Microorganisms

21 pages, 3190 KiB

Open AccessArticle

Inulin and Freeze-Dried Blueberry Intervention Lead to Changes in the Microbiota and Metabolites within In Vitro Studies and in Cognitive Function within a Small Pilot Trial on Healthy Children

by Buket Horasan Sagbasan, Claire M. Williams, Lynne Bell, Katie L. Barfoot, Carlos Poveda and Gemma E. Walton

Microorganisms 2024, 12(7), 1501; https://doi.org/10.3390/microorganisms12071501 - 22 Jul 2024

Viewed by 1097

Abstract

The relationship between the gut microbiota and cognitive health is complex and bidirectional, being significantly impacted by our diet. Evidence indicates that polyphenols and inulin can impact cognitive function via various mechanisms, one of which is the gut microbiota. In this study, effects [...] Read more.

The relationship between the gut microbiota and cognitive health is complex and bidirectional, being significantly impacted by our diet. Evidence indicates that polyphenols and inulin can impact cognitive function via various mechanisms, one of which is the gut microbiota. In this study, effects of a wild blueberry treatment (WBB) and enriched chicory inulin powder were investigated both in vitro and in vivo. Gut microbiota composition and metabolites, including neurotransmitters, were assessed upon faecal microbial fermentation of WBB and inulin in a gut model system. Secondly, microbiota changes and cognitive function were assessed in children within a small pilot (n = 13) trial comparing WBB, inulin, and a maltodextrin placebo, via a series of tests measuring executive function and memory function, with faecal sampling at baseline, 4 weeks post-intervention and after a 4 week washout period. Both WBB and inulin led to microbial changes and increases in levels of short chain fatty acids in vitro. In vivo significant improvements in executive function and memory were observed following inulin and WBB consumption as compared to placebo. Cognitive benefits were accompanied by significant increases in Faecalibacterium prausnitzii in the inulin group, while in the WBB group, Bacteroidetes significantly increased and Firmicutes significantly decreased (p < 0.05). As such, WBB and inulin both impact the microbiota and may impact cognitive function via different gut-related or other mechanisms. This study highlights the important influence of diet on cognitive function that could, in part, be mediated by the gut microbiota. Full article

(This article belongs to the Section Food Microbiology)

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18 pages, 2725 KiB

Open AccessArticle

Inhibition of Microbial Growth and Biofilm Formation in Pure and Mixed Bacterial Samples

by John D. Cate, Young Z. Sullivan and Maria D. King

Microorganisms 2024, 12(7), 1500; https://doi.org/10.3390/microorganisms12071500 - 22 Jul 2024

Viewed by 1020

Abstract

Hydraulic fracturing, or fracking, requires large amounts of water to extract fossil fuel from rock formations. As a result of hydraulic fracturing, the briny wastewater, often termed back-produced fracturing or fracking water (FW), is pumped into holding ponds. One of the biggest challenges [...] Read more.

Hydraulic fracturing, or fracking, requires large amounts of water to extract fossil fuel from rock formations. As a result of hydraulic fracturing, the briny wastewater, often termed back-produced fracturing or fracking water (FW), is pumped into holding ponds. One of the biggest challenges with produced water management is controlling microbial activity that could reduce the pond water’s reusable layer and pose a significant environmental hazard. This study focuses on the characterization of back-produced water that has been hydraulically fractured using chemical and biological analysis and the development of a high-throughput screening method to evaluate and predict the antimicrobial effect of four naturally and commercially available acidic inhibitors (edetic acid, boric acid, tannic acid, and lactic acid) on the growth of the FW microbiome. Liquid cultures and biofilms of two laboratory model strains, the vegetative Escherichia coli MG1655, and the spore-forming Bacillus atrophaeus (also known as Bacillus globigii, BG) bacteria, were used as reference microorganisms. Planktonic bacteria in FW were more sensitive to antimicrobials than sessile bacteria in biofilms. Spore-forming BG bacteria exhibited more sensitivity to acidic inhibitors than the vegetative E. coli cells. Organic acids were the most effective bacterial growth inhibitors in liquid culture and biofilm. Full article

(This article belongs to the Special Issue Bacterial and Antibiotic Resistance in the Environment)

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20 pages, 1901 KiB

Open AccessArticle

Transcriptomic Signatures of Zika Virus Infection in Patients and a Cell Culture Model

by Gillian Berglund, Claudia D. Lennon, Pheonah Badu, John Andrew Berglund and Cara T. Pager

Microorganisms 2024, 12(7), 1499; https://doi.org/10.3390/microorganisms12071499 - 22 Jul 2024

Cited by 1 | Viewed by 925

Abstract

Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked [...] Read more.

Zika virus (ZIKV), a re-emerging flavivirus, is associated with devasting developmental and neurological disease outcomes particularly in infants infected in utero. Towards understanding the molecular underpinnings of the unique ZIKV disease pathologies, numerous transcriptome-wide studies have been undertaken. Notably, these studies have overlooked the assimilation of RNA-seq analysis from ZIKV-infected patients with cell culture model systems. In this study we find that ZIKV-infection of human lung adenocarcinoma A549 cells, mirrored both the transcriptional and alternative splicing profiles from previously published RNA-seq data of peripheral blood mononuclear cells collected from pediatric patients during early acute, late acute, and convalescent phases of ZIKV infection. Our analyses show that ZIKV infection in cultured cells correlates with transcriptional changes in patients, while the overlap in alternative splicing profiles was not as extensive. Overall, our data indicate that cell culture model systems support dissection of select molecular changes detected in patients and establishes the groundwork for future studies elucidating the biological implications of alternative splicing during ZIKV infection. Full article

(This article belongs to the Special Issue Zika Virus Infection and Immune Response)

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16 pages, 1686 KiB

Open AccessArticle

Impact of Biotic and Abiotic Factors on Listeria monocytogenes, Salmonella enterica, and Enterohemorrhagic Escherichia coli in Agricultural Soil Extracts

by Dimple Sharma, Autumn L. Kraft, Joshua O. Owade, Mateja Milicevic, Jiyoon Yi and Teresa M. Bergholz

Microorganisms 2024, 12(7), 1498; https://doi.org/10.3390/microorganisms12071498 - 22 Jul 2024

Viewed by 928

Abstract

Outbreaks of Enterohemorrhagic Escherichia coli (EHEC), Salmonella enterica, and Listeria monocytogenes linked to fresh produce consumption pose significant food safety concerns. These pathogens can contaminate pre-harvest produce through various routes, including contaminated water. Soil physicochemical properties and flooding can influence pathogen survival [...] Read more.

Outbreaks of Enterohemorrhagic Escherichia coli (EHEC), Salmonella enterica, and Listeria monocytogenes linked to fresh produce consumption pose significant food safety concerns. These pathogens can contaminate pre-harvest produce through various routes, including contaminated water. Soil physicochemical properties and flooding can influence pathogen survival in soils. We investigated survival of EHEC, S. enterica, and L. monocytogenes in soil extracts designed to represent soils with stagnant water. We hypothesized pathogen survival would be influenced by soil extract nutrient levels and the presence of native microbes. A chemical analysis revealed higher levels of total nitrogen, phosphorus, and carbon in high-nutrient soil extracts compared to low-nutrient extracts. Pathogen survival was enhanced in high-nutrient, sterile soil extracts, while the presence of native microbes reduced pathogen numbers. A microbiome analysis showed greater diversity in low-nutrient soil extracts, with distinct microbial compositions between extract types. Our findings highlight the importance of soil nutrient composition and microbial dynamics in influencing pathogen behavior. Given key soil parameters, a long short-term memory model (LSTM) effectively predicted pathogen survival. Integrating these factors can aid in developing predictive models for pathogen persistence in agricultural systems. Overall, our study contributes to understanding the complex interplay in agricultural ecosystems, facilitating informed decision-making for crop production and food safety enhancement. Full article

(This article belongs to the Special Issue Microbiome Research for Animal, Plant and Environmental Health)

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17 pages, 3034 KiB

Open AccessArticle

Discovery and Characterization of Epichloë Fungal Endophytes from Elymus spp. in Northwest China

by Mingxiang Du, Tian Wang, Chunjie Li and Taixiang Chen

Microorganisms 2024, 12(7), 1497; https://doi.org/10.3390/microorganisms12071497 - 22 Jul 2024

Viewed by 696

Abstract

Epichloë fungal endophytes hold promise in sustainable agriculture by fortifying cool-season grasses such as Elymus spp. against various stresses. Elymus spp. are widely distributed in Northwest China with a high incidence of endophyte infections. In this study, we identified 20 Epichloë endophytic fungal [...] Read more.

