Author:
Meng Yujie,Li Shuang,Zhang Chong,Zheng Hao
Abstract
Abstract
Background
Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts’ health. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same species. Innovative droplet-based microfluidic cultivation may help to elucidate the inter-strain interactions. A limited number of bacterial phylotypes colonize the honeybee gut, while individual strains possess unique genomic potential and critical capabilities, which provides a particularly good model for strain-level analyses.
Results
Here, we construct a droplet-based microfluidic platform and generated ~ 6 × 108 droplets encapsulated with individual bacterial cells from the honeybee gut and cultivate in different media. Shotgun metagenomic analysis reveals significant changes in community structure after droplet-based cultivation, with certain species showing higher strain-level diversity than in gut samples. We obtain metagenome-assembled genomes, and comparative analysis reveal a potential novel cluster from Bifidobacterium in the honeybee. Interestingly, Lactobacillus panisapium strains obtained via droplet cultivation from Apis mellifera contain a unique set of genes encoding l-arabinofuranosidase, which is likely important for the survival of bacteria in competitive environments.
Conclusions
By encapsulating single bacteria cells inside microfluidic droplets, we exclude potential interspecific competition for the enrichment of rare strains by shotgun sequencing at high resolution. The comparative genomic analysis reveals underlying mechanisms for host-specific adaptations, providing intriguing insights into microbe-microbe interactions. The current approach may facilitate the hunting for elusive bacteria and paves the way for large-scale studies of more complex animal microbial communities.
Publisher
Springer Science and Business Media LLC
Subject
Microbiology (medical),Microbiology
Reference70 articles.
1. Lynch JB, Hsiao EY. Microbiomes as sources of emergent host phenotypes. Science. 2019;365:1405–9.
2. Lee W-J, Hase K. Gut microbiota–generated metabolites in animal health and disease. Nat Chem Biol. 2014;10:416–24.
3. Knight R, Callewaert C, Marotz C, Hyde ER, Debelius JW, McDonald D, et al. The microbiome and human biology. Annu Rev Genomics Hum Genet. 2017;18:65–86.
4. Zou Y, Xue W, Luo G, Deng Z, Qin P, Guo R, et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat Biotechnol. 2019;37:179–85.
5. Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ, et al. A new view of the tree of life. Nat Microbiol. 2016;1:1–6.
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