Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes

AbstractGut microbial reference genomes and gene catalogs are necessary for understanding the chicken gut microbiome. Here, we assembled 12,339 microbial genomes and constructed a gene catalog consisting of ~16.6 million genes by integrating 799 public chicken gut microbiome samples from ten countries. We found that 893 and 38 metagenome-assembled genomes (MAGs) in our dataset were putative novel species and genera, respectively. In the chicken gut, Lactobacillus aviarius and Lactobacillus crispatus were the most common lactic acid bacteria, and glycoside hydrolases were the most abundant carbohydrate-active enzymes (CAZymes). Antibiotic resistome profiling results indicated that Chinese chicken samples harbored a higher relative abundance but less diversity of antimicrobial resistance genes (ARGs) than European samples. We also proposed the effects of geography and host species on the gut resistome. Our study provides the largest integrated metagenomic dataset from the chicken gut to date and demonstrates its value in exploring chicken gut microbial genes.

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Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

Scientific Reports ◽

10.1038/s41598-021-81668-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Laura Glendinning ◽

Buğra Genç ◽

R. John Wallace ◽

Mick Watson

Keyword(s):

Cervus Elaphus ◽

Rangifer Tarandus ◽

Red Deer ◽

Bos Taurus ◽

Novel Species ◽

Ovis Aries ◽

Metagenomic Analysis ◽

Reference Dataset ◽

Microbial Genomes ◽

Ruminant Species

AbstractThe rumen microbiota comprises a community of microorganisms which specialise in the degradation of complex carbohydrates from plant-based feed. These microbes play a highly important role in ruminant nutrition and could also act as sources of industrially useful enzymes. In this study, we performed a metagenomic analysis of samples taken from the ruminal contents of cow (Bos Taurus), sheep (Ovis aries), reindeer (Rangifer tarandus) and red deer (Cervus elaphus). We constructed 391 metagenome-assembled genomes originating from 16 microbial phyla. We compared our genomes to other publically available microbial genomes and found that they contained 279 novel species. We also found significant differences between the microbiota of different ruminant species in terms of the abundance of microbial taxonomies, carbohydrate-active enzyme genes and KEGG orthologs. We present a dataset of rumen-derived genomes which in combination with other publicly-available rumen genomes can be used as a reference dataset in future metagenomic studies.

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Carnobacterium iners sp. nov., a psychrophilic, lactic acid-producing bacterium from the littoral zone of an Antarctic pond

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.042861-0 ◽

2013 ◽

Vol 63 (Pt_4) ◽

pp. 1370-1375 ◽

Cited By ~ 23

Author(s):

Isabel Snauwaert ◽

Bart Hoste ◽

Katrien De Bruyne ◽

Karolien Peeters ◽

Luc De Vuyst ◽

...

Keyword(s):

Lactic Acid ◽

16S Rrna ◽

16S Rrna Gene ◽

Littoral Zone ◽

Type Species ◽

Novel Species ◽

Sequence Similarity ◽

Rrna Gene ◽

Content Type ◽

Link Type

Two lactic acid-producing, Gram-stain-positive rods were isolated from a microbial mat actively growing in the littoral zone of an Antarctic lake (Forlidas Pond) in the Pensacola mountains and studied using a polyphasic taxonomic approach. The isolates were examined by phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of pheS, rpoA and atpA, and biochemical and genotypic characteristics. One strain, designated LMG 26641, belonged to Carnobacterium alterfunditum and the other strain, designated LMG 26642T, could be assigned to a novel species, with Carnobacterium funditum DSM 5970T as its closest phylogenetic neighbour (99.2 % 16S rRNA gene sequence similarity). Carnobacterium iners sp. nov. could be distinguished biochemically from other members of the genus Carnobacterium by the lack of acid production from carbohydrates. DNA–DNA relatedness confirmed that strain LMG 26642T represented a novel species, for which we propose the name Carnobacterium iners sp. nov. (type strain is LMG 26642T = CCUG 62000T).