Epichloë fungal endophytes hold promise in sustainable agriculture by fortifying cool-season grasses such as Elymus spp. against various stresses. Elymus spp. are widely distributed in Northwest China with a high incidence of endophyte infections. In this study, we identified 20 Epichloë endophytic fungal strains carried by five Elymus spp. from five areas of Northwest China and systematically characterized their morphology, molecular phylogeny, mating type, and alkaloid diversity for the first time. The morphological characterization underscores strain diversity, with variable colony textures and growth rates. A phylogenetic analysis confirms all strains are E. bromicola, emphasizing their taxonomic status. Alkaloid-encoding gene profiling delineates distinct alkaloid synthesis capabilities among the strains, which are crucial for host adaptability and resistance. A mating-type analysis reveals uniformity (mtAC) across the Epichloë strains, simplifying breeding strategies. Notably, the Epichloë strains exhibit diverse alkaloid synthesis gene profiles, impacting host interactions. This research emphasizes the ecological significance of Epichloë endophytes in Elymus spp. ecosystems, offering insights into their genetic diversity and potential applications in sustainable agriculture. Full article

(This article belongs to the Section Plant Microbe Interactions)

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7 pages, 1232 KiB

Open AccessCommunication

N-Acyl Homoserine Lactone Production by the Marine Isolate, Dasania marina

by Fnu Alimiran, Samuel David, Scott Birks, Athenia Oldham and Douglas Henderson

Microorganisms 2024, 12(7), 1496; https://doi.org/10.3390/microorganisms12071496 - 22 Jul 2024

Viewed by 710

Abstract

Dasania marina (isolate SD1D, with 98.5% sequence similarity to Dasania marina DMS 21967 KOPRI 20902) is a marine bacterium that was isolated from ballast tank fluids as part of a biofilm study in 2014. Our previous work indicated that although this strain produced [...] Read more.

Dasania marina (isolate SD1D, with 98.5% sequence similarity to Dasania marina DMS 21967 KOPRI 20902) is a marine bacterium that was isolated from ballast tank fluids as part of a biofilm study in 2014. Our previous work indicated that although this strain produced no detectable biofilm, it was the only isolate to produce N-acyl homoserine lactones (AHLs) in assays using the broad-range reporter strain, Agrobacterium tumefaciens KYC55. The goal of the current study was to determine the types of AHL molecules produced by the D. marina isolate using gas chromatography–mass spectroscopy (GCMS) and C4- to C14-AHL as standards. A time course assay indicated that the D. marina strain produced the highest level of AHLs at 20 h of growth. When extracts were subjected to GCMS, detectable levels of C8- and C10-AHL and higher levels of C12-AHL were observed. Interestingly, several biofilm-forming isolates obtained from the same source also produced detectable amounts of several AHLs. Of the isolates tested, a strain designated SD5, with 99.83% sequence similarity to Alteromonas tagae BCRC 17571, produced unstable biofilms, yet detectable levels of C6-, C8-, C10- and C12-AHL, and isolate SD8, an Alteromonas oceani S35 strain (98.85% sequence similarity), produced robust and stable biofilms accompanied by detectable levels of C8- and C12-AHL. All isolates tested produced C12-AHL at higher levels than the other AHLs. Results from this study suggest that quorum sensing and biofilm formation are uncoupled in D. marina. Whether the suite of AHLs produced by this isolate could modulate biofilm formation in other strains requires further study. Full article

(This article belongs to the Section Biofilm)

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17 pages, 19074 KiB

Open AccessArticle

Exosomal miR-7-25207 Increases Subgroup J Avian Leukosis Virus Titers by Targeting the Akt-CyclinQ1 and PRC1-YAF2 Dual Pathways

by Xiaona Zeng, Tongfei Liu, Shengqiu Tang, Xiaoying Dong, Yajuan Li, Liqin Liao, Sheng Chen, Liyi Chen, Jie Kong, Zhenkai Dai, Keyu Feng, Yung-Hou Wong and Qingmei Xie

Microorganisms 2024, 12(7), 1495; https://doi.org/10.3390/microorganisms12071495 - 22 Jul 2024

Viewed by 727

Abstract

Subgroup J avian leukosis virus (ALV-J) is a major pathogen in poultry, causing substantial economic losses to the poultry industry worldwide. Exosomal small RNAs derived from virus-infected cells or biological fluids can serve as viral transmission vectors. However, the role and [...] Read more.

Subgroup J avian leukosis virus (ALV-J) is a major pathogen in poultry, causing substantial economic losses to the poultry industry worldwide. Exosomal small RNAs derived from virus-infected cells or biological fluids can serve as viral transmission vectors. However, the role and mechanism of exosomal miRNA in ALV-J infection are unclear. In this study, we demonstrated that exosomal microRNA-7-25207 (miR-7-25207) could increase the titers of ALV-J. Exosomes isolated from ALV-J-infected DF-1 cells (Exo-ALV-J) contained partial viral proteins from ALV-J and could transmit the infection to uninfected DF-1 cells, leading to productive infection. Additionally, the RNA expression profile of exosomes was altered following ALV-J infection. miRNA analysis revealed that the expression of exosomal miR-7-25207 increased. Overexpression of miR-7-25207 significantly increased the titers of ALV-J in transfected cells. Furthermore, miR-7-25207 directly suppressed the expression of Akt and PRC1. Akt, in turn, directly inhibited CyclinQ1 expression, while PRC1 directly interfered with YAF2 expression. In conclusion, ALV-J infection activates the expression of miR-7-25207, which is subsequently delivered via exosomes to uninfected cells, increasing ALV-J titers by targeting Akt-CyclinQ1 and PRC1-YAF2 dual pathways. These findings suggest that exosomal miR-7-25207 may serve as a potential biomarker for clinical parameters in ALV-J infection. Full article

(This article belongs to the Section Virology)

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11 pages, 853 KiB

Open AccessArticle

Occurrence and Persistence of Saccharomyces cerevisiae Population in Spontaneous Fermentation and the Relation with “Winery Effect”

by Alice Agarbati, Francesca Comitini, Maurizio Ciani and Laura Canonico

Microorganisms 2024, 12(7), 1494; https://doi.org/10.3390/microorganisms12071494 - 21 Jul 2024

Cited by 1 | Viewed by 887

Abstract

The yeast Saccharomyces cerevisiae ensures successful fermentation in winemaking, although the persistent use of commercial strains lead to the loss of aroma complexity of wines. Hence, the research of indigenous S. cerevisiae with proper oenological features and well adapted to specific wine-growing areas [...] Read more.

