Coolia spp. was documented. The biosensor analysis outperformed RT-PCR, allowing us to document certain tropical toxic dinoflagellates, viz., Gambierdiscus and Coolia, that produce human ciguatoxins and Coolia toxins, respectively. These non-native algal toxins can accumulate, pervade the food web and negatively impact human food security. This supports the northerly movement of microalgae with climate change in offshore Iberian peninsular waters. This study highlights biosensors as a cost-effective tool for the offshore monitoring of HAB species and advances molecular technologies for long-term CPR datasets that have limited records of harmful algae. DNA from formalin-preserved CPR samples is degraded, so the use of a short, multiprobe biosensor can augment historical plankton records with contemporary methods that also capture infrequently occurring benthic taxa carried in surface waters. The integration of probe-based biosensor technologies offers a promising avenue for exploring plankton dynamics in response to environmental changes. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 3500 KiB

Open AccessArticle

Culture-Independent Quantification of Legionella pneumophila in Evaporative Cooling Systems Using Immunomagnetic Separation Coupled with Flow Cytometry

by Philipp Streich, Johannes Redwitz, Sandra Walser-Reichenbach, Caroline E. W. Herr, Martin Elsner and Michael Seidel

Appl. Microbiol. 2024, 4(1), 284-296; https://doi.org/10.3390/applmicrobiol4010019 - 27 Jan 2024

Cited by 2 | Viewed by 1439

Abstract

Legionella pneumophila are pathogenic bacteria that repeatedly occur in high concentrations in the process water of evaporative cooling systems (ECS). When released into the environment, the resulting bioaerosols can cause outbreaks with fatal consequences. The official, internationally accepted detection method for Legionella spp. [...] Read more.

Legionella pneumophila are pathogenic bacteria that repeatedly occur in high concentrations in the process water of evaporative cooling systems (ECS). When released into the environment, the resulting bioaerosols can cause outbreaks with fatal consequences. The official, internationally accepted detection method for Legionella spp. in water samples is based on cultivation. However, cultivation is time-consuming and may underestimate the total count of viable L. pneumophila in ECS. Therefore, culture-independent methods are receiving attention for rapid monitoring. Cartridge-based immunomagnetic separation (IMS) coupled with flow cytometry (FCM) is an innovative, antibody-based method for the culture-independent quantification of L. pneumophila, using a panel of antibodies against serogroup (Sg) 1–15. We characterized the IMS-FCM method as a quantitative rapid test by general analytical procedures. Viable cryopreserved L. pneumophila standards were used in calibration experiments for the method. We achieved detection limits for Sg 1, Sg 4, and Sg 6 of 100, 105 and 88 viable cells per 100 mL, respectively. Furthermore, we demonstrated the practical applicability of IMS-FCM with real ECS samples and compared the performance against cultivation. Cultivation showed here no positive results, but IMS-FCM evidenced L. pneumophila in a range of 0–80,000 viable cells per 100 mL. This work demonstrates that IMS-FCM is a suitable, culture-independent, quantitative method for rapidly monitoring L. pneumophila. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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9 pages, 1482 KiB

Open AccessCommunication

First Description of Simplicillium lanosoniveum, a Potential Antagonist of the Coffee Leaf Rust from Cuba

by Yamilé Baró Robaina, Isel González Marrero, María Elena Lorenzo Nicao, Rafael F. Castañeda Ruiz, De-Wei Li, Amaia Ponce de la Cal, Haifa Ben Gharsa, Romina G. Manfrino, Christina Schuster and Andreas Leclerque

Appl. Microbiol. 2024, 4(1), 275-283; https://doi.org/10.3390/applmicrobiol4010018 - 26 Jan 2024

Cited by 1 | Viewed by 1480

Abstract

(1) The fungal genus Simplicillium (Cordycipitaceae: Hypocreales) has an extensive distribution and a broad spectrum of hosts and substrates. The species Simplicillium lanosoniveum is a mycoparasite with potential for biological control of coffee leaf rust, Hemileia vastatrix. Morphologically, Simplicillium closely resembles mycoparasitic [...] Read more.

(1) The fungal genus Simplicillium (Cordycipitaceae: Hypocreales) has an extensive distribution and a broad spectrum of hosts and substrates. The species Simplicillium lanosoniveum is a mycoparasite with potential for biological control of coffee leaf rust, Hemileia vastatrix. Morphologically, Simplicillium closely resembles mycoparasitic and entomopathogenic Lecanicillium fungi, often resulting in misidentification. A fungal isolate was obtained from leaf-rust-infested coffee plants from Cienfuegos Province, Cuba. (2) Combined analyses of morphology and molecular markers (ITS, LSU, EF-1alpha) were used for fungal identification. (3) In the NJ, ML, and BI phylogenies which were reconstructed, the isolate LBSim-01 was located in the Simplicillium lanosoniveum clade. This species-level identification was supported by morphological features. (4) The isolate LBSim-01 was assigned to the species Simplicillium lanosoniveum. This is the first description of a Simplicillium fungus associated with coffee leaf rust in Cuba. The presented results hold implications for the biological control of this economically relevant plant disease. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 2314 KiB

Open AccessArticle

Combination Screening of a Naïve Antibody Library Using E. coli Display and Single-Step Colony Assay

by Mieko Kato and Yoshiro Hanyu

Appl. Microbiol. 2024, 4(1), 237-249; https://doi.org/10.3390/applmicrobiol4010016 - 23 Jan 2024

Viewed by 1692

Abstract

The use of single-domain camelid antibodies, termed VHHs or nanobodies, has found increasing application in diagnosis, pharmaceutical development, and research because of their superior properties, such as small size, elevated stability, high water solubility, and excellent affinity for the antigen. Antigen-specific VHHs are [...] Read more.

The use of single-domain camelid antibodies, termed VHHs or nanobodies, has found increasing application in diagnosis, pharmaceutical development, and research because of their superior properties, such as small size, elevated stability, high water solubility, and excellent affinity for the antigen. Antigen-specific VHHs are generated by screening VHH display libraries via bio-panning. However, the bio-panning step needs to be repeated multiple times, which is time-consuming and laborious. Here, we developed a simple and rapid screening method that combined Escherichia coli display and a single-step colony assay to successfully identify positive clones from a naïve VHH library. The library was constructed from peripheral blood mononuclear cells of alpaca, and VHHs were displayed on the surface of E. coli using the inverse autotransporter intimin. Libraries enriched by magnetic cell sorting were screened directly using a single-step colony assay. Colonies formed on the hydrophilic filter and antigen-coated membrane. The expression of VHHs was induced, and those bound to the antigen on the membrane were detected as positive clones. Screening and identification of positive clones required only two days, which saves considerable time and resources compared to existing protocols. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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22 pages, 2350 KiB

Open AccessArticle

Toward Effects of Hydrophobicity on Biosurfactant Production by Bacillus subtilis Isolates from Crude-Oil-Exposed Environments

by Seyedeh Zahra Hashemi, Jamshid Fooladi, Maliheh Vahidinasab, Philipp Hubel, Jens Pfannstiel, Evelina Pillai, Holger Hrenn, Rudolf Hausmann and Lars Lilge

Appl. Microbiol. 2024, 4(1), 215-236; https://doi.org/10.3390/applmicrobiol4010015 - 18 Jan 2024

Cited by 1 | Viewed by 1576

Abstract

Background: Due to their structural features, biosurfactants reveal promising physicochemical properties, making them interesting for various applications in different fields, such as the food, cosmetics, agriculture, and bioremediation sectors. In particular, the bioproduction of surfactin, one of the most potent microbially synthesized biosurfactant [...] Read more.

