-
Nature Communications Jan 2024Bacteria use a variety of defense systems to protect themselves from phage infection. In turn, phages have evolved diverse counter-defense measures to overcome host...
Bacteria use a variety of defense systems to protect themselves from phage infection. In turn, phages have evolved diverse counter-defense measures to overcome host defenses. Here, we use protein structural similarity and gene co-occurrence analyses to screen >66 million viral protein sequences and >330,000 metagenome-assembled genomes for the identification of anti-phage and counter-defense systems. We predict structures for ~300,000 proteins and perform large-scale, pairwise comparison to known anti-CRISPR (Acr) and anti-phage proteins to identify structural homologs that otherwise may not be uncovered using primary sequence search. This way, we identify a Bacteroidota phage Acr protein that inhibits Cas12a, and an Akkermansia muciniphila anti-phage defense protein, termed BxaP. Gene bxaP is found in loci encoding Bacteriophage Exclusion (BREX) and restriction-modification defense systems, but confers immunity independently. Our work highlights the advantage of combining protein structural features and gene co-localization information in studying host-phage interactions.
Topics: Bacteriophages; CRISPR-Cas Systems; Viral Proteins; Bacteria; Bacteroidetes
PubMed: 38245560
DOI: 10.1038/s41467-024-45068-7 -
Science (New York, N.Y.) Nov 2023Nutrient starvation of beneficial bacteria helps them colonize the human gut.
Nutrient starvation of beneficial bacteria helps them colonize the human gut.
Topics: Humans; Symbiosis; Gastrointestinal Microbiome; Firmicutes; Bacteroidetes; Probiotics; Animals; Mice; Genetic Fitness; Genetic Engineering; Diet; Intestines; Gastrointestinal Diseases
PubMed: 37972163
DOI: 10.1126/science.adh9165 -
Microbiome Oct 2018Clostridiales and Bacteroidales are uniquely adapted to the gut environment and have co-evolved with their hosts resulting in convergent microbiome patterns within...
BACKGROUND
Clostridiales and Bacteroidales are uniquely adapted to the gut environment and have co-evolved with their hosts resulting in convergent microbiome patterns within mammalian species. As a result, members of Clostridiales and Bacteroidales are particularly suitable for identifying sources of fecal contamination in environmental samples. However, a comprehensive evaluation of their predictive power and development of computational approaches is lacking. Given the global public health concern for waterborne disease, accurate identification of fecal pollution sources is essential for effective risk assessment and management. Here, we use random forest algorithm and 16S rRNA gene amplicon sequences assigned to Clostridiales and Bacteroidales to identify common fecal pollution sources. We benchmarked the accuracy, consistency, and sensitivity of our classification approach using fecal, environmental, and artificial in silico generated samples.
RESULTS
Clostridiales and Bacteroidales classifiers were composed mainly of sequences that displayed differential distributions (host-preferred) among sewage, cow, deer, pig, cat, and dog sources. Each classifier correctly identified human and individual animal sources in approximately 90% of the fecal and environmental samples tested. Misclassifications resulted mostly from false-positive identification of cat and dog fecal signatures in host animals not used to build the classifiers, suggesting characterization of additional animals would improve accuracy. Random forest predictions were highly reproducible, reflecting the consistency of the bacterial signatures within each of the animal and sewage sources. Using in silico generated samples, we could detect fecal bacterial signatures when the source dataset accounted for as little as ~ 0.5% of the assemblage, with ~ 0.04% of the sequences matching the classifiers. Finally, we developed a proxy to estimate proportions among sources, which allowed us to determine which sources contribute the most to observed fecal pollution.
CONCLUSION
Random forest classification with 16S rRNA gene amplicons offers a rapid, sensitive, and accurate solution for identifying host microbial signatures to detect human and animal fecal contamination in environmental samples.
