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

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Nice study illustrating the prokaryotic diversity in so-called higher termites: Phylogenomic analysis of 589 metagenome-assembled genomes from termite guts https://t.co/odNHAoMPla via @PeerJPreprints https://t.co/1gly02ykw0
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RT @phy_papers: PJpreprint: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the…
RT @phy_papers: PJpreprint: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the…
RT @phy_papers: PJpreprint: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the…
RT @phy_papers: PJpreprint: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the…
RT @phy_papers: PJpreprint: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the…
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RT @phy_papers: PJpreprint: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the…
20 days ago
PJpreprint: Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites https://t.co/cMvQAllrSD
20 days ago
Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites https://t.co/ielLSioJw9 https://t.co/Pa2TMSgXrI
Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites https://t.co/FfXL1EUEvI https://t.co/JHdo5gVmaa
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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.

DOI: 10.7287/peerj.preprints.27929v1/supp-1

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-2

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-3

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-4

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-5

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-6

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-7

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-8

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-9

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-10

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-11

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-12

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-13

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-14

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-15

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.

DOI: 10.7287/peerj.preprints.27929v1/supp-16

Final taxonomic assignment and characteristics of the MAGs

DOI: 10.7287/peerj.preprints.27929v1/supp-18

Initial taxonomic assignment of the MAGs

DOI: 10.7287/peerj.preprints.27929v1/supp-19

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Vincent Hervé conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Pengfei Liu performed the experiments, analyzed the data, approved the final draft.

Carsten Dietrich conceived and designed the experiments, performed the experiments, approved the final draft.

David Sillam-Dussès contributed reagents/materials/analysis tools, approved the final draft.

Petr Stiblik contributed reagents/materials/analysis tools, approved the final draft.

Jan Šobotník contributed reagents/materials/analysis tools, approved the final draft.

Andreas Brune conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Field experiments were approved by the French Ministry for the Ecological and Solidarity Transition (UID: ABSCH-CNA-FR-240495-2).

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The data have been deposited at GenBank under the BioProject accession number PRJNA560329; genomes are available with accession numbers SRR9983610-SRR9984198.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA560329

Data Deposition

The following information was supplied regarding data availability:

The accession numbers of the MAGs are provided in the Supplementary Table 2.

The data have been deposited at GenBank under the BioProject accession number PRJNA560329; genomes are available with accession numbers SRR9983610-SRR9984198.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA560329

Funding

This study was funded by the Deutsche Forschungsgemeinschaft in the collaborative research center SFB 987 (Microbial Diversity in Environmental Signal Response) and by the Max-Planck-Gesellschaft. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. PS and JŠ were supported by grant "EVA4.0", No. CZ.02.1.01/0.0/0.0/16_019/0000803 financed by OP RDE. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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