Assessing the strength and sensitivity of the core microbiota approach on a highly diverse sponge reef

ABSTRACT Revealing the ecological roles of the core microbiota in community maintaining and soil nutrient cycling is crucial for understanding ecosystem function, yet there is a dearth of continental-scale studies on this fundamental topic in microbial ecology. Here, we collected 251 soil samples from adjacent pairs of maize and rice fields at a continental scale in eastern China. We revealed the major ecological roles of the core microbiota in maintaining complex connections between bacterial taxa and their associations with belowground multinutrient cycling. By identifying the habitat preferences of the core microbiota, we built a continental atlas for mapping the spatial distributions of bacteria in agro-soils, which helps forecast the responses of agricultural ecosystems to anthropogenic disturbance. The multinutrient cycling index for maize and rice soils was related to bacterial α-diversity and β-diversity, respectively. Rice soils exhibited higher bacterial diversity and closer bacterial cooccurrence relationships than maize soils. In contrast to the macro- or microecological latitudinal richness patterns in natural terrestrial ecosystems, the bacteria in maize soils showed higher richness at high latitudes; however, this trend was not observed in rice soils. This study provides a new perspective on the distinct bacterial biogeographic patterns to predict the ecological roles of the core microbiota in agro-soils and thus helps manage soil bacterial communities for better provisioning of key ecosystem services. IMPORTANCE Disentangling the roles of the core microbiota in community maintaining and soil nutrient cycling is an important yet poorly understood topic in microbial ecology. This study presents an exploratory effort to gain predictive understanding of the spatial atlas and ecological roles of the core microbiota. A systematic, continental-scale survey was conducted using agro-soils in adjacent pairs of maize (dryland) and rice (wetland) fields across eastern China. The results indicate that the core microbiota play major ecological roles in maintaining complex connections between bacterial taxa and are associated with belowground multinutrient cycling. A continental atlas was built for mapping the bacterial spatial distributions in agro-soils through identifying their habitat preferences. This study represents a significant advance in forecasting the responses of agricultural ecosystems to anthropogenic disturbance and thus helps manage soil bacterial communities for better provisioning of key ecosystem services—the ultimate goal of microbial ecology.

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Investigating the core microbiota and its influencing factors in traditional Chinese pickles

Food Research International ◽

10.1016/j.foodres.2021.110543 ◽

2021 ◽

pp. 110543

Author(s):

Feiyu An ◽

Huijun Sun ◽

Junrui Wu ◽

Chunyan Zhao ◽

Tong Li ◽

...

Keyword(s):

Influencing Factors ◽

Core Microbiota ◽

The Core

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Construction of synthetic microbiota for reproducible flavor metabolism in Chinese light aroma type liquor produced by solid-state fermentation

10.1101/510610 ◽

2019 ◽

Author(s):

Shilei Wang ◽

Qun Wu ◽

Yao Nie ◽

Yan Xu

Keyword(s):

