Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites
- Published
- Accepted
- Subject Areas
- Bioinformatics, Ecology, Genomics, Microbiology
- Keywords
- metagenome-assembled genomes, gut microbiology, higher termites, bacteria, archaea, phylogenomics, metagenomics
- Copyright
- © 2019 Hervé et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2019. Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites. PeerJ Preprints 7:e27929v1 https://doi.org/10.7287/peerj.preprints.27929v1
Abstract
“Higher” termites have been able to colonize all tropical and subtropical regions because of their ability to digest lignocellulose with the aid of their prokaryotic gut microbiota. Over the last decade, numerous studies based on 16S rRNA gene amplicon libraries have largely described both the taxonomy and structure of the prokaryotic communities associated with termite guts. Host diet and microenvironmental conditions have emerged as the main factors structuring the microbial assemblages in the different gut compartments. Additionally, these molecular inventories have revealed the existence of termite-specific clusters that indicate coevolutionary processes in numerous prokaryotic lineages. However, for lack of representative isolates, the functional role of most lineages remains unclear. We reconstructed 589 metagenome-assembled genomes (MAGs) from the different gut compartments of eight higher termite species that encompass 17 prokaryotic phyla. By iteratively building genome trees for each clade, we significantly improved the initial automated assignment, frequently up to the genus level. We recovered MAGs from most of the termite-specific clusters in the radiation of, e.g., Planctomycetes, Fibrobacteres, Bacteroidetes, Euryarchaeota, Bathyarchaeota, Spirochaetes, Saccharibacteria, and Firmicutes, which to date contained only few or no representative genomes. Moreover, the MAGs included abundant members of the termite gut microbiota. This dataset represents the largest genomic resource for arthropod-associated microorganisms available to date and contributes substantially to populating the tree of life. More importantly, it provides a backbone for studying the metabolic potential of the termite gut microbiota, including the key members involved in carbon and nitrogen biogeochemical cycles, and important clues that may help cultivating representatives of these understudied clades.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Phylogenomic distribution of the MAGs according to the host diet
The outer rings show the occurrence of MAGs in termites with different diets. The maximum likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I model of amino-acid evolution.
Phylogenomic distribution of the MAGs according to the gut compartment of the host
The outer rings show the occurrence of MAGs in the different termite gut compartments: C crop (foregut), M midgut, P1–P5 proctodeal compartments (hindgut). The maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I model of amino-acid evolution.
Phylogenomic tree of the Archaea
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Asgard group was used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Ruminococcaceae family (Firmicutes)
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Dorea and Butyrivibrio (Lachnospiraceae) species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Actinobacteria
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Chloroflexi species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Spirochaetes
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Elusimicrobia and Cyanobacteria were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Fibrobacteres
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Bacteroidetes were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Desulfovibrionaceae family (Deltaproteobacteria)
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Desulfonatronum species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Bacteroidetes
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Chlorobi species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Chloroflexi, Saccharibacteria and Microgenomates
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Actinobacteria species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Synergistetes
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Elusimicrobia species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Planctomycetes
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Verrucomicrobia species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Elusimicrobia
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Spirochaetes species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Cloacimonetes
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Fibrobacteres species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Kiritimatiellaeota
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Chlamydiae species were used as outgroup. Names in bold included MAGs recovered in the present study.
Phylogenomic tree of the Acidobacteria
This maximum-likelihood tree was inferred from a concatenated alignment of 43 proteins using the LG+G+I+F model of amino-acid evolution. Branch supports were calculated using a Chi2-based parametric approximate likelihood-ratio test. Proteobacteria species were used as outgroup. Names in bold included MAGs recovered in the present study.