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MBio May 2024is a prominent member of the human gut microbiota contributing to nutrient exchange, gut function, and maturation of the host's immune system. This obligate anaerobe...
is a prominent member of the human gut microbiota contributing to nutrient exchange, gut function, and maturation of the host's immune system. This obligate anaerobe symbiont can adopt a biofilm lifestyle, and it was recently shown that biofilm formation is promoted by the presence of bile. This process also requires a extracellular DNase, which is not, however, regulated by bile. Here, we showed that bile induces the expression of several Resistance-Nodulation-Division (RND) efflux pumps and that inhibiting their activity with a global competitive efflux inhibitor impaired bile-dependent biofilm formation. We then showed that, among the bile-induced RND-efflux pumps, only the tripartite BT3337-BT3338-BT3339 pump, re-named BipABC [for Bile Induced Pump A (), B (), and C ()], is required for biofilm formation. We demonstrated that BipABC is involved in the efflux of magnesium to the biofilm extracellular matrix, which leads to a decrease of extracellular DNA concentration. The release of magnesium in the biofilm matrix also impacts biofilm structure, potentially by modifying the electrostatic repulsion forces within the matrix, reducing interbacterial distance and allowing bacteria to interact more closely and form denser biofilms. Our study therefore, identified a new molecular determinant of biofilm formation in response to bile salts and provides a better understanding on how an intestinal chemical cue regulates biofilm formation in a major gut symbiont.IMPORTANCE is a prominent member of the human gut microbiota able to degrade dietary and host polysaccharides, altogether contributing to nutrient exchange, gut function, and maturation of the host's immune system. This obligate anaerobe symbiont can adopt a biofilm community lifestyle, providing protection against environmental factors that might, in turn, protect the host from dysbiosis and dysbiosis-related diseases. It was recently shown that exposure to intestinal bile promotes biofilm formation. Here, we reveal that a specific membrane efflux pump is induced in response to bile, leading to the release of magnesium ions, potentially reducing electrostatic repulsion forces between components of the biofilm matrix. This leads to a reduction of interbacterial distance and strengthens the biofilm structure. Our study, therefore, provides a better understanding of how bile promotes biofilm formation in a major gut symbiont, potentially promoting microbiota resilience to stress and dysbiosis events.
Topics: Biofilms; Bacteroides thetaiotaomicron; Magnesium; Bacterial Proteins; Bile; Humans; Membrane Transport Proteins; Gastrointestinal Microbiome; Gene Expression Regulation, Bacterial
PubMed: 38534200
DOI: 10.1128/mbio.03488-23 -
Pharmacological Research Feb 2024Plant-derived exosome-like nanoparticles (ELNs) have drawn considerable attention for oral treatment of colonic diseases. However, the roles of ELNs derived from garlic...
Plant-derived exosome-like nanoparticles (ELNs) have drawn considerable attention for oral treatment of colonic diseases. However, the roles of ELNs derived from garlic on colitis remain unclear. Here, we demonstrate that garlic ELNs (GELNs), with desirable particle sizes (79.60 nm) and trafficking large amounts of functional proteins and microRNAs, stably roam in the gut and confer protection against ulcerative colitis (UC). In mice with DSS-induced colitis, orally administered GELNs effectively ameliorated bloody diarrhea, normalized the production of proinflammatory cytokines, and prevented colonic barrier impairment. Mechanistically, GELNs were taken up by gut microbes and reshaped DSS-induced gut microbiota dysbiosis, in which Bacteroides was the dominant respondent genus upon GELNs treatment. Notably, GELNs-enriched peu-MIR2916-p3 specifically promoted the growth of Bacteroides thetaiotaomicron, an intestinal symbiotic bacterium with palliative effects on colitis. Our findings provide new insights into the medicinal application of GELNs and highlight their potential as natural nanotherapeutic agents for preventing and treating UC.
Topics: Mice; Animals; Garlic; Bacteroides thetaiotaomicron; Gastrointestinal Microbiome; Exosomes; Colitis; Colitis, Ulcerative; Colon; Dextran Sulfate; Disease Models, Animal; Mice, Inbred C57BL
PubMed: 38218354
DOI: 10.1016/j.phrs.2024.107071 -
Biomicrofluidics Sep 2023Despite the large number of microfluidic devices that have been described over the past decade for the study of tissues and organs, few have become widely adopted. There...
