Microorganisms

18 pages, 2847 KiB

Open AccessArticle

Microplastic Categories Distinctively Impact Wastewater Bacterial Taxonomic Composition and Antimicrobial Resistance Genes

by Tam Thanh Tran, Kabelo Stephans Stenger, Marte Strømmen, Cornelius Carlos Bezuidenhout and Odd-Gunnar Wikmark

Microorganisms 2025, 13(2), 260; https://doi.org/10.3390/microorganisms13020260 - 24 Jan 2025

Abstract

Wastewater treatment plants (WWTPs) may serve as hotspots for pathogens and promote antimicrobial resistance (AMR). Plastic debris in wastewater could further contribute to AMR dissemination. The aim of this study was to investigate the impact of various microplastic types on bacterial communities and [...] Read more.

Wastewater treatment plants (WWTPs) may serve as hotspots for pathogens and promote antimicrobial resistance (AMR). Plastic debris in wastewater could further contribute to AMR dissemination. The aim of this study was to investigate the impact of various microplastic types on bacterial communities and AMR gene abundance in wastewater that were obtained from two WWTPs, one in Tromsø, Norway, and the other one in Potchefstroom, South Africa. The microcosm experiments were designed as follows: Five manufactured microplastic pellet types were used for testing, and two rock aggregate types were used as controls. In addition, each material type was subjected to artificial aging treatments using either ultra-violet light or hydrogen peroxide. Each material was incubated in flasks containing inlet/outlet wastewater obtained from these two WWTPs. Nucleic acids were extracted after a one-week incubation period. The detection of the bla_FOXand bla_MOX genes was performed using quantitative PCR. Extracted DNA was sequenced using a MinION device. Non-metric multi-dimensional scaling plot on full-length 16S sequencing data at the species level showed that samples were clustered into distinct material groups, which were in line with the ANOSIM test. The Indicator Species Analysis showed a strong association between many Acinetobacter species with the plastic group than the rock group. Aging treatment using hydrogen peroxide showed some effects on microbial composition in the outlet wastewater. The abundance of bla_FOX and bla_MOX genes in the Norwegian wastewater outlet were generally lower compared to those in the inlet, though the results were contrary in South African wastewater samples. The relative abundance of AMR genes seemed to be increased on several plastic types (PET, PE, and PLA) but decreased on PVC-A. WWTP treatments in this study did not effectively reduce the abundance of AMR genes. An in-depth understanding the role of specific microplastic type on bacterial communities and AMR profiles is, therefore, needed to combat AMR threat. Full article

(This article belongs to the Special Issue Virulence and Antimicrobial Resistance of Microorganisms in Wastewater Environments)

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13 pages, 2852 KiB

Open AccessArticle

Effect of Multiyear Biodegradable Plastic Mulch on Soil Microbial Community, Assembly, and Functioning

by Xiaowei Liu, Zongyu Wen, Wei Zhou, Wentao Dong, Huiqing Ren, Gang Liang and Wenwen Gong

Microorganisms 2025, 13(2), 259; https://doi.org/10.3390/microorganisms13020259 - 24 Jan 2025

Abstract

The increasing use of biodegradable plastic mulch like polybutylene adipate terephthalate (PBAT) has raised concerns about its long-term environmental impact. In this study, we investigated the effects of multiyear PBAT mulch application on bacterial and fungal communities, assembly mechanisms, and key ecological functions. [...] Read more.

The increasing use of biodegradable plastic mulch like polybutylene adipate terephthalate (PBAT) has raised concerns about its long-term environmental impact. In this study, we investigated the effects of multiyear PBAT mulch application on bacterial and fungal communities, assembly mechanisms, and key ecological functions. The microbial community diversity and composition were significantly altered after multiyear biodegradable plastic mulching. We observed that PBAT treatment enriched specific bacterial genera, such as Pantoea, potentially involved in plastic degradation, and fungal genera like Cephaliophora and Stephanosporaceae, which may play a role in organic matter decomposition. A null model analysis revealed that bacterial community assembly was largely shaped by deterministic processes, with stronger environmental selection pressures in PBAT-treated soils, while fungal communities were more influenced by stochastic processes. In addition, multiyear PBAT mulch application also impacted the functionality of the soil microbial communities. PBAT exposure enhanced biofilm formation in aerobic bacteria, promoting aerobic degradation processes while also reducing the abundance of stress-tolerant bacteria. Additionally, PBAT altered key microbial functions related to carbon, nitrogen, and sulfur cycling. Notably, the fungal communities exhibited functional shifts, with an increase in saprotrophic fungi being beneficial for nutrient cycling, alongside a potential rise in plant pathogenic fungi. These findings underscore the multiyear ecological impacts of biodegradable plastics, suggesting microbial adaptation to plastic degradation and changes in key ecological functions, with implications for agricultural sustainability and bioremediation strategies. Full article

(This article belongs to the Section Environmental Microbiology)

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17 pages, 1080 KiB

Open AccessArticle

Genomic and Proteomic Analyses of Bacterial Communities of Ixodes scapularis Ticks from Broome County, New York

by Michel Shamoon-Pour, Emily H. Canessa, John Macher, Amaan Fruitwala, Emma Draper, Benjamin Policriti, Matthew Chin, Matthew Nunez, Paul Puccio, Yuan Fang, Xin-Ru Wang and Yetrib Hathout

Microorganisms 2025, 13(2), 258; https://doi.org/10.3390/microorganisms13020258 - 24 Jan 2025

Abstract

The microbial communities of Ixodes scapularis, the primary vector of Lyme disease in North America, exhibit regional variations that may affect pathogen transmission and vector competence. We analyzed bacterial communities in I. scapularis ticks collected from Broome County, New York, using 16S [...] Read more.

