A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle

Abstract

Background The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries. Results Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes. Conclusions Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task.

Host innate immune responses and microbiome profile of neonatal calves challenged with Cryptosporidium parvum and the effect of bovine colostrum supplementation

“…By shotgun metagenomic sequencing assembled with previously reconstructed genomes ( Teseo et al., 2022 ), and newly assembled MAGs with the data from this study, the entire microbial community and predicted virulence features were analyzed. From the metagenomic reads, 1,338 MAGs were mapped, and their abundance examined across fecal samples of 0 and 6 dpc.…”

“…The MAGs were built using MEGAHIT assembler ( Li et al., 2015 ) and autometa ( Miller et al., 2019 ) and filtered using CheckM to remove the ones below 85% completeness and > 5% contamination ( Parks et al., 2015 ). The newly built MAGs and the ones from a previous study ( Teseo et al., 2022 ) using dRep ( Olm et al., 2017 ) were compared, thus creating a non-redundant dataset of representative genomes for the samples. For abundance matrices, the read counts per sample were estimated using KMA and corrected by converting counts to proportions [(MAG contig counts/contig length)/average genome size] calculated using MicrobeCensus ( Nayfach and Pollard, 2015 ).…”

A comprehensive catalog encompassing 1376 species-level genomes reveals the core community and functional diversity of anammox microbiota

“…More simple and explicit exchange of vitamins may occur in anammox systems; for example, only four taxa (including anammox bacteria) can provide cobalamin for other community members. Additionally, the incomplete biosynthesis pathways of speci c bacteria may indicate that the production of nutrients relies on the complementary contributions of multiple symbionts [93]. These cross-feeding interactions should be further investigated and veri ed via multiomics and/or genome-scale models [94].…”

Microbial Antioxidants and Their Interactions with Gastrointestinal Tract Epithelial Cells in the Cattle

“…Based on our to-date largest bovine gastrointestinal microbial MAG database, "Bovine Gastro Microbial Genome Map" (BGMGM), we further expanded and elevated it with newly published resources and sequenced samples. Speci cally, we collected 2,114 new MAGs from cattle hindgut 22 and 106 MAGs hybrid assembled from long-read sequencing data obtained from omasum, jejunum, and rectum content, resulting in a total of 47,241 MAGs. After dereplicating using dRep (v.2.5.4) 74 with a 95% ANI threshold (comp 0 -con 1000 -sa 0.95 -nc 0.2), 14,093 non-redundant MAGs were retained.…”