Background: Due to their structural features, biosurfactants reveal promising physicochemical properties, making them interesting for various applications in different fields, such as the food, cosmetics, agriculture, and bioremediation sectors. In particular, the bioproduction of surfactin, one of the most potent microbially synthesized biosurfactant molecules, is of great interest. However, since the wild-type productivities are comparably low, stimulatory environmental conditions have to be identified for improved bioproduction This study aims to find a correlation between the hydrophobicity and production of the biosurfactant surfactin by B. subtilis isolates from crude-oil-contaminated soil and water. Methods: The surfactin production yield was characterized in adapted batch cultivations using high-performance thin-layer liquid chromatography (HPTLC). Defined hydrophobic environmental conditions were achieved by supplementation with hexadecane or polystyrene beads, and the effects on biosurfactant production were measured. Adaptations at the protein level were analyzed using mass spectrometry measurements. Results: The correlation between hydrophobicity and surfactin production was characterized using Bacillus subtilis strains ZH1 and P7 isolated from crude-oil-contaminated soil and water. Since these isolates show the biodegradation of crude oil and hexadecane as hydrophobic substrates, respectively, a first-time approach, using polystyrene beads, was applied to provide a hydrophobic environment. Interestingly, contrary to popular opinion, reduced biosurfactant production was determined. Using mass spectrometric approaches, the physiological effects of co-cultivation and the cellular response at the protein level were investigated, resulting in altered quantities of stress proteins and proteins involved in the carbon metabolism counter to polystyrene beads. Conclusions: Contrary to common opinion, increasing hydrophobicity does not have a stimulating effect, and even reduces the effect on the bioproduction of surfactin as the main biosurfactant using selected B. subtilis strains. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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21 pages, 2787 KiB

Open AccessArticle

Development of a Standardised International Protocol for Evaluation of the Disinfection Efficacy of Healthcare Laundry Wash Processes

by Lucy Owen, Caroline Cayrou, Georgina Page, Martin Grootveld and Katie Laird

Appl. Microbiol. 2024, 4(1), 194-214; https://doi.org/10.3390/applmicrobiol4010014 - 18 Jan 2024

Viewed by 1814

Abstract

This research aims to develop a standardised protocol for monitoring the disinfection efficacy of healthcare laundry processes in view of numerous differential methodologies currently being employed within the healthcare laundry sector, including agitation and surface sampling for post-laundering decontamination assessment and swatch and [...] Read more.

This research aims to develop a standardised protocol for monitoring the disinfection efficacy of healthcare laundry processes in view of numerous differential methodologies currently being employed within the healthcare laundry sector, including agitation and surface sampling for post-laundering decontamination assessment and swatch and bioindicator testing for in-wash-process efficacy. Enterococcus faecium as an indicator species within industrial wash systems is preferable due to its high thermal and disinfectant tolerance. Methods for measuring laundry disinfection were compared; commercially available E. faecium bioindicators and contaminated cotton swatches (loose, in cloth bags or within nylon membranes) were laundered industrially at ambient temperature and microbial recovery determined. E. faecium was lost from cotton during laundering but retained by the bioindicator membrane, which allows disinfection efficacy to be measured without loss of microorganisms from the test swatch. Commercially available bioindicators were only permeable to disinfectants and detergents at ≥60 °C. Subsequently, polyethersulphone membranes for enclosing contaminated swatches were developed for low-temperature laundering, with permeability to industrial laundry chemistries at below ≤60 °C. This study demonstrates that bioindicators are the recommended methodology for laundry disinfection validation. The use of a universal healthcare laundry disinfection methodology will lead to standardised microbiological testing across the industry and improvements in infection control. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 1693 KiB

Open AccessArticle

16S rRNA Gene Sequencing-Based Identification and Comparative Analysis of the Fecal Microbiota of Five Syntopic Lizard Species from a Low-Mountain Area in Western Bulgaria

by Irina Lazarkevich, Stephan Engibarov, Simona Mitova, Emiliya Vacheva, Steliyana Popova, Nikola Stanchev, Rumyana Eneva, Yana Gocheva, Ivanka Boyadzhieva and Maria Gerginova

Appl. Microbiol. 2024, 4(1), 181-193; https://doi.org/10.3390/applmicrobiol4010013 - 18 Jan 2024

Cited by 1 | Viewed by 1461

Abstract

Studies on the gut microbiome of free-living reptiles in Europe are generally fragmentary and still missing in Bulgaria. We aimed to identify and compare the fecal microbiota profiles of five syntopic lizard species from three families: the European green lizard (Lacerta viridis [...] Read more.

Studies on the gut microbiome of free-living reptiles in Europe are generally fragmentary and still missing in Bulgaria. We aimed to identify and compare the fecal microbiota profiles of five syntopic lizard species from three families: the European green lizard (Lacerta viridis), the common wall lizard (Podarcis muralis), the meadow lizard (Darevskia praticola) (Lacertidae), the European snake-eyed skink (Ablepharus kitaibelii) (Scincidae), and the European slow worm (Anguis fragilis) (Anguidae), which coinhabit a low mountainous area in the western part of the country. A high-throughput sequencing of the hypervariable V3-V4 region of the 16S rRNA gene, performed on the Illumina HiSeq2500 platform, was used. The core microbiota of lizard hosts seems to be species-specific. A dynamic phyla proportion between hosts was found. The richest alpha diversity was observed in D. praticola, and the lowest alpha diversity was observed in P. muralis and A. fragilis. Within the three lacertids, the microbiota of D. praticola and L. viridis were more closely related to each other than they were to those of P. muralis. Sharing a largely common trophic resource (all species except A. fragilis are mainly insectivorous) was not an indication of similarity in their gut microbial communities. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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19 pages, 2833 KiB

Open AccessArticle

Methanogenic Archaea Quantification in the Human Gut Microbiome with F₄₂₀ Autofluorescence-Based Flow Cytometry

by Yorick Minnebo, Kim De Paepe, Ruben Props, Tim Lacoere, Nico Boon and Tom Van de Wiele

Appl. Microbiol. 2024, 4(1), 162-180; https://doi.org/10.3390/applmicrobiol4010012 - 17 Jan 2024

Viewed by 2012

Abstract

Methane-producing Archaea can be found in a variety of habitats, including the gastrointestinal tract, where they are linked to various diseases. The majority of current monitoring methods can be slow and laborious. To facilitate gut methanogenic Archaea detection, we investigated flow cytometry for [...] Read more.

Methane-producing Archaea can be found in a variety of habitats, including the gastrointestinal tract, where they are linked to various diseases. The majority of current monitoring methods can be slow and laborious. To facilitate gut methanogenic Archaea detection, we investigated flow cytometry for rapid quantification based on the autofluorescent F₄₂₀ cofactor, an essential coenzyme in methanogenesis. The methanogenic population was distinguishable from the SYBR green (SG) and SYBR green/propidium iodide (SGPI) stained background microbiome based on elevated 452 nm emission in Methanobrevibacter smithii spiked controls. As a proof-of-concept, elevated F₄₂₀-autofluorescence was used to detect and quantify methanogens in 10 faecal samples and 241 in vitro incubated faecal samples. The methanogenic population in faeces, determined through Archaea-specific 16S rRNA gene amplicon sequencing, consisted of Methanobrevibacter and Methanomassiliicoccus. F₄₂₀-based methanogen quantification in SG and SGPI-stained faecal samples showed an accuracy of 90 and 100% against Archaea proportions determined with universal primers. When compared to methane and Archaea presence, methanogen categorisation in in vitro incubated faeces exhibited an accuracy of 71 and 75%, with a precision of 42 and 70%, respectively. To conclude, flow cytometry is a reproducible and fast method for the detection and quantification of gut methanogenic Archaea. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 3038 KiB

Open AccessArticle

Effect of kuratsuki Bacillus and Priestia on Taste of Sake

by Karin Kobayashi and Hiromi Nishida

Appl. Microbiol. 2024, 4(1), 147-161; https://doi.org/10.3390/applmicrobiol4010011 - 15 Jan 2024

Cited by 2 | Viewed by 1224

Abstract

The co-cultivation of sake yeast (AK25, K901, K1401, or K1801 strain) and the kuratsuki Bacillus A-10 and/or Priestia B-12 strains in koji solution was performed to demonstrate the effects of these two kuratsuki bacteria on sake taste. The results showed that the Brix [...] Read more.

