Glyphosate perturbs the gut microbiota of honey bees

Glyphosate, the primary herbicide used globally for weed control, targets the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme in the shikimate pathway found in plants and some microorganisms. Thus, glyphosate may affect bacterial symbionts of animals living near agricultural sites, including pollinators such as bees. The honey bee gut microbiota is dominated by eight bacterial species that promote weight gain and reduce pathogen susceptibility. The gene encoding EPSPS is present in almost all sequenced genomes of bee gut bacteria, indicating that they are potentially susceptible to glyphosate. We demonstrated that the relative and absolute abundances of dominant gut microbiota species are decreased in bees exposed to glyphosate at concentrations documented in the environment. Glyphosate exposure of young workers increased mortality of bees subsequently exposed to the opportunistic pathogen Serratia marcescens. Members of the bee gut microbiota varied in susceptibility to glyphosate, largely corresponding to whether they possessed an EPSPS of class I (sensitive to glyphosate) or class II (insensitive to glyphosate). This basis for differences in sensitivity was confirmed using in vitro experiments in which the EPSPS gene from bee gut bacteria was cloned into Escherichia coli. All strains of the core bee gut species, Snodgrassella alvi, encode a sensitive class I EPSPS, and reduction in S. alvi levels was a consistent experimental result. However, some S. alvi strains appear to possess an alternative mechanism of glyphosate resistance. Thus, exposure of bees to glyphosate can perturb their beneficial gut microbiota, potentially affecting bee health and their effectiveness as pollinators.

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Bifidobacterium adolescentis shows potential to strengthen host defence against gastrointestinal infection via inhibition of the opportunistic pathogen Candida albicans and stimulation of human-isolated macrophages killing capacity in vitro

Access Microbiology ◽

10.1099/acmi.ac2020.po0743 ◽

2020 ◽

Vol 2 (7A) ◽

Author(s):

Liviana Ricci ◽

Joanna Mackie ◽

Megan D. Lenardon ◽

Caitlin Jukes ◽

Ahmed N. Hegazy ◽

...

Keyword(s):

Candida Albicans ◽

Bacterial Species ◽

Opportunistic Pathogen ◽

Limited Information ◽

Human Gut ◽

Bifidobacterium Adolescentis ◽

Host Immune Responses ◽

Opportunistic Fungal Pathogen ◽

Antimicrobial Metabolites

The human gut microbiota enhances the host’s resistance to enteric pathogens via colonisation resistance, a phenomenon that is driven by multiple mechanisms, such as production of antimicrobial metabolites and activation of host immune responses. However, there is limited information on how individual gut bacterial species, particularly many of the dominant anaerobes, might impact the host’s defence. This study investigated the potential of specific human gut isolates to bolster the host’s resistance to infection. First, by antagonising the opportunistic fungal pathogen Candida albicans, and secondly, by modulating the killing capacity of human-isolated macrophages in vitro. Co-culturing C. albicans with faecal microbiota from different healthy individuals revealed varying levels of fungal inhibition. In vitro assays with a panel of representative human gut anaerobes confirmed that culture supernatants from certain bacterial isolates, in particular of Bifidobacterium adolescentis, significantly inhibited C. albicans growth. Mechanistic studies revealed that microbial fermentation acids including acetate and lactate, in combination with the associated decrease in pH, were strong drivers of this inhibitory activity. In the second in vitro assay, human-isolated macrophages were exposed to bacterial supernatants, and subsequently tested for their capacity to eliminate adherent-invasive Escherichia coli. Among the gut anaerobes tested, B. adolescentis was revealed to exert the strongest immunostimulatory and killing effect when compared to the unstimulated macrophages control. B. adolescentis is known to be stimulated by dietary consumption of resistant starch andmay therefore represent an attractive target for the development of probiotic and prebiotic interventions tailored to enhancethe host’s natural defences against infection.