Fermentation Process ◽

System Level ◽

Flavor Compounds ◽

Fermented Foods ◽

Natural Fermentation ◽

Food Fermentation ◽

Core Microbiota ◽

The Core ◽

Natural Microbiota ◽

Dynamic Profile

ABSTRACTNatural microbiota plays an essential role in flavor compounds producing for traditional food fermentation. Whereas, the fluctuation of natural microbiota results in the inconstancy of food quality. Thus, it is critical to reveal the core microbiota for flavor compounds producing and construct a synthetic core microbiota for constant food fermentation. Here, we revealed the core microbiota based on their flavor-producing and co-occurrence performance, using Chinese light aroma type liquor as a model system. Five genera were identified to be the core microbiota, including Lactobacillus, Saccharomyces, Pichia, Geotrichum, and Candida. The synthetic core microbiota of these five genera presented a reproducible dynamic profile with that in the natural microbiota. Monte Carlo test showed that the interpretation of five environmental factors (lactic acid, ethanol and acetic acid contents, moisture and pH) on the synthetic microbiota distribution were highly significant (P < 0.01), which was similar with that in the natural fermentation system. In addition, 77.27% of the flavor compounds produced by the synthetic core microbiota showed a similar dynamic profile (ρ > 0) with that in the natural liquor fermentation process, and the flavor profile presented a similar composition. It indicated that the synthetic core microbiota is efficient for reproducible flavor metabolism. This work established a method for identifying core microbiota and constructing a synthetic microbiota for reproducible flavor compounds. It is of great significance for the tractable and constant production of various fermented foods.IMPORTANCEThe transformation from natural fermentation to synthetic fermentation is essential to construct a constant food fermentation process, which is the premise for stably making high-quality food. According to the functions of flavor-producing and co-occurring in dominant microbes, we provided a system-level approach to identify the core microbiota in Chinese light aroma type liquor fermentation. In addition, we successfully constructed a synthetic core microbiota to simulate the microbial community succession and flavor compounds production in the in vitro system. The constructed synthetic core microbiota could not only facilitate a mechanistic understanding of the structure and function of the microbiota, but also be beneficial for constructing a tractable and reproducible food fermentation process.

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Evaluating the core microbiota in complex communities: A systematic investigation

Environmental Microbiology ◽

10.1111/1462-2920.13647 ◽

2017 ◽

Vol 19 (4) ◽

pp. 1450-1462 ◽

Cited By ~ 69

Author(s):

Carmen Astudillo-García ◽

James J. Bell ◽

Nicole S. Webster ◽

Bettina Glasl ◽

Jamaluddin Jompa ◽

...

Keyword(s):

Systematic Investigation ◽

Core Microbiota ◽

The Core

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A Single Dose of Synbiotics and Vitamins at Birth Affects Piglet Microbiota before Weaning and Modifies Post-Weaning Performance

Animals ◽

10.3390/ani11010084 ◽

2021 ◽

Vol 11 (1) ◽

pp. 84

Author(s):

Marion Girard ◽

Marco Tretola ◽

Giuseppe Bee

Keyword(s):

Single Dose ◽

Average Daily Gain ◽

Experimental Period ◽

Fecal Microbiota ◽

Microbial Colonization ◽

Suckling Period ◽

Core Microbiota ◽

The Core ◽

Abundance And Diversity ◽

Daily Gain

Early-life microbial colonization is an important driver for the development and maturation of the gut. The present study aimed to determine whether a single-dose supplement given only at birth would improve piglet performance and modify their fecal microbiota during the suckling and post-weaning periods. At birth, piglets from eight litters received a supplement (SUP+) while piglets from six other litters received water (SUP−). All piglets were monitored until two weeks post-weaning, and fecal samples were collected on Day 16 of age and two weeks post-weaning (Day 39 ± 1). The supplementation resulted in an improvement of average daily gain during the whole experimental period, mainly due to a better growth and a reduction in the incidence of diarrhea in the post-weaning period. There were no differences in the abundance and diversity of the main taxa, although the supplementation increased the relative abundance of rare taxa, such as bacteria from the Saccharibacteria and Cyanobacteria phyla, and the Lentisphaeria class in the suckling period. In addition, at 16 days of age, SUP+ piglets had a more diverse core microbiota, with bacteria from the Lactobacillus genus being present in the core microbiota of SUP+ piglets and absent from SUP− piglets. Therefore, the enhanced growth performance and reduction in diarrhea seem to be related to changes in fecal microbiota during the suckling period rather than at two weeks post-weaning.

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Comparative Evaluation of Microbiota Dynamics and Metabolites Correlation Between Spontaneous and Inoculated Fermentations of Nanfeng Tangerine Wine

Frontiers in Microbiology ◽

10.3389/fmicb.2021.649978 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xiangyu Qiu ◽

Linlin Yu ◽

Weiying Wang ◽

Riming Yan ◽

Zhibin Zhang ◽

...