The microbial communities of Ixodes scapularis, the primary vector of Lyme disease in North America, exhibit regional variations that may affect pathogen transmission and vector competence. We analyzed bacterial communities in I. scapularis ticks collected from Broome County, New York, using 16S rRNA gene sequencing (18 ticks) as well as mass spectrometry-based proteomics (36 ticks). According to the 16S rRNA analysis, the endosymbiont Rickettsia buchneri was the most abundant species, with significantly higher (p = 0.0011) abundance in females (54.76%) compared to males (31.15%). We detected Borreliella burgdorferi in 44.44% of ticks and Anaplasma phagocytophilum in two nymphs but in high relative abundances (12.73% and 46.46%). Male ticks exhibited higher bacterial diversity, although the community composition showed no significant clustering by sex or life stage. Co-occurrence analysis revealed negative associations between R. buchneri and Pseudomonas (p = 0.0245), but no associations with B. burgdorferi. Proteomic analysis identified 12 R. buchneri-specific proteins, additionally detecting the protozoan pathogen Babesia microti in 18.18% of females. These findings provide the first comprehensive characterization of I. scapularis microbiomes in the Southern Tier region of New York and suggest broader distribution of R. buchneri across tick life stages than previously recognized, with potential implications for pathogen transmission dynamics. Full article

(This article belongs to the Special Issue Advanced Research on Ticks and Tick-Borne Diseases: 2nd Edition)

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21 pages, 1637 KiB

Open AccessReview

Probiotics in Poultry: Unlocking Productivity Through Microbiome Modulation and Gut Health

by Muhammad Naeem and Dianna Bourassa

Microorganisms 2025, 13(2), 257; https://doi.org/10.3390/microorganisms13020257 - 24 Jan 2025

Abstract

This review explores the role of probiotics in improving productivity and gut health in poultry through microbiome modulation, particularly during early life. Gut health is pivotal to poultry performance, influencing nutrient absorption, immune function, and disease resistance. Early-life interventions target the microbiome to [...] Read more.

This review explores the role of probiotics in improving productivity and gut health in poultry through microbiome modulation, particularly during early life. Gut health is pivotal to poultry performance, influencing nutrient absorption, immune function, and disease resistance. Early-life interventions target the microbiome to shape long-term health and productivity. Probiotics, live microorganisms providing health benefits, improve gut health through the competitive exclusion of pathogens, immune modulation, antimicrobial compound production, and enhancing gut barrier integrity. Applying probiotics improves growth performance, feed conversion efficiency, body weight gain, and carcass quality by promoting lean muscle growth and reducing fat deposition. For laying hens, probiotics enhance egg production and quality. These benefits are linked to better nutrient utilization, a well-balanced microbiome, and reduced gastrointestinal disorders. However, the efficacy of probiotics depends on strain specificity, dosage, and administration methods. Factors like environmental conditions, storage stability, and interactions with other feed additives also influence their effectiveness. Despite these challenges, advancements in microbiome research and probiotic technologies, such as precision probiotics and synbiotics, provide promising solutions. Future research should focus on optimizing formulations, understanding host–microbiome interactions, and leveraging new technologies for targeted microbiome management. Full article

(This article belongs to the Special Issue Probiotics, Prebiotics, and Synbiotics in Animal Nutrition and Health, and Food Safety)

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11 pages, 1090 KiB

Open AccessCommunication

Causal Association Between the Mucosal and Luminal Microbiotas from the Gastrointestinal Tract of Weaned Piglets Using Bayesian Network

by Shu Yoshimura, Takamitsu Tsukahara, Toru Takahashi, Hiroto Miura, So Morishima, Masaaki Kise, Jiye Shin, Yoshihiro Yahara and Ryo Inoue

Microorganisms 2025, 13(2), 256; https://doi.org/10.3390/microorganisms13020256 - 24 Jan 2025

Abstract

The aim of this study was to investigate the microbiota composition and its potential interactions across seven gut locations (stomachs, jejuna, ilea, ceca, proximal colons, distal colons, and recta) in weaned pigs to identify key influencing microbiotas. To compare between microbiota compositions, 16S [...] Read more.

The aim of this study was to investigate the microbiota composition and its potential interactions across seven gut locations (stomachs, jejuna, ilea, ceca, proximal colons, distal colons, and recta) in weaned pigs to identify key influencing microbiotas. To compare between microbiota compositions, 16S rRNA gene amplicon sequencing was performed. Six 70-day-old healthy crossbred (Duroc × Large White × Landrace) piglets were introduced as donors. A Bayesian network (BN) was used to examine the directional interactions among the microbiotas evaluated (seven mucosal and seven digesta microbiotas). Based on edge connectivity frequency, the microbiota in jejunal mucosa was the central hub node, influencing other microbiotas, especially the mucosal microbiotas of the ileum, cecum, distal colon, and rectum. The jejunal mucosa was dominated by Prevotella and lactobacilli, both recognized for their contributions to pig health. Among Prevotella, Prevotella copri and Prevotella sp. were predominant in jejunal mucosa (4.6% and 2.9%, respectively). Lactobacilli, including eight distinct species, were distributed throughout the gastrointestinal tract. Notably, Ligilactobacillus salivarius and Lactobacillus amylovorus, known as immune-enhancing bacteria, were abundant in jejunal mucosa (1.0% and 0.8%) and digestas (0.9% and 19.2%), respectively. The BN identified rectal mucosa and digestas as two terminal nodes, influenced by upstream microbiotas in the gastrointestinal tract. This finding supports the link between fecal microbiota and pig productivity, as the fecal microbiota, closely resembling the rectal microbiota, reflects the conditions of the microbiota throughout the gastrointestinal tract. Full article