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Human gut bacteria as potent class I histone deacetylase inhibitors in vitro through production of butyric acid and valeric acid

PLoS ONE ◽

10.1371/journal.pone.0201073 ◽

2018 ◽

Vol 13 (7) ◽

pp. e0201073 ◽

Cited By ~ 49

Author(s):

Samantha Yuille ◽

Nicole Reichardt ◽

Suchita Panda ◽

Hayley Dunbar ◽

Imke E. Mulder

Keyword(s):

Histone Deacetylase ◽

Butyric Acid ◽

Histone Deacetylase Inhibitors ◽

Gut Bacteria ◽

Valeric Acid ◽

Class I ◽

Human Gut

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Analysis of adherence, biofilm formation and cytotoxicity suggests a greater virulence potential of Gardnerella vaginalis relative to other bacterial-vaginosis-associated anaerobes

Microbiology ◽

10.1099/mic.0.034280-0 ◽

2010 ◽

Vol 156 (2) ◽

pp. 392-399 ◽

Cited By ~ 112

Author(s):

Jennifer L. Patterson ◽

Annica Stull-Lane ◽

Philippe H. Girerd ◽

Kimberly K. Jefferson

Keyword(s):

Bacterial Vaginosis ◽

Cytotoxic Activity ◽

Bacterial Species ◽

Opportunistic Pathogen ◽

Collective Effects ◽

Gardnerella Vaginalis ◽

Childbearing Age ◽

Virulence Potential ◽

Virulence Properties

Worldwide, bacterial vaginosis (BV) is the most common vaginal disorder in women of childbearing age. BV is characterized by a dramatic shift in the vaginal microflora, involving a relative decrease in lactobacilli, and a proliferation of anaerobes. In most cases of BV, the predominant bacterial species found is Gardnerella vaginalis. However, pure cultures of G. vaginalis do not always result in BV, and asymptomatic women are sometimes colonized with low numbers of G. vaginalis. Thus, there is controversy about whether G. vaginalis is an opportunistic pathogen and the causative agent of many cases of BV, or whether BV is a polymicrobial condition caused by the collective effects of an altered microbial flora. Recent studies of the biofilm-forming potential and cytotoxic activity of G. vaginalis have renewed interest in the virulence potential of this organism. In an effort to tease apart the aetiology of this disorder, we utilized in vitro assays to compare three virulence properties of G. vaginalis relative to other BV-associated anaerobes. We designed a viable assay to analyse bacterial adherence to vaginal epithelial cells, we compared biofilm-producing capacities, and we assessed cytotoxic activity. Of the BV-associated anaerobes tested, only G. vaginalis demonstrated all three virulence properties combined. This study suggests that G. vaginalis is more virulent than other BV-associated anaerobes, and that many of the bacterial species frequently isolated from BV may be relatively avirulent opportunists that colonize the vagina after G. vaginalis has initiated an infection.

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Poly (acetyl arginyl) glucosamine attenuates Pseudomonas aeruginosa in a rat lung infection model

10.1101/2021.09.15.460521 ◽

2021 ◽

Author(s):

Bryan Garcia ◽

Melissa S. McDaniel ◽

Allister J. Loughran ◽

J. Dixon Johns ◽

Vidya Narayanaswamy ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Respiratory Infections ◽