Topics: Animals; Bacteroidetes; Cats; Cattle; Clostridiales; Decision Trees; Deer; Dogs; Environmental Monitoring; Feces; Fresh Water; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; RNA, Ribosomal, 16S; Sewage; Swine; Water Pollution
PubMed: 30336775
DOI: 10.1186/s40168-018-0568-3 -
International Journal of Molecular... Mar 2021Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend... (Review)
Review
Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.
Topics: Animals; Bacteroidetes; Cell Wall; Gastrointestinal Microbiome; Humans; Models, Biological; Plants; Polysaccharides
PubMed: 33802923
DOI: 10.3390/ijms22063077 -
Nature Microbiology Jul 2022Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid...
Inositol lipids are ubiquitous in eukaryotes and have finely tuned roles in cellular signalling and membrane homoeostasis. In Bacteria, however, inositol lipid production is relatively rare. Recently, the prominent human gut bacterium Bacteroides thetaiotaomicron (BT) was reported to produce inositol lipids and sphingolipids, but the pathways remain ambiguous and their prevalence unclear. Here, using genomic and biochemical approaches, we investigated the gene cluster for inositol lipid synthesis in BT using a previously undescribed strain with inducible control of sphingolipid synthesis. We characterized the biosynthetic pathway from myo-inositol-phosphate (MIP) synthesis to phosphoinositol dihydroceramide, determined the crystal structure of the recombinant BT MIP synthase enzyme and identified the phosphatase responsible for the conversion of bacterially-derived phosphatidylinositol phosphate (PIP-DAG) to phosphatidylinositol (PI-DAG). In vitro, loss of inositol lipid production altered BT capsule expression and antimicrobial peptide resistance. In vivo, loss of inositol lipids decreased bacterial fitness in a gnotobiotic mouse model. We identified a second putative, previously undescribed pathway for bacterial PI-DAG synthesis without a PIP-DAG intermediate, common in Prevotella. Our results indicate that inositol sphingolipid production is widespread in host-associated Bacteroidetes and has implications for symbiosis.
Topics: Animals; Bacteria; Bacteroides thetaiotaomicron; Bacteroidetes; Inositol; Lipid Metabolism; Mice; Phosphatidylinositols; Sphingolipids
PubMed: 35725777
DOI: 10.1038/s41564-022-01152-6 -
Journal of Molecular Medicine (Berlin,... Jan 2017Bacterial species composition in the gut has emerged as an important factor in obesity and its related metabolic diseases such as type 2 diabetes. Out of thousands of... (Review)
Review
Bacterial species composition in the gut has emerged as an important factor in obesity and its related metabolic diseases such as type 2 diabetes. Out of thousands of bacterial species-level phylotypes inhabiting the human gut, the majority belong to two dominant phyla, the Bacteroidetes and Firmicutes. Members of the Bacteroidetes in particular have been associated with human metabolic diseases. However, their associations with disease are not always consistent between studies. Delving deeper into the diversity within the Bacteroidetes reveals a vast diversity in genomes and capacities, which partly explain how not all members respond equally to similar environmental conditions in their hosts. Here, we discuss the Bacteroidetes phylum, associations of its members with metabolic phenotypes, and efforts to characterize functionally their interactions with their hosts. Harnessing the Bacteroidetes to promote metabolic health will require a nuanced understanding of how specific strains interact with their microbial neighbors and their hosts under various conditions.
Topics: Animals; Bacteroidetes; Diet; Gastrointestinal Microbiome; Host-Pathogen Interactions; Humans; Metabolic Diseases; Microbiota
PubMed: 27900395
DOI: 10.1007/s00109-016-1492-2 -
Microbiology Spectrum Aug 2023Microbial secondary metabolites play crucial roles in microbial competition, communication, resource acquisition, antibiotic production, and a variety of other...