(This article belongs to the Special Issue Gut Microbiota: Metagenomics to Study Ecology, 2nd Edition)

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14 pages, 736 KiB

Open AccessReview

Gut Microbes as the Major Drivers of Rheumatoid Arthritis: Our Microbes Are Our Fortune!

by Veena Taneja

Microorganisms 2025, 13(2), 255; https://doi.org/10.3390/microorganisms13020255 - 24 Jan 2025

Abstract

Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology. While certain genes provide strong susceptibility factors, the role of environmental factors is becoming increasingly recognized. Among genetic factors, human leukocyte antigen (HLA) genes, encoded within the major histocompatibility complex (MHC), have [...] Read more.

Rheumatoid arthritis (RA) is an autoimmune disease with an unknown etiology. While certain genes provide strong susceptibility factors, the role of environmental factors is becoming increasingly recognized. Among genetic factors, human leukocyte antigen (HLA) genes, encoded within the major histocompatibility complex (MHC), have been linked to predisposition to RA, while among environmental factors, smoking, infections and diet are the major contributors. Genetic and environmental factors impact microbial composition in the host. Based on the dysbiosis observed in the gut and lung microbiome, a mucosal origin of RA has been suggested. However, proving whether genes or microbes provide a stronger risk factor has been difficult. Studies from RA patients and various mouse models, specifically humanized mice expressing HLA class II genes, have been instrumental in defining the role of environmental factors such as smoking and endogenous small intestinal microbes in modulating arthritis severity. The consensus based on most studies support an interaction between host genetic and environmental factors in the onset and severity of disease. However, until now, no microbial markers for disease prognosis or treatment efficacy have been available. Here, the role of gut microbes as markers of disease severity, and the potential for using endogenous commensals for modulating immune responses to suppress inflammation in the context of genetic factors, are discussed. Full article

(This article belongs to the Special Issue Gut Microbiome in Homeostasis and Disease, 2nd Edition)

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26 pages, 1624 KiB

Open AccessArticle

Supplementation with Lactiplantibacillus plantarum CNPC003 and Pilosocereus gounellei Flour Enhances the Properties of Goat Cream Cheese

by Daniela Karla Medeiros Vasconcelos, Evandro Leite de Souza, Márcia Gabrielle Silva Viana, Maria Isabel Ferreira Campos, Lorena Lucena de Medeiros, Lary Souza Olegário, Mércia de Sousa Galvão, Karina Maria Olbrich dos Santos, Antônio Silvio do Egito, Marta Suely Madruga, Marcos dos Santos Lima, Tatiane Santi Gadelha, Maria Teresa Bertoldo Pacheco, Kataryne Árabe Rimá de Oliveira and Maria Elieidy Gomes de Oliveira

Microorganisms 2025, 13(2), 254; https://doi.org/10.3390/microorganisms13020254 - 24 Jan 2025

Abstract

This study evaluated the impacts of Lactiplantibacillus plantarum CNPC003 and xique-xique flour supplementation on the technological, physicochemical, nutritional, and sensory properties of goat cream cheese over 21 days of refrigerated storage. Four cheese formulations were prepared: a control (CC), one with L. plantarum [...] Read more.

This study evaluated the impacts of Lactiplantibacillus plantarum CNPC003 and xique-xique flour supplementation on the technological, physicochemical, nutritional, and sensory properties of goat cream cheese over 21 days of refrigerated storage. Four cheese formulations were prepared: a control (CC), one with L. plantarum CNPC003 (PC), one with xique-xique flour (XC), and one with L. plantarum CNPC003 and xique-xique flour (PXC). XC and PXC had a yellowish-green hue with less brightness. PC and PXC were less firm and adhesive with greater elasticity, cohesiveness, and gumminess, and they had reduced total protein and increased total free amino acids (p < 0.05) during storage. The contents of specific volatile compounds increased in PXC during storage. PXC had higher L. plantarum counts than PC on day 21 of storage. PC and PXC had distinct colors and textures and were well accepted regarding sensory attributes. Xique-xique flour and L. plantarum CNPC003 supplementation positively impact the nutritional and functional characteristics of goat cream cheese without negatively affecting the technological and sensory attributes. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series on Fermented Foods: Diversity, Traditional Heritage and Innovation)

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12 pages, 3005 KiB

Open AccessArticle

SARS-CoV-2 XEC: A Genome-Based Survey

by Fabio Scarpa, Francesco Branda, Giancarlo Ceccarelli, Chiara Romano, Chiara Locci, Noemi Pascale, Ilenia Azzena, Pier Luigi Fiori, Marco Casu, Stefano Pascarella, Miriana Quaranta, Domenico Benvenuto, Roberto Cauda, Massimo Ciccozzi and Daria Sanna

Microorganisms 2025, 13(2), 253; https://doi.org/10.3390/microorganisms13020253 - 24 Jan 2025

Abstract

Recombination, a process of genetic exchange between distinct organisms, has played a critical role in the emergence of SARS-CoV-2 variants such as the XEC recombinant. This study provides a detailed genomic and structural characterization of XEC, derived from the recombination of lineages KP.3.3 [...] Read more.