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Companilactobacillus pabuli sp. nov., a lactic acid bacterium isolated from animal feed

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004670 ◽

2021 ◽

Author(s):

Ji Young Jung ◽

Hye Kyeong Kang ◽

Hyun Mi Jin ◽

Sang-Soo Han ◽

Young Chul Kwon ◽

...

Keyword(s):

Lactic Acid ◽

16S Rrna ◽

Dna Hybridization ◽

Type Species ◽

Novel Species ◽

Rrna Gene ◽

Average Nucleotide Identity ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA–DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11T belonged to the genus Companilactobacillus . The 16S rRNA gene sequence of strain NFFJ11T exhibited high similarity to Companilactobacillus formosensis S215T (99.66 %), Companilactobacillus farciminis Rv4 naT (99.53 %), Companilactobacillus crustorum LMG 23699T (99.19 %), Companilactobacillus futsaii YM 0097T (99.06 %), Companilactobacillus zhachilii HBUAS52074T (98.86 %) and Companilactobacillus heilongiiangensis S4-3T (98.66 %). However, average nucleotide identity and in silico DNA–DNA hybridization values for these type strains were in the range of 79.90–92.93 % and 23.80–49.30 %, respectively, which offer evidence that strain NFFJ11T belongs to a novel species of the genus Companilactobacillus . The cell-wall peptidoglycan type was A4α (l-Lys–d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11T were C18 : 1 ω9c (43.3 %), C16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C19 : 1 ω7c, C19 : 1 ω6c and C19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11T represents a novel species belonging to the genus Companilactobacillus , for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11T (= KACC 21771T= JCM 34088T).

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MSC: a metagenomic sequence classification algorithm

Bioinformatics ◽

10.1093/bioinformatics/bty1071 ◽

2019 ◽

Vol 35 (17) ◽

pp. 2932-2940 ◽

Cited By ~ 1

Author(s):

Subrata Saha ◽

Jethro Johnson ◽

Soumitra Pal ◽

George M Weinstock ◽

Sanguthevar Rajasekaran

Keyword(s):

Low Cost ◽

Sequence Classification ◽

Natural Habitats ◽

Metagenomic Sequence ◽

Microbial Genomes ◽

Next Generation Sequencing Technology ◽

Alternative Approaches ◽

Computational Resources ◽

Computing Machines ◽

Reference Genomes

Abstract Motivation Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbial genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article, we propose a highly efficient metagenomic sequence classification (MSC) algorithm that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the reference sequences. Results Microbiome researchers are generally interested in two objectives of a taxonomic classifier: (i) to detect prevalence, i.e. the taxa present in a sample, and (ii) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory and runtime. Moreover, MSC outputs an approximate estimate of the abundances. Availability and implementation The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.

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A unified catalog of 204,938 reference genomes from the human gut microbiome

Nature Biotechnology ◽

10.1038/s41587-020-0603-3 ◽

2020 ◽

Cited By ~ 19

Author(s):

Alexandre Almeida ◽

Stephen Nayfach ◽

Miguel Boland ◽

Francesco Strozzi ◽

Martin Beracochea ◽

...

Keyword(s):

Gut Microbiome ◽

Human Gut ◽

Human Gut Microbiome ◽

Reference Genomes

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Genomic and Transcriptome Analyses of a Thermophilic Bacterium Geobacillus stearothermophilus B5 Isolated from Compost Reveal Its Enzymatic Basis for Lignocellulose Degradation

Microorganisms ◽

10.3390/microorganisms8091357 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1357

Author(s):

Mengmeng Wang ◽

Jiaxi Miao ◽

Xuanqing Wang ◽

Tuo Li ◽

Han Zhu ◽

...