The yeast Saccharomyces cerevisiae ensures successful fermentation in winemaking, although the persistent use of commercial strains lead to the loss of aroma complexity of wines. Hence, the research of indigenous S. cerevisiae with proper oenological features and well adapted to specific wine-growing areas become of great interest for winemakers. Here, 206 pure cultures of S. cerevisiae were isolated from two wineries during a two-year sampling campaign and bio-typed through interdelta sequences analyses with the aim to evaluate the occurrence and persistence of the S. cerevisiae wild population linked to each winery. Both wineries belong to the same Verdicchio DOC wine area (Castelli di Jesi), and never used commercial yeasts during fermentation. Results showed 19 different biotypes with a specific population of S. cerevisiae in each winery, without cross-contamination with each other and with commercial starter strains. Moreover, inside each winery a persistence of some dominant biotypes was observed over time (three biotypes in winery 1; 95% of isolates in the two years and one biotype in winery 2; 20% of isolates in the two years), indicating a sort of “winery-effect”. The evaluation of S. cerevisiae populations for the oenological characters by microfermentations showed a proper and well distinct aromatic imprinting on the resulted wines supporting the concept of “winery effect”. Full article

(This article belongs to the Special Issue Microbiology of the Grape-Wine System)

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13 pages, 258 KiB

Open AccessReview

Synbiotics as Treatment for Irritable Bowel Syndrome: A Review

by Henning Sommermeyer and Jacek Piątek

Microorganisms 2024, 12(7), 1493; https://doi.org/10.3390/microorganisms12071493 - 21 Jul 2024

Viewed by 1210

Abstract

Irritable bowel syndrome is a persistent disturbance of the function of the gastrointestinal tract with a prevalence of about 11.2% in the population at large. While the etiology of the disorder remains unclear, there is mounting evidence that the disturbance of the gut [...] Read more.

Irritable bowel syndrome is a persistent disturbance of the function of the gastrointestinal tract with a prevalence of about 11.2% in the population at large. While the etiology of the disorder remains unclear, there is mounting evidence that the disturbance of the gut microbiota is at least one contributing factor. This insight resulted in clinical trials investigating the therapeutic effects of products containing probiotic microorganisms. Most studies with IBS patients have evaluated the therapeutic effects of mono- and multi-strain probiotics, but only a few studies have investigated the efficacy of synbiotics (combinations of probiotic bacteria and one or more prebiotic components). This review summarizes the results from eight randomized, placebo-controlled clinical trials that investigated the efficacy of synbiotic preparations (three mono-strain and five multi-strain products) in adult IBS patients. While data remain sparse, some of the surveyed clinical trials have demonstrated interesting efficacy results in IBS patients. To allow a judgment of the role played by synbiotics in the treatment of IBS patients, more high-quality clinical trials are needed. Full article

(This article belongs to the Special Issue Probiotics: The Current State of Scientific Knowledge)

15 pages, 1653 KiB

Open AccessArticle

Immunological and Safety Considerations When Selecting the Dose Formulation of a Purified Inactivated Zika Virus Vaccine (PIZV)

by Camilo J. Acosta, Francesco Nordio, Eloi Kpamegan, Kelley J. Moss, Pradeep Kumar and Kazuhiro Hirata

Microorganisms 2024, 12(7), 1492; https://doi.org/10.3390/microorganisms12071492 - 21 Jul 2024

Viewed by 911

Abstract

We previously reported the first-in-human assessment of three doses (2, 5, and 10 µg) of purified inactivated Zika virus vaccine (PIZV or TAK-426) in the Phase 1 ZIK-101 study (NCT03343626). Here, we report dose selection based on extended safety and immunogenicity data (6 [...] Read more.

We previously reported the first-in-human assessment of three doses (2, 5, and 10 µg) of purified inactivated Zika virus vaccine (PIZV or TAK-426) in the Phase 1 ZIK-101 study (NCT03343626). Here, we report dose selection based on extended safety and immunogenicity data (6 months post-vaccination) and discuss considerations (e.g., immunological, historic, flavivirus immunological cross-reactions) for selecting a Zika virus (ZIKV) vaccine dose formulation. TAK-426 dose selection was conducted at the first interim analysis, and was based on cumulative safety data from both flavivirus-naïve (up to ≥28 days post-dose PD2) and flavivirus-primed participants (up to ≥28 days PD1), and on immunogenicity data from flavivirus-naïve participants only (at 28 days PD1 and 28 days PD2). The safety profile from TAK-426 recipients was compared to placebo recipients. Immunogenicity was assessed by geometric mean titer ratios of neutralizing anti-ZIKV antibodies and differences in seroconversion rates. There was no significant difference in safety between the three TAK-426 doses. The 10 μg dose provided the earliest and strongest immune response (with close to 100% seroconversion and higher antibody titers PD1 in flavivirus-naïve participants), and was well tolerated with acceptable safety profiles in both flavivirus-naïve and flavivirus-primed participants; this dose was selected for further development. Full article

(This article belongs to the Special Issue Zika Virus Infection and Immune Response)

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14 pages, 3895 KiB

Open AccessArticle

Characteristics of the Perianthic Endophytic Fungal Communities of the Rare Horticultural Plant Lirianthe delavayi and Their Changes under Artificial Cultivation

by Lang Yuan, Tongxing Zhao, Jing Yang, Nannan Wu, Pinzheng Zhang, Hanbo Zhang and Tao Xu

Microorganisms 2024, 12(7), 1491; https://doi.org/10.3390/microorganisms12071491 - 21 Jul 2024

Viewed by 674

Abstract

Flower endophytic fungi play a major role in plant reproduction, stress resistance, and growth and development. However, little is known about how artificial cultivation affects the endophytic fungal community found in the tepals of rare horticultural plants. In this research, we used high-throughput [...] Read more.

Flower endophytic fungi play a major role in plant reproduction, stress resistance, and growth and development. However, little is known about how artificial cultivation affects the endophytic fungal community found in the tepals of rare horticultural plants. In this research, we used high-throughput sequencing technology combined with bioinformatics analysis to reveal the endophytic fungal community of tepals in Lirianthe delavayi and the effects of artificial cultivation on the community composition and function of these plants, using tepals of L. delavayi from wild habitat, cultivated campus habitat, and cultivated field habitat as research objects. The results showed that the variety of endophytic fungi in the tepals of L. delavayi was abundant, with a total of 907 Amplicon sequencing variants (ASVs) obtained from all the samples, which were further classified into 4 phyla, 23 classes, 51 orders, 97 families, 156 genera, and 214 species. We also found that artificial cultivation had a significant impact on the community composition of endophytic fungi. Although there was no significant difference at the phylum level, with Ascomycota and Basidiomycota being the main phyla, there were significant differences in dominant and unique genera. Artificial cultivation has led to the addition of new pathogenic fungal genera, such as Phaeosphaeria, Botryosphaeria, and Paraconiothyrium, increasing the risk of disease in L. delavayi. In addition, the abundance of the endophytic fungus Rhodotorula, which is typical in plant reproductive organs, decreased. Artificial cultivation also altered the metabolic pathways of endophytic fungi, decreasing their ability to resist pests and diseases and reducing their ability to reproduce. A comparison of endophytic fungi in tepals and leaves revealed significant differences in community composition and changes in the endophytic diversity caused by artificial cultivation. To summarize, our results indicate that endophytic fungi in the tepals of L. delavayi mainly consist of pathogenic and saprophytic fungi. Simultaneously, artificial cultivation introduces a great number of pathogenic fungi that alter the metabolic pathways associated with plant resistance to disease and pests, as well as reproduction, which can increase the risk of plant disease and reduce plant reproductive capacity. Our study provides an important reference for the conservation and breeding of rare horticultural plants. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture)

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13 pages, 4766 KiB

Open AccessArticle

Identification and Characterization of an Alphacoronavirus in Rhinolophus sinicus and a Betacoronavirus in Apodemus ilex in Yunnan, China

by Qian Liu, Dan-Shu Wang, Zhong-Hao Lian, Jie Fang, Pei-Yu Han, Ye Qiu, Jun-Ying Zhao, Li-Dong Zong, Yun-Zhi Zhang and Xing-Yi Ge

Microorganisms 2024, 12(7), 1490; https://doi.org/10.3390/microorganisms12071490 - 21 Jul 2024

Viewed by 837

Abstract

Coronaviruses (CoVs), the largest positive-sense RNA viruses, have caused infections in both humans and animals. The cross-species transmission of CoVs poses a serious threat to public health. Rodents and bats, the two largest orders of mammals, serve as significant natural reservoirs for CoVs. [...] Read more.