Microbial secondary metabolites play crucial roles in microbial competition, communication, resource acquisition, antibiotic production, and a variety of other biotechnological processes. The retrieval of full-length BGC (biosynthetic gene cluster) sequences from uncultivated bacteria is difficult due to the technical constraints of short-read sequencing, making it impossible to determine BGC diversity. Using long-read sequencing and genome mining, 339 mainly full-length BGCs were recovered in this study, illuminating the wide range of BGCs from uncultivated lineages discovered in seawater from Aoshan Bay, Yellow Sea, China. Many extremely diverse BGCs were discovered in bacterial phyla such as , , , and as well as the previously uncultured archaeal phylum " Thermoplasmatota." The data from metatranscriptomics showed that 30.1% of secondary metabolic genes were being expressed, and they also revealed the expression pattern of BGC core biosynthetic genes and tailoring enzymes. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional expression of BGCs in environmental processes. Genome mining of metagenomic data has become the preferred method for the bioprospecting of novel compounds by cataloguing secondary metabolite potential. However, the accurate detection of BGCs requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until recently with new long-read technologies. We used high-quality metagenome-assembled genomes generated from long-read data to determine the biosynthetic potential of microbes found in the surface water of the Yellow Sea. We recovered 339 highly diverse and mostly full-length BGCs from largely uncultured and underexplored bacterial and archaeal phyla. Additionally, we present long-read metagenomic sequencing combined with metatranscriptomic analysis as a potential method for gaining access to the largely underutilized genetic reservoir of specialized metabolite gene clusters in the majority of microbes that are not cultured. The combination of long-read metagenomic and metatranscriptomic analyses is significant because it can more accurately assess the mechanisms of microbial adaptation to the environment through BGC expression based on metatranscriptomic data.
Topics: Metagenomics; Bacteria; Metagenome; Archaea; Bacteroidetes
PubMed: 37409950
DOI: 10.1128/spectrum.01501-23 -
Scientific Reports Jul 2022Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally...
Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally studied for their community composition, but less is known about their genetic structure and heterogeneity. In this study, we analyzed a coastal sabkha for its microbial composition using 16S rDNA and whole metagenome, as well as for its population genetic structure. Our 16S rDNA analysis show high alpha diversity in both inner and edge sabkha than outer sabkha. Beta diversity result showed similar kind of microbial composition between inner and edge sabkha, while outer sabkha samples show different microbial composition. At phylum level, Bacteroidetes (~ 22 to 34%), Euryarchaeota (~ 18 to ~ 30%), unclassified bacteria (~ 24 to ~ 35%), Actinobacteria (~ 0.01 to ~ 11%) and Cyanobacteria (less than 1%) are predominantly found in both inside and edge sabkha regions, whereas Proteobacteria (~ 92 to ~ 97%) and Parcubacteria (~ 1 to ~ 2%) are predominately found in outer sabkha. Our 225 metagenomes assembly from this study showed similar bacterial community profile as observed in 16S rDNA-based analysis. From the assembled genomes, we found important genes that are involved in biogeochemical cycles and secondary metabolite biosynthesis. We observed a dynamic, thriving ecosystem that engages in metabolic activity that shapes biogeochemical structure via carbon fixation, nitrogen, and sulfur cycling. Our results show varying degrees of horizontal gene transfers (HGT) and homologous recombination, which correlates with the observed high diversity for these populations. Moreover, our pairwise population differentiation (Fst) for the abundance of species across the salinity gradient of sabkhas identified genes with strong allelic differentiation, lower diversity and elevated nonsynonymous to synonymous ratio of variants, which suggest selective sweeps for those gene variants. We conclude that the process of HGT, combined with recombination and gene specific selection, constitute the driver of genetic variation in bacterial population along a salinity gradient in the unique sabkha ecosystem.
Topics: Bacteroidetes; Cyanobacteria; DNA, Ribosomal; Ecosystem; Salinity; Sodium Chloride; Sodium Chloride, Dietary
PubMed: 35788147
DOI: 10.1038/s41598-022-15347-8 -
Applied and Environmental Microbiology Apr 2020Beneficial gut microbes can facilitate insect growth on diverse diets. The omnivorous American cockroach, (Insecta: Blattodea), thrives on a diet rich in plant...