Recombination, a process of genetic exchange between distinct organisms, has played a critical role in the emergence of SARS-CoV-2 variants such as the XEC recombinant. This study provides a detailed genomic and structural characterization of XEC, derived from the recombination of lineages KP.3.3 (donor) and KS.1.1 (acceptor). Phylogenomic analyses reveal that XEC and its descendant XEC.1 form a monophyletic clade with close evolutionary ties to KP.3.3. The genomic breakpoint, spanning nucleotide positions 22,363–22,463, marks the shift from KS.1.1 to KP.3.3 within the spike protein gene. Mutational analysis highlights shared traits with its parental lineages, including mutations associated with immune evasion, receptor affinity, and fusogenicity. Notable changes, such as Q493E and L455S, may confer unique immunogenic properties, though XEC’s overall immune escape potential is limited by the absence of new mutations in conserved epitopes. Despite these mutations, XEC demonstrates restricted geographical spread, low genetic variability, and an evolutionary trajectory indicative of an evolutionary dead-end. Bayesian Skyline Plot analysis corroborates this, showing stable but declining population size. These findings underscore the need for ongoing genomic surveillance to monitor recombinant variants’ characteristics and public health impact. This study contributes to understanding viral evolution and highlights the importance of distinguishing variants of concern from those with minimal epidemiological significance. Full article

(This article belongs to the Special Issue Microbial Genome Analysis and Interpretation Using Computational Approaches—Second Edition)

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15 pages, 1735 KiB

Open AccessArticle

The Impact of Compounds Released from Damaged Salad Leaves on the Growth and Virulence of Listeria monocytogenes

by Asma Alsharif, Lama Aldawsari, Giannis Koukkidis and Primrose Freestone

Microorganisms 2025, 13(2), 252; https://doi.org/10.3390/microorganisms13020252 - 24 Jan 2025

Abstract

Background: Fresh produce such as leafy green salads have recently become recognized as a potential source of food-borne infection by enteric pathogens This study investigated whether compounds released from damaged salad leaves were recognized by Listeria monocytogenes strain EGD and if they impacted [...] Read more.

Background: Fresh produce such as leafy green salads have recently become recognized as a potential source of food-borne infection by enteric pathogens This study investigated whether compounds released from damaged salad leaves were recognized by Listeria monocytogenes strain EGD and if they impacted its growth and virulence. Methods: The effects of extracts of salad leaves or salad bag fluids were tested on the growth, biofilm formation, and colonization of salad leaves and host cell virulence. Results: The presence of salad extract at a concentration of less than 0.5% v/v and salad bag fluids at a concentration of 10% v/v enhanced the growth in water and serum-based medium by more than 10,000 times over un-supplemented control cultures. Light and scanning electron microscopy, as well as eukaryotic Caco-2 and Galleria mellonella models of infection, showed that leafy green extracts from rocket, lettuce, spinach, and their salad bag fluids significantly increased the ability of Listeria to establish biofilms and infect host cells. Conclusions: This investigation showed that salad leaf extracts can markedly enhance bacterial virulence, which has implications for bagged salad leaf consumer safety if the leaves become contaminated with pathogenic bacteria such as Listeria. Full article

(This article belongs to the Special Issue Plant Extracts and Antimicrobials, Second Edition)

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22 pages, 3198 KiB

Open AccessArticle

Metabolic Responses, Cell Recoverability, and Protein Signatures of Three Extremophiles: Sustained Life During Long-Term Subzero Incubations

by Marcela Ewert, Brook L. Nunn, Erin Firth and Karen Junge

Microorganisms 2025, 13(2), 251; https://doi.org/10.3390/microorganisms13020251 - 24 Jan 2025

Abstract

Few halophilic strains have been examined in detail for their culturability and metabolic activity at subzero temperatures, within the ice matrix, over the longer term. Here, we examine three Arctic strains with varied salinity tolerances: Colwellia psychrerythraea str. 34H (Cp34H), Psychrobacter sp. str. [...] Read more.

Few halophilic strains have been examined in detail for their culturability and metabolic activity at subzero temperatures, within the ice matrix, over the longer term. Here, we examine three Arctic strains with varied salinity tolerances: Colwellia psychrerythraea str. 34H (Cp34H), Psychrobacter sp. str. 7E (P7E), and Halomonas sp. str. 3E (H3E). As a proxy for biosignatures, we examine observable cells, metabolic activity, and recoverability on 12-month incubations at −5, −10 and −36 °C. To further develop life-detection strategies, we also study the short-term tracking of new protein synthesis on Cp34H at −5 °C for the first time, using isotopically labeled ¹³C₆-leucine and mass spectrometry-based proteomics. All three bacterial species remained metabolically active after 12 months at −5 °C, while recoverability varied greatly among strains. At −10 and −36 °C, metabolic activity was drastically reduced and recoverability patterns were strain-specific. Cells were observable at high numbers in all treatments, validating their potential as biosignatures. Newly synthesized proteins were detectable and identifiable after one hour of incubation. Proteins prioritized for synthesis with the provided substrate are involved in motility, protein synthesis, and in nitrogen and carbohydrate metabolism, with an emphasis on structural proteins, enzymatic activities in central metabolic pathways, and regulatory functions. Full article