Keyword(s):

High Throughput Sequencing ◽

Wine Fermentation ◽

Gas Chromatography Mass Spectrometry ◽

Microbial Succession ◽

Spontaneous Fermentation ◽

Core Microbiota ◽

The Core ◽

Volatile Flavor ◽

Functional Shift ◽

Dominant Bacteria

Understanding the evolution of microorganisms and metabolites during wine fermentation is essential for controlling its production. The structural composition and functional capacity of the core microbiota determine the quality and quantity of fruit wine. Nanfeng tangerine wine fermentation 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 product fermentation remain unclear. Therefore, high-throughput sequencing (HTS) and headspace-gas chromatography-mass spectrometry (HS/GC-MS) were employed to reveal the core functional microbiota for the production of volatile flavors during spontaneous fermentation (SF) and inoculated fermentation (IF) with Saccharomyces cerevisiae of Nanfeng tangerine wine. A total of 13 bacterial and 8 fungal genera were identified as the core microbiota; Lactobacillus and Acetobacter were the dominant bacteria in SF and IF, respectively. The main fungal genera in SF and IF were Hanseniaspora, Pichia, and Saccharomyces with a clear succession. In addition, the potential correlations analysis between microbiota succession and volatile flavor dynamics revealed that Lactobacillus, Acetobacter, Hanseniaspora, and Saccharomyces were the major contributors to the production of the volatile flavor of Nanfeng tangerine wine. The results of the present study provide insight into the effects of the core functional microbiota in Nanfeng tangerine wine and can be used to develop effective strategies for improving the quality of fruit wines.

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Soil Probiotic Utilizes Plant and Pollinator Transport for Territorial Expansion

10.20944/preprints201905.0294.v1 ◽

2019 ◽

Author(s):

Da-Ran Kim ◽

Gyeongjun Cho ◽

Chang-Wook Jeon ◽

David M. Weller ◽

Linda S. Thomashow ◽

...

Keyword(s):

Botrytis Cinerea ◽

Vascular Bundle ◽

Plant Interactions ◽

Territorial Expansion ◽

Core Microbiota ◽

Plant Parts ◽

The Core ◽

Space And Time ◽

Below Ground ◽

Tripartite Interaction

Microbe-plant interactions are linked with the core microbiota, and both the plant and the microbial partners depend on one other to thrive in nature. However, why and how the below-ground core microbiota become established aboveground is poorly understood. We tracked the movement of a probiotic Streptomyces endophyte throughout a managed strawberry ecosystem. Probiotics in the rhizosphere and anthosphere were genetically identical, yet these niches were segregated in space and time. The probiotic in the rhizosphere moved upward via the vascular bundle, relocated to aboveground plant parts, and protected against Botrytis cinerea. It also moved from flowers to roots, and among flowers via pollinators that were protected against pollinator pathogens. Our results reveal a solid evidence in tripartite interaction with Streptomyces exploiting plant and pollinator partners.

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Construction of Synthetic Microbiota for Reproducible Flavor Compound Metabolism in Chinese Light-Aroma-Type Liquor Produced by Solid-State Fermentation

Applied and Environmental Microbiology ◽

10.1128/aem.03090-18 ◽

2019 ◽

Vol 85 (10) ◽

Cited By ~ 19

Author(s):

Shilei Wang ◽

Qun Wu ◽

Yao Nie ◽

Jianfeng Wu ◽

Yan Xu

Keyword(s):