Bacterial Species ◽

Membrane Integrity ◽

Opportunistic Pathogen ◽

Infection Model ◽

Total Biomass ◽

Chronic Infections

Pseudomonas aeruginosa is a common opportunistic pathogen that can cause chronic infections in multiple disease states, including respiratory infections in patients with cystic fibrosis (CF) and non-CF bronchiectasis. Like many opportunists, P. aeruginosa forms multicellular biofilm communities that are widely thought to be an important determinant of bacterial persistence and resistance to antimicrobials and host immune effectors during chronic/recurrent infections. Poly (acetyl, arginyl) glucosamine (PAAG) is a glycopolymer which has antimicrobial activity against a broad range of bacterial species, and also has mucolytic activity which can normalize rheologic properties of cystic fibrosis mucus. In this study, we sought to evaluate the effect of PAAG on P. aeruginosa bacteria within biofilms in vitro, and in the context of experimental pulmonary infection in a rodent infection model. PAAG treatment caused significant bactericidal activity against P. aeruginosa biofilms, and a reduction in the total biomass of preformed P. aeruginosa biofilms on abiotic surfaces, as well as on the surface of immortalized cystic fibrosis human bronchial epithelial cells. Studies of membrane integrity indicated that PAAG causes changes to P. aeruginosa cell morphology and dysregulates membrane polarity. PAAG treatment reduced infection and consequent tissue inflammation in experimental P. aeruginosa rat infections. Based on these findings we conclude that PAAG represents a novel means to combat P. aeruginosa infection, which may warrant further evaluation as a therapeutic.

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Gut Microbiota of Ostrinia Nubilalis Larvae Degrade Maize Cellulose

10.21203/rs.3.rs-589374/v1 ◽

2021 ◽

Author(s):

Junfeng Li ◽

Sifan Chen ◽

Xuxiong Tao ◽

Tao Shao

Keyword(s):

Gut Microbiota ◽

Ostrinia Nubilalis ◽

European Corn Borer ◽

Gut Bacteria ◽

Cellulose Content ◽

Bacterial Isolates ◽

Corn Borer ◽

Gut Microbes ◽

Maize Plants

Abstract BackgroundWhile most insects rely on gut bacteria to digest cellulose and produce sugars or fatty acids that are then available to the host, this has been disputed in Lepidopteran larvae due to their simple gut morphology and rapid digestive throughput. The European corn borer (ECB), Ostrinia nubilalis (Hübner), is a devastating pest that feeds the lignocellulose-rich tissues of maize plants. However, the potential role of ECB gut microbes in degrading maize cellulose remains unexplored. Here, we investigate the gut microbiota of ECB fed with different diets and the potential function of their gut bacteria in maize lignocellulose degradation.ResultsThe diversity and composition of gut bacterial communities varied dramatically between the ECB larva fed with artificial diets (ECB-D) and maize plants (ECB-M). Draft genomes of the bacterial isolates from ECB-D and ECB-M show that the principal degraders of cellulose mainly belonged to Firmicutes or Proteobacteria and were primarily found in the midgut. The bacterial isolates contained genes encoding various carbohydrate-active enzymes (CAZyme). Furthermore, scanning electron microscopy (SEM) revealed significant breakdown of lignocellulose in maize treated by the two bacterial isolates for nine days in vitro. Cellulose content in maize particles treated with BI-M were significantly lower than those treated with BI-D or the control (Kruskal–Wallis test: Χ2 = 6.72, df = 2; P = 0.0259). Metabolomic analyses reveal that maize particles treated by two bacterial isolates generate distinctive metabolomic profiles, with enrichment for different monosaccharides and amino acids.ConclusionThe results indicated that the diet of the host impacts the composition and the function of its gut microbiota, and that ECB exploits specific gut microbes to digest maize lignocellulose with distinctive products. Our study provides valuable microbiota resources for lignocellulose bioconversion.

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Revealing the in vivo growth and division patterns of mouse gut bacteria

Science Advances ◽

10.1126/sciadv.abb2531 ◽

2020 ◽

Vol 6 (36) ◽

pp. eabb2531

Author(s):

Liyuan Lin ◽

Qiuyue Wu ◽

Jia Song ◽

Yahui Du ◽

Juan Gao ◽

...