(This article belongs to the Special Issue Advances in Halophilic Microorganisms)

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22 pages, 1653 KiB

Open AccessReview

The Role of Gut Microbiota Dysbiosis in Erectile Dysfunction: From Pathophysiology to Treatment Strategies

by Aris Kaltsas, Ilias Giannakodimos, Eleftheria Markou, Konstantinos Adamos, Marios Stavropoulos, Zisis Kratiras, Athanasios Zachariou, Fotios Dimitriadis, Nikolaos Sofikitis and Michael Chrisofos

Microorganisms 2025, 13(2), 250; https://doi.org/10.3390/microorganisms13020250 - 23 Jan 2025

Abstract

Erectile dysfunction (ED) is a prevalent male sexual disorder characterized by the persistent inability to achieve or maintain an erection sufficient for satisfactory sexual performance. While its etiology is multifactorial, encompassing vascular, neurological, hormonal, and psychological components, emerging evidence suggests a significant role [...] Read more.

Erectile dysfunction (ED) is a prevalent male sexual disorder characterized by the persistent inability to achieve or maintain an erection sufficient for satisfactory sexual performance. While its etiology is multifactorial, encompassing vascular, neurological, hormonal, and psychological components, emerging evidence suggests a significant role for gut microbiota dysbiosis in its development. The gut microbiota influences various metabolic, inflammatory, and neuropsychological processes critical to erectile function. Dysbiosis can lead to systemic inflammation, endothelial dysfunction, hormonal imbalances, and altered neurotransmitter production, all of which are key factors in ED pathogenesis. This narrative review synthesizes current research on the association between gut microbiota alterations and ED, highlighting specific bacterial taxa implicated in ED through mechanisms involving inflammation, metabolic disturbances, and hormonal regulation. This review explores potential mechanisms linking gut microbiota and ED, including pro-inflammatory cytokines, gut barrier integrity disruption, metabolic disorders, psychological factors via the gut–brain axis, and hormonal regulation. Furthermore, the gut microbiota offers promising avenues for developing non-invasive biomarkers and therapeutic interventions such as probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation. Future research should focus on longitudinal studies, mechanistic explorations, and clinical trials to validate these findings and translate them into clinical practice. Understanding the interplay between the gut microbiota and erectile function could unveil novel diagnostic biomarkers and pave the way for innovative treatments targeting the microbiota, ultimately improving men’s sexual and overall health. Full article

(This article belongs to the Collection Feature Papers in Medical Microbiology)

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16 pages, 2811 KiB

Open AccessArticle

Electro-Enhanced Gas Fermentation for Bioproduction of Volatile Fatty Acids and Alcohols

by Clemens Hiebl and Werner Fuchs

Microorganisms 2025, 13(2), 249; https://doi.org/10.3390/microorganisms13020249 - 23 Jan 2025

Abstract

This study investigates sub-stoichiometric electron supply, also termed electro-fermentation, to influence product formation in gas fermentation. Two species, Clostridium carboxidivorans and Alkalibaculum bacchi, as well as a co-culture of A. bacchi and Clostridium kluyveri, were tested in batch cultures with and [...] Read more.

This study investigates sub-stoichiometric electron supply, also termed electro-fermentation, to influence product formation in gas fermentation. Two species, Clostridium carboxidivorans and Alkalibaculum bacchi, as well as a co-culture of A. bacchi and Clostridium kluyveri, were tested in batch cultures with and without an external cell potential of 800 mV. The supplied gas mixture was 50:40:10 N₂:H₂:CO₂. The test unit was a single-chamber reactor with a cathode made from an electrically conducting composite of PP and black carbon. The observed current densities were generally very low, around 0.22 mA/m². Despite that, a significant and reproducible change in product patterns and formation rates occurred. C. carboxidivorans increased the formation of acetate (+32%), butyrate (+300% relative to the control), and caproate (+600% relative to the control). In a similar manner, A. bacchi produced more acetate (+38%), butyrate (13 times more than the control), and caproate (only observed in the electrified setup). Additional trials using a modified gas phase composition, 80:20 H₂:CO₂, confirmed the finding that the application of an electric potential enhances chain elongation as well as alcohol formation. Moreover, an experiment with reversed electric polarity showed that a high cathode surface area is essential for inducing metabolic modifications. The results demonstrate that electro-fermentation holds significant potential for improving bioconversion processes aimed at producing green chemicals. Full article

(This article belongs to the Section Microbial Biotechnology)

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27 pages, 8698 KiB

Open AccessArticle

Analysis of Midgut Bacterial Communities in Larvae and Adult Mosquitoes of Aedes aegypti Invaded by Three Different Microorganisms

by Yanan Yin, Yanhui Liu, Jieli Fan, Lingling Yu, Meng Nie, Zhiqi Zhang, Qian Han and Chenghong Liao

Microorganisms 2025, 13(2), 248; https://doi.org/10.3390/microorganisms13020248 - 23 Jan 2025

Abstract

The midgut microbiota of Aedes aegypti is crucial for the mosquito’s development, nutrition, and immunity. However, its communities are also distinctively influenced by the colonization of different microorganisms, influencing its susceptibility to pathogens and transmission capacity. In this study, we investigated the effects [...] Read more.

