Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees

Sarton-Lohéac, Garance; Nunes-Silva, Carlos Gustavo; Mazel, Florent; Baud, Gilles; Bakker, Vincent de; Das, Sudip; Chazli, Yassine El; Ellegaard, Kirsten; García-Garcerá, Marc; Glover, Natasha; Liberti, Joanito; Marçal, Lorena Nacif; Prasad, Aiswarya; Somerville, Vincent; Bonilla-Rosso, Germán; Engel, Philipp

doi:10.1128/mbio.03538-22

Cited by 14 publications

(25 citation statements)

References 86 publications

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“…Next, we predicted metabolic functions and macromolecular machineries using a custom rule-based based pipeline that included the GapMind, dbCAN and MacSysFinder tools (28–32) to comprehensively investigate the common catabolic and biosynthetic pathways, secretion systems, bacterial competence and carbohydrate-active enzymes (CAZymes)(33)(Figure 3, Table S6). The most prevalent mechanism for carbon catabolism in all streptococci including the lung isolates was the Embden-Meyerhof-Parnas (EMP) pathway.…”

Section: Resultsmentioning

confidence: 99%

“…The accessory system including relaxases (MOBs)(44) were more variable across genomes with 5 MOB families (MOB B , MOB C , MOB Q , MOB T , MOB V ) detected (Figure S5). Hence, we classified these as conjugation system proteins (CONJ)(28).…”

Section: Resultsmentioning

confidence: 99%

“…The mixture was incubated for 30 min at 37°C with gentle agitation. After this, the volume was brought up to 500 μl with Gram-positive lysis buffer and the mixture was transferred to screw cap tubes in tubes containing 200 mg of 0.1-mm acid-washed zirconia beads and homogenized using a FastPrep-25 5G instrument (2 rounds of 30 s with the power set to 6), as previously described(28). This was followed by centrifugation at maximum speed for 5 minutes at room temperature.…”

Section: Methodsmentioning

confidence: 99%

“…Predictions of key metabolic pathways and macromolecular structures were performed by using a custom genome profiler as previously described(28). A set of rules were applied to conclude the presence and completeness of predicted pathways.…”

Section: Functional Annotation and Analysismentioning

confidence: 99%

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Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota

Kanungo,

Bonilla-Rosso,

Sarton-Lohéac

et al. 2023

Preprint

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Streptococci are one of the predominant and the most diverse genus in the human lung. Previously, we isolated human distal lung Streptococci from bronchoalvolear lavage fluid (BALF) as part of the human Lung Microbiota culture Collection (LuMiCol). Here, we performed whole genome sequencing, comparative phylogenomics and phenotypic characterization of six Streptococcal isolates representing the phylogenetic diversity of the genus in distal human lung. Here, we report five new species and one new subspecies including phylogenetic intermediates of commonly found Streptococci not limited to human lung. Pangenome analysis reveals gene content, evolutionary relationships, and metabolic functions shedding light on contribution of these Streptococci to lung microbial metabolism. Antimicrobial resistance gene analysis followed by MIC determination revealed macrolide, lincosamide and tetracycline resistance in lung Streptococci. We show the presence of capsular genes in lung streptococci both matching to the prototypical capsular genes (cps) and unique genes. Interestingly, the newStreptococcusisolate sp. nov. P2E5, genetically identical to the most prevalentStreptococcusin the human distal lung was revealed to be a phylogenetic intermediate between theS. mitisgroup andS. pneumoniae.It also harbors the pneumolysin (ply) gene and was found to have the serotype 21E. Finally, core genome phylogeny reveals that lung Streptococci the are evolutionary distinct from oral Streptococcal isolates in expanded Human Oral Microbiome Database (eHOMD). Hence, these findings we reveal new phylogenetically distinct Streptococcal species from the human distal lung microbiota and its genetic diversity and metabolism to understand the microbial ecology of human lung.ImportanceA healthy human distal lung harbour characteristic microbial communities mostly composed of oropharyngeal taxa, which are facultative or obligative anaerobes despite lung being the medium of oxygen intake. However, little is known about the genetic and functional diversity of these bacteria owing to the lack of resources including availability of primary lung isolate from human samples. Therefore, we have established a large bacterial collection that covers all major phyla by cultivating human bronchoalveolar lavage fluid (BALF) under various conditions.Streptococcusis the most prevalent and diverse genera in the human lung microbiota. Using genetic and biochemical approaches, we studied six diverse lung isolates from our collection representing the actual Streptococcal diversity and identify these as new species and subspecies. We hypothesize that learning about the phylogenetic genetic diversity, preferred metabolism and molecular structures of these Streptococci will provide with new insights on the understudied microbial ecosystem of the human lung.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Functional Annotation and Analysismentioning

confidence: 99%

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Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota

Kanungo,

Bonilla-Rosso,

Sarton-Lohéac

et al. 2023

Preprint

Self Cite

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“…Most of the Meliponini species, on the other hand, harbor an Acetobacter -like phylotype that is seldom detected in other eusocial bees. These differences between stingless bees and other eusocial bees seem to be due to the loss and gain of these phylotypes during host bee evolution [ 38 ], which is further discussed in the recent study using neotropical stingless bees [ 75 ].…”

Section: Eusocial Bee Gut Microbiotamentioning

confidence: 99%

Basic Structures of Gut Bacterial Communities in Eusocial Insects

Suenami

Koto

Miyazaki

2023

Insects

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Gut bacterial communities assist host animals with numerous functions such as food digestion, nutritional provision, or immunity. Some social mammals and insects are unique in that their gut microbial communities are stable among individuals. In this review, we focus on the gut bacterial communities of eusocial insects, including bees, ants, and termites, to provide an overview of their community structures and to gain insights into any general aspects of their structural basis. Pseudomonadota and Bacillota are prevalent bacterial phyla commonly detected in those three insect groups, but their compositions are distinct at lower taxonomic levels. Eusocial insects harbor unique gut bacterial communities that are shared within host species, while their stability varies depending on host physiology and ecology. Species with narrow dietary habits, such as eusocial bees, harbor highly stable and intraspecific microbial communities, while generalists, such as most ant species, exhibit relatively diverse community structures. Caste differences could influence the relative abundance of community members without significantly altering the taxonomic composition.

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Mitochondrial genome heteroplasmy and phylogenomics of the stingless bee Tetragonula laeviceps (Apidae, Apinae, Meliponini)

Yong,

Song,

Chua

et al. 2024

Apidologie

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Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees

Cited by 14 publications

References 86 publications

Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota

Comparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota

Basic Structures of Gut Bacterial Communities in Eusocial Insects

Mitochondrial genome heteroplasmy and phylogenomics of the stingless bee Tetragonula laeviceps (Apidae, Apinae, Meliponini)

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