Keyword(s):

Amino Acid ◽

Gut Microbiota ◽

Growth Dynamics ◽

Gut Bacteria ◽

Metabolic Labeling ◽

Taxonomic Identification ◽

In Vivo Growth

Current techniques for studying gut microbiota are unable to answer some important microbiology questions, like how different bacteria grow and divide in the gut. We propose a method that integrates the use of sequential d-amino acid–based in vivo metabolic labeling with fluorescence in situ hybridization (FISH), for characterizing the growth and division patterns of gut bacteria. After sequentially administering two d-amino acid–based probes containing different fluorophores to mice by gavage, the resulting dual-labeled peptidoglycans provide temporal information on cell wall synthesis of gut bacteria. Following taxonomic identification with FISH probes, the growth and division patterns of the corresponding bacterial taxa, including species that cannot be cultured separately in vitro, are revealed. Our method offers a facile yet powerful tool for investigating the in vivo growth dynamics of the bacterial gut microbiota, which will advance our understanding of bacterial cytology and facilitate elucidation of the basic microbiology of this gut “dark matter.”

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Bacterial biodiversity drives the evolution of CRISPR-based phage resistance in Pseudomonas aeruginosa

10.1101/586115 ◽

2019 ◽

Author(s):

Ellinor O Alseth ◽

Elizabeth Pursey ◽

Adela M Luján ◽

Isobel McLeod ◽

Clare Rollie ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Dna Sequences ◽

Bacterial Species ◽

Opportunistic Pathogen ◽

Phage Resistance ◽

Natural Environments ◽

Human Pathogens ◽

Resistance Evolution ◽

Trade Offs

Approximately half of all bacterial species encode CRISPR-Cas adaptive immune systems1, which provide immunological memory by inserting short DNA sequences from phage and other parasitic DNA elements into CRISPR loci on the host genome2. Whereas CRISPR loci evolve rapidly in natural environments3, bacterial species typically evolve phage resistance by the mutation or loss of phage receptors under laboratory conditions4,5. Here, we report how this discrepancy may in part be explained by differences in the biotic complexity of in vitro and natural environments6,7. Specifically, using the opportunistic pathogen Pseudomonas aeruginosa and its phage DMS3vir, we show that coexistence with other human pathogens amplifies the fitness trade-offs associated with phage receptor mutation, and therefore tips the balance in favour of CRISPR-based resistance evolution. We also demonstrate that this has important knock-on effects for P. aeruginosa virulence, which became attenuated only if the bacteria evolved surface-based resistance. Our data reveal that the biotic complexity of microbial communities in natural environments is an important driver of the evolution of CRISPR-Cas adaptive immunity, with key implications for bacterial fitness and virulence.

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Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

Microorganisms ◽

10.3390/microorganisms8101483 ◽

2020 ◽

Vol 8 (10) ◽

pp. 1483

Author(s):

Miloslava Kollarcikova ◽

Marcela Faldynova ◽

Jitka Matiasovicova ◽

Eva Jahodarova ◽

Tereza Kubasova ◽

...

Keyword(s):

Gut Microbiota ◽

Intestinal Tract ◽

Single Gene ◽

Bacterial Species ◽

Host Adaptation ◽

Human Gut ◽

Bacteroides Species ◽

The Family ◽

New Generation

Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.

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Method comparison for the direct enumeration of bacterial species using a chemostat model of the human colon

BMC Microbiology ◽

10.1186/s12866-019-1669-2 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Ines B. Moura ◽

Charmaine Normington ◽

Duncan Ewin ◽

Emma Clark ◽

Mark H. Wilcox ◽

...

Keyword(s):