The midgut microbiota of Aedes aegypti is crucial for the mosquito’s development, nutrition, and immunity. However, its communities are also distinctively influenced by the colonization of different microorganisms, influencing its susceptibility to pathogens and transmission capacity. In this study, we investigated the effects of infections with Escherichia coli, Staphylococcus aureus, and Beauveria bassiana on the midgut microbial composition of Ae. aegypti. These microorganisms were inoculated into the midguts of third-instar larvae using a soaking method. Midgut samples were then analyzed through high-throughput 16S rDNA sequencing to assess bacterial load and microbiota composition of fourth-instar larvae and female adult mosquitoes. The results reveal that E. coli-colonized fourth-instar larvae (CO_4W) exhibited 20 unique genera, whereas the S. aureus-colonized group (S_4W) had operational taxonomic units assigned to 194 bacterial taxa, including a notable decrease in Elizabethkingia. In addition, B. bassiana infection led to a significant reduction of Elizabethkingia meningoseptica in larvae, decreasing from 42.9% in the control group (CK_4W) to 0.9% in the B. bassiana-infected group (B_4W). Distinct microbial profiles were also compared between adult mosquitoes and fourth-instar larvae. Significant abundance changes were found in Firmicutes, Bacteroidota, and Proteobacteria among different groups. Metabolic pathway predictions using PICRUSt suggested that microorganism invasion enriched the pathways involved in carbohydrate metabolism and amino acid metabolism. This enrichment suggests that the microbiota may undergo specific adaptive responses to pathogen presence. Overall, our results provide new insights into the relationship between the invasion of microorganisms and midgut bacterial communities in mosquitoes. Full article

(This article belongs to the Section Microbiomes)

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22 pages, 361 KiB

Open AccessReview

Using In Vitro Models to Study the Interactions Between Environmental Exposures and Human Microbiota

by Qiwen Cheng and Shengxi Chen

Microorganisms 2025, 13(2), 247; https://doi.org/10.3390/microorganisms13020247 - 23 Jan 2025

Abstract

Research has demonstrated a close correlation between human microbiota and overall health, highlighting their intimate connection. Exposure to environmental factors, such as chemical contaminants and biological agents, has the potential to alter the composition and function of microbiota, thereby influencing health outcomes. Meanwhile, [...] Read more.

Research has demonstrated a close correlation between human microbiota and overall health, highlighting their intimate connection. Exposure to environmental factors, such as chemical contaminants and biological agents, has the potential to alter the composition and function of microbiota, thereby influencing health outcomes. Meanwhile, microbiota may contribute to host protection by degrading, or rendering harmless, exposures. Environmental exposures demonstrate significant diversity and dynamism; however, conventional methods for exposure–microbiota research, such as animal and epidemiological studies, are often both time-consuming and costly. Additionally, they may raise ethical concerns. This review aimed to examine the existing understanding of employing in vitro models to investigate the interactions between environmental exposures and human microbiota, particularly those located outside the large intestine. A comprehensive search was conducted across the Web of Science, PubMed, and Scopus databases, employing a range of keywords related to microbiota, exposures, and in vitro models. A total of 58 studies fulfilled the search criteria, revealing instances of microbial modulation of exposures and vice versa. It was observed that, although considerable research has been conducted on these interactions in vitro, there remains a pressing need for enhanced model designs and application contexts. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens, Second Edition)

35 pages, 14424 KiB

Open AccessArticle

Quick In Vitro Screening of PGPMs for Salt Tolerance and Evaluation of Induced Tolerance to Saline Stress in Tomato Culture

by Lucas Arminjon and François Lefort

Microorganisms 2025, 13(2), 246; https://doi.org/10.3390/microorganisms13020246 - 23 Jan 2025

Abstract

Soil salinity, affecting 20–50% of irrigated farmland globally, poses a significant threat to agriculture and food security, worsened by climate change and increasing droughts. Traditional methods for managing saline soils—such as leaching, gypsum addition, and soil excavation—are costly and often unsustainable. An alternative [...] Read more.

Soil salinity, affecting 20–50% of irrigated farmland globally, poses a significant threat to agriculture and food security, worsened by climate change and increasing droughts. Traditional methods for managing saline soils—such as leaching, gypsum addition, and soil excavation—are costly and often unsustainable. An alternative approach using plant growth-promoting microorganisms (PGPMs) offers promise for improving crop productivity in saline conditions. This study tested twenty-three bacterial strains, one yeast, and one fungal strain, isolated from diverse sources including salicornia plants, sandy soils, tomato stems or seeds, tree leaves, stems, and flowers. They were initially submitted to in vitro selection tests to assess their ability to promote plant growth under salt stress. In vitro tests included auxin production, phosphate solubilization, and co-culture of microorganisms and tomato seedlings in salt-supplemented media. The Bacillus sp. strain 44 showed the highest auxin production, while Bacillus megaterium MJ had the strongest phosphate solubilization ability. Cryptococcus sp. STSD 4 and Gliomastix murorum (4)10-1(iso1) promoted germination and the growth of tomato seedlings in an in vitro co-culture test performed on a salt-enriched medium. This innovative test proved particularly effective in selecting relevant strains for in planta trials. The microorganisms that performed best in the various in vitro tests were then evaluated in vivo on tomato plants grown in greenhouses. The results showed significant improvements in growth, including increases in fresh and dry biomass and stem size. Among the strains tested, Gliomastix murorum (4)10-1(iso1) stood out, delivering an increase in fresh biomass of 94% in comparison to the negative control of the salt modality. These findings highlight the potential of specific PGPM strains to enhance crop resilience and productivity in saline soils, supporting sustainable agricultural practices. Full article