Despite the large number of microfluidic devices that have been described over the past decade for the study of tissues and organs, few have become widely adopted. There are many reasons for this lack of adoption, primarily that devices are constructed for a single purpose or because they are highly complex and require relatively expensive investment in facilities and training. Here, we describe a microphysiological system (MPS) that is simple to use and provides fluid channels above and below cells, or tissue biopsies, maintained on a disposable, poly(methyl methacrylate), carrier held between polycarbonate outer plates. All other fittings are standard Luer sizes for ease of adoption. The carrier can be coated with cells on both sides to generate membrane barriers, and the devices can be established in series to allow medium to flow from one cell layer to another. Furthermore, the carrier containing cells can be easily removed after treatment on the device and the cells can be visualized or recovered for additional off-chip analysis. A 0.4 m membrane with cell monolayers proved most effective in maintaining separate fluid flows, allowing apical and basal surfaces to be perfused independently. A panel of different cell lines (Caco-2, HT29-MTX-E12, SH-SY5Y, and HUVEC) were successfully maintained in the MPS for up to 7 days, either alone or on devices connected in series. The presence of tight junctions and mucin was expressed as expected by Caco-2 and HT-29-MTX-E12, with Concanavalin A showing uniform staining. Addition of Annexin V and PI showed viability of these cells to be >80% at 7 days. Bacterial extracellular vesicles (BEVs) produced by and labeled with 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbo-cyanine perchlorate (DiD) were used as a model component of the human colonic microbiota and were visualized translocating from an apical surface containing Caco-2 cells to differentiated SH-SY5Y neuronal cells cultured on the basal surface of connected devices. The newly described MPS can be easily adapted, by changing the carrier to maintain spheroids, pieces, or slices of biopsy tissue and joined in series to study a variety of cell and tissue processes. The cell layers can be made more complex through the addition of multiple cell types and/or different patterning of extracellular matrix and the ability to culture cells adjacent to one another to allow study of cell:cell transfer, e.g., passive or active drug transfer, virus or bacterial entry or BEV uptake and transfer.
PubMed: 37840538
DOI: 10.1063/5.0168953 -
Loss of bile acid-altering enzymes impacts bacterial fitness and the global metabolic transcriptome.Microbiology Spectrum Jan 2024Recent work on bile salt hydrolases (BSHs) in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the...
Recent work on bile salt hydrolases (BSHs) in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it are not well understood. In this study, we set out to define if and how () uses its BSHs and hydroxysteroid dehydrogenase to modify bile acids to provide a fitness advantage for itself and . Genes encoding bile acid-altering enzymes were able to impact how responds to nutrient limitation in the presence of bile acids, specifically carbohydrate metabolism, affecting many polysaccharide utilization loci. This suggests that may be able to shift its metabolism, specifically its ability to target different complex glycans including host mucin, when it comes into contact with specific bile acids in the gut.
Topics: Bacteroides thetaiotaomicron; Transcriptome; Bile Acids and Salts; Bacteroides; Polysaccharides; Bacteria
PubMed: 38018975
DOI: 10.1128/spectrum.03576-23 -
International Journal of Molecular... Nov 2023The farnesoid X receptor (FXR)/βKlotho/fibroblast growth factors (FGFs) pathway is crucial for maintaining the intestinal barrier and preventing colorectal cancer...
Farnesoid X Receptor Agonist GW4064 Protects Lipopolysaccharide-Induced Intestinal Epithelial Barrier Function and Colorectal Tumorigenesis Signaling through the αKlotho/βKlotho/FGFs Pathways in Mice.
