Evaluating the core microbiota in complex communities: A systematic investigation

Astudillo‐García, Carmen; Bell, James J.; Webster, Nicole S.; Glasl, Bettina; Jompa, Jamaluddin; Montoya, José M.; Taylor, Michael W.

doi:10.1111/1462-2920.13647

Cited by 170 publications

(147 citation statements)

References 79 publications

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“…However, Marino et al used 97% OTU clustering, which means individual OTUs are likely to encompass wider microbial taxonomic variation in contrast to 99% clustering of OTUs as used in this study. The core microbial genera in our study formed 63% and 69% of the total microbiome in Long Key and Kemp Channel, respectively, suggesting that the differences observed relative to previous work primarily reflect methodical differences (Astudillo‐García et al, ). Furthermore, the higher the number of replicates, the smaller the apparent ‘core’ microbiome appears (Turon et al, ), and in this study, the number of within‐species replicates we used ( n = 33) was substantially larger than in many previous studies.…”

Section: Discussioncontrasting

confidence: 54%

Host genetics and geography influence microbiome composition in the spongeIrcinia campana

Griffiths

Antwis

Lenzi

et al. 2019

Journal of Animal Ecology

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Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome.Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome.We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing.We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location.Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco‐evolutionary dynamics of host‐associated microbiomes.

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Section: Discussioncontrasting

confidence: 54%

Host genetics and geography influence microbiome composition in the spongeIrcinia campana

Griffiths

Antwis

Lenzi

et al. 2019

Journal of Animal Ecology

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“…Using prevalence rather than abundance to examine the C. orientalis microbiome facilitated identification of additional taxa likely to perform important symbiotic functions (Ainsworth et al., ; Astudillo‐García et al., ; Hernandez‐Agreda, Leggat, Bongaerts, & Ainsworth, ; Thomas et al., ). Multiple members of the “core” community matched microbial taxa involved in nitrogen metabolism and may play a role in nitrogen cycling within the C. orientalis holobiont.…”

Section: Discussionmentioning

confidence: 99%

Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge

et al. 2018

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Bioeroding sponges break down calcium carbonate substratum, including coral skeleton, and their capacity for reef erosion is expected to increase in warmer and more acidic oceans. However, elevated temperature can disrupt the functionally important microbial symbionts of some sponge species, often with adverse consequences for host health. Here, we provide the first detailed description of the microbial community of the bioeroding sponge Cliona orientalis and assess how the community responds to seawater temperatures incrementally increasing from 23°C to 32°C. The microbiome, identified using 16S rRNA gene sequencing, was dominated by Alphaproteobacteria, including a single operational taxonomic unit (OTU; Rhodothalassium sp.) that represented 21% of all sequences. The "core" microbial community (taxa present in >80% of samples) included putative nitrogen fixers and ammonia oxidizers, suggesting that symbiotic nitrogen metabolism may be a key function of the C. orientalis holobiont. The C. orientalis microbiome was generally stable at temperatures up to 27°C; however, a community shift occurred at 29°C, including changes in the relative abundance and turnover of microbial OTUs. Notably, this microbial shift occurred at a lower temperature than the 32°C threshold that induced sponge bleaching, indicating that changes in the microbiome may play a role in the destabilization of the C. orientalis holobiont. C. orientalis failed to regain Symbiodinium or restore its baseline microbial community following bleaching, suggesting that the sponge has limited ability to recover from extreme thermal exposure, at least under aquarium conditions.

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“…The microbiota in natural environments is complex and often includes thousands of genera from a diverse range of species (Astudillo-Garcia et al, 2017). In industrial fermentation, the microbiota depends on the conditions and nutrient availability (Sekwati-Monang et al, 2012).…”

Section: Introductionmentioning

confidence: 99%

“…In recent years, the concept of core microbiota has emerged (Astudillo-Garcia et al, 2017). The core microbiota play important roles in natural ecological systems, human health and industrial processes (Schmitt et al, 2012; Zhang et al, 2015; Kable et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

Song¹,

Du²,

Zhang³

et al. 2017

Front. Microbiol.

192

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Fermentation microbiota is specific microorganisms that generate different types of metabolites in many productions. In traditional solid-state fermentation, the structural composition and functional capacity of the core microbiota determine the quality and quantity of products. As a typical example of food fermentation, Chinese Maotai-flavor liquor production involves a complex of various microorganisms and a wide variety of metabolites. However, the microbial succession and functional shift of the core microbiota in this traditional food fermentation remain unclear. Here, high-throughput amplicons (16S rRNA gene amplicon sequencing and internal transcribed space amplicon sequencing) and metatranscriptomics sequencing technologies were combined to reveal the structure and function of the core microbiota in Chinese soy sauce aroma type liquor production. In addition, ultra-performance liquid chromatography and headspace-solid phase microextraction-gas chromatography-mass spectrometry were employed to provide qualitative and quantitative analysis of the major flavor metabolites. A total of 10 fungal and 11 bacterial genera were identified as the core microbiota. In addition, metatranscriptomic analysis revealed pyruvate metabolism in yeasts (genera Pichia, Schizosaccharomyces, Saccharomyces, and Zygosaccharomyces) and lactic acid bacteria (genus Lactobacillus) classified into two stages in the production of flavor components. Stage I involved high-level alcohol (ethanol) production, with the genus Schizosaccharomyces serving as the core functional microorganism. Stage II involved high-level acid (lactic acid and acetic acid) production, with the genus Lactobacillus serving as the core functional microorganism. The functional shift from the genus Schizosaccharomyces to the genus Lactobacillus drives flavor component conversion from alcohol (ethanol) to acid (lactic acid and acetic acid) in Chinese Maotai-flavor liquor production. Our findings provide insight into the effects of the core functional microbiota in soy sauce aroma type liquor production and the characteristics of the fermentation microbiota under different environmental conditions.

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Evaluating the core microbiota in complex communities: A systematic investigation

Cited by 170 publications

References 79 publications

Host genetics and geography influence microbiome composition in the spongeIrcinia campana

Host genetics and geography influence microbiome composition in the spongeIrcinia campana

Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

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