The co-cultivation of sake yeast (AK25, K901, K1401, or K1801 strain) and the kuratsuki Bacillus A-10 and/or Priestia B-12 strains in koji solution was performed to demonstrate the effects of these two kuratsuki bacteria on sake taste. The results showed that the Brix and acidity patterns of sake preparations produced with and without these kuratsuki bacteria were very similar. This indicated that the addition of these kuratsuki bacteria did not inhibit ethanol fermentation or organic acid production by sake yeast. A taste recognition device showed that the effects of these kuratsuki bacteria on the saltiness and sourness of sake were greater than those on other taste properties. Astringency stimulation and saltiness of sake produced using the sake yeast K901 were increased by Bacillus A-10 and decreased by Priestia B-12. Except for these two cases, the taste intensities of sake preparations produced with the Bacillus A-10 and Priestia B-12 strains were very similar, but differed from those of sake produced with kuratsuki Kocuria. These results support our hypothesis that the flavor and taste of sake can be controlled by utilizing the interactions between kuratsuki bacteria and sake yeast. For crating the desired sake taste, a combination of kuratsuki bacteria and sake yeast should be considered. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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9 pages, 991 KiB

Open AccessCommunication

Evaluation of Genomic Contamination Detection Tools and Influence of Horizontal Gene Transfer on Their Efficiency through Contamination Simulations at Various Taxonomic Ranks

by Luc Cornet, Valérian Lupo, Stéphane Declerck and Denis Baurain

Appl. Microbiol. 2024, 4(1), 124-132; https://doi.org/10.3390/applmicrobiol4010009 - 10 Jan 2024

Viewed by 1595

Abstract

Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer [...] Read more.

Genomic contamination remains a pervasive challenge in (meta)genomics, prompting the development of numerous detection tools. Despite the attention that this issue has attracted, a comprehensive comparison of the available tools is absent from the literature. Furthermore, the potential effect of horizontal gene transfer on the detection of genomic contamination has been little studied. In this study, we evaluated the efficiency of detection of six widely used contamination detection tools. To this end, we developed a simulation framework using orthologous group inference as a robust basis for the simulation of contamination. Additionally, we implemented a variable mutation rate to simulate horizontal transfer. Our simulations covered six distinct taxonomic ranks, ranging from phylum to species. The evaluation of contamination levels revealed the suboptimal precision of the tools, attributed to significant cases of both over-detection and under-detection, particularly at the genus and species levels. Notably, only so-called “redundant” contamination was reliably estimated. Our findings underscore the necessity of employing a combination of tools, including Kraken2, for accurate contamination level assessment. We also demonstrate that none of the assayed tools confused contamination and horizontal gene transfer. Finally, we release CRACOT, a freely accessible contamination simulation framework, which holds promise in evaluating the efficacy of future algorithms. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 1097 KiB

Open AccessArticle

Insights into Genetic and Physiological Characteristics of Clover Rhizobia in Afghanistan Soils

by Safiullah Habibi, Michiko Yasuda, Shafiqullah Aryan, Tadashi Yokoyama, Kalimullah Saighani and Naoko Ohkama-Ohtsu

Appl. Microbiol. 2024, 4(1), 112-123; https://doi.org/10.3390/applmicrobiol4010008 - 8 Jan 2024

Viewed by 1163

Abstract

Livestock production in Afghanistan highly relies on grazing and clover feed, which is a key component of pastures and forage crops. This study elucidated the genetic diversity of clover-nodulating rhizobia in different ecological regions and their effects on clover growth. A total of [...] Read more.

Livestock production in Afghanistan highly relies on grazing and clover feed, which is a key component of pastures and forage crops. This study elucidated the genetic diversity of clover-nodulating rhizobia in different ecological regions and their effects on clover growth. A total of 57 rhizobia were isolated and their genetic diversities were studied through 16S rRNA and nifD genes. The isolates were inoculated to clover (Afghan local variety), to investigate the potential of nitrogen fixation and influences of clover growth. The 16S rRNA gene analysis showed two distinct groups of Rhizobium (94.7%) and Ensifer (5.3%) species. The nifD phylogenetic relationship revealed a high similarity to Rhizobium and a novel lineage group close to Rhizobium leguminosarum species. In the plant test, different genotypes significantly (p < 0.01) exhibited an increase in plant biomass production, compared to the un-inoculated plants. Among genotypes, the highest plant biomass was recorded in PC8 (1769.0 mg/plant) and PC9 (1409.2 mg/plant) isolates as compared to un-inoculated plants (144.0 mg/plant). Moreover, these isolates showed maximum nitrogen fixation rates of 8.2 and 6.5 µM/plant, respectively. These isolates were identified as the most promising rhizobial strains for developing biofertilizers in the context of Afghanistan. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 851 KiB

Open AccessArticle

Occurrence of Mobile Colistin Resistance Genes mcr-1–mcr-10 including Novel mcr Gene Variants in Different Pathotypes of Porcine Escherichia coli Isolates Collected in Germany from 2000 to 2021

by Lisa Göpel, Ellen Prenger-Berninghoff, Silver A. Wolf, Torsten Semmler, Rolf Bauerfeind and Christa Ewers

Appl. Microbiol. 2024, 4(1), 70-84; https://doi.org/10.3390/applmicrobiol4010005 - 28 Dec 2023

Cited by 6 | Viewed by 1666

Abstract

In the European Union, gastrointestinal disease in pigs is the main indication for the use of colistin, but large-scale epidemiologic data concerning the frequency of mobile colistin resistance (mcr) genes in pig-associated pathotypes of Escherichia coli (E. coli) are [...] Read more.

In the European Union, gastrointestinal disease in pigs is the main indication for the use of colistin, but large-scale epidemiologic data concerning the frequency of mobile colistin resistance (mcr) genes in pig-associated pathotypes of Escherichia coli (E. coli) are lacking. Multiplex polymerase chain reactions were used to detect virulence-associated genes (VAGs) and mcr-1–mcr-10 genes in 10,573 porcine E. coli isolates collected in Germany from July 2000 to December 2021. Whole genome sequencing was performed on 220 representative mcr-positive E. coli strains. The total frequency of mcr genes was 10.2%, the most frequent being mcr-1 (8.4%) and mcr-4 (1.6%). All other mcr genes were rarely identified (mcr-2, mcr-3, mcr-5) or absent (mcr-6 to mcr-10). The highest frequencies of mcr genes were found in enterotoxigenic and shiga toxin-encoding E. coli (ETEC/STEC hybrid) and in edema disease E. coli (EDEC) strains (21.9% and 17.7%, respectively). We report three novel mcr variants, mcr-1.36, mcr-4.8, and mcr-5.5. In 39 attaching and effacing E. coli (AEEC) isolates analyzed in our study, the eae subtype β1 was the most prevalent (71.8%). Constant surveillance for the presence of mcr genes in various sectors should consider the different frequency of mcr-positive isolates in pathogenic E. coli. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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20 pages, 4423 KiB

Open AccessArticle

Customizing Sanitization Protocols for Food-Borne Pathogens Based on Biofilm Formation, Surfaces and Disinfectants—Their Two- and Three-Way Interactions

by Manju Kundu, Amin Omar, Brenton Buziak, Nick Allan, Lyriam Marques, Merle Olson, Ronald Howard and Michael W. Harding

Appl. Microbiol. 2024, 4(1), 27-46; https://doi.org/10.3390/applmicrobiol4010003 - 23 Dec 2023

Cited by 1 | Viewed by 1862

Abstract

Food-borne pathogens are a serious challenge in food handling, processing, and packaging systems. The growth of microbial biofilms on food handling surfaces further complicates the management of the microbial contamination of food. Microorganisms within biofilms are difficult to eradicate with chemical disinfectants, with [...] Read more.