Keyword(s):

Thermophilic Bacterium ◽

Glycoside Hydrolases ◽

Lignocellulose Degradation ◽

Geobacillus Stearothermophilus ◽

Carbohydrate Active Enzymes ◽

Transcriptional Responses ◽

Protein Coding ◽

Clusters Of Orthologous Groups ◽

Different Temperatures ◽

Shock Proteins

A lignocellulose-degrading strain isolated from thermophilic compost was identified as Geobacillus stearothermophilus B5, and found able to secrete considerable amounts of enzymes at optimal temperature (60 °C) and pH (7.5). One circular contig of 3.37 Mbp was assembled from raw data, and 3371 protein-coding genes were predicted. Clusters of orthologous groups (COG) analysis revealed various genes with functions in polymeric substrate degradation, especially for Carbohydrate Active enZymes (CAZymes), such as glycoside hydrolases (GHs) and glycosyl transferases (GTs). Furthermore, the transcriptional responses of B5 at different temperatures—with rice straw provided as the sole carbon source—were analyzed. The results revealed that B5 could resist high temperature by upregulating heat shock proteins (HSPs), enhancing protein synthesis, and decreasing carbon catabolism. Briefly, B5 possesses the ability of lignocellulose degradation, and might be considered a potential inoculant for improving composting efficiency.

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Global Profiling of Carbohydrate Active Enzymes in Human Gut Microbiome

PLoS ONE ◽

10.1371/journal.pone.0142038 ◽

2015 ◽

Vol 10 (11) ◽

pp. e0142038 ◽

Cited By ~ 35

Author(s):

Tanudeep Bhattacharya ◽

Tarini Shankar Ghosh ◽

Sharmila S. Mande

Keyword(s):

Gut Microbiome ◽

Carbohydrate Active Enzymes ◽

Human Gut ◽

Human Gut Microbiome

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Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor

Gut ◽

10.1136/gutjnl-2019-319635 ◽

2020 ◽

Vol 69 (11) ◽

pp. 1998-2007 ◽

Cited By ~ 4

Author(s):

Yun Kit Yeoh ◽

Zigui Chen ◽

Martin C S Wong ◽

Mamie Hui ◽

Jun Yu ◽

...

Keyword(s):

Colorectal Cancer ◽

Fusobacterium Nucleatum ◽

Disease Status ◽

Rural Populations ◽

Microbial Genomes ◽

Microbiome Composition ◽

Chinese Populations ◽

Southern Chinese ◽

Relative Abundances ◽

Reference Genomes

ObjectiveFusobacteria are not common nor relatively abundant in non-colorectal cancer (CRC) populations, however, we identified multiple Fusobacterium taxa nearly absent in western and rural populations to be comparatively more prevalent and relatively abundant in southern Chinese populations. We investigated whether these represented known or novel lineages in the Fusobacterium genus, and assessed their genomes for features implicated in development of cancer.MethodsPrevalence and relative abundances of fusobacterial species were calculated from 3157 CRC and non-CRC gut metagenomes representing 16 populations from various biogeographies. Microbial genomes were assembled and compared with existing reference genomes to assess novel fusobacterial diversity. Phylogenetic distribution of virulence genes implicated in CRC was investigated.ResultsIrrespective of CRC disease status, southern Chinese populations harboured increased prevalence (maximum 39% vs 7%) and relative abundances (average 0.4% vs 0.04% of gut community) of multiple recognised and novel fusobacterial taxa phylogenetically distinct from Fusobacterium nucleatum. Genomes assembled from southern Chinese gut metagenomes increased existing fusobacterial diversity by 14.3%. Homologues of the FadA adhesin linked to CRC were consistently detected in several monophyletic lineages sister to and inclusive of F. varium and F. ulcerans, but not F. mortiferum. We also detected increased prevalence and relative abundances of F. varium in CRC compared with non-CRC cohorts, which together with distribution of FadA homologues supports a possible association with gut disease.ConclusionThe proportion of fusobacteria in guts of southern Chinese populations are higher compared with several western and rural populations in line with the notion of environment/biogeography driving human gut microbiome composition. Several non-nucleatum taxa possess FadA homologues and were enriched in CRC cohorts; whether this imposes a risk in developing CRC and other gut diseases deserves further investigation.

