Fibrobacter communities in the gastrointestinal tracts of diverse hindgut‐fermenting herbivores are distinct from those of the rumen

Abstract

Summary The genus Fibrobacter contains cellulolytic bacteria originally isolated from the rumen. Culture-independent investigations have since identified Fibrobacter populations in gastrointestinal tracts of numerous hindgut-fermenting herbivores, but their physiology is poorly characterized due to few representative axenic cultures. To test the hypothesis that novel Fibrobacter diversity exists in hindgut fermenters, we performed culture and 16S rRNA gene amplicon sequencing on samples collected from phylogenetically diverse herbivorous hosts. Using a unique approach for recovering axenic Fibrobacter cultures, we isolated 45 novel strains from 11 different hosts. Full-length 16S rRNA gene sequencing of these isolates identified nine discrete phylotypes (cutoff = 0.03%) among them, including several that were only isolated from hindgut-fermenting hosts, and four previously unrepresented by axenic cultures. Our phylogenetic analysis indicated that six of the phylotypes are more closely related to previously described subspecies of Fibrobacter succinogenes, while the remaining three were more closely related to F. intestinalis. Culture-independent bacterial community profiling confirmed that most isolates were representative of numerically dominant phylotypes in their respective samples and strengthened the association of certain phylotypes with either ruminants or hindgut-fermenters. Despite considerable phylogenetic diversity observed among the Fibrobacter strains isolated here, phenotypic characterization suggests a conserved specialization for growth on cellulose.

Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites

“…Interestingly, we did not recover MAGs within the Fibrobacterales, which harbors the Fibrobacter genus, a clade that was also absent from 16S rRNA gene-based surveys of termite gut microbiota (Hongoh et al, 2006;Mikaelyan et al, 2015b;Bourguignon et al, 2018). Members of this genus have been isolated from the gastrointestinal tracts of mammals and bird herbivores (Neumann, McCormick & Suen, 2017), where they are potentially involved in cellulose and hemicellulose degradation (Neumann & Suen, 2018). This suggests co-evolution patterns among different Fibrobacteres clades within animal hosts with a lignocellulose-based diet.…”

Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites

“…None of the MAGs fell into the genus Fibrobacter, which was absent also in all 16S rRNA gene-based surveys of termite gut microbiota (Hongoh et al, 2006;Mikaelyan et al, 2015b;Bourguignon et al, 2018). Members of this genus have been isolated from the gastrointestinal tracts of mammals and bird herbivores (Neumann, McCormick & Suen, 2017), where they are potentially involved in cellulose and hemicellulose degradation (Neumann & Suen, 2018). This suggests co-evolutionary patterns among different Fibrobacteres clades within animal hosts with a lignocellulose-based diet.…”

The Phylogenomic Diversity of Herbivore-AssociatedFibrobacterspp. Is Correlated to Lignocellulose-Degrading Potential

“…Fibrobacter is a conserved member of the rumen microbiota, and Fibrobacter species possess several characteristics that contribute to efficient rumen function (16). Although Fibrobacter species readily solubilize hemicelluloses and pectins, available evidence indicates that energy generation in these bacteria results exclusively from the catabolism of hexoses and that these bacteria preferentially target cellulose as a substrate for growth (17 – 19). As a result, xylooligosaccharides and pentoses liberated from insoluble forms of hemicellulose and pectin, respectively, via Fibrobacter become available for consumption by other rumen microbes.…”

“…Recently, we reported a novel isolation technique that was used to greatly expand the diversity of Fibrobacter strains available for study as well as to provide additional evidence strengthening the association of certain phylotypes with the rumen or the hindgut (17). Here, we build upon our previous work by making functional predictions explaining the ecological basis of diversity among Fibrobacter spp.…”