Food-borne pathogens are a serious challenge in food handling, processing, and packaging systems. The growth of microbial biofilms on food handling surfaces further complicates the management of the microbial contamination of food. Microorganisms within biofilms are difficult to eradicate with chemical disinfectants, with an increased likelihood of survival and the subsequent contamination of food. Therefore, a biofilm approach is needed in food safety and hygiene studies. Since many factors, such as strain, cell density, surface type and texture, environmental stress, and so forth, can affect biofilm formation and disinfectant efficacy, we evaluated the responses of biofilms formed by three food-borne bacterial pathogens on eight hard surfaces to seven chemical disinfectants. The three bacteria showed different capacities to colonize the surfaces. Similarly, chemical disinfectants also varied in efficacy, on surfaces and with pathogen species. One-, two-, and three-way interactions of strain, surface, and disinfectant were observed. The results generated demonstrate that the fine-tuning of sanitization strategies along the food production, processing, and packaging chain can be achieved in specific scenarios by accounting for two- and three-way interactions among bacteria, surface, and disinfectant. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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11 pages, 991 KiB

Open AccessArticle

Antimicrobial Resistance Profile of Planctomycetota Isolated from Oyster Shell Biofilm: Ecological Relevance within the One Health Concept

by Bárbara Guedes, Ofélia Godinho, Sandra Quinteira and Olga Maria Lage

Appl. Microbiol. 2024, 4(1), 16-26; https://doi.org/10.3390/applmicrobiol4010002 - 20 Dec 2023

Viewed by 1523

Abstract

Background: Planctomycetota isolation in pure culture is still challenging with most of the reported data coming from molecular-based methods. Here, we intended to isolate Planctomycetota from the filter-feeder Pacific oyster Magallana gigas, extending the search to a not yet explored natural reservoir [...] Read more.

Background: Planctomycetota isolation in pure culture is still challenging with most of the reported data coming from molecular-based methods. Here, we intended to isolate Planctomycetota from the filter-feeder Pacific oyster Magallana gigas, extending the search to a not yet explored natural reservoir and to characterize their antimicrobial resistance phenotype. Methods: Oyster samples from different supermarkets and from a farm producer were subject to isolation in selective medium. Inoculation was performed from the shell biofilm and after an enrichment of the edible content. Results: Planctomycetota isolates (n = 65) were only obtained from the shell biofilm with four different species identified: Rhodopirellula baltica (n = 62), Rhodopirellula rubra (n = 1), Rhodopirellula heiligendammensis (n = 1) and Gimesia chilikensis (n = 1). This study reports the first association of Planctomycetota members with oysters and the first description of R. heiligendammensis in Portugal. Moreover, R. rubra, originally identified in Portugal, was isolated from oysters of French origin. Antibiotic susceptibility testing, conducted in strains belonging to two species never assayed before revealed multidrug resistance phenotypes with bacteria showing resistance to several classes of clinically relevant antibiotics (e.g., β-lactams and aminoglycosides). Conclusion: The ecological role and impact of Planctomycetota on oyster holobiont and, ultimately, in public health, under the One Health concept, is discussed. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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17 pages, 2425 KiB

Open AccessArticle

The Impact of Lytic Viruses on Bacterial Carbon Metabolism in a Temperate Freshwater Reservoir (Naussac, France)

by Angia Sriram Pradeep Ram, Marie-Eve Mauduit, Jonathan Colombet, Fanny Perriere, Antoine Thouvenot and Télesphore Sime-Ngando

Appl. Microbiol. 2023, 3(4), 1407-1423; https://doi.org/10.3390/applmicrobiol3040095 - 15 Dec 2023

Cited by 2 | Viewed by 1115

Abstract

In aquatic systems, the impact of the viral regulation of bacterial carbon metabolism (BCM) is often overlooked compared with nutrient supply. To address this gap, an investigation was conducted in the euphotic and aphotic zones of a mesotrophic freshwater reservoir (Naussac, France) to [...] Read more.

In aquatic systems, the impact of the viral regulation of bacterial carbon metabolism (BCM) is often overlooked compared with nutrient supply. To address this gap, an investigation was conducted in the euphotic and aphotic zones of a mesotrophic freshwater reservoir (Naussac, France) to assess the relative influence of lytic viral infection on key bacterial metabolic parameters, specifically bacterial production (BP) and respiration (BR), as indicators of BCM. Measured using flow cytometry, the abundance of viral sub-groups (V1–V3) exhibited a consistent pattern in tandem with their bacterial hosts across both time and space. A more significant relationship between bacterial and viral parameters than between physicochemical factors suggested a prevailing internal control mechanism that was potentially driven by viral lysis. Viral-mediated bacterial mortality up to 65% was evident in the euphotic zone. The observed variation in BCM (ranging from 7% to 32%) was explained by an uncoupling between BR and BP. Notably, BR was significantly higher (three-fold) than BP in bacterial communities subjected to low in situ phosphate concentrations (<0.5 µM P) and high nutrient stoichiometric ratios (N:P > 60, C:P > 900). An antagonistic relationship between lytic viruses and BCM, whereby the repression of bacterial growth results in elevated respiratory demands, could potentially be attributed to substrate availability constraints. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 1146 KiB

Open AccessArticle

Campylobacter Bacteriophage Infection at Refrigeration Temperatures

by Yang Hu, Bader Al Shaaer, Lu Liang and Ian F. Connerton

Appl. Microbiol. 2023, 3(4), 1392-1406; https://doi.org/10.3390/applmicrobiol3040094 - 13 Dec 2023

Cited by 1 | Viewed by 1601

Abstract

The application of bacteriophages to control foodborne bacterial pathogens in foods has gained traction in recent years. Poultry meat is a major source of Campylobacter jejuni, and a target for the application of bacteriophages. To offer the prospect of a post-harvest control [...] Read more.

The application of bacteriophages to control foodborne bacterial pathogens in foods has gained traction in recent years. Poultry meat is a major source of Campylobacter jejuni, and a target for the application of bacteriophages. To offer the prospect of a post-harvest control measure, the bacteriophage must function at refrigeration temperatures, where C. jejuni does not grow but can survive. Here, we report actions of three classes of Campylobacter bacteriophage at 4 °C. The pre-incubation of broth cultures at 4 °C before a shift to 42 °C under conditions that support the growth of the host bacteria revealed differences in the time to lysis compared with cultures incubated at 42 °C. The pre-adsorption of the bacteriophage to a sub-population of bacteria is consistent with the observation of asynchronous infection. To ascertain whether the bacteriophages adsorb and infect (the commitment to replicate), we investigated bacteriophage transcription at 4 °C. RNA transcripts for all the bacteriophage host combinations were detected after 15 min, indicating that the interaction is not merely passive. Bacteriophages can infect C. jejuni at refrigeration temperatures, but the infection does not proceed to lysis in the absence of host cell division. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 2365 KiB

Open AccessArticle

Employing Active Learning in Medium Optimization for Selective Bacterial Growth

by Shuyang Zhang, Honoka Aida and Bei-Wen Ying

Appl. Microbiol. 2023, 3(4), 1355-1369; https://doi.org/10.3390/applmicrobiol3040091 - 3 Dec 2023

Cited by 1 | Viewed by 2402

Abstract

Medium optimization and development for selective bacterial cultures are essential for isolating and functionalizing individual bacteria in microbial communities; nevertheless, it remains challenging due to the unknown mechanisms between bacterial growth and medium components. The present study first tried combining machine learning (ML) [...] Read more.

Medium optimization and development for selective bacterial cultures are essential for isolating and functionalizing individual bacteria in microbial communities; nevertheless, it remains challenging due to the unknown mechanisms between bacterial growth and medium components. The present study first tried combining machine learning (ML) with active learning to fine-tune the medium components for the selective culture of two divergent bacteria, i.e., Lactobacillus plantarum and Escherichia coli. ML models considering multiple growth parameters of the two bacterial strains were constructed to predict the fine-tuned medium combinations for higher specificity of bacterial growth. The growth parameters were designed as the exponential growth rate (r) and maximal growth yield (K), which were calculated according to the growth curves. The eleven chemical components in the commercially available medium MRS were subjected to medium optimization and specialization. High-throughput growth assays of both strains grown separately were performed to obtain thousands of growth curves in more than one hundred medium combinations, and the resultant datasets linking the growth parameters to the medium combinations were used for the ML training. Repeated rounds of active learning (i.e., ML model construction, medium prediction, and experimental verification) successfully improved the specific growth of a single strain out of the two. Both r and K showed maximized differentiation between the two strains. A further analysis of all the data accumulated in active learning identified the decision-making medium components for growth specificity and the differentiated, determinative manner of growth decisions of the two strains. In summary, this study demonstrated the efficiency and practicality of active learning in medium optimization for selective cultures and offered novel insights into the contribution of the chemical components to specific bacterial growth. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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9 pages, 747 KiB

Open AccessArticle

Assessment of Live Lactobacilli Recovery from Probiotic Products for Vaginal Application

by Diana Neves Sousa, Carlos Gaspar, Joana Rolo, Gilbert G. G. Donders, José Martinez-de-Oliveira, Rita Palmeira-de-Oliveira and Ana Palmeira-de-Oliveira

Appl. Microbiol. 2023, 3(4), 1195-1203; https://doi.org/10.3390/applmicrobiol3040082 - 14 Oct 2023

Viewed by 1610

Abstract

The interest in the use of probiotics to treat and prevent vaginal infections is known. The new regulation of medical devices by the European Medical Agency (EMA) introduced big changes in Europe regarding probiotic products for vaginal application, as they are no longer [...] Read more.