The farnesoid X receptor (FXR)/βKlotho/fibroblast growth factors (FGFs) pathway is crucial for maintaining the intestinal barrier and preventing colorectal cancer (CRC). We used an FXR agonist, GW4064, and FXR-knockout (FXR-KO) mice to investigate the role of FXR/Klothos/FGFs pathways in lipopolysaccharide (LPS)-induced intestinal barrier dysfunction and colon carcinogenesis. The results showed that upregulation of FXR in enterocytes effectively ameliorated intestinal tight-junction markers (claudin1 and zonula occludens-1), inflammation, and bile acid levels, thereby protecting mice from intestinal barrier dysfunction and colon carcinogenesis. GW4064 treatment increased FXR, αKlotho, βKlotho, FGF19, FGF21, and FGF23 in wild-type mice exposed to LPS, while FXR-KO mice had decreased levels. FXR-KO mice exhibited elevated colon cancer markers (β-catenin, LGR5, CD44, CD34, and cyclin D1) under LPS, underscoring the pivotal role of FXR in inhibiting the development of colon tumorigenesis. The varying gut microbiota responses in FXR-KO mice versus wild-type mice post LPS exposure emphasize the pivotal role of FXR in preserving intestinal microbial health, involving , , and . Our study validates the effectiveness of GW4064 in alleviating LPS-induced disruptions to the intestinal barrier and colon carcinogenesis, emphasizing the importance of the FXR/αKlotho/βKlotho/FGFs pathway and the interplay between bile acids and gut microbiota.
Topics: Mice; Animals; Lipopolysaccharides; Receptors, Cytoplasmic and Nuclear; Cell Transformation, Neoplastic; Intestinal Diseases; Bile Acids and Salts; Fibroblast Growth Factors; Colorectal Neoplasms; Mice, Inbred C57BL
PubMed: 38069256
DOI: 10.3390/ijms242316932 -
ACS Omega Oct 2023Gut microbial dysbiosis during later life may contribute to health conditions, possibly due to an increase in intestinal permeability, immune changes, and systemic...
Gut microbial dysbiosis during later life may contribute to health conditions, possibly due to an increase in intestinal permeability, immune changes, and systemic inflammation. Mouse models have been employed to determine the influence of gut microbes on aging; however, suitable gut microbial indicators are currently lacking. Therefore, this study aimed to determine the gut microbial indicators and their potential guilds in a natural aging mouse model. In agreement with previous studies, alpha diversity indices-including observed OTUs, ACE, Chao1, and Simpson-were significantly lower in aged mice than in younger mice. The results of beta diversity analysis revealed the compositional differences between young and aged mice, and the MRPP, ANOSIM, and Adonis tests indicated that the results were representative. By employing ANCOM and LEfSe analyses, () and were identified as the indicators of young and aged mice, respectively. Notably, these indicators were still present after 3 months. The result of network analysis confirmed the negative correlation of these genera in mice, and the potential guild members were identified based on the increased abundance of in aged mice. The gut microbes of aged mice tend to correspond to those involved in human diseases, selenocompound metabolism, and glycolysis/gluconeogenesis in functional predictions. In this study, the gut microbial indicators in aged mice have been identified, and it is envisaged that these findings could provide a new approach for future studies of antiaging.
PubMed: 37810685
DOI: 10.1021/acsomega.3c05949 -
The ISME Journal Oct 2023Microbial communities host many auxotrophs-organisms unable to synthesize one or more metabolites required for their growth. Auxotrophy is thought to confer an...
Microbial communities host many auxotrophs-organisms unable to synthesize one or more metabolites required for their growth. Auxotrophy is thought to confer an evolutionary advantage, yet auxotrophs must rely on other organisms that produce the metabolites they require. The mechanisms of metabolite provisioning by "producers" remain unknown. In particular, it is unclear how metabolites such as amino acids and cofactors, which are found inside the cell, are released by producers to become available to auxotrophs. Here, we explore metabolite secretion and cell lysis as two distinct possible mechanisms that result in the release of intracellular metabolites from producer cells. We measured the extent to which secretion or lysis of Escherichia coli and Bacteroides thetaiotaomicron amino acid producers can support the growth of engineered Escherichia coli amino acid auxotrophs. We found that cell-free supernatants and mechanically lysed cells provide minimal levels of amino acids to auxotrophs. In contrast, bacteriophage lysates of the same producer bacteria can support as many as 47 auxotroph cells per lysed producer cell. Each phage lysate released distinct levels of different amino acids, suggesting that in a microbial community the collective lysis of many different hosts by multiple phages could contribute to the availability of an array of intracellular metabolites for use by auxotrophs. Based on these results, we speculate that viral lysis could be a dominant mechanism of provisioning of intracellular metabolites that shapes microbial community structure.