Beneficial gut microbes can facilitate insect growth on diverse diets. The omnivorous American cockroach, (Insecta: Blattodea), thrives on a diet rich in plant polysaccharides and harbors a species-rich gut microbiota responsive to host diet. are among the most abundant taxa in and other cockroaches, based on cultivation-independent gut community profiling, and these potentially polysaccharolytic bacteria may contribute to host diet processing. Eleven isolates were cultivated from digestive tracts, and phylogenomic analyses suggest that they were new , , , and species distinct from those previously isolated from other insects, humans, and environmental sources. In addition, complete genomes were generated for each isolate, and polysaccharide utilization loci (PULs) and several non-PUL-associated carbohydrate-active enzyme (CAZyme)-coding genes that putatively target starch, pectin, and/or cellulose were annotated in each of the isolate genomes. Type IX secretion system (T9SS)- and CAZyme-coding genes tagged with the corresponding T9SS recognition and export C-terminal domain were observed in some isolates, suggesting that these CAZymes were deployed via non-PUL outer membrane translocons. Additionally, single-substrate growth and enzymatic assays confirmed genomic predictions that a subset of the and isolates could degrade starch, pectin, and/or cellulose and grow in the presence of these substrates as a single sugar source. Plant polysaccharides enrich diets, and many of these gut isolates are well equipped to exploit host dietary inputs and potentially contribute to gut community and host nutrient accessibility. Gut microbes are increasingly being recognized as critical contributors to nutrient accessibility in animals. The globally distributed omnivorous American cockroach () harbors many bacterial phyla (e.g., ) that are abundant in vertebrates. thrives on a highly diverse plant-enriched diet, making this insect a rich potential source of uncharacterized polysaccharolytic bacteria. We have cultivated, completely sequenced, and functionally characterized several novel species that are endemic to the gut, and many of these isolates can degrade simple and complex polysaccharides. Cultivation and genomic characterization of these isolates further enable deeper insight into how these taxa participate in polysaccharide metabolism and, more broadly, how they affect animal health and development.
Topics: Animals; Bacteroidetes; Diet; Periplaneta; Polysaccharides; Symbiosis
PubMed: 32060023
DOI: 10.1128/AEM.00091-20 -
Nihon Saikingaku Zasshi. Japanese... 2017Many bacteria symbiotic and parasitic in humans are included in the genera Bacteroides, Prevotella, Porphyromonas and others, which belong to the phylum Bacteroidetes.... (Review)
Review
Many bacteria symbiotic and parasitic in humans are included in the genera Bacteroides, Prevotella, Porphyromonas and others, which belong to the phylum Bacteroidetes. We have been studying gingipain, a major secretory protease of Porphyromonas gingivalis which is a periodontopathogenic bacterium belonging to the genus Porphyromonas, and pili which contribute to host colonization in the bacterium. In the process, it was found that gingipain was secreted by a system not reported previously. Furthermore, this secretion system was found to exist widely in the Bacteroidetes phylum bacteria and closely related to the gliding motility of bacteroidete bacteria, and it was named the Por secretion system (later renamed the type IX secretion system). Regarding P. gingivalis pili, it was found that the pilus protein is transported as a lipoprotein to the cell surface, and the pilus formation occurs due to degradation by arginine-gingipain. Pili with this novel formation mechanism was found to be widely present in bacteria belonging to the class Bacteroidia in the phylum Bacteroidetes and was named the type V pili.
Topics: Adhesins, Bacterial; Animals; Arginine; Bacterial Adhesion; Bacterial Proteins; Bacterial Secretion Systems; Bacteroidetes; Cell Membrane; Cysteine Endopeptidases; Fimbriae, Bacterial; Genome, Bacterial; Gingipain Cysteine Endopeptidases; Humans; Lipoproteins; Mice; Periodontitis; Porphyromonas gingivalis; Protein Transport
PubMed: 29109335
DOI: 10.3412/jsb.72.219