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PMID: 15816930 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing.

Environmental microbiology ·Vol. 7 ·No. 4 ·2005-04-00 ·Pages 530-43

Larue R, Yu Z, Parisi VA, Egan AR, Morrison M

Abstract

It is well recognized that a dynamic biofilm develops upon plant biomass in the herbivore gastrointestinal tract, but this component of the microbiome has not previously been specifically sampled, or directly compared with the biodiversity present in the planktonic fraction of digesta. In this study, the digesta collected from four sheep fed two different diets was separated into three fractions: the planktonic phase, and the microbial populations either weakly or tightly adherent to plant biomass. The community DNA prepared from each fraction was then subjected to both ribosomal intergenic spacer analysis (RISA) and denaturing gradient gel electrophoresis (DGGE). Both types of analysis showed that dietary factors influence community structure, and that the adherent fractions produced more complex profiles. The RIS-clone libraries prepared from the planktonic and adherent populations were then subjected to restriction fragment length polymorphism (RFLP) and DNA sequence analyses, which resulted in a far greater degree of discrimination among the fractions. Although many of the sequenced clones from the adherent populations were assigned to various clusters within the low G+C Gram-positive bacteria, the clone libraries from animals consuming an all-grass diet were largely comprised of novel lineages of Clostridium, while in animals consuming the starch-containing diet, Selenomonas and Ruminococcus spp. were the dominant low G+C Gram-positive bacteria. Additionally, the libraries from hay-fed animals also contained clones most similar to asaccharolytic Clostridia, and other Gram-positive bacteria that specialize in the transformation of plant phenolic compounds and the formation of cinnamic, phenylacetic and phenylpropionic acids. These results reveal, for the first time, the phylogeny of adherent subpopulations that specialize in the transformation of plant lignins and other secondary compounds, which potentiate polysaccharide hydrolysis by other members of the biofilm.

MeSH Terms

Animals Bacteria/classification,genetics,isolation & purification Biodiversity Biofilms Biomass Clostridium/classification,genetics,isolation & purification DNA Fingerprinting DNA, Bacterial/chemistry,isolation & purification DNA, Ribosomal Spacer/analysis,isolation & purification Electrophoresis, Polyacrylamide Gel Gastrointestinal Tract/microbiology Molecular Sequence Data Phylogeny Polymorphism, Restriction Fragment Length Ruminococcus/classification,genetics,isolation & purification Selenomonas/classification,genetics,isolation & purification Sequence Analysis, DNA Sheep/microbiology

Chemicals

DNA, Bacterial DNA, Ribosomal Spacer

Authors & Affiliations

5 authors, click to expand affiliations / ORCID

Larue Ross

The MAPLE Research Initiative, Department of Animal Sciences, The Ohio State University, Columbus, OH 43210, USA.

Yu Zhongtang

Parisi Victoria A

Egan Adrian R

Morrison Mark

Article Info

Journal

Environmental microbiology

Abbr.

Environ Microbiol

ISSN

1462-2912

DOI

10.1111/j.1462-2920.2005.00721.x

Published

2005-04-00

Pages

530-43

Language

English

Region

England

NLM ID

100883692

Subset

Databases

GENBANK

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External Links

PubMed source DOI: 10.1111/j.1462-2920.2005.00721.x View journal details

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Novel microbial diversity adherent to plant biomass in the herbivore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing.

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