Topics: Amino Acids; Bacteriophages; Escherichia coli
PubMed: 37322284
DOI: 10.1038/s41396-023-01452-7 -
Science Advances Dec 2023Bacille Calmette-Guerin (BCG) vaccine can elicit good T1 responses in neonates. We hypothesized that the pioneer gut microbiota affects vaccine T cell responses. Infants...
Bacille Calmette-Guerin (BCG) vaccine can elicit good T1 responses in neonates. We hypothesized that the pioneer gut microbiota affects vaccine T cell responses. Infants who are HIV exposed but uninfected (iHEU) display an altered immunity to vaccination. BCG-specific immune responses were analyzed at 7 weeks of age in iHEU, and responses were categorized as high or low. subsp. was enriched in the stools of high responders, while was enriched in low responders at time of BCG vaccination. Neonatal germ-free or SPF mice orally gavaged with live exhibited significantly higher BCG-specific T cells compared with pups gavaged with and differentially affected stool metabolome and colonic transcriptome. Human colonic epithelial cells stimulated with induced a unique gene expression profile versus . We thus identified a causal role of in early-life antigen-specific immunity.
Topics: Humans; Infant; Mice; Animals; Bifidobacterium longum subspecies infantis; BCG Vaccine; T-Lymphocytes; Gastrointestinal Microbiome; Feces
PubMed: 38064556
DOI: 10.1126/sciadv.ade1370 -
Journal of Bacteriology Nov 2023The human gut microbiota, including , is required for the degradation of otherwise undigestible polysaccharides. The gut microbiota uses polysaccharides as an energy...
The human gut microbiota, including , is required for the degradation of otherwise undigestible polysaccharides. The gut microbiota uses polysaccharides as an energy source, and fermentation products such as short-chain fatty acids are beneficial to the human host. This use of polysaccharides is dependent on the proper pairing of a TonB protein with polysaccharide-specific TonB-dependent transporters; however, the formation of these protein complexes is poorly understood. In this study, we examine the role of 11 predicted TonB homologs in polysaccharide uptake. We show that two proteins, TonB4 and TonB6, may be functionally redundant. This may allow for the development of drugs targeting species containing only a TonB4 homolog with limited impact on species encoding the redundant TonB6.
Topics: Humans; Bacteroides thetaiotaomicron; Polysaccharides; Bacteroides
PubMed: 37874167
DOI: 10.1128/jb.00218-23 -
BioRxiv : the Preprint Server For... Jul 2023Bacteroidota are abundant members of the human gut microbiota that shape the enteric landscape by modulating host immunity and degrading dietary- and host-derived...
Bacteroidota are abundant members of the human gut microbiota that shape the enteric landscape by modulating host immunity and degrading dietary- and host-derived glycans. These processes are at least partially mediated by O uter M embrane V esicles (OMVs). In this work, we developed a high-throughput screen to identify genes required for OMV biogenesis and its regulation in ( ). Our screening led us to the identification of a novel family of D ual M embrane-spanning A nti-sigma factors (Dma), which regulate OMV biogenesis in . We employed molecular and multiomic analyses to demonstrate that deletion of Dma1, the founding member of the Dma family, results in hypervesiculation by modulating the expression of NigD1, which belongs to a family of uncharacterized proteins found throughout Bacteroidota. Dma1 has an unprecedented domain organization: it contains a C-terminal β-barrel embedded in the OM; its N-terminal domain interacts with its cognate sigma factor in the cytoplasm, and both domains are tethered via an intrinsically disordered region that traverses the periplasm. Phylogenetic analyses reveal that the Dma family is a unique feature of Bacteroidota. This study provides the first mechanistic insights into the regulation of OMV biogenesis in human gut bacteria.
PubMed: 37503209
DOI: 10.1101/2023.07.13.548920