The interest in the use of probiotics to treat and prevent vaginal infections is known. The new regulation of medical devices by the European Medical Agency (EMA) introduced big changes in Europe regarding probiotic products for vaginal application, as they are no longer considered as medical devices. As the future classification will be as drugs, it will stress the need to define robust and reliable pre-clinical in vitro testing in order to assess the quality, safety and efficacy of probiotics for human use. Before discussing the efficacy in human pathology, it is mandatory to evaluate the survival and multiplication potential of probiotic strains when brought into contact with vaginal fluid. In this work, our objective was to assess the recovery and stability profile of lactobacilli from six vaginal probiotic formulations brought in contact with specific culture media or vaginal fluid simulants (VFS). Overall, the recovery of viable lactobacilli cells from a modified vaginal fluid simulant (MVFS) solution was comparable to the recovery pattern obtained in standard culture medium. Therefore, we conclude that the MVFS seems to better simulate the conditions of the human vaginal fluid, in contrast with other simulants, and may be used to predict the viability of probiotics over time in the normal vaginal milieu. We discovered that each probiotic product has a unique profile that requires stand-alone studies in conditions that mimic the in vivo status in order to assess their preclinical effectiveness and promote their differential use by the medical community. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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18 pages, 2855 KiB

Open AccessArticle

Genome Comparison of ‘Candidatus Phytoplasma rubi’ with Genomes of Other 16SrV Phytoplasmas Highlights Special Group Features

by Jan Werner Böhm, Dominik Duckeck, Bojan Duduk, Bernd Schneider and Michael Kube

Appl. Microbiol. 2023, 3(3), 1083-1100; https://doi.org/10.3390/applmicrobiol3030075 - 12 Sep 2023

Cited by 4 | Viewed by 1812

Abstract

Phytoplasmas are associated with important bacterial diseases, causing severe symptoms in agricultural and ornamental crops. ‘Candidatus Phytoplasma rubi’, associated with the Rubus stunt in raspberries (Rubus idaeus) and blackberries (Rubus subgenus Rubus), causes shortened internodes, elongated sepals, proliferation, [...] Read more.

Phytoplasmas are associated with important bacterial diseases, causing severe symptoms in agricultural and ornamental crops. ‘Candidatus Phytoplasma rubi’, associated with the Rubus stunt in raspberries (Rubus idaeus) and blackberries (Rubus subgenus Rubus), causes shortened internodes, elongated sepals, proliferation, phyllody, and virescence. The recently published genome of ‘Ca. P. rubi’ RS enabled a comprehensive genomic comparison to the complete genomes of 16SrV phytoplasmas, comprising strains of the flavescence dorée-associated phytoplasma CH and two ‘Candidatus Phytoplasma ziziphi’ strains. Besides the typical transporters and metabolic features of phytoplasmas, the phosphorolysis of sucrose and the utilization of the carboxylic acid L-lactate became apparent for the 16SrV-group. With respect to the effector repertoire and the encoded immunodominant membrane proteins involved in host colonization, the group revealed conserved features that comprise the variable membrane proteins A and B. However, SAP11- and SAP54 orthologs were limited to ‘Ca. P. rubi’ RS and ‘Ca. P. ziziphi’. Genome-sequence-based phylogenetic analysis supports the close relationship of these genomes relative to alder yellows phytoplasmas. The analyses supported the impact of the mobilome on phytoplasma evolution but also highlighted that there is the possibility of identifying phytoplasmas with a larger metabolic repertoire in the future. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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15 pages, 957 KiB

Open AccessArticle

High-Throughput Viability Testing of Microbial Communities in a Probiotic Product Using Flow Cytometry

by Joanna V. Pereira, Hasinika K. A. H. Gamage, Amy K. Cain, Evan Hayes, Ian T. Paulsen and Sasha G. Tetu

Appl. Microbiol. 2023, 3(3), 1068-1082; https://doi.org/10.3390/applmicrobiol3030074 - 11 Sep 2023

Cited by 4 | Viewed by 2787

Abstract

There is growing scientific and commercial interest in multi-species probiotic products due to their potential benefits in maintaining gut health. Determining the viability of probiotic microorganisms in these products is essential to ensure that they confer maximal health benefits. The gold standard for [...] Read more.

There is growing scientific and commercial interest in multi-species probiotic products due to their potential benefits in maintaining gut health. Determining the viability of probiotic microorganisms in these products is essential to ensure that they confer maximal health benefits. The gold standard for enumerating probiotic viability is the plate count method. However, this may be inaccurate for enumerating mixed probiotic populations, with recognised limitations including difficulty measuring metabolically active yet unculturable, very slow growing microbes, microencapsulated, enteric coated microbes, or multi-strain formulations that require differing growth media. Here, we developed a flow-cytometry-based approach using SYTOX^TM Green dye to assess the viability of probiotic microorganisms in a multi-species, fibre-containing probiotic product and compared this to the traditional plate count method. This method was suitable for enumerating both total bacterial cells and the viable cell fraction in the complete product mixture, and could also be used to assess how stressors, such as gastric digestion and exposure to bile acids, affect bacterial cell viability. Flow cytometry measurements routinely detected higher viable cell counts than plate counting. This work demonstrates that flow cytometry assays can be established as a suitable method for rapid enumeration of viable cells in complex, multi-species probiotics. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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10 pages, 3326 KiB

Open AccessArticle

Population Dynamics in the Biogenesis of Single-/Multi-Layered Membrane Vesicles Revealed by Encapsulated GFP-Monitoring Analysis

by Sangho Koh, Shuhei Noda and Seiichi Taguchi

Appl. Microbiol. 2023, 3(3), 1027-1036; https://doi.org/10.3390/applmicrobiol3030070 - 2 Sep 2023

Cited by 2 | Viewed by 1731

Abstract

Various generations of membrane vesicles (MV) have been observed in Escherichia coli in terms of triggering events and populations of single-layered (s)/multi-layered (m) forms. Previously, we proposed a novel mechanism for MV generation triggered by the intracellular accumulation of biopolyester polyhydroxybutyrate (PHB). This [...] Read more.

Various generations of membrane vesicles (MV) have been observed in Escherichia coli in terms of triggering events and populations of single-layered (s)/multi-layered (m) forms. Previously, we proposed a novel mechanism for MV generation triggered by the intracellular accumulation of biopolyester polyhydroxybutyrate (PHB). This was designated as the Polymer Intracellular Accumulation-triggered system for Membrane Vesicle Production (PIA-MVP). Herein, we attempted to determine the conditions for the change in the population between s-MV and m-MV using glucose concentration-dependent PIA-MVP. PIA-MVP was established using the good correlation between the glucose concentration-dependent PHB accumulation and MV generation. Thus, we assumed the presence of a critical glucose concentration could determine the population ratio of s-MV to m-MV, indicating that s-MV generation is a dominant component in the extracellular environment. Cytoplasmic green fluorescent protein (GFP) was used to evaluate the glucose concentration, enabling the selective generation of s-MV. The glucose concentration was determined to be 15 g/L to satisfy this purpose under the culture conditions. In conclusion, we established a biological system allowing us to selectively generate both single- and multi-layered MVs based on PIA-VIP encapsulation of GFP, providing a versatile toolkit to gain insights into the MV generation mechanism and achieve progress in various engineering applications. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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25 pages, 4022 KiB

Open AccessArticle

Development of a Chicken Gastrointestinal Tract (GIT) Simulation Model: Impact of Cecal Inoculum Storage Preservation Conditions

by Nelson Mota de Carvalho, Célia Maria Costa, Cláudia Castro, Mayra Anton Dib Saleh, Manuela Estevez Pintado, Diana Luazi Oliveira and Ana Raquel Madureira

Appl. Microbiol. 2023, 3(3), 968-992; https://doi.org/10.3390/applmicrobiol3030066 - 22 Aug 2023

Cited by 2 | Viewed by 2812

Abstract

A chicken gastrointestinal tract (GIT) simulation model was developed to help predict the potential effects of feed additives supplementation on chicken’ microbiota. The chemical and enzymatic conditions for oral, gastric, intestinal, and cecum fermentation phases were designed to closely resemble the chicken GIT [...] Read more.

