Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur <i>Indri indri</i>

The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur's virtually unexplored gut microbiome will deepen our understanding of the species' health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri fecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups, suggesting physical interaction is key in promoting microbiome acquisition. Strain sharing rates were highest between mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroup interactions and stable territory occupancy coupled with ongoing habitat fragmentation. No evidence of microbiome acquisition through geophagy was detected. These findings underscore the profound influence of social structure on microbiome transmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies.

Authors

Institutions

Publication Details

Journal
The ISME Journal
Published
2025-01-01
DOI
https://doi.org/10.1093/ismejo/wraf136
Citations
1
Primary Topic
Gut microbiota and health
Type
article
Field-Weighted Citation Impact
0.81

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri

Luigimaria Borruso, Donatella Scarafile, Chiara De Gregorio, Daria Valente et al.
1 citations
The ISME Journal
Gut microbiota and health
0.81
article

Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri

Luigimaria Borruso, Donatella Scarafile, Chiara De Gregorio, Daria Valente, Albert García-Valiente, Camillo Sandri, Francesco Asnicar, Davide Golzato, Serena Manara, Aitor Blanco‐Míguez, Paola Mattarelli, Valeria Torti, Cristina Giacoma, Nicola Segata, Caterina Spiezio, Elisa Piperni, Monica Modesto, Mireia Valles‐Colomer, Michal Punčochář, Paolo Manghi, Harilala Andriamaniraka, Federica Armanini, Francisca Labisa-Morais
article en
1 citations

Abstract

The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur's virtually unexplored gut microbiome will deepen our understanding of the species' health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri fecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups, suggesting physical interaction is key in promoting microbiome acquisition. Strain sharing rates were highest between mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroup interactions and stable territory occupancy coupled with ongoing habitat fragmentation. No evidence of microbiome acquisition through geophagy was detected. These findings underscore the profound influence of social structure on microbiome transmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies.

The ISME JournalVol. 19(1)
Fondazione Edmund Mach (IT), University of Antananarivo (MG), Universitat Pompeu Fabra (ES), Free University of Bozen-Bolzano (IT), University of Trento (IT), University of Warwick (GB), Accademia Albertina delle Belle Arti (IT), Casa di Cura Villa Garda (IT), Istituti di Ricovero e Cura a Carattere Scientifico (IT), University of Turin (IT), European Institute of Oncology (IT), University of Bologna (IT)
“la Caixa” Foundation, Università degli Studi di Trento, Ministerio de Ciencia e Innovación
Life in Land
Openalex Percentile: Top 25%
Gut microbiota and health
0.81
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.