Fermentation Process ◽

Flavor Compounds ◽

Flavor Compound ◽

Content Type ◽

Natural Fermentation ◽

Food Fermentation ◽

Core Microbiota ◽

The Core ◽

Natural Microbiota ◽

Dynamic Profile

ABSTRACT Natural microbiota plays an essential role in flavor compounds used in traditional food fermentation; however, the fluctuation in natural microbiota results in inconsistency in food quality. Thus, it is critical to reveal the core microbiota for flavor compound production and to construct a synthetic core microbiota for use in constant food fermentation. Here, we reveal the core microbiota based on their flavor production and cooccurrence performance, using Chinese light-aroma-type liquor as a model system. Five genera, Lactobacillus, Saccharomyces, Pichia, Geotrichum, and Candida, were identified to be the core microbiota. The synthetic core microbiota of these five genera presented a reproducible dynamic profile similar to that in the natural microbiota. A Monte Carlo test showed that the effects of five environmental factors (lactic acid, ethanol, and acetic acid contents, moisture, and pH) on the synthetic microbiota distribution were highly significant (P < 0.01), similar to those effects on a natural fermentation system. In addition, 77.27% of the flavor compounds produced by the synthetic core microbiota showed a similar dynamic profile (ρ > 0) with that in the natural liquor fermentation process, and the flavor profile presented a similar composition. It indicated that the synthetic core microbiota is efficient for reproducible flavor metabolism. This work established a method for identifying core microbiota and constructing a synthetic microbiota for reproducible flavor compounds. This work is of great significance for the tractable and constant production of various fermented foods. IMPORTANCE The transformation from natural fermentation to synthetic fermentation is essential in constructing a constant food fermentation process, which is the premise for stably making high-quality food. According to flavor-producing and cooccurring functions in dominant microbes, we provided a system-level approach to identify the core microbiota in Chinese light-aroma-type liquor fermentation. In addition, we successfully constructed a synthetic core microbiota to simulate the microbial community succession and flavor compound production in the in vitro system. The constructed synthetic core microbiota could not only facilitate a mechanistic understanding of the structure and function of the microbiota but also be beneficial for constructing a tractable and reproducible food fermentation process.

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Let the Core Microbiota Be Functional

Trends in Plant Science ◽

10.1016/j.tplants.2017.04.008 ◽

2017 ◽

Vol 22 (7) ◽

pp. 583-595 ◽

Cited By ~ 84

Author(s):

Philippe Lemanceau ◽

Manuel Blouin ◽

Daniel Muller ◽

Yvan Moënne-Loccoz

Keyword(s):

Core Microbiota ◽

The Core

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Characteristics of Ruminal Microbial Community: Evolutionary and Ecological Perspectives

10.20944/preprints202012.0628.v1 ◽

2020 ◽

Author(s):

Amlan Kumar Patra

Keyword(s):

Microbial Community ◽

Ruminal Fermentation ◽

Plant Leaves ◽

Ecological Traits ◽

Core Microbiome ◽

Core Microbiota ◽

The Core ◽

Ruminant Species ◽

Ruminal Microbiota ◽

Evolutionary Perspectives

Ruminants perhaps appeared about 50 million years ago (Ma). Five ruminant families had been extinct and about 200 species in 6 ruminant families are living today. The first ruminant family probably was small omnivore without functional ruminal microbiota to digest fiber. Subsequently, other ruminant families evolved around 18-23 Ma along with woodlands and grasslands. Probably, ruminants started to consume selective and highly nutritious plant leaves and grasses similar to concentrates. By 5-11 Ma, grasslands expanded and some ruminants used more grass in their diets with comparatively low nutritive values and high fibers. Historically, humans have domesticated 9 ruminant species that are mostly utilizer of low quality forages for human benefits. Thus, the non-functional rumen microbiota to predominantly concentrate fermenting microbiota, followed by predominantly fiber digesting microbiota had evolved for mutual complementary benefits of holobiont over the million years. The core microbiome of ruminant species seems the resultant of hologenome interaction in an evolutionary unit. The inertia and resilience properties of ruminal ecosystem seem to be due to this core microbiota, which makes the ecosystem most stable in response to perturbations because this core microbiota has evolutionary advantages with logically more generalists (i.e., wide metabolic versatile and redundancy). Also, a part of the ruminal microbiome shows highly plasticity, which is likely useful for evolutionary adaptability of holobiont. This review discusses ecological characteristics of ruminal microbial community in evolutionary perspectives. The updated understanding of ecological traits of ruminal microbiome would be helpful to better modulate the ruminal fermentation favorably for human benefits.

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