Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis

Custer, Gordon F.; Gans, Maya; Diepen, Linda T. A. van; Dini‐Andreote, Francisco; Buerkle, C. Alex

doi:10.1128/msystems.01066-22

Cited by 27 publications

(23 citation statements)

References 52 publications

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“…Forests had the highest proportion of specialist indicator taxa (45% or 214 taxa) of all successional stages, whereas 183 indicator taxa were shared between all three stages of grasslands (Figure 4D). Core microbiomes can be characterised by bacterial taxa that are highly enriched across certain environments or host plant species, as defined through prevalence or occupancy thresholds (Custer et al, 2023), and can be of disproportionate relevance for host fitness or ecosystem function (D Ainsworth et al, 2015; Toju et al, 2018). Based on our results, the asymptotic convergence of zeta decline and taxa retention curves for all land‐use categories into core sets of taxa shared across multiple sites provides compelling complementary evidence for core microbiomes in both grasslands and forests, that generally reflect the overall community turnover patterns.…”

Section: Discussionmentioning

confidence: 99%

“…This was interpreted as indicating the presence of core taxa within the successional stages. Next, we derived these putative core microbiomes for further analyses by prevalence filtering based on occupancy thresholds (Custer et al, 2023). For this, we considered taxa occupying a minimum of 80% of the sites within any given successional stage to be part of the core microbiome.…”

Section: Methodsmentioning

confidence: 99%

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Core taxa underpin soil microbial community turnover during secondary succession

Sveen,

Viketoft,

Bengtsson

et al. 2023

Environmental Microbiology

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Understanding the processes that underpin the community assembly of bacteria is a key challenge in microbial ecology. We studied soil bacterial communities across a large‐scale successional gradient of managed and abandoned grasslands paired with mature forest sites to disentangle drivers of community turnover and assembly. Diversity partitioning and phylogenetic null‐modelling showed that bacterial communities in grasslands remain compositionally stable following abandonment and secondary succession but they differ markedly from fully afforested sites. Zeta diversity analyses revealed the persistence of core microbial taxa that both reflected and differed from whole‐scale community turnover patterns. Differences in soil pH and C:N were the main drivers of community turnover between paired grassland and forest sites and the variability of pH within successional stages was a key factor related to the relative dominance of deterministic assembly processes. Our results indicate that grassland microbiomes could be compositionally resilient to abandonment and secondary succession and that the major changes in microbial communities between grasslands and forests occur fairly late in the succession when trees have established as the dominant vegetation. We also show that core taxa may show contrasting responses to management and abandonment in grasslands.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Core taxa underpin soil microbial community turnover during secondary succession

Sveen,

Viketoft,

Bengtsson

et al. 2023

Environmental Microbiology

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“…2020 ), and overlapping KEGG Orthologs (KO) between PICRUSt2 and Tax4Fun2 outputs were used for final data visualization with PICRUSt2 abundance values. The coral core microbiome was determined for species-specific community taxa at a prevalence threshold of 30, 60, and 90% using the “occupancy method” defined by Custer et al. (2023) , e.g., present in equal to or greater than X% of samples ( Ainsworth et al.…”

Section: Methodsmentioning

confidence: 99%

Characteristics of The Bleached Microbiome of The Generalist CoralPocillopora damicornisfrom Two Distinct Reef Habitats

Bergman

Ricci

Leggat

et al. 2023

Integrative Organismal Biology

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Generalist coral species may play an important role in predicting, managing, and responding to the growing coral reef crisis as sea surface temperatures are rising and reef-wide bleaching events are becoming more common. Pocilloporids are amongst the most widely distributed and studied of generalist corals, characterised by a broad geographic distribution, phenotypic plasticity, and tolerance of sub-optimal conditions for coral recruitment and survival. Emerging research indicates that microbial communities associated with Pocilloporid corals may be contributing to their persistence on coral reefs impacted by thermal stress, however, we lack detailed information on shifts in the coral-bacterial symbiosis during bleaching events across many of the reef habitats these corals are found. Here we characterized the bacterial communities of healthy and bleached Pocillopora damicornis corals during the bleaching events that occurred during the austral summer of 2020 on Heron Island, on the southern Great Barrier Reef, and the austral summer of 2019 on Lord Howe Island, the most southerly coral reef in Australia. Regardless of reef location, significant differences in α and β diversity, core bacterial community, and inferred functional profile of the bleached microbiome of P. damicornis were not detected. Consistent with previous reports, patterns in the Pocilloporid coral microbiome, including no increase in pathogenic taxa or evidence of dysbiosis, are conserved during bleaching responses. We hypothesize that the resilience of holobiont interactions may aid the Pocilloporids to survive Symbiodiniaceae loss and contribute to the success of Pocilloporids.

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“…To estimate the degree of differentiation between the common core microbiota [44] of the Dutch and SAS samples, Principal Coordinate Analysis (PCoA) [45] was applied based on the RAs of the taxa. First, a prevalence threshold of 50% [46] was applied. Then, the first two principal components were plotted in a two-dimensional space.…”

Section: Methodsmentioning

confidence: 99%

Disrupted Ecology andH. parainfluenzaeDistinguish the Gut Microbiota of an Ethnic Minority Predisposed to Type 2 Diabetes Mellitus

Nayman,

Schwartz,

Polmann

et al. 2023

Preprint

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PurposeDecreased gut microbiota production of short-chain fatty acids (SCFAs) has been implicated in type 2 diabetes mellitus (T2DM) disease progression. Most microbiome studies focus on ethnic majorities. This study aims to understand microbiome differences between an ethnic majority (the Dutch) and minority (the South-Asian Surinamese (SAS)) group with a lower and higher prevalence of T2DM, respectively.MethodsMicrobiome data from the Healthy Life in an Urban Setting (HELIUS) cohort were used. The 16S rRNA V4 region was sequenced. Two age– and gender-matched groups were compared: the Dutch (n = 41) and SAS (n = 43). Microbial compositions were generated via DADA2. Alpha and beta-diversity and Principal Coordinate Analysis (PCoA) were computed. DESeq2 differential bacterial abundance and LEfSe biomarker analyses were performed to determine discriminating features. Co-occurrence networks were constructed to examine gut ecology.ResultsA tight cluster of bacterial abundances was observed in the Dutch women, which overlapped with some of the SAS microbiomes. The Dutch gut contained a more interconnected microbial ecology, whereas the SAS network was dispersed.Bacteroides caccae, Butyricicoccus, Alistipes putredinis, Coprococcus comes,Odoribacter splanchnicus,andLachnospiracharacterized the Dutch gut.Haemophilus,Bifidobacterium,andAnaerostipes hadruscharacterized the SAS gut. All butLachnospiraand certain strains ofHaemophilusare known SCFA producers.ConclusionThe Dutch gut microbiome was distinguished from the SAS by diverse, differentially abundant SCFA-producing taxa with significant cooperation. The dynamic ecology observed in the Dutch was lost in the SAS. The higher prevalence of T2DM in the SAS may be associated with the dysbiosis observed.

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Comparative Analysis of Core Microbiome Assignments: Implications for Ecological Synthesis

Cited by 27 publications

References 52 publications

Core taxa underpin soil microbial community turnover during secondary succession

Core taxa underpin soil microbial community turnover during secondary succession

Characteristics of The Bleached Microbiome of The Generalist CoralPocillopora damicornisfrom Two Distinct Reef Habitats

Disrupted Ecology andH. parainfluenzaeDistinguish the Gut Microbiota of an Ethnic Minority Predisposed to Type 2 Diabetes Mellitus

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