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

Bertucci

et al. 2020

Preprint

Self Cite

26Miscanthus sp. is regarded as suitable biomass for different biorefinery value chains. However, due 27 to high recalcitrance, its wide use is yet untapped. Termite is the most efficient lignocellulose 28 degrading insect, and its success results from synergistic cooperation with its gut microbiome. 29Here, we investigated at holobiont level the dynamic adaptation of a higher termite Cortaritermes 30 sp. to imposed Miscanthus diet, with a long-term objective of overcoming lignocellulose 31 recalcitrance. We used an integrative omics approach, comprising amplicon sequencing, 32 metagenomics and metatranscriptomics that we combined with enzymatic characterisation of 33 carbohydrate active enzymes from termite gut Fibrobacteres and Spirochaetae. Adaptation to the 34 new diet was evidenced by reduced gut bacterial diversity and modified gene expression profiles, 35 further suggesting a shift towards utilisation of cellulose and arabinoxylan, two main components of 36Miscanthus lignocellulose. Low identity of reconstructed microbial genomes to microbes from 37 closely related termite species, supported the hypothesis of a strong phylogenetic relationship 38 between host and its gut microbiome. Application-wise, this makes each termite gut system an 39 endless source of enzymes that are potentially industrially relevant. 40This study provides a framework for better understanding the complex lignocellulose degradation by 41 the higher termite gut system and paves a road towards its future bioprospecting. 42 43

Section: Resultssupporting

confidence: 66%

Targeted biomass degradation by the higher termite gut system - integrative omics applied to host and its gut microbiome

Całusińska

Bertucci

et al. 2020

Preprint

Self Cite

“…Following the taxonomic assignment, transcripts of putative prokaryotic origin were selected for further analysis. To improve the taxonomic classi cation, transcripts were also compared to the metagenome assembled genomes (MAGs) reconstructed in metagenomic study of higher termites gut microbiota [34]. In the case where the identity to MAGs was higher than to the entries in IMG-MER genomes database, the initial IMG-MER taxonomy was corrected.…”

Section: Prokaryotic Mrna Sequencing and Data Analysismentioning

confidence: 99%

“…1) and the taxonomic distribution of assigned prokaryotic gene transcripts (Fig. 2), even though the initial database dependent taxonomy was further improved by comparing transcripts to MAGs reconstructed from termite gut microbiomes [34]. In particular, large under-representation of Fibrobacteres and overrepresentation of Firmicutes were observed in the termite gut prokaryotic metatranscriptomes, especially within the plant bre-feeding termite cluster.…”

Section: Transcripts Annotation To Broad Functional Categories Revealmentioning

confidence: 99%

Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites

Goux

Sillam‐Dussès

et al. 2020

Preprint

Background: Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories. Results: Despite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly 0.18 % of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts.Conclusions: Our results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass.

“…1) and the taxonomic distribution of assigned prokaryotic gene transcripts (Fig. 2), even though the initial database dependent taxonomy was further improved by comparing transcripts to MAGs reconstructed from termite gut microbiomes [30]. In particular, large under-representation of Fibrobacteres and over-representation of Firmicutes were observed in the termite gut prokaryotic metatranscriptomes, especially within the plant fibrefeeding termite cluster.…”

Section: Resultsmentioning

confidence: 99%

Compositional and functional characterisation of biomass-degrading microbial communities in guts of plant fibre- and soil-feeding higher termites

Goux

Sillam‐Dussès

et al. 2020

Preprint

Background: Termites are among the most successful insect lineages on the globe and are responsible for providing numerous ecosystem services. They mainly feed on wood and other plant material at different stages of humification. Lignocellulose is often a principal component of such plant diet and termites largely rely on their symbiotic microbiota and associated enzymes to decompose their food efficiently. While lower termites and their gut flagellates were given larger scientific attention in the past, the gut lignocellulolytic bacteria of higher termites remain less explored. Therefore, in this study, we investigated the structure and function of gut prokaryotic microbiomes from 11 higher termite genera representative of Syntermitinae, Apicotermitinae, Termitidae and Nasutitermitinae subfamilies, broadly grouped into plant fibre- and soil-feeding termite categories. Results: Despite the different compositional structures of the studied termite gut microbiomes, reflecting well the diet and host lineage, we observed a surprisingly high functional congruency between gut metatranscriptomes from both feeding groups. The abundance of transcripts encoding for carbohydrate active enzymes as well as expression and diversity profiles of assigned glycoside hydrolase families were also similar between plant fibre- and soil-feeding termites. Yet, dietary imprints highlighted subtle metabolic differences specific to each feeding category. Roughly 0.18 % of de novo re-constructed gene transcripts were shared between the different termite gut microbiomes, making each termite gut a unique reservoir of genes encoding for potentially industrially applicable enzymes, e.g. relevant to biomass degradation. Taken together, we demonstrated the functional equivalence in microbial populations across different termite hosts. Conclusions: Our results provide valuable insight into the bacterial component of the termite gut system and significantly expand the inventory of termite prokaryotic genes participating in the deconstruction of plant biomass.