Coronaviruses (CoVs), the largest positive-sense RNA viruses, have caused infections in both humans and animals. The cross-species transmission of CoVs poses a serious threat to public health. Rodents and bats, the two largest orders of mammals, serve as significant natural reservoirs for CoVs. It is important to monitor the CoVs carried by bats and rodents. In this study, we collected 410 fecal samples from bats and 74 intestinal samples from rats in Yunnan Province, China. Using RT-PCR, we identified one positive sample for alphacoronavirus (TC-14) from Rhinolophus sinicus (Chinese rufous horseshoe bat) and two positive samples for betacoronavirus (GS-53, GS-56) from Apodemus ilex (Rodentia: Muridae). We successfully characterized the complete genomes of TC-14 and GS-56. Phylogenetic analysis revealed that TC-14 clustered with bat CoV HKU2 and SADS-CoV, while GS-56 was closely related to rat CoV HKU24. The identification of positive selection sites and estimation of divergence dates further helped characterize the genetic evolution of TC-14 and GS-56. In summary, this research reveals the genetic evolution characteristics of TC-14 and GS-56, providing valuable references for the study of CoVs carried by bats and rodents in Yunnan Province. Full article

(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)

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16 pages, 4699 KiB

Open AccessReview

Cyanobacterial Bloom Formation by Enhanced Ecological Adaptability and Competitive Advantage of Microcystis—Non-Negligible Role of Quorum Sensing

by Ziqing Zhang and Jieming Li

Microorganisms 2024, 12(7), 1489; https://doi.org/10.3390/microorganisms12071489 - 20 Jul 2024

Viewed by 826

Abstract

Microcystis-dominated cyanobacterial blooms (MCBs) frequently occur in freshwaters worldwide due to massive Microcystis colony formation and severely threaten human and ecosystem health. Quorum sensing (QS) is a direct cause of Microcystis colony formation that drives MCBs outbreak by regulating Microcystis population characteristics [...] Read more.

Microcystis-dominated cyanobacterial blooms (MCBs) frequently occur in freshwaters worldwide due to massive Microcystis colony formation and severely threaten human and ecosystem health. Quorum sensing (QS) is a direct cause of Microcystis colony formation that drives MCBs outbreak by regulating Microcystis population characteristics and behaviors. Many novel findings regarding the fundamental knowledge of the Microcystis QS phenomenon and the signaling molecules have been documented. However, little effort has been devoted to comprehensively summarizing and discussing the research progress and exploration directions of QS signaling molecules-mediated QS system in Microcystis. This review summarizes the action process of N-acyl homoserine lactones (AHLs) as major signaling molecules in Microcystis and discusses the detailed roles of AHL-mediated QS system in cellular morphology, physiological adaptability, and cell aggregation for colony formation to strengthen ecological adaptability and competitive advantage of Microcystis. The research progress on QS mechanisms in Microcystis are also summarized. Compared to other QS systems, the LuxI/LuxR-type QS system is more likely to be found in Microcystis. Also, we introduce quorum quenching (QQ), a QS-blocking process in Microcystis, to emphasize its potential as QS inhibitors in MCBs control. Finally, in response to the research deficiencies and gaps in Microcystis QS, we propose several future research directions in this field. This review deepens the understanding on Microcystis QS knowledge and provide theoretical guidance in developing strategies to monitor, control, and harness MCBs. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 7665 KiB

Open AccessArticle

Optimization of H₂O₂ Production in Biological Systems for Design of Bio-Fenton Reactors

by Peiguo Zhou, Liping Yang, Wenjing Yang, Jiaxin Hou and Ziqiao Liao

Microorganisms 2024, 12(7), 1488; https://doi.org/10.3390/microorganisms12071488 - 20 Jul 2024

Viewed by 745

Abstract

The treatment of antibiotic wastewater, which is known for its micro-toxicity, inhibition, and poor biochemistry, poses significant challenges, including complex processes, high energy demands, and secondary pollution. Bio-Fenton, a novel Fenton technology, enables the in situ production of H₂O₂ at [...] Read more.

The treatment of antibiotic wastewater, which is known for its micro-toxicity, inhibition, and poor biochemistry, poses significant challenges, including complex processes, high energy demands, and secondary pollution. Bio-Fenton, a novel Fenton technology, enables the in situ production of H₂O₂ at near-neutral pH, having low energy requirements and sustainable properties, and reduces the hazards of H₂O₂ transportation and storage. We preliminary self-designed a heterogeneous Bio-Fenton reactor. An aerobic SBBR system with pure algae, pure bacteria, and bacteria–algae symbiosis was first constructed to investigate the optimal process conditions through the effects of carbon source concentration, light duration, bamboo charcoal filling rate, and dissolved oxygen (DO) content on the H₂O₂ production and COD removal. Second, the reactor was constructed by adding iron-carrying catalysts to remove ROX and SDZ wastewater. The results demonstrated that the optimal operating parameters of aerobic SBBR were an influent carbon source concentration of 500 mg/L, a water temperature of 20 ± 2 °C, pH = 7.5, a dissolved oxygen content of 5 mg/L, a light–dark ratio of 12 h:12 h, a light intensity of 2500 Lux, an HRT of 10 h, and a bamboo charcoal filling rate of 33%. Given these conditions, the bacterial–algal system was comprehensively found to be the most suitable biosystem for this experiment. Ultimately, the dynamically coupled Bio-Fenton process succeeded in the preliminary removal of 41.32% and 42.22% of the ROX and SDZ from wastewater, respectively. Full article

(This article belongs to the Special Issue Microbial Ecosystems in Water and Wastewater Treatment: 2nd Edition)

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17 pages, 5544 KiB

Open AccessArticle

The Metabolism of Leuconostoc Genus Decoded by Comparative Genomics

by Francesco Candeliere, Laura Sola, Enrico Busi, Maddalena Rossi, Alberto Amaretti and Stefano Raimondi

Microorganisms 2024, 12(7), 1487; https://doi.org/10.3390/microorganisms12071487 - 20 Jul 2024

Viewed by 886

Abstract

Leuconostoc encompasses a number of species that frequently appear in foods where they play different roles, ranging from ripening to spoiling. The number of available Leuconostoc genomes has recently increased and enabled the precise taxonomic and phylogenetic delineation of species. Nonetheless, a thorough [...] Read more.

Leuconostoc encompasses a number of species that frequently appear in foods where they play different roles, ranging from ripening to spoiling. The number of available Leuconostoc genomes has recently increased and enabled the precise taxonomic and phylogenetic delineation of species. Nonetheless, a thorough investigation of the functions and the metabolic potential of Leuconostoc species has never been accomplished. In this study, all the currently available 553 Leuconostoc genomes were downloaded from NCBI GenBank and annotated utilizing specific tools in order to reconstruct the metabolic potential of the genus in terms of carbohydrate hydrolysis and fermentative pathways, transporters, and anabolic potential. The analysis revealed that species cluster based on their metabolic potential, showing unique adaptation and ecological roles. Pentose phosphate and phosphoketolase pathways were highlighted as the main ones of central metabolism. The various identified PTS and ABC transporters showed adaptability to different sugars. The metabolic diversity described in this study not only supports the role of Leuconostoc spp. in natural ecosystems but also highlights their potential in industrial applications, particularly in the fermentation industry where their ability to metabolize a wide range of substrates can be harnessed for the production of various fermented foods and bioproducts. Full article

(This article belongs to the Special Issue Food Microorganisms and Genomics)

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17 pages, 4503 KiB

Open AccessArticle

Microbial Electrolysis Cells Based on a Bacterial Anode Encapsulated with a Dialysis Bag Including Graphite Particles

by Irina Amar Dubrovin, Lea Ouaknin Hirsch, Abhishiktha Chiliveru, Avinash Jukanti, Shmuel Rozenfeld, Alex Schechter and Rivka Cahan

Microorganisms 2024, 12(7), 1486; https://doi.org/10.3390/microorganisms12071486 - 20 Jul 2024

Viewed by 649

Abstract

One of the main barriers to MEC applicability is the bacterial anode. Usually, the bacterial anode contains non-exoelectrogenic bacteria that act as a physical barrier by settling on the anode surface and displacing the exoelectrogenic microorganisms. Those non-exoelectrogens can also compete with exoelectrogenic [...] Read more.