A chicken gastrointestinal tract (GIT) simulation model was developed to help predict the potential effects of feed additives supplementation on chicken’ microbiota. The chemical and enzymatic conditions for oral, gastric, intestinal, and cecum fermentation phases were designed to closely resemble the chicken GIT conditions. For cecum fermentation, the inoculum was obtained from the cecal contents of 18 38-day broiler chickens. The impact of inoculum preservation on bacteria viability was assessed by comparing two methods of preservation with fresh inoculum: (1) 5% dimethyl sulfoxide (DMSO) at −80 °C and (2) 30% glycerol at −20 °C. The fermentation with fresh and frozen (DMSO method) inoculums was performed and compared using standard chicken feed (SCF) and SCF with 1% fructooligosaccharides (FOS), and inoculum control (IC) condition without feed matrix was used as a baseline. Inoculum’s viability was assessed throughout 90 days of storage by culture media platting, while bacterial growth and metabolites production during fermentation was evaluated by quantitative polymerase chain reaction (qPCR), high-performance liquid chromatography (HPLC), and total ammonia nitrogen quantification. The DMSO method was shown to be the most suitable for cecal inoculum storage. Higher growth of beneficial cecal bacteria for fresh inoculum was observed in SCF while for frozen inoculum, was the SCF + FOS condition. Also, frozen inoculum had lower activity of butyrate producers and proteolytic bacteria, showing different fermentation profiles. The GIT model developed showed to be useful to test the effect of feed additives supplementation. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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19 pages, 1032 KiB

Open AccessReview

Salmonella: Role in Internal and External Environments and Potential as a Therapeutic Tool

by Patrick J. Naughton, Violetta R. Naughton and James S. G. Dooley

Appl. Microbiol. 2024, 4(4), 1515-1533; https://doi.org/10.3390/applmicrobiol4040104 - 8 Nov 2024

Viewed by 1301

Abstract

Salmonella has had a long and intimate relationship with humans and continues to raise concerns for human health, but this close bond also provides opportunities for new therapeutics and treatments. Although Salmonella enterica serovar Typhi is the principal organism that comes to mind [...] Read more.

Salmonella has had a long and intimate relationship with humans and continues to raise concerns for human health, but this close bond also provides opportunities for new therapeutics and treatments. Although Salmonella enterica serovar Typhi is the principal organism that comes to mind in terms of death and morbidity, it is the non-typhoidal Salmonellae that have the most health and economic implications. The developed world has had a challenging relationship with Salmonella, particularly in the UK and the EC/EU, experiencing significant Salmonella outbreaks in the 1980s and 1990s. As a consequence, the research focus was on understanding the nature of infection in food animals and on developing ways and means of controlling zoonotic infections. This led to the development of numerous model systems for the study of Salmonella both in vitro and in vivo. The introduction of vaccination has all but eliminated Salmonella in eggs and reduced perceived risk held by the general public. At the same time as Salmonella in eggs was being brought under control in the UK and EU, the danger posed by antibiotic resistance was beginning to emerge. In the past, with the efficacy of antibiotics against Gram-negative bacteria being unchallenged, there was limited focus on the threat posed by antibiotic resistance in non-typhoidal Salmonella. However, the identification of Salmonella as the first ‘multidrug-resistant’ organism, the presence of invasive non-typhoidal Salmonella in North Africa and the emergence of monophasic Salmonella enterica serovar Typhimurium across Europe, Asia and the Americas have prompted renewed interest in Salmonella research, particularly in the context of non-infectious disease, biofilm studies and antibiotic resistance. At the same time, research has continued to develop ways of taking advantage of what Salmonella offers in the way of pathogenic factors and the therapeutic and treatment applications in areas such as vaccine development, cancer therapeutics and drug delivery and the role of Salmonella in non-infectious diseases supported by developments in molecular and genomic methods. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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12 pages, 1124 KiB

Open AccessReview

The Rumen and Gastrointestinal Microbial Environment and Its Association with Feed Efficiency and Pregnancy in Female Beef Cattle

by M. Gabbi Martin, Juan F. Cordero-Llarena, Brynn H. Voy, Kyle J. McLean and Phillip R. Myer

Appl. Microbiol. 2024, 4(4), 1422-1433; https://doi.org/10.3390/applmicrobiol4040098 - 27 Sep 2024

Viewed by 1315

Abstract

With the anticipated population growth by 2050, the demand for high-quality protein for human consumption is set to rise. To enhance the sustainability of U.S. cattle production, producers and researchers have traditionally concentrated on improving the feed efficiency of steers through advancements in [...] Read more.

With the anticipated population growth by 2050, the demand for high-quality protein for human consumption is set to rise. To enhance the sustainability of U.S. cattle production, producers and researchers have traditionally concentrated on improving the feed efficiency of steers through advancements in genetics, nutrition, and microbiome tools, resulting in a more marketable beef product. However, without successful pregnancies, there would be no marketable animals to feed. Despite extensive research on hormonal impacts on cattle physiology, including nutrition and reproduction, there is limited knowledge about how the rumen microbial environment is impacted by pregnancy and feed efficiency in female beef cattle. Understanding the rumen microbiome’s role in feed efficiency and its response to hormonal changes during pregnancy is crucial for advancing sustainable beef cattle production. Therefore, this review highlights the importance of understanding the microbial dynamics in the rumen of pregnant beef females. Although progress has been made, gaps remain in understanding how varying nutritional requirements throughout pregnancy affect the rumen microbiome, highlighting the need for continued research. Addressing these areas will lead to more efficient and sustainable cattle production practices, benefiting beef production and contributing to global food security. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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14 pages, 883 KiB

Open AccessReview

Changes in the Skin Microbiome Following Dermatological Procedures: A Scoping Review

by Jeremy R. Ellis, Eron J. Powell, Luke M. Tomasovic, Rachel L. Marcheskie, Vishruth Girish, Anmol Warman and Darshan Sivaloganathan

Appl. Microbiol. 2024, 4(2), 972-985; https://doi.org/10.3390/applmicrobiol4020066 - 18 Jun 2024

Cited by 1 | Viewed by 2356

Abstract

The skin microbiome consists of bacteria, fungi, viruses, and mites, which play a crucial role in maintaining skin health and immune function. Imbalances in this microbial community, known as dysbiosis, are implicated in various dermatological conditions. While skincare products are known to influence [...] Read more.

The skin microbiome consists of bacteria, fungi, viruses, and mites, which play a crucial role in maintaining skin health and immune function. Imbalances in this microbial community, known as dysbiosis, are implicated in various dermatological conditions. While skincare products are known to influence the skin microbiome, the effects of dermatological procedures have not been extensively studied. Here, we perform a scoping review to outline the studies investigating the impacts of dermatological interventions on the skin microbiome. Phototherapy emerged as the most studied intervention, encompassing UV phototherapy, light therapy, laser therapy, and photodynamic therapy. Chemical interventions, such as chemical peels, micropigmentation, and debridement, have comparatively limited studies describing their impacts on the skin microbiome. To date, no studies have been done on a wide variety of common dermatological procedures such as cryotherapy, skin grafts, and dermabrasion, which may have stronger likelihoods of affecting the skin microbiome. This underscores the need for further research on the influences of dermatological procedures, especially chemical and physical interventions, on the skin microbiome. More comprehensive pre-clinical and clinical studies are essential not only for understanding the long-term consequences of these procedures, but also for optimizing patient outcomes in dermatological care. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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24 pages, 634 KiB

Open AccessReview

The Industrial Fermentation Process and Clostridium Species Used to Produce Biobutanol

by David T. Jones

Appl. Microbiol. 2024, 4(2), 894-917; https://doi.org/10.3390/applmicrobiol4020061 - 31 May 2024

Viewed by 1362

Abstract

The fermentation route for producing biobutanol from renewable plant biomass was used extensively during the last century. The key factors affecting performance in the standard batch industrial fermentation process are highlighted. Four species of Clostridium were utilized for the industrial production of solvents, [...] Read more.

