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Updated: Dec 31, 2025
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Assessing the Viability of a Synthetic Bacterial Consortium on the In Vitro Gut Host-microbe Interface
Published on: July 4, 2018
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Evolutionary relationships among bifidobacteria and their hosts and environments
Cynthia I Rodriguez1, Jennifer B H Martiny2
1Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA. cirodri1@uci.edu.
BMC Genomics
|January 10, 2020
Summary
Bifidobacteria genomes show adaptation to specific hosts and environments, with variations in traits like genome size and carbohydrate metabolism. However, human-derived strains lack this distinct host-associated phylogenetic signal.
Area of Science:
- Microbiology
- Genomics
- Evolutionary Biology
Background:
- The assembly of animal microbiomes is influenced by environmental factors and host genetics.
- Bifidobacteria are common gut colonizers in humans and other mammals, often associated with health benefits.
- Understanding Bifidobacteria adaptation requires investigating genomic diversity across various hosts and environments.
Purpose of the Study:
- To investigate the phylogenetic signal of Bifidobacteria based on isolation sources (hosts and environments).
- To determine if key genomic traits of Bifidobacteria are dependent on their host or environment of origin.
- To explore the adaptation of Bifidobacteria diversity through comparative genomics.
Main Methods:
- Comparative analysis of publicly available Bifidobacterium genome sequences from PATRIC and NCBI.
- Multilocus phylogenetic analysis to assess genetic relatedness among strains from different sources.
- Examination of genomic traits, including genome size, accessory gene composition, amino acid biosynthesis, and carbohydrate degradation genes (CAZymes).
Main Results:
- Bifidobacteria diversity exhibits a phylogenetic signal associated with their hosts, with strains from the same host showing non-random phylogenetic relatedness.
- Genomic traits, such as genome size and accessory gene content, differ among Bifidobacteria from various sources.
- Specific traits related to amino acid production and carbohydrate degradation varied with isolation source, but not within human-derived strains.
Conclusions:
- Bifidobacteria diversity is significantly adapted to specific hosts and environments, with genomic traits reflecting these associations.
- The host-associated phylogenetic signal and trait differentiation are not evident in human-derived Bifidobacteria strains alone.
- Genomic analysis of Bifidobacteria provides insights into their environmental adaptation mechanisms and the traits crucial for survival in different niches.
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