One of the main barriers to MEC applicability is the bacterial anode. Usually, the bacterial anode contains non-exoelectrogenic bacteria that act as a physical barrier by settling on the anode surface and displacing the exoelectrogenic microorganisms. Those non-exoelectrogens can also compete with exoelectrogenic microorganisms for nutrients and reduce hydrogen production. In this study, the bacterial anode was encapsulated by a dialysis bag including suspended graphite particles to improve current transfer from the bacteria to the anode material. An anode encapsulated in a dialysis bag without graphite particles, and a bare anode, were used as controls. The MEC with the graphite-dialysis-bag anode was fed with artificial wastewater, leading to a current density, hydrogen production rate, and areal capacitance of 2.73 A·m⁻², 134.13 F·m⁻², and 7.6 × 10⁻² m³·m⁻³·d⁻¹, respectively. These were highest when compared to the MECs based on the dialysis-bag anode and bare anode (1.73 and 0.33 A·m⁻², 82.50 and 13.75 F·m⁻², 4.2 × 10⁻² and 5.2 × 10⁻³ m³·m⁻³·d⁻¹, respectively). The electrochemical impedance spectroscopy of the modified graphite-dialysis-bag anode showed the lowest charge transfer resistance of 35 Ω. The COD removal results on the 25th day were higher when the MEC based on the graphite-dialysis-bag anode was fed with Geobacter medium (53%) than when it was fed with artificial wastewater (40%). The coulombic efficiency of the MEC based on the graphite-dialysis-bag anode was 12% when was fed with Geobacter medium and 15% when was fed with artificial wastewater. Full article

(This article belongs to the Special Issue Application of Microbes in Environmental Remediation)

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9 pages, 836 KiB

Open AccessCommunication

Isolation and Genomic Analysis of a Case of Staphylococcus argenteus ST2250 Related to Sepsis in Italy

by Giulia Gatti, Francesca Taddei, Anna Marzucco, Maria Sofia Montanari, Giorgio Dirani, Silvia Zannoli, Laura Grumiro, Martina Brandolini, Claudia Colosimo, Laura Dionisi, Ludovica Ingletto, Alessandra Mistral De Pascali, Alessandra Scagliarini, Vittorio Sambri and Monica Cricca

Microorganisms 2024, 12(7), 1485; https://doi.org/10.3390/microorganisms12071485 - 20 Jul 2024

Viewed by 856

Abstract

Staphylococcus argenteus, identified in 2006, represents a challenging case of bacterial taxonomic identification because of its high similarity to Staphylococcus aureus. In this context, neither mass spectrometry (MS) nor 16S gene analysis cannot precisely reveal the difference between the two species. [...] Read more.

Staphylococcus argenteus, identified in 2006, represents a challenging case of bacterial taxonomic identification because of its high similarity to Staphylococcus aureus. In this context, neither mass spectrometry (MS) nor 16S gene analysis cannot precisely reveal the difference between the two species. In our study, the sensitivity to antibiotics of S. argenteus isolated from blood culture was tested, and the investigation of the bacterial genome was performed by Multi-Locus Sequence Typing (MLST) and Whole-Genome Next-Generation Sequencing (WG-NGS). The pathogen was identified as ST2250 and presented perfectly matched resistance genes, namely aph(3′)-III, mgrA, and sepA, whereas the virulence gene detected was scn. Two plasmids were found: the pSAS plasmid, belonging to the family of Inc18, and plasmid pN315, belonging to the Rep3 group. The epidemiological distribution and the spread of S. argenteus infection are scarcely documented, particularly when associated with sepsis. Therefore, a correct taxonomy identification, antibiogram, and resistance gene analysis may help in acquiring knowledge about this bacterium and implement its detection and treatment. Full article

(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research)

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7 pages, 1645 KiB

Open AccessOpinion

Compositional Data and Microbiota Analysis: Imagination and Reality

by Tatsuki Itagaki, Hirokazu Kobayashi, Ken-ichiro Sakata, Ikuya Miyamoto, Akira Hasebe and Yoshimasa Kitagawa

Microorganisms 2024, 12(7), 1484; https://doi.org/10.3390/microorganisms12071484 - 20 Jul 2024

Viewed by 1021

Abstract

The relationships among bacterial flora, diseases, and diet have been described by many authors. An operational taxonomic units (OTUs) are the result of clustering the 16S rRNA gene sequences at a certain cutoff value, and they are considered compositional data. As Pearson’s correlation [...] Read more.

The relationships among bacterial flora, diseases, and diet have been described by many authors. An operational taxonomic units (OTUs) are the result of clustering the 16S rRNA gene sequences at a certain cutoff value, and they are considered compositional data. As Pearson’s correlation coefficient is difficult to interpret, Aitchison’s ratio analysis was used to develop a method to handle compositional data. Multivariate analysis was developed because univariate analysis can be subject to large biases. Simulations regarding absolute abundance based on certain assumptions and some analyses, such as nonparametric multidimensional scaling (NMDS), principal component analysis (PCA), and ratio analysis, were conducted in this study. The same content as a 100% stacked bar graph could be expressed in low dimensions using PCA. However, the relative diversity was not reproducible with NMDS. Various assumptions were made regarding absolute abundance based on the relative abundance. However, which assumptions are true could not be determined. In summary, ratio analysis and PCA are useful for analyzing compositional data and the gut microbiota. Full article

(This article belongs to the Special Issue Novel Strategies in the Study of the Human Gut Microbiota 2.0)

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10 pages, 677 KiB

Open AccessArticle

Antimicrobial Resistance of Enterococcus Isolates from Poultry Farms in the Republic of Serbia (Autonomous Province of Vojvodina)

by Maja Velhner, Bojana Prunić, Nevenka Aleksić, Dalibor Todorović, Slobodan Knežević and Dragana Ljubojević Pelić

Microorganisms 2024, 12(7), 1483; https://doi.org/10.3390/microorganisms12071483 - 20 Jul 2024

Viewed by 878

Abstract

Enterococcus species are significant intestinal commensals of animals, including poultry. However, they have emerged as important opportunistic infective agents in both veterinary and human medicine as well as major nosocomial pathogens, owing to their increasing antimicrobial resistance. This research aimed to investigate the [...] Read more.

Enterococcus species are significant intestinal commensals of animals, including poultry. However, they have emerged as important opportunistic infective agents in both veterinary and human medicine as well as major nosocomial pathogens, owing to their increasing antimicrobial resistance. This research aimed to investigate the prevalence and antimicrobial resistance patterns of Enterococcus spp. isolated from poultry farms in the north of Serbia. A total of 40 samples of overshoes or feces were collected from 40 poultry farms and analyzed for the presence of Enterococcus spp. using PCR or MALDI-TOF mass spectrometry for their identification. The number of isolates was 40 and included 11 isolates from laying hens, 2 isolates from turkeys, 3 from broiler breeders, and 24 from broilers. The Kirby–Bauer disk diffusion method was used to test for antibiotic susceptibility in accordance with the Clinical and Laboratory Standards Institute and EUCAST guidelines. The results showed that Enterococcus faecalis was isolated from 37.5% farms, and E. faecium from 42.5%. E. hirae was identified in 15% of poultry establishments, and E. durans and E. thialandicus on 2.5%. Notably, resistance to erythromycin, streptomycin, fluoroquinolones, and tetracyclines among the frequently used antibiotics was found. Furthermore, 35% of the isolates had multidrug resistance (MDR). In order to prevent the spread of antibiotic resistance in chicken farming and protect the health of the public and animals alike, our findings highlight the critical need for improved surveillance and control measures. To effectively establish a containment strategy for Enterococcus spp. isolated from poultry farms, more research into the processes behind their antibiotic resistance is required. Full article

(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)

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16 pages, 623 KiB

Open AccessReview

The Role of Oncogenic Viruses in Head and Neck Cancers: Epidemiology, Pathogenesis, and Advancements in Detection Methods

by Pinelopi Samara, Michail Athanasopoulos, Stylianos Mastronikolis, Efthymios Kyrodimos, Ioannis Athanasopoulos and Nicholas S. Mastronikolis

Microorganisms 2024, 12(7), 1482; https://doi.org/10.3390/microorganisms12071482 - 19 Jul 2024

Cited by 1 | Viewed by 1196

Abstract

Head and neck cancers (HNCs) constitute a wide range of malignancies originating from the epithelial lining of the upper aerodigestive tract, including the oral cavity, pharynx, larynx, nasal cavity, paranasal sinuses, and salivary glands. Although lymphomas affecting this region are not conventionally classified [...] Read more.

