Geography as non-genetic modulation factor of chicken cecal microbiota

PLoS One. 2021 Jan 6;16(1):e0244724. doi: 10.1371/journal.pone.0244724. eCollection 2021.

Abstract

The gastrointestinal tract of chickens harbors a highly diverse microbiota contributing not only to nutrition, but also to the physiological development of the gastrointestinal tract. Microbiota composition depends on many factors such as the portion of the intestine as well as the diet, age, genotype, or geographical origin of birds. The aim of the present study was to demonstrate the influence of the geographical location over the cecal microbiota from broilers. We used metabarcoding sequencing datasets of the 16S rRNA gene publicly available to compare the composition of the Argentine microbiota against the microbiota of broilers from another seven countries (Germany, Australia, Croatia, Slovenia, United States of America, Hungary, and Malaysia). Geographical location played a dominant role in shaping chicken gut microbiota (Adonis R2 = 0.6325, P = 0.001; Mantel statistic r = 0.1524, P = 4e-04) over any other evaluated factor. The geographical origin particularly affected the relative abundance of the families Bacteroidaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Clostridiaceae. Because of the evident divergence of microbiota among countries we coined the term "local microbiota" as convergent feature that conflates non-genetic factors, in the perspective of human-environmental geography. Local microbiota should be taken into consideration as a native overall threshold value for further appraisals when testing the production performance and performing correlation analysis of gut microbiota modulation against different kind of diet and/or management approaches. In this regard, we described the Argentine poultry cecal microbiota by means of samples both from experimental trials and commercial farms. Likewise, we were able to identify a core microbiota composed of 65 operational taxonomic units assigned to seven phyla and 38 families, with the four most abundant taxa belonging to Bacteroides genus, Rikenellaceae family, Clostridiales order, and Ruminococcaceae family.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animal Feed
  • Animals
  • Australia
  • Cecum / microbiology*
  • Chickens / microbiology*
  • Croatia
  • DNA Barcoding, Taxonomic
  • Gastrointestinal Microbiome / genetics*
  • Germany
  • Hungary
  • Malaysia
  • RNA, Ribosomal, 16S / genetics
  • Slovenia
  • United States

Substances

  • RNA, Ribosomal, 16S

Grants and funding

This work was supported by the Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and National Institute of Agricultural Technology (INTA). N.P.V. has a fellowship from CONICET; L.R, J.M.D.C, M.F.M. and M.D.F. are members of research career of CONICET and INTA, Argentina. INTA- PNBIO 1131043/PNSA I106 to M.D.F and PNSA 1115056/I104 to M.F.M. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.