(This article belongs to the Special Issue Microbial Biostimulants: From the Lab to the Field for a New Agriculture 3.0)

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15 pages, 1172 KiB

Open AccessReview

Microbiota Dysbiosis: A Key Modulator in Preeclampsia Pathogenesis and Its Therapeutic Potential

by Johnatan Torres-Torres, Jorge Alberto Basurto-Serrano, Zaira Alexi Camacho-Martinez, Francisco Rafael Guadarrama-Sanchez, Irma Eloisa Monroy-Muñoz, Javier Perez-Duran, Juan Mario Solis-Paredes, Raigam Martinez-Portilla, Salvador Espino-y-Sosa, Andrea Ramirez-Gonzalez, Rodrigo Guadarrama-Mora and Lourdes Rojas-Zepeda

Microorganisms 2025, 13(2), 245; https://doi.org/10.3390/microorganisms13020245 - 23 Jan 2025

Abstract

Preeclampsia is a leading cause of maternal and perinatal morbidity and mortality worldwide. Emerging evidence implicates gut and vaginal microbiota dysbiosis in preeclampsia pathogenesis through its roles in immune regulation, inflammation, and placental function. This review explores the mechanisms linking microbiota alterations to [...] Read more.

Preeclampsia is a leading cause of maternal and perinatal morbidity and mortality worldwide. Emerging evidence implicates gut and vaginal microbiota dysbiosis in preeclampsia pathogenesis through its roles in immune regulation, inflammation, and placental function. This review explores the mechanisms linking microbiota alterations to preeclampsia and evaluates the therapeutic potential of microbiota-targeted interventions. A systematic search using MeSH terms related to “preeclampsia”, “microbiota”, and “dysbiosis” identified studies on microbiota and preeclampsia pathophysiology. Data extraction focused on microbial alterations and mechanistic insights. Gut dysbiosis, characterized by reduced beneficial bacteria and short-chain fatty acid production, weakens the intestinal barrier, exacerbates systemic inflammation, and impairs placental development. Vaginal dysbiosis, marked by reduced Lactobacillus species, promotes local inflammation, increasing placental dysfunction risk. Therapeutic strategies, including probiotics, prebiotics, and dietary modifications, show promise in restoring microbial balance and mitigating preeclampsia risk. Microbiota dysbiosis significantly contributes to preeclampsia pathogenesis through inflammation, endothelial dysfunction, and placental impairment. Interventions targeting microbial balance, such as probiotics and dietary modifications, show promise for prevention, but further research and large-scale trials are essential to validate their efficacy and safety. Full article

(This article belongs to the Section Medical Microbiology)

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21 pages, 2333 KiB

Open AccessArticle

The Microbiome of Catfish (Ictalurus punctatus) Treated with Natural Preservatives During Refrigerated Storage

by Jung-Lim Lee and Gregory Yourek

Microorganisms 2025, 13(2), 244; https://doi.org/10.3390/microorganisms13020244 - 23 Jan 2025

Abstract

Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers’ growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we [...] Read more.

Fish is an essential lean protein source worldwide. Unfortunately, fresh fish food products deteriorate rapidly due to microbial spoilage. With consumers’ growing concerns about using chemical preservatives, we propose using natural preservatives as safer alternatives to prevent microbial spoilage. In this study, we used Next-Generation Sequencing (NGS) metagenomics to study microbiomes on catfish fillets at early (day one for all samples), middle (day seven for control store-bought and aquaculture-raised samples, day nine for other treatment store-bought samples, and day eleven for other treatment aquaculture-raised samples), and late (day fifteen for all store-bought, day eleven for control aquaculture-raised samples, and day twenty-seven for other treatment aquaculture-raised samples) points. Store-bought and aquaculture-raised catfish were treated individually with natural preservatives (vinegar, lemon, and grapefruit seed [GSE]). We observed bacterial populations and sequenced 16S NGS libraries of catfish microbes. Vinegar treatment showed the greatest suppression of bacterial growth in both groups, and GSE and lemon treatment had similar levels of suppression in the mid and late points (−4 to −5 Log CFU/g vinegar and −0.1 to −4 Log CFU/g other treatments in aquaculture and −1 to −2 Log CFU/g vinegar and −0.2 to −0.5 Log CFU/g other treatments in store-bought). Aquaculture-raised vinegar treatment samples had similar proportional taxonomy abundance values through storage duration. Pseudomonas, Janthinobacterium, and Camobacteriaceae were the dominant bacteria species in the early point for store-bought fish. Still, Pseudomonas was suppressed by vinegar treatment in the middle point, which allowed for less biased relative abundance compared to other treatments. Chryseobacterium, CK-1C4-19, and Cetobacterium were the dominant bacteria species for early point treatments in aquaculture-raised fish. Still, they remained the predominant bacteria for only aquaculture-raised vinegar samples in the middle and late points, which allowed for a similar relative abundance to fresh catfish. Meanwhile, Pseudomonas in most lemon and GSE samples became the dominant species at a later point. This study provides a better understanding of bacterial spoilage of catfish during storage. Additionally, we showed that natural preservative treatments can effectively extend the shelf-life of fishery products. Full article