Head and neck cancers (HNCs) constitute a wide range of malignancies originating from the epithelial lining of the upper aerodigestive tract, including the oral cavity, pharynx, larynx, nasal cavity, paranasal sinuses, and salivary glands. Although lymphomas affecting this region are not conventionally classified as HNCs, they may occur in lymph nodes or mucosa-associated lymphoid tissues within the head and neck. Oncogenic viruses play a crucial role in HNC onset. Human papillomavirus (HPV) is extensively studied for its association with oropharyngeal cancers; nevertheless, other oncogenic viruses also contribute to HNC development. This review provides an overview of the epidemiology, pathogenesis, and advancements in detection methods of oncogenic viruses associated with HNCs, recognizing HPV’s well-established role while exploring additional viral connections. Notably, Epstein–Barr virus is linked to nasopharyngeal carcinoma and lymphomas. Human herpesvirus 8 is implicated in Kaposi’s sarcoma, and Merkel cell polyomavirus is associated with subsets of HNCs. Additionally, hepatitis viruses are examined for their potential association with HNCs. Understanding the viral contributions in the head and neck area is critical for refining therapeutic approaches. This review underlines the interaction between viruses and malignancies in this region, highlighting the necessity for ongoing research to elucidate additional mechanisms and enhance clinical outcomes. Full article

(This article belongs to the Section Medical Microbiology)

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35 pages, 12751 KiB

Open AccessReview

Native Infective Endocarditis: A State-of-the-Art-Review

by Francesco Nappi

Microorganisms 2024, 12(7), 1481; https://doi.org/10.3390/microorganisms12071481 - 19 Jul 2024

Cited by 1 | Viewed by 2040

Abstract

Native valve infective endocarditis (NVE) is a global phenomenon, defined by infection of a native heart valve and involving the endocardial surface. The causes and epidemiology of the disease have evolved in recent decades, with a doubling of the average patient age. A [...] Read more.

Native valve infective endocarditis (NVE) is a global phenomenon, defined by infection of a native heart valve and involving the endocardial surface. The causes and epidemiology of the disease have evolved in recent decades, with a doubling of the average patient age. A higher incidence was observed in patients with implanted cardiac devices that can result in right-sided infection of the tricuspid valve. The microbiology of the disease has also changed. Previously, staphylococci, which are most often associated with health-care contact and invasive procedures, were the most common cause of the disease. This has now been superseded by streptococci. While innovative diagnostic and therapeutic strategies have emerged, mortality rates have not improved and remain at 30%, which is higher than that for many cancer diagnoses. The lack of randomized trials and logistical constraints impede clinical management, and long-standing controversies such as the use of antibiotic prophylaxis persist. This state of the art review addresses clinical practice, controversies, and strategies to combat this potentially devastating disease. A multidisciplinary team will be established to provide care for patients with presumptive NVE. The composition of the team will include specialists in cardiology, cardiovascular surgery, and infectious disease. The prompt administration of combination antimicrobial therapy is essential for effective NVE treatment. Additionally, a meticulous evaluation of each patient is necessary in order to identify any indications for immediate valve surgery. With the intention of promoting a more comprehensive understanding of the procedural management of native infective endocarditis and to furnish clinicians with a reference, the current evidence for the utilization of distinct strategies for the diagnosis and treatment of NVE are presented. Full article

(This article belongs to the Section Medical Microbiology)

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18 pages, 2280 KiB

Open AccessArticle

Climate Change Stressors, Phosphate Limitation, and High Irradiation Interact to Increase Alexandrium minutum Toxicity and Modulate Encystment Rates

by Marta Sixto, Pilar Riobó, Francisco Rodríguez, Patricio A. Díaz and Rosa I. Figueroa

Microorganisms 2024, 12(7), 1480; https://doi.org/10.3390/microorganisms12071480 - 19 Jul 2024

Viewed by 993

Abstract

The changes in the cell physiology (growth rate, cell size, and cell DNA content), photosynthetic efficiency, toxicity, and sexuality under variable light and nutrient (phosphates) conditions were evaluated in cultures of the dinoflagellate Alexandrium minutum obtained from a red tide in the Ría [...] Read more.

The changes in the cell physiology (growth rate, cell size, and cell DNA content), photosynthetic efficiency, toxicity, and sexuality under variable light and nutrient (phosphates) conditions were evaluated in cultures of the dinoflagellate Alexandrium minutum obtained from a red tide in the Ría de Vigo (NW Spain). The cells were grown at low (40 and 150 µE m⁻² s⁻¹), moderate (400 µE m⁻² s⁻¹), and high (800 µE m⁻² s⁻¹) light intensities in a medium with phosphate (P+) and without (P−). Cultures were acclimated to the irradiance conditions for one week, and the experiment was run for ~1 month. The cell size and DNA content were monitored via flow cytometry. Two different clonal strains were employed as a monoculture (in a P− or P+ medium) or, to foster sexuality and resting cyst formation, as a mixed culture (only in a P− medium). A. minutum growth was favored by increasing light intensities until 400 µE m⁻² s⁻¹. The DNA content analyses indicated the accumulation of S-phase cells at the highest light intensities (400 and 800 µE m⁻² s⁻¹) and therefore the negative effects on cell cycle progression. Only when the cells were grown in a P− medium did higher light intensities trigger dose-dependent, significantly higher toxicities in all the A. minutum cultures. This result suggests that the toxicity level is responsive to the combined effects of (high) light and (low) P stress. The cell size was not significantly affected by the light intensity or P conditions. The optimal light intensity for resting cyst formation was 150 µE m⁻² s⁻¹, with higher irradiances reducing the total encystment yield. Encystment was not observed at the lowest light intensity tested, indicative of the key role of low-level irradiance in gamete and/or zygote formation, in contrast to the stressor effect of excessive irradiance on planozygote formation and/or encystment. Full article

(This article belongs to the Special Issue Phytoplankton Ecology and Harmful Algal Bloom Surveillance in Marine Ecosystems)

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11 pages, 1098 KiB

Open AccessArticle

Enteropathogenic Providencia alcalifaciens: A Subgroup of P. alcalifaciens That Causes Diarrhea

by Dieter Bulach, Glen P. Carter and M. John Albert

Microorganisms 2024, 12(7), 1479; https://doi.org/10.3390/microorganisms12071479 - 19 Jul 2024

Cited by 1 | Viewed by 962

Abstract

Despite being considered a normal flora, Providencia alcalifaciens can cause diarrhea. In a previous study, strain 2939/90, obtained from a diarrheal patient, caused invasion and actin condensation in mammalian cells, and diarrhea in a rabbit model. Four TnphoA mutants of 2939/90 produced [...] Read more.