The fermentation route for producing biobutanol from renewable plant biomass was used extensively during the last century. The key factors affecting performance in the standard batch industrial fermentation process are highlighted. Four species of Clostridium were utilized for the industrial production of solvents, and although they share many features in common, they also exhibit significant differences. The salient features of the existing industrial species and strains are reviewed. These include their suitability for the type of process and fermentation substrate used. The strains are also assessed with respect to their potential for future applications. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 619 KiB

Open AccessReview

The Influence of Technological Shifts in the Food Chain on the Emergence of Foodborne Pathogens: An Overview

by Saja Hamaideh, Amin N. Olaimat, Murad A. Al-Holy, Ahmad Ababneh, Hafiz Muhammad Shahbaz, Mahmoud Abughoush, Anas Al-Nabulsi, Tareq Osaili, Mutamed Ayyash and Richard A. Holley

Appl. Microbiol. 2024, 4(2), 594-606; https://doi.org/10.3390/applmicrobiol4020041 - 25 Mar 2024

Cited by 1 | Viewed by 2229

Abstract

The transformation of the food chain due to technological advances has had significant implications in regard to food safety. A noteworthy trend in this evolution relates to the emergence of new or previously unseen pathogens within products, thereby altering the landscape of foodborne [...] Read more.

The transformation of the food chain due to technological advances has had significant implications in regard to food safety. A noteworthy trend in this evolution relates to the emergence of new or previously unseen pathogens within products, thereby altering the landscape of foodborne illness epidemiology. The escalating frequency of these events underscores the need for a comprehensive re-evaluation of preventive strategies. The occurrence of novel species of bacteria, viruses, parasites, and unusual biotoxins from unexpected sources has challenged the previous limits that had been set to prevent foodborne illness outbreaks. The repercussions, ranging from detrimental effects on public health to economic burden, are influenced by a myriad of factors affecting the evolution of foodborne pathogens and emerging ailments. Among these factors are shifts in population demographics and behaviors, especially dietary patterns, as well as climate extremes, advances in more precise pathogen detection, microbial adaptation, evolving agricultural practices, and transformative changes within the food industry. This review critically examines the impact of technological metamorphosis along the food chain, encompassing production, processing, handling, packaging, storage, transportation, and industry demographics on the dynamics influencing the emergence of foodborne pathogens. Additionally, potential solutions to mitigate and manage this escalating issue are proposed. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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21 pages, 1481 KiB

Open AccessReview

Sustainability of Biogas Production from Anaerobic Digestion of Food Waste and Animal Manure

by Sharath Kumar Ankathi, Utkarsh S. Chaudhari, Robert M. Handler and David R. Shonnard

Appl. Microbiol. 2024, 4(1), 418-438; https://doi.org/10.3390/applmicrobiol4010029 - 21 Feb 2024

Cited by 5 | Viewed by 5831

Abstract

Anaerobic digestion (AD) involves a set of microbiological reactions and physio-chemical processes to generate biogas, a mixture of predominantly CH₄ and CO₂. It is commercialized globally; however, AD has limited commercial applications in the U.S. compared to other regions of [...] Read more.

Anaerobic digestion (AD) involves a set of microbiological reactions and physio-chemical processes to generate biogas, a mixture of predominantly CH₄ and CO₂. It is commercialized globally; however, AD has limited commercial applications in the U.S. compared to other regions of the world. The main objective of this article is to review different studies on socio-economic and environmental aspects and policies of biogas/biomethane production and to focus on resource availability. The key outcome from this review shows that the anaerobic digestion of food waste and animal manure has great potential to achieve economic and environmental benefits compared to other waste management techniques such as landfilling or conventional manure management. The 12 life cycle assessment (LCA) studies reviewed showed lower impacts for biogas systems and indicated a need for standardization of methodology so that alternative production concepts can be objectively compared. Similarly, economic analyses showed higher profitability for a biogas combined heat and power facility compared to a biomethane facility. By considering a review of the sustainability of biogas, we presented a new multi-criteria sustainable assessment framework that includes three domains: i. resource availability and logistics, ii. process modeling, and iii. impact assessment with primary application to the optimum location and installation of sustainable biogas/biomethane plants in the U.S. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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25 pages, 3237 KiB

Open AccessReview

Role of Bacteria-Derived Exopolysaccharides in Inflammatory Bowel Disease with a Special Focus on Cyanobacterial Exopolysaccharides

by Devaprakash Manoharan, Sivakumar Natesan, Muriel Billamboz and Samir Jawhara

Appl. Microbiol. 2024, 4(1), 250-274; https://doi.org/10.3390/applmicrobiol4010017 - 23 Jan 2024

Cited by 3 | Viewed by 2061

Abstract

Instances of inflammatory bowel disease (IBD), a chronic inflammatory condition of the gastrointestinal tract, are rapidly increasing in western and newly industrialized countries. Exopolysaccharides (EPSs) are one of the strategies to enhance the gut microbiota and modulate the immune-inflammatory response deregulation in IBD [...] Read more.

Instances of inflammatory bowel disease (IBD), a chronic inflammatory condition of the gastrointestinal tract, are rapidly increasing in western and newly industrialized countries. Exopolysaccharides (EPSs) are one of the strategies to enhance the gut microbiota and modulate the immune-inflammatory response deregulation in IBD patients. EPSs are produced by commensal bacteria such as Lactobacillus and Bifidobacterium. Additionally, Cyanobacteria species are promising sources of novel EPS and have potential pharmaceutical and therapeutic applications. The presence of uronic acids and sulphate groups in Cyanobacterial EPSs is an important factor that gives EPSs an anionic charge that is not seen in other prokaryotic species. This feature may impact their physico-chemical characteristics and biological properties. Additionally, Cyanobacterial EPSs have a wide range of biotechnological applications that include use as thickeners, stabilizers, and gelling agents in the food and pharmaceutical sectors. The present review focuses on the role of EPSs in IBD, with a special focus on EPSs derived from Cyanobacteria. This review also covers the biological properties of Cyanobacterial EPS in immuno-inflammatory responses and against pathogens as well as its role in biotechnological applications. Overall, Cyanobacterial EPSs have therapeutic potential against IBD due to their anti-inflammatory and immunoregulatory properties that can reduce inflammation and regulate the immune response and restore the gut microbiota of patients. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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23 pages, 2001 KiB

Open AccessReview

Systematic Review of Probiotics and Their Potential for Developing Functional Nondairy Foods

by Ricardo S. Aleman and Ajitesh Yadav

Appl. Microbiol. 2024, 4(1), 47-69; https://doi.org/10.3390/applmicrobiol4010004 - 26 Dec 2023

Cited by 6 | Viewed by 4742

Abstract

The gastrointestinal tract is an environment that hosts various microorganisms, including pathogens. Generally, pathogenic bacteria enter the host body through food and the gastrointestinal tract. These pathogenic bacteria can colonize or infiltrate host cells and tissues, causing various infectious diseases. In recent years, [...] Read more.