(This article belongs to the Special Issue Evaluation of Risks of Microbiological Origin Associated with Food Consumption, Third Edition)

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11 pages, 7409 KiB

Open AccessArticle

A Genomic Characterization of Clinical Brucella melitensis Isolates from Tunisia: Integration into the Global Population Structure

by Asma Ferjani, Hellen Buijze, Germán Kopprio, Susanne Köhler, Amel Rehaiem, Hajer Battikh, Lamia Ammari, Sana Ferjani, Lamia Kanzari, Meriam Zribi, Badreddine Kilani, Nicolle Hanschmann, Holger Scholz and Ilhem Boutiba

Microorganisms 2025, 13(2), 243; https://doi.org/10.3390/microorganisms13020243 - 23 Jan 2025

Abstract

Brucellosis represents a significant global health concern that is endemic in many regions of the world, especially in Maghreb (Tunisia, Morocco and Algeria). In Tunisia the diagnosis of human brucellosis is primarily based on serological tests and cultivation of the causative pathogen, without [...] Read more.

Brucellosis represents a significant global health concern that is endemic in many regions of the world, especially in Maghreb (Tunisia, Morocco and Algeria). In Tunisia the diagnosis of human brucellosis is primarily based on serological tests and cultivation of the causative pathogen, without the knowledge of the underlying Brucella species or biovar. In addition, the scarcity of laboratories with adequate biosecurity measures to handle suspected specimens constitutes a significant challenge. Furthermore, the absence of full genome data limits our understanding of the genetic diversity of Brucella in Tunisia in comparison to the strains circulating in the North African region and the world. In the present study, a total of 36 bacterial isolates derived from human patients diagnosed with brucellosis in Tunisia were subjected to examination. Real-time PCR confirmed all isolates as B. melitensis. In the subsequent core genome-based MLST analysis (cgMLST) based on 2706 target genes, the isolates formed two separate but closely related clusters with a distance of 140 alleles. The intra-cluster diversity was one to six alleles. In the larger geographical context and in comparison to almost 1000 other Brucella genomes, the isolates showed the highest genetic relationship to B. melitensis isolates from Italy and Egypt with distances of 130 and 150 alleles, respectively. All the isolates were most similar to the biovar 3 genotype. Markedly, strains from a reported brucellosis outbreak in Austria were grouped closely (26 and 27 alleles, respectively) together with strains from Tunisia, suggesting that this country may represent their geographical origin. This research represents a significant advancement in our understanding of B. melitensis strains circulating in the Maghreb region, as it is the first study to elucidate the molecular characterization of strains isolated from humans in Tunisia. The cgMLST analysis of the strains provided information on the regional distribution of the strains and the association with neighboring countries and significant outbreaks in the region. The data will form the basis of a future reference framework for strains circulating in the Mediterranean region. Full article

(This article belongs to the Section Medical Microbiology)

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13 pages, 1361 KiB

Open AccessArticle

Molecular Detection of Trypanosomatids in Rodents and Marsupials in the State of Amapá, Brazil

by Lourdes Marina Bezerra Pessoa, Claudia Regina Silva, Kamila Gaudêncio da Silva Sales, Darlison Chagas de Souza, Lucas Lisboa Nunes Bonifácio, Rafaela Lira Nogueira de Luna, Filipe Dantas-Torres and Lúcio André Viana

Microorganisms 2025, 13(2), 242; https://doi.org/10.3390/microorganisms13020242 - 23 Jan 2025

Abstract

Trypanosomatids of the genera Trypanosoma and Leishmania are parasites of medical and veterinary importance that infect mammals, including humans and domestic and wild animals. Among mammals, rodents and marsupials play a crucial role in maintaining and spreading the zoonotic transmission cycle of these [...] Read more.

Trypanosomatids of the genera Trypanosoma and Leishmania are parasites of medical and veterinary importance that infect mammals, including humans and domestic and wild animals. Among mammals, rodents and marsupials play a crucial role in maintaining and spreading the zoonotic transmission cycle of these parasites. The present study aimed to detect the natural occurrence of Trypanosoma spp. and Leishmania spp. in rodents and marsupials in the state of Amapá, northern Brazil. In total, 137 samples were analyzed, of which 19 (6 marsupials and 13 rodents) were positive for trypanosomatid DNA. Partial sequences of the 18S rRNA gene of trypanosomatids were obtained from 10 out of 19 positive samples. Specifically, an undescribed Trypanosoma sp. was detected in Marmosa demerarae, Marmosa murina, Zygodontomys brevicauda, and Neacomys paracou. Trypanosoma cruzi was detected in a Philander opossum, whereas sequences close to Trypanosoma wauwau and Trypanosoma freitasi were obtained from Didelphis imperfecta and N. paracou, respectively. Finally, Leishmania (Viannia) sp. was detected in Mesomys hispidus, Hylaeamys megacephalus, and Z. brevicauda. The present study expands the knowledge about marsupials and rodents as hosts of trypanosomatids and emphasizes the need for further studies on the role of these animals as potential reservoirs of these parasites in the Amazon region. Full article

(This article belongs to the Special Issue Pathobiology, Infection Biology and Control of Protozoan Parasites—the ONE HEALTH Approach)

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