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Inulin Fermentation by Lactobacilli and Bifidobacteria from Dairy Calves

Applied and Environmental Microbiology ◽

10.1128/aem.01738-20 ◽

2020 ◽

Vol 87 (1) ◽

Author(s):

Yuanting Zhu ◽

Jinxin Liu ◽

Julian M. Lopez ◽

David A. Mills

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Gut Microbiome ◽

Animal Health ◽

Dairy Calves ◽

Milk Replacer ◽

Comparative Genomic ◽

Bacterial Strains ◽

Content Type ◽

Long Chain

ABSTRACT Prebiotics are increasingly examined for their ability to modulate the neonate gut microbiota of livestock, and products such as inulin are commonly added to milk replacer used in calving. However, the ability of specific members of the bovine neonate microbiota to respond to inulin remains to be determined, particularly among indigenous lactobacilli and bifidobacteria, beneficial genera commonly enriched by inulin. Screening of Bifidobacterium and Lactobacillus isolates obtained from fresh feces of dairy calves revealed that lactobacilli had a higher prevalence of inulin fermentation capacity (58%) than bifidobacteria (17%). Several Ligilactobacillus agilis (synonym Lactobacillus agilis) isolates exhibited vigorous growth on, and complete degradation of, inulin; however, the phenotype was strain specific. The most vigorous inulin-fermenting strain, L. agilis YZ050, readily degraded long-chain inulin not consumed by bifidobacterial isolates. Comparative genomic analysis of both L. agilis fermenter and nonfermenter strains indicated that strain YZ050 encodes an inulinase homolog, previously linked to extracellular degradation of long-chain inulin in Lacticaseibacillus paracasei, that was strongly induced during growth on inulin. Inulin catabolism by YZ050 also generates extracellular fructose, which can cross-feed other non-inulin-fermenting lactic acid bacteria isolated from the same bovine feces. The presence of specific inulin-responsive bacterial strains within calf gut microbiome provides a mechanistic rationale for enrichment of specific lactobacilli and creates a foundation for future synbiotic applications in dairy calves aimed at improving health in early life. IMPORTANCE The gut microbiome plays an important role in animal health and is increasingly recognized as a target for diet-based manipulation. Inulin is a common prebiotic routinely added to animal feeds; however, the mechanism of inulin consumption by specific beneficial taxa in livestock is ill defined. In this study, we examined Lactobacillus and Bifidobacterium isolates from calves fed inulin-containing milk replacer and characterized specific strains that robustly consume long-chain inulin. In particular, novel Ligilactobacillus agilis strain YZ050 consumed inulin via an extracellular fructosidase, resulting in complete consumption of all long-chain inulin. Inulin catabolism resulted in temporal release of extracellular fructose, which can promote growth of other non-inulin-consuming strains of lactic acid bacteria. This work provides the mechanistic insight needed to purposely modulate the calf gut microbiome via the establishment of networks of beneficial microbes linked to specific prebiotics.

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Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

Nature Communications ◽

10.1038/s41467-020-16438-8 ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 10

Author(s):

Edoardo Pasolli ◽

Francesca De Filippis ◽

Italia E. Mauriello ◽

Fabio Cumbo ◽

Aaron M. Walsh ◽

...

Keyword(s):

Lactic Acid ◽

Lactic Acid Bacteria ◽

Gut Microbiome ◽

Large Scale ◽

Streptococcus Thermophilus ◽

Fermented Food ◽

Fermented Foods ◽

Genome Wide Analysis ◽

Genome Wide ◽

Stool Samples

Abstract Lactic acid bacteria (LAB) are fundamental in the production of fermented foods and several strains are regarded as probiotics. Large quantities of live LAB are consumed within fermented foods, but it is not yet known to what extent the LAB we ingest become members of the gut microbiome. By analysis of 9445 metagenomes from human samples, we demonstrate that the prevalence and abundance of LAB species in stool samples is generally low and linked to age, lifestyle, and geography, with Streptococcus thermophilus and Lactococcus lactis being most prevalent. Moreover, we identify genome-based differences between food and gut microbes by considering 666 metagenome-assembled genomes (MAGs) newly reconstructed from fermented food microbiomes along with 154,723 human MAGs and 193,078 reference genomes. Our large-scale genome-wide analysis demonstrates that closely related LAB strains occur in both food and gut environments and provides unprecedented evidence that fermented foods can be indeed regarded as a possible source of LAB for the gut microbiome.

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