The gastrointestinal microbiome of browsing goats (Capra hircus)

PLoS One. 2022 Oct 17;17(10):e0276262. doi: 10.1371/journal.pone.0276262. eCollection 2022.

Abstract

Despite the growing interest in the ruminants' gastrointestinal tract (GIT) microbiomes' ability to degrade plant materials by animal husbandry and industrial sectors, only a few studies addressed browsing ruminants. The present work describes the taxonomic and functional profile of the bacterial and archaeal communities from five different gastrointestinal sections (rumen, omasum-abomasum, jejunum, cecum and colon) of browsing Capra hircus, by metabarcoding using 16S rRNA genes hypervariable regions. The bacterial communities across the GITs are mainly composed of Bacillota and Bacteroidota. Prevotella was the leading bacterial group found in the stomachs, Romboutsia in the jejuna, and Rikenellaceae_RC9_gut_group, Bacteroides, UCG-010_ge, UCG-005, and Alistipes in large intestines. The archaeal communities in the stomachs and jejuna revealed to be mainly composed of Methanobrevibacter, while in the large intestines its dominance is shared with Methanocorpusculum. Across the GITs, the main metabolic functions were related to carbohydrate, amino acid, and energy metabolisms. Significant differences in the composition and potential biological functions of the bacterial communities were observed among stomachs, jejuna and large intestines. In contrast, significant differences were observed among stomachs and jejuna verse large intestines for archaeal communities. Overall different regions of the GIT are occupied by different microbial communities performing distinct biological functions. A high variety of glycoside hydrolases (GHs) indispensable for degrading plant cell wall materials were predicted to be present in all the GIT sections.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / metabolism
  • Animals
  • Archaea / genetics
  • Bacteria
  • Bacteroidetes / genetics
  • Carbohydrates
  • Gastrointestinal Microbiome* / genetics
  • Glycoside Hydrolases / metabolism
  • Goats / genetics
  • RNA, Ribosomal, 16S / genetics
  • RNA, Ribosomal, 16S / metabolism
  • Rumen / microbiology

Substances

  • Amino Acids
  • Carbohydrates
  • RNA, Ribosomal, 16S
  • Glycoside Hydrolases

Grants and funding

This work was funded by a PhD Studentship to V.G. from the Fundação para a Ciência e Tecnologia (SFRH/BDE/103606/2014). This work also received financial support from Association BLC3 - Technology and Innovation Campus, Centre Bio R&D Unit (UID/ 05083/2020), R&D Unit Centre for Functional Ecology - Science for People & the Planet (UIDB/04004/2020), financed by FCT/MCTES through national funds (PIDDAC), and Center for Neuroscience and Cell Biology (UIDP/04539/2020). Also, contributing to conclude this research was the research contract of V.G. funded by CENTRO-04-3559-FSE-000146 - Centro Portugal Regional Operational Program (Centro2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.