Despite being considered a normal flora, Providencia alcalifaciens can cause diarrhea. In a previous study, strain 2939/90, obtained from a diarrheal patient, caused invasion and actin condensation in mammalian cells, and diarrhea in a rabbit model. Four TnphoA mutants of 2939/90 produced negligible invasion and actin condensation in mammalian cells. Now, the parent strain and the mutants have been sequenced to locate TnphoA insertion sites and determine the effect on virulence. A TnphoA insertion was detected in the type three secretion system (T3SS) locus on a large plasmid and not in a T3SS locus on the chromosome. In 52 genomes of P. alcalifaciens surveyed, the chromosomal T3SS locus was present in all strains, including both P. alcalifaciens genomic clades, which we classified as group A and group B. Plasmid T3SS was present in 21 of 52 genomes, mostly in group A genomes, which included isolates from an outbreak of hemorrhagic diarrhea in dogs. The TnphoA insertion only in the plasmid T3SS locus affected the invasion phenotype, suggested that this locus is critical for causation of diarrhea. We conclude that a subgroup of P. alcalifaciens that possesses this plasmid-mediated T3SS is an enteric pathogen that can cause diarrheal disease. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Multidrug-Resistant Bacteria in Infectious Patients)

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11 pages, 1281 KiB

Open AccessArticle

Growth and Yield Dynamics in Three Japanese Soybean Cultivars with Plant Growth-Promoting Pseudomonas spp. and Bradyrhizobium ottawaense Co-Inoculation

by Khin Thuzar Win, Fukuyo Tanaka, Kiwamu Minamisawa and Haruko Imaizumi-Anraku

Microorganisms 2024, 12(7), 1478; https://doi.org/10.3390/microorganisms12071478 - 19 Jul 2024

Cited by 1 | Viewed by 832

Abstract

Co-inoculation of soybeans with Bradyrhizobium and plant growth-promoting bacteria has displayed promise for enhancing plant growth, but concrete evidence of its impact on soybean yields is limited. Therefore, this study assessed the comparative efficacy of two 1-aminocyclopropane-1-carboxylate deaminase-producing Pseudomonas species (OFT2 and OFT5) [...] Read more.

Co-inoculation of soybeans with Bradyrhizobium and plant growth-promoting bacteria has displayed promise for enhancing plant growth, but concrete evidence of its impact on soybean yields is limited. Therefore, this study assessed the comparative efficacy of two 1-aminocyclopropane-1-carboxylate deaminase-producing Pseudomonas species (OFT2 and OFT5) co-inoculated with Bradyrhizobium ottawaense (SG09) on the growth, physiology, nodulation efficiency, and grain yield of three major Japanese soybean cultivars: Enrei, Fukuyutaka, and Satonohohoemi. The experiments were conducted in a warehouse under natural light conditions. The treatments included the inoculation of SG09, SG09 + OFT2, and SG09 + OFT5. Compared with Bradyrhizobium inoculation alone, co-inoculation led to significant improvements in nodulation efficiency, growth, and physiological performance in the Enrei and Fukuyutaka cultivars, but not in the Satonohohoemi cultivar. Furthermore, co-inoculation significantly boosted the total nitrogen content and ion uptake in the shoots, ultimately leading to a remarkable improvement in the grain yield in the Enrei and Fukuyutaka cultivars. These findings contribute to clarifying the interplay among Bradyrhizobium, Pseudomonas, and the plant host cultivar. Notably, Bradyrhizobium–Pseudomonas co-inoculation represents a potentially effective biofertilization strategy for soybean production, highlighting promising avenues for sustainable agricultural practices. Full article

(This article belongs to the Special Issue Interactions between Plant Beneficial Pseudomonas spp. and Their Host, 2nd Edition)

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13 pages, 498 KiB

Open AccessArticle

Characterising Eastern Grey Kangaroos (Macropus giganteus) as Hosts of Coxiella burnetii

by Anita Tolpinrud, Elizabeth Dobson, Catherine A. Herbert, Rachael Gray, John Stenos, Anne-Lise Chaber, Joanne M. Devlin and Mark A. Stevenson

Microorganisms 2024, 12(7), 1477; https://doi.org/10.3390/microorganisms12071477 - 19 Jul 2024

Viewed by 873

Abstract

Macropods are often implicated as the main native Australian reservoir hosts of Coxiella burnetii (Q fever); however, the maintenance and transmission capacity of these species are poorly understood. The objective of this cross-sectional study was to describe the epidemiology of C. burnetii in [...] Read more.

Macropods are often implicated as the main native Australian reservoir hosts of Coxiella burnetii (Q fever); however, the maintenance and transmission capacity of these species are poorly understood. The objective of this cross-sectional study was to describe the epidemiology of C. burnetii in a high-density population of eastern grey kangaroos (Macropus giganteus) in a peri-urban coastal nature reserve in New South Wales, Australia. Blood, faeces and swabs were collected from forty kangaroos as part of a population health assessment. Frozen and formalin-fixed tissues were also collected from 12 kangaroos euthanised on welfare grounds. Specimens were tested for C. burnetii using PCR, serology, histopathology and immunohistochemistry. A total of 33/40 kangaroos were seropositive by immunofluorescence assay (estimated true seroprevalence 84%, 95% confidence interval [CI] 69% to 93%), with evidence of rising titres in two animals that had been tested four years earlier. The PCR prevalence was 65% (95% CI 48% to 79%), with positive detection in most sample types. There was no evidence of pathology consistent with C. burnetii, and immunohistochemistry of PCR-positive tissues was negative. These findings indicate that kangaroos are competent maintenance hosts of C. burnetii, likely forming a significant part of its animal reservoir at the study site. Full article

(This article belongs to the Special Issue Pathogen Infection in Wildlife 2.0)

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7 pages, 614 KiB

Open AccessCommunication

Gut Microbiota Composition Is Causally Linked to Multiple Sclerosis: A Mendelian Randomization Analysis

by Valeria Zancan, Martina Nasello, Rachele Bigi, Roberta Reniè, Maria Chiara Buscarinu, Rosella Mechelli, Giovanni Ristori, Marco Salvetti and Gianmarco Bellucci

Microorganisms 2024, 12(7), 1476; https://doi.org/10.3390/microorganisms12071476 - 19 Jul 2024

Viewed by 1075

Abstract

Accumulating evidence links the microbial communities inhabiting the gut to the pathophysiological processes underlying multiple sclerosis (MS). However, most studies on the microbiome in MS are correlative in nature, thus being at risk of confounding and reverse causality. Mendelian randomization (MR) analyses allow [...] Read more.

Accumulating evidence links the microbial communities inhabiting the gut to the pathophysiological processes underlying multiple sclerosis (MS). However, most studies on the microbiome in MS are correlative in nature, thus being at risk of confounding and reverse causality. Mendelian randomization (MR) analyses allow the estimation of the causal relationship between a risk factor and an outcome of interest using genetic variants as proxies for environmental exposures. Here, we performed a two-sample MR to assess the causality between the gut microbiome and MS. We extracted genetic instruments from summary statistics from three large genome-wide association studies (GWASs) on the gut microbiome (18,340, 8959, and 7738 subjects). The exposure data were derived from the latest GWAS on MS susceptibility (47,429 patients and 68,374 controls). We pinpointed several microbial strains whose abundance is linked with enhanced MS risk (Actinobacteria class, Bifidobacteriaceae family, Lactobacillus genus) or protection (Prevotella spp., Lachnospiranaceae genus, Negativibacillus genus). The largest risk effect was seen for Ruminococcus Torques (OR, 2.89, 95% C.I. 1.67–5, p = 1.51 × 10⁻⁴), while Akkermansia municiphila emerged as strongly protective (OR, 0.43, 95% C.I. 0.32–0.57, p = 1.37 × 10⁻⁸). Our findings support a causal relationship between the gut microbiome and MS susceptibility, reinforcing the relevance of the microbiome–gut–brain axis in disease etiology, opening wider perspectives on host–environmental interactions for MS prevention. Full article

(This article belongs to the Special Issue Effects of Gut Microbiota on Human Health and Disease)

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20 pages, 2734 KiB

Open AccessArticle

Oat Brewery Waste Decreased Methane Production and Alters Rumen Fermentation, Microbiota Composition, and CAZymes Profiles

by Pradeep Kumar Malik, Shraddha Trivedi, Archit Mohapatra, Atul Purshottam Kolte, Anjumoni Mech, Tsuma Victor, Elena Ahasic and Raghavendra Bhatta

Microorganisms 2024, 12(7), 1475; https://doi.org/10.3390/microorganisms12071475 - 19 Jul 2024

Viewed by 648

Abstract

The transformation of oat brewery waste (OBW) into livestock feed could be a potential replacement for the expensive concentrate and one of the effective approaches for avoiding health hazards due to the accumulation of oat brewery waste in the environment. To explore the [...] Read more.