The gastrointestinal tract is an environment that hosts various microorganisms, including pathogens. Generally, pathogenic bacteria enter the host body through food and the gastrointestinal tract. These pathogenic bacteria can colonize or infiltrate host cells and tissues, causing various infectious diseases. In recent years, the protective role of probiotic bacteria against gastrointestinal pathogens has been carefully investigated. Probiotics have been found to modulate intestinal microbial flora and play a significant role in the gastrointestinal tract’s function, especially by inhibiting the growth of pathogenic bacteria. However, the mechanism of action of probiotics has yet to be sufficiently proven and recognized. Several important mechanisms support the antagonistic effects of probiotics on various microorganisms, which is achieved, for example, through the production of different antimicrobial compounds, such as bacteriocins, various organic acids, antibiotics, antimicrobial proteins, and exopolysaccharides; mucosal barriers with mucosa and bacteria binding blockers; competition for nutrient uptake; and strengthening of the immune system. Accordingly, this review summarizes the recent studies that have examined the mechanism of action of probiotic bacteria and their beneficial effects in preventing pathogenic bacterial growth and improving gastrointestinal functions. Comprehending their mechanisms of action allows the selection of appropriate probiotic strains for specific applications in gastrointestinal dysfunction. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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13 pages, 731 KiB

Open AccessReview

Exopolysaccharides Synthesized by Rhizospheric Bacteria: A Review Focused on Their Roles in Protecting Plants against Stress

by María Evangelina Carezzano, Florencia Belén Alvarez Strazzi, Verónica Pérez, Pablo Bogino and Walter Giordano

Appl. Microbiol. 2023, 3(4), 1249-1261; https://doi.org/10.3390/applmicrobiol3040086 - 16 Nov 2023

Cited by 8 | Viewed by 2090

Abstract

Plants are constantly exposed to a wide range of environmental factors that cause different kinds of stress, such as drought, salinity, heat, frost, and low nutrient availability. There are also biotic sources of stress, which include pathogens (bacteria, viruses, pests), herbivores, and plant [...] Read more.

Plants are constantly exposed to a wide range of environmental factors that cause different kinds of stress, such as drought, salinity, heat, frost, and low nutrient availability. There are also biotic sources of stress, which include pathogens (bacteria, viruses, pests), herbivores, and plant competitors. These various types of stress affect normal plant physiology and development, and may lead to significantly lower yields. However, certain microorganisms (MOs), known as plant growth-promoting rhizobacteria (PGPR), can interact with and benefit plants in stressful environments. They do so through a series of mechanisms which contribute to minimizing the negative effects of plants’ responses to stress. This review summarizes current knowledge about those mechanisms, with a focus on the production of exopolysaccharides (EPSs). These compounds can act as osmoprotectants, promote the production of phytohormones, prevent the entry of pathogens through roots, bioremediate metals, and improve soil structure and permeability, among many other beneficial effects. This makes them suitable alternatives to guarantee food security while reducing the excessive use of chemical agricultural inputs and their harmful consequences for the environment. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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10 pages, 1240 KiB

Open AccessBrief Report

Phenotypic and Draft Genome Sequence Analyses of a Paenibacillus sp. Isolated from the Gastrointestinal Tract of a North American Gray Wolf (Canis lupus)

by Jennifer McCabe, Jessika L. Bryant, C. Cristoph Klews, MiCayla Johnson, Ariel N. Atchley, Thomas W. Cousins, Analiska Dominguez, Marie Gabriel, Katie Middleton, Natasha A. Bowles, Heather M. Broughton, Kristina M. Smith, Mark R. Ackermann, Robert Bildfell, Patrick N. Ball, Evan S. Forsythe and Bruce S. Seal

Appl. Microbiol. 2023, 3(4), 1120-1129; https://doi.org/10.3390/applmicrobiol3040077 - 23 Sep 2023

Cited by 1 | Viewed by 12620

Abstract

The discovery of novel probiotic bacteria from free-ranging animals for the treatment of inflammatory bowel disease in domestic pets is a unique approach. The chloroform extraction of gastrointestinal (GI) tract material was used to inactivate vegetative cells and select for spore-forming bacteria. A [...] Read more.

The discovery of novel probiotic bacteria from free-ranging animals for the treatment of inflammatory bowel disease in domestic pets is a unique approach. The chloroform extraction of gastrointestinal (GI) tract material was used to inactivate vegetative cells and select for spore-forming bacteria. A bacterium identified as a novel Paenibacillus sp. strain via small ribosomal RNA (16S) gene sequencing was isolated from the GI tract of a gray wolf (Canis lupus). The bacterium was typed as Gram-variable, both catalase/oxidase-positive and positive via starch hydrolysis and lipase assays. The bacterium inhibited the growth of Staphylococcus aureus, Escherichia coli and Micrococcus luteus. The draft whole genome sequence (WGS) assembly was 7,034,206 bp in length, encoding 6543 genes, and is similar in size and coding capacity to other closely related Paenibacillus spp. The isolate’s genome encodes several germination and sporulation gene products along with antimicrobials such as a bacteriocin system and chitinase. Enzyme genes such as alpha amylase, cellulase, lipases and pectin lyase are also present in the genome. An incomplete lysogenic bacteriophage genome was also present in the isolate’s genome. Phenotypic characteristics combined with a WGS genotype analysis indicate that this bacterium, designated Paenibacillus sp. ClWae2A, could be a potential candidate probiotic for domestic dogs. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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11 pages, 1022 KiB

Open AccessCase Report

Salmonella Enteritidis ST11 Prosthetic Valve Endocarditis Complicated by a Paravalvular Abscess: Case Report and Literature Review

by Shiori Kitaya, Shintaro Katahira, Hiroaki Baba, Yoshikatsu Saiki, Yukio Katori, Koichi Tokuda and Hajime Kanamori

Appl. Microbiol. 2023, 3(3), 1057-1067; https://doi.org/10.3390/applmicrobiol3030073 - 8 Sep 2023

Viewed by 1631

Abstract

Salmonella infection typically causes self-limiting gastroenteritis. However, in rare cases, it can lead to prosthetic valve endocarditis (PVE), especially in older adults with a history of valve replacement surgery. In this case study, we describe a case of Salmonella PVE in a man [...] Read more.

Salmonella infection typically causes self-limiting gastroenteritis. However, in rare cases, it can lead to prosthetic valve endocarditis (PVE), especially in older adults with a history of valve replacement surgery. In this case study, we describe a case of Salmonella PVE in a man with a prosthetic aortic valve. Complications of PVE include abscess formation, which is associated with increased mortality. If a patient with a history of prosthetic valve replacement presents with symptoms suggestive of gastroenteritis or bacteremia, a thorough investigation should be conducted with suspicion of PVE. The prognosis of Salmonella PVE can be improved by promptly initiating appropriate antibiotics and administering them for an adequate duration, as well as by considering surgical intervention when necessary. Additionally, confirming negative blood cultures after treatment of Salmonella bacteremia is important to prevent the development of PVE and paravalvular abscesses. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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11 pages, 2012 KiB

Open AccessCase Report

Diabetic Foot Osteomyelitis Caused by Co-Infection with Methicillin-Resistant Staphylococcus aureus and Multidrug-Resistant Extended-Spectrum ß-Lactamase-Producing Escherichia coli: A Case Report

by Shiori Kitaya, Chieko Miura, Ayano Suzuki, Yoshimichi Imai, Koichi Tokuda and Hajime Kanamori

Appl. Microbiol. 2023, 3(3), 1046-1056; https://doi.org/10.3390/applmicrobiol3030072 - 7 Sep 2023

Cited by 1 | Viewed by 2394

Abstract

This case report describes a 47-year-old man with type 2 diabetes and its associated complications. The patient developed co-infection with methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant (MDR) extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli following surgical amputation for osteomyelitis caused by diabetic foot infection (DFI). [...] Read more.

This case report describes a 47-year-old man with type 2 diabetes and its associated complications. The patient developed co-infection with methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant (MDR) extended-spectrum ß-lactamase (ESBL)-producing Escherichia coli following surgical amputation for osteomyelitis caused by diabetic foot infection (DFI). The patient had a history of recurrent hospitalization due to DFI and had received multiple antimicrobials. Intraoperative wound cultures identified MRSA and MDR ESBL-producing E. coli as the causative agents of the co-infection. Intravenous vancomycin and meropenem were administered. After surgery, daily debridement and hyperbaric oxygen therapy were performed. The patient underwent surgical wound closure and was discharged on day 86. Polymicrobial infections in DFIs worsen antimicrobial resistance, impede wound healing, and increase the risk of osteomyelitis and amputation. Furthermore, infections caused by MDR bacteria exacerbate challenges in infection control, clinical treatment, and patient outcomes. In DFI cases caused by co-infection with MDR bacteria, prompt and appropriate antimicrobial therapy, debridement, and regular wound care while considering transmission are essential. Full article

(This article belongs to the Special Issue Exclusive Papers Collection of Editorial Board Members and Invited Scholars in Applied Microbiology (2023, 2024))

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