Lifestyles in transition: evolution and natural history of the genus Lactobacillus

Duar, Rebbeca M.; Lin, Xiaoxi B.; Zheng, Jinshui; Martino, Maria Elena; Grenier, Théodore; Pérez-Muñoz, María Elisa; Leulier, François; Gänzle, Michael G.; Walter, Jens

doi:10.1093/femsre/fux030

Cited by 412 publications

(536 citation statements)

References 189 publications

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“…() for the taxonomic composition of the microbiome in individual flies of four mycophagous drosophilid species, including the three studied here, these results are surprising from the broad perspective of gut microbiome research. The default prediction is that the composition and functional traits of the gut microbiome would be shaped by the conditions and resources in the gut habitat and that the gut habitat would differ between host species, depending on diet and phylogeny (Brooks et al., ; Duar et al., ; Ley, Luzupone, Hamady, Knight & Gordon, ; Moeller et al., ). The latter expectation is borne out by the gut transcriptome data in this study, with gene expression differentiating by species on the first two PC axes (Figure f).…”

Section: Discussionmentioning

confidence: 99%

Functional variation in the gut microbiome of wild Drosophila populations

et al. 2018

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Most of the evidence that the gut microbiome of animals is functionally variable, with consequences for the health and fitness of the animal host, is based on laboratory studies, often using inbred animals under tightly controlled conditions. It is largely unknown whether these microbiome effects would be evident in outbred animal populations under natural conditions. In this study, we quantified the functional traits of the gut microbiota (metagenome) and host (gut transcriptome) and the taxonomic composition of the gut microorganisms (16S rRNA gene sequence) in natural populations of three mycophagous Drosophila species. Variation in microbiome function and composition was driven principally by the period of sample collection, while host function varied mostly with Drosophila species, indicating that variation in microbiome traits is determined largely by environmental factors, and not host taxonomy. Despite this, significant correlations between microbiome and host functional traits were obtained. In particular, microbiome functions dominated by metabolism were positively associated with host functions relating to gut epithelial turnover. Much of the functional variation in the microbiome could be attributed to variation in abundance of Bacteroidetes, rather than the two other abundant groups, the γ-Proteobacteria or Lactobacillales. We conclude that functional variation in the interactions between animals and their gut microbiome can be detectable in natural populations, and, in mycophagous Drosophila, this variation relates primarily to metabolism and homeostasis of the gut epithelium.

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Section: Discussionmentioning

confidence: 99%

Functional variation in the gut microbiome of wild Drosophila populations

et al. 2018

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“…The current literature depicts L. plantarum as a paradigm for a nomadic lifestyle, with an increasing interest as a model bacterium and for industrial applications (Siezen and van Hylckama Vlieg, ; Martino et al ., ). Most of the studies dealing with L. plantarum have used genome approaches and/or have investigated strains having weak link with the habitat of origin (Bron et al ., ; Esteban‐Torres et al ., ; Reverón et al ., ; Turpin et al ., ). We used triplets of strains isolated from nine different habitats.…”

Section: Discussionmentioning

confidence: 99%

How Lactobacillus plantarum shapes its transcriptome in response to contrasting habitats

Filannino

Angelis

Cagno

et al. 2018

Environmental Microbiology

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Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin. Subsequently, selected strains from each habitat switched to repeated cultivation on MRS medium and transcriptomes homogenized into a unique cluster. Adaptation to this common medium mainly relied on activation of genes for phage- and prophage-related proteins and transposases. Finally, the comparison of growth across model media and with respect to MRS medium showed that 44% of the overall 3112 gene transcripts changed depending on the specific habitat. Regulation and shaping of transcriptomes mainly concerned carbohydrate acquisition, pyruvate catabolism, proteolytic system and amino acid, lipid and inorganic ion transport and metabolism, with contrasting responses for contrasting habitats. Pathways reconstruction demonstrated how the large genome size of L. plantarum imparts transcriptome and metabolic flexibility as the basic mechanism for a nomadic lifestyle.

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“…Lactic acid bacteria are known to often co-occur with other microorganisms in a variety of natural niches (Duar et al, 2017;Ponomarova and Patil, 2015). One such niche is the adult Drosophila gut where Acetobacteracaea and Lactobacilli are often found together (Pais et al, 2018;Ren et al, 2007;Ryu et al, 2008;Wong et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Metabolic cross-feeding allows a gut microbial community to overcome detrimental diets and alter host behaviour

Henriques

Serra

Francisco

et al. 2019

Preprint

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The impact of commensal bacteria on the host arises from complex microbial-diet-host interactions. Mapping metabolic interactions in gut microbial communities is therefore key to understand how the microbiome influences the host. Here we use an interdisciplinary approach including isotope-resolved metabolomics to show that in Drosophila melanogaster, Acetobacter pomorum (Ap) and Lactobacillus plantarum (Lp) establish a syntrophic relationship to overcome detrimental host diets and identify Ap as the bacterium altering the host's feeding decisions. Specifically, we show that Lp generates lactate which is used by Ap to produce and provide amino acids that are essential to Lp allowing it to grow in imbalanced diets. Lactate is also necessary and sufficient for Ap to alter the fly's protein appetite. Our data show that gut bacterial communities use metabolic interactions to become resilient to detrimental host diets and to ensure the constant flow of metabolites used by effector bacteria to alter host behaviour.Drosophila, feeding behaviour, microbiome, commensal bacteria, nutrition, bacterial communities, essential amino acids, syntrophy, metabolic crossfeeding, Acetobacteracaea, Lactobacilli Correspondence: carlos.ribeiro@neuro.fchampalimaud.org

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Lifestyles in transition: evolution and natural history of the genus Lactobacillus

Cited by 412 publications

References 189 publications

Functional variation in the gut microbiome of wild Drosophila populations

Functional variation in the gut microbiome of wild Drosophila populations

How Lactobacillus plantarum shapes its transcriptome in response to contrasting habitats

Metabolic cross-feeding allows a gut microbial community to overcome detrimental diets and alter host behaviour

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