Gut Microbiota ◽

Real Time ◽

Quantitative Methods ◽

Pearson Correlation ◽

Bacterial Species ◽

Method Comparison ◽

Recurrent Infection ◽

Human Colon ◽

Chemostat Model

Abstract Background Clostridioides difficile infection (CDI) has a high recurrent infection rate. Faecal microbiota transplantation (FMT) has been used successfully to treat recurrent CDI, but much remains unknown about the human gut microbiota response to replacement therapies. In this study, antibiotic-mediated dysbiosis of gut microbiota and bacterial growth dynamics were investigated by two quantitative methods: real-time quantitative PCR (qPCR) and direct culture enumeration, in triple-stage chemostat models of the human colon. Three in vitro models were exposed to clindamycin to induce simulated CDI. All models were treated with vancomycin, and two received an FMT. Populations of total bacteria, Bacteroides spp., Lactobacillus spp., Enterococcus spp., Bifidobacterium spp., C. difficile, and Enterobacteriaceae were monitored using both methods. Total clostridia were monitored by selective culture. Using qPCR analysis, we additionally monitored populations of Prevotella spp., Clostridium coccoides group, and Clostridium leptum group. Results Both methods showed an exacerbation of disruption of the colonic microbiota following vancomycin (and earlier clindamycin) exposure, and a quicker recovery (within 4 days) of the bacterial populations in the models that received the FMT. C. difficile proliferation, consistent with CDI, was also observed by both qPCR and culture. Pearson correlation coefficient showed an association between results varying from 98% for Bacteroides spp., to 62% for Enterobacteriaceae. Conclusions Generally, a good correlation was observed between qPCR and bacterial culture. Overall, the molecular assays offer results in real-time, important for treatment efficacy, and allow the monitoring of additional microbiota groups. However, individual quantification of some genera (e.g. clostridia) might not be possible without selective culture.

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In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials

mBio ◽

10.1128/mbio.00019-20 ◽

2020 ◽

Vol 11 (2) ◽

Cited By ~ 5

Author(s):

Kurt Selle ◽

Joshua R. Fletcher ◽

Hannah Tuson ◽

Daniel S. Schmitt ◽

Lana McMillan ◽

...

Keyword(s):

Gut Microbiota ◽

Broad Spectrum ◽

Bacterial Species ◽

Bacterial Genome ◽

The United States ◽

Type I ◽

Content Type ◽

Clostridioides Difficile

ABSTRACT Clostridioides difficile is an important nosocomial pathogen that causes approximately 500,000 cases of C. difficile infection (CDI) and 29,000 deaths annually in the United States. Antibiotic use is a major risk factor for CDI because broad-spectrum antimicrobials disrupt the indigenous gut microbiota, decreasing colonization resistance against C. difficile. Vancomycin is the standard of care for the treatment of CDI, likely contributing to the high recurrence rates due to the continued disruption of the gut microbiota. Thus, there is an urgent need for the development of novel therapeutics that can prevent and treat CDI and precisely target the pathogen without disrupting the gut microbiota. Here, we show that the endogenous type I-B CRISPR-Cas system in C. difficile can be repurposed as an antimicrobial agent by the expression of a self-targeting CRISPR that redirects endogenous CRISPR-Cas3 activity against the bacterial chromosome. We demonstrate that a recombinant bacteriophage expressing bacterial genome-targeting CRISPR RNAs is significantly more effective than its wild-type parent bacteriophage at killing C. difficile both in vitro and in a mouse model of CDI. We also report that conversion of the phage from temperate to obligately lytic is feasible and contributes to the therapeutic suitability of intrinsic C. difficile phages, despite the specific challenges encountered in the disease phenotypes of phage-treated animals. Our findings suggest that phage-delivered programmable CRISPR therapeutics have the potential to leverage the specificity and apparent safety of phage therapies and improve their potency and reliability for eradicating specific bacterial species within complex communities, offering a novel mechanism to treat pathogenic and/or multidrug-resistant organisms. IMPORTANCE Clostridioides difficile is a bacterial pathogen responsible for significant morbidity and mortality across the globe. Current therapies based on broad-spectrum antibiotics have some clinical success, but approximately 30% of patients have relapses, presumably due to the continued perturbation to the gut microbiota. Here, we show that phages can be engineered with type I CRISPR-Cas systems and modified to reduce lysogeny and to enable the specific and efficient targeting and killing of C. difficile in vitro and in vivo. Additional genetic engineering to disrupt phage modulation of toxin expression by lysogeny or other mechanisms would be required to advance a CRISPR-enhanced phage antimicrobial for C. difficile toward clinical application. These findings provide evidence into how phage can be combined with CRISPR-based targeting to develop novel therapies and modulate microbiomes associated with health and disease.

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