A Phylogenomic Analysis of the Bacterial Phylum Fibrobacteres

Abstract

The Fibrobacteres has been recognized as a bacterial phylum for over a decade, but little is known about the group beyond its environmental distribution, and characterization of its sole cultured representative genus, Fibrobacter, after which the phylum was named. Based on these incomplete data, it is thought that cellulose hydrolysis, anaerobic metabolism, and lack of motility are unifying features of the phylum. There are also contradicting views as to whether an uncultured sister lineage, candidate phylum TG3, should be included in the Fibrobacteres. Recently, chitin-degrading cultured representatives of TG3 were isolated from a hypersaline soda lake, and the genome of one species, Chitinivibrio alkaliphilus, sequenced and described in detail. Here, we performed a comparative analysis of Fibrobacter succinogenes, C. alkaliphilus and eight near or substantially complete Fibrobacteres/TG3 genomes of environmental populations recovered from termite gut, anaerobic digester, and sheep rumen metagenomes. We propose that TG3 should be amalgamated with the Fibrobacteres phylum based on robust monophyly of the two lineages and shared character traits. Polymer hydrolysis, using a distinctive set of glycoside hydrolases and binding domains, appears to be a prominent feature of members of the Fibrobacteres. Not all members of this phylum are strictly anaerobic as some termite gut Fibrobacteres have respiratory chains adapted to the microaerophilic conditions found in this habitat. Contrary to expectations, flagella-based motility is predicted to be an ancestral and common trait in this phylum and has only recently been lost in F. succinogenes and its relatives based on phylogenetic distribution of flagellar genes. Our findings extend current understanding of the Fibrobacteres and provide an improved basis for further investigation of this phylum.

Keywords: TG3; anaerobic digester; comparative genomics; fibrobacteres; termite gut.

Figure 1

Phylogenetic analysis of the phylum Fibrobacteres. (A) Maximum likelihood tree of the phylum Fibrobacteres based on alignment of 83 concatenated proteins as previously described (Soo et al., 2014). The tree was inferred using an outgroup comprising 2358 genomes from 33 phyla. For clarity, only the immediate phylum-level neighborhood of the Fibrobacteres is shown. Fibrobacteraceae genomes are shown in red; Fibromonadaceae in blue; and Chitinivibronia in green. Fibrobacteres genomes encoding nitrogen-fixing, flagellar and/or respiratory genes are indicated by N, F, and R in boxes (dotted box indicates incomplete genes), respectively. Bootstrap support for interior nodes using multiple inference methods is shown according to the legend at the lower left of the figure; ML, Maximum Likelihood; MP, Maximum Parsimony; NJ, Neighbor Joining. (B) Maximum likelihood tree based on 16S rRNA genes from Fibrobacteres and TG3 obtained from SILVA database release 119 (Quast et al., 2012). The closest matches to the partial 16S rRNA sequences obtained from the population genomes are indicated by color matching to (A), noting that the position of MC_77 is estimated since this genome lacks a 16S rRNA sequence. Isolates are bolded in black. Taxonomic group names by rank are proposed to the right of the tree, also see main text. Node support values are as described for (A).

Figure 2

Glycoside hydrolase families with a significant difference in mean proportions ≥1% between Fibrobacteres and other cellulolytic bacteria and a p ≤ 0.05. Statistical significance was assessed using Welch's t-test with Bonferroni multiple test correction.

Figure 3

Composite metabolic reconstruction of members of the phylum Fibrobacteres. Presence of genes and pathways in a given lineage is indicated by colored dots (legend at lower left). Steps in metabolic pathways absent in all investigated Fibrobacteres genomes are indicated by red crosses. Multistep reactions are shown by red arrows. Abbreviations are described in Table S3.