The transformation of oat brewery waste (OBW) into livestock feed could be a potential replacement for the expensive concentrate and one of the effective approaches for avoiding health hazards due to the accumulation of oat brewery waste in the environment. To explore the potential of OBW as a methane (CH₄) mitigating agent, an in vitro study was undertaken to investigate the effect of graded replacement of concentrate with OBW on CH₄ production, microbiota, feed fermentation, and CAZymes. A total of five treatments with variable proportions of OBW were formulated. The results indicated a linear decrease in the total gas production and a 38–52% decrease in CH₄ production with a 60 and 100% replacement of concentrate with OBW. The inclusion of OBW also affected the abundance of microbes such as Firmicutes, Euryarchaeota, Methanobrevibacter, and protozoa numbers. This study demonstrated that OBW can partially replace the concentrate and effectively mitigate CH₄ production; however, the concurrent decrease in fermentation cautioned for the partial replacement of concentrate with OBW at an appropriate level at which the fermentation remains unaffected while decreasing CH₄ production. Therefore, waste from oat breweries can contribute to curtailing the accumulation of greenhouse gases (GHGs) in the atmosphere. Full article

(This article belongs to the Section Veterinary Microbiology)

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18 pages, 5670 KiB

Open AccessArticle

Isolation and Characterization of Potassium-Solubilizing Rhizobacteria (KSR) Promoting Cotton Growth in Saline–Sodic Regions

by Yue Zhao, Hongbang Liang, Jihong Zhang, Yu Chen, Yam Prasad Dhital, Tao Zhao and Zhenhua Wang

Microorganisms 2024, 12(7), 1474; https://doi.org/10.3390/microorganisms12071474 - 19 Jul 2024

Viewed by 963

Abstract

Cotton is highly sensitive to potassium, and Xinjiang, China’s leading cotton-producing region, faces a severe challenge due to reduced soil potassium availability. Biofertilizers, particularly potassium-solubilizing rhizobacteria (KSR), convert insoluble potassium into plant-usable forms, offering a sustainable solution for evergreen agriculture. This study isolated [...] Read more.

Cotton is highly sensitive to potassium, and Xinjiang, China’s leading cotton-producing region, faces a severe challenge due to reduced soil potassium availability. Biofertilizers, particularly potassium-solubilizing rhizobacteria (KSR), convert insoluble potassium into plant-usable forms, offering a sustainable solution for evergreen agriculture. This study isolated and characterized KSR from cotton, elucidated their potassium solubilization mechanisms, and evaluated the effects of inoculating KSR strains on cotton seedlings. Twenty-three KSR strains were isolated from cotton rhizosphere soil using modified Aleksandrov medium. Their solubilizing capacities were assessed in a liquid medium. Strain A10 exhibited the highest potassium solubilization capacity (21.8 ppm) by secreting organic acids such as lactic, citric, acetic, and succinic acid, lowering the pH and facilitating potassium release. A growth curve analysis and potassium solubilization tests of A10 under alkali stress showed its vigorous growth and maintained solubilization ability at pH 8–9, with significant inhibition at pH 10. Furthermore, 16S rRNA sequencing identified strain A10 as Pseudomonas aeruginosa. Greenhouse pot experiments showed that inoculating cotton plants with strain A10 significantly increased plant height and promoted root growth. This inoculation also enhanced dry biomass accumulation in both the aerial parts and root systems of the plants, while reducing the root–shoot ratio. These results suggest that Pseudomonas aeruginosa A10 has potential as a biofertilizer, offering a new strategy for sustainable agriculture. Full article

(This article belongs to the Special Issue Using Microorganisms to Increase Crop Productivity and Sustainability)

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27 pages, 4308 KiB

Open AccessArticle

The Microbiome of Fertilization-Stage Maize Silks (Style) Encodes Genes and Expresses Traits That Potentially Promote Survival in Pollen/Style Niches and Host Reproduction

by Michelle E. H. Thompson and Manish N. Raizada

Microorganisms 2024, 12(7), 1473; https://doi.org/10.3390/microorganisms12071473 - 19 Jul 2024

Cited by 2 | Viewed by 1320

Abstract

Within flowers, the style channel receives pollen and transmits male gametes inside elongating pollen tubes to ovules. The styles of maize/corn are called silks. Fertilization-stage silks possess complex microbiomes, which may partially derive from pollen. These microbiomes lack functional analysis. We hypothesize that [...] Read more.

Within flowers, the style channel receives pollen and transmits male gametes inside elongating pollen tubes to ovules. The styles of maize/corn are called silks. Fertilization-stage silks possess complex microbiomes, which may partially derive from pollen. These microbiomes lack functional analysis. We hypothesize that fertilization-stage silk microbiomes promote host fertilization to ensure their own vertical transmission. We further hypothesize that these microbes encode traits to survive stresses within the silk (water/nitrogen limitation) and pollen (dehydration/aluminum) habitats. Here, bacteria cultured from fertilization-stage silks of 14 North American maize genotypes underwent genome mining and functional testing, which revealed osmoprotection, nitrogen-fixation, and aluminum-tolerance traits. Bacteria contained auxin biosynthesis genes, and testing confirmed indole compound secretion, which is relevant, since pollen delivers auxin to silks to stimulate egg cell maturation. Some isolates encoded biosynthetic/transport compounds known to regulate pollen tube guidance/growth. The isolates encoded ACC deaminase, which degrades the precursor for ethylene that otherwise accelerates silk senescence. The findings suggest that members of the microbiome of fertilization-stage silks encode adaptations to survive the stress conditions of silk/pollen and have the potential to express signaling compounds known to impact reproduction. Overall, whereas these microbial traits have traditionally been assumed to primarily promote vegetative plant growth, this study proposes they may also play selfish roles during host reproduction. Full article

(This article belongs to the Section Plant Microbe Interactions)

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18 pages, 4538 KiB

Open AccessArticle

A Clean and Health-Care-Focused Way to Reduce Indoor Airborne Bacteria in Calf House with Long-Wave Ultraviolet

by Luyu Ding, Qing Zhang, Chaoyuan Wang, Chunxia Yao, Feifei Shan and Qifeng Li

Microorganisms 2024, 12(7), 1472; https://doi.org/10.3390/microorganisms12071472 - 19 Jul 2024

Viewed by 617

Abstract

Long-term exposure to a relatively high concentration of airborne bacteria emitted from intensive livestock houses could potentially threaten the health and welfare of animals and workers. There is a dual effect of air sterilization and promotion of vitamin D synthesis for the specific [...] Read more.

Long-term exposure to a relatively high concentration of airborne bacteria emitted from intensive livestock houses could potentially threaten the health and welfare of animals and workers. There is a dual effect of air sterilization and promotion of vitamin D synthesis for the specific bands of ultraviolet light. This study investigated the potential use of A-band ultraviolet (UVA) tubes as a clean and safe way of reducing airborne bacteria and improving calf health. The composition and emission characteristics of airborne bacteria were investigated and used to determine the correct operating regime of UVA tubes in calf houses. Intermittent exceedances of indoor airborne bacteria were observed in closed calf houses. The measured emission intensity of airborne bacteria was 1.13 ± 0.09 × 10⁷ CFU h⁻¹ per calf. Proteobacteria were the dominant microbial species in the air inside and outside calf houses. After UVA radiation, the indoor culturable airborne bacteria decreased in all particle size ranges of the Anderson sampler, and it showed the highest reduction rate in the size range of 3.3–4.7 μm. The results of this study would enrich the knowledge of the source characteristics of the airborne bacteria in intensive livestock farming and contribute to the environmental control of cattle in intensive livestock production. Full article

(This article belongs to the Section Environmental Microbiology)

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