PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities

Ren, Tiantian; Wu, Martin

doi:10.1016/j.gene.2016.08.032

Cited by 13 publications

(14 citation statements)

References 22 publications

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“…Although it is beyond the scope of the present study, the proposed approach would benefit from further research aiming to establish which clustering method better preserves the phylogenetic relationships among sequences 31 , as well as the similarity limit below which OTUs loose biological or technical congruency. On the other hand, OTUs could be substituted by nodes in a phylogenetic tree 32 . Such approach should produce an enhanced phylogenetic resolution of the core groups, with the likely downside of escalating computing requirements and/or having to resort to the use of reference phylogenetic trees, with the (possible) concomitant loss of information.…”

Section: Discussionmentioning

confidence: 99%

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units

Cárcer

2018

Sci Rep

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The complex community of microbes living in the human gut plays an important role in host wellbeing. However, defining a ‘healthy’ gut microbiome in terms of composition has remained an elusive task, despite its anticipated medical and scientific importance. In this regard, a central question has been if there is a ‘core’ microbiome consisting of bacterial groups common to all healthy humans. Recent studies have been able to define a compositional core in human gut microbiome datasets in terms of taxonomic assignments. However, the description of the core microbiome in terms of taxonomic assignments may not be adequate when considering subsequent analyses and applications. Through the implementation of a dynamic clustering approach in the meta-analyisis of comprehensive 16S rRNA marker gene datasets, this study found that the human gut pan-microbiome presents a preeminent compositional core comprised of discrete units of varying phylogenetic depth present in all individuals studied. Since both microbial traits and ecological coherence show signs of phylogenetic conservation, this outcome provides a new conceptual framework in the study of the ecosystem, as well as important practical considerations which should be taken into account in future research.

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Section: Discussionmentioning

confidence: 99%

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units

Cárcer

2018

Sci Rep

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“…The amplicon sequence variants (ASVs) were aligned with MAFFT [ 67 ] (via q2-alignment) and used to construct a phylogeny with FastTree 2 [ 68 ] (via q2-phylogeny). Taxonomy was assigned to ASVs using a classify-sklearn naïve Bayes taxonomic classifier [ 69 ] based on SILVA database (release 132) [ 70 ], only the target sequences fragment was used in the classifier (i.e., classifier trained with the primers) [ 71 , 72 ]. The ubiquitousness of the bacterial families was addressed in each data set by identifying the taxa that persisted across serial fractions of the samples, performed with the QIIME 2 plugin feature-table (core-features) [ 65 ].…”

Section: Methodsmentioning

confidence: 99%

Anti-Tick Microbiota Vaccine Impacts Ixodes ricinus Performance during Feeding

Mateos-Hernández

Obregón

Mayé³

et al. 2020

Vaccines

118

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The tick microbiota is a highly complex ensemble of interacting microorganisms. Keystone taxa, with a central role in the microbial networks, support the stability and fitness of the microbial communities. The keystoneness of taxa in the tick microbiota can be inferred from microbial co-occurrence networks. Microbes with high centrality indexes are highly connected with other taxa of the microbiota and are expected to provide important resources to the microbial community and/or the tick. We reasoned that disturbance of vector microbiota by removal of ubiquitous and abundant keystone bacteria may disrupt the tick-microbiota homeostasis causing harm to the tick host. These observations and reasoning prompted us to test the hypothesis that antibodies targeting keystone bacteria may harm the ticks during feeding on immunized hosts. To this aim, in silico analyses were conducted to identify keystone bacteria in the microbiota of Ixodes nymphs. The family Enterobacteriaceae was among the top keystone taxa identified in Ixodes microbiota. Immunization of α-1,3-galactosyltransferase-deficient-C57BL/6 (α1,3GT KO) mice with a live vaccine containing the Enterobacteriaceae bacterium Escherichia coli strain BL21 revealed that the production of anti-E. coli and anti-α-Gal IgM and IgG was associated with high mortality of I. ricinus nymphs during feeding. However, this effect was absent in two different strains of wild type mice, BALB/c and C57BL/6. This result concurred with a wide distribution of α-1,3-galactosyltransferase genes, and possibly α-Gal, in Enterobacteriaceae and other bacteria of tick microbiota. Interestingly, the weight of I. ricinus nymphs that fed on E. coli-immunized C57BL/6 was significantly higher than the weight of ticks that fed on C57BL/6 immunized with a mock vaccine. Our results suggest that anti-tick microbiota vaccines are a promising tool for the experimental manipulation of vector microbiota, and potentially the control of ticks and tick-borne pathogens.

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“…The phylogenetic core microbiota was screened out using PhyloCore, which uses a phylogeny-based algorithm to identify core taxa at OTU level (Ren and Wu 2016 ). For each internal node, PhyloCore calculated a prevalence value, defined as the cumulative presence of all its descendant OTUs.…”

Section: Methodsmentioning

confidence: 99%

Disease outbreak accompanies the dispersive structure of shrimp gut bacterial community with a simple core microbiota

et al. 2018

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Increasing evidence has emerged supporting a tight link between gut bacterial community and shrimp health. However, the knowledge about the variation of gut bacterial community, especially with different disease onset time, remains elusive. Here, healthy and diseased shrimps were collected at 3 disease-outbreak times (day 70, 80 and 85) to investigate the variation of gut bacterial community and its underlying ecological process with 16S rRNA gene amplicon sequencing. The gut bacterial community of diseased shrimp was distinct from the healthy one and temporally less stable, characterized by decreased alpha-diversity and dispersive structure. And its dominant ecological process experienced a transition with disease onset time, although deterministic process mainly governed the healthy gut bacterial assembly. In addition, the core microbiota of healthy shrimp gut harbored more diverse bacterial taxa with more cooperative interactions, while the diseased core microbiota showed opposite pattern with significantly higher abundance of opportunistic pathogens as well. These findings indicate that shrimp heath is highly relevant to the homeostasis of its gut bacterial community. Preservation and restoration of the bacterial community equilibrium could represent an effective strategy for shrimp disease prevention.Electronic supplementary materialThe online version of this article (10.1186/s13568-018-0644-x) contains supplementary material, which is available to authorized users.

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PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities

Cited by 13 publications

References 22 publications

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units

Anti-Tick Microbiota Vaccine Impacts Ixodes ricinus Performance during Feeding

Disease outbreak accompanies the dispersive structure of shrimp gut bacterial community with a simple core microbiota

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