scholarly journals Microbial Diversity and Characteristics of Kombucha as Revealed by Metagenomic and Physicochemical Analysis

Nutrients ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 4446
Author(s):  
Mayank Kaashyap ◽  
Marc Cohen ◽  
Nitin Mantri
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Health Benefits ◽  
Biochemical Properties ◽  
Physicochemical Analysis ◽  
Functional Health ◽  
Its Sequencing ◽  
Human Gut ◽  
Microbial Composition ◽  
History Of Use

Kombucha is a fermented tea made from a Symbiotic Culture of Bacteria and Yeast (SCOBY) with a long history of use as a health tonic. It is likely that most health benefits come from the tea and fermentation metabolites from specific microbial communities. Despite its growing importance as a functional health drink, the microbial ecosystem present in kombucha has not been fully documented. To characterize the microbial composition and biochemical properties of ‘The Good Brew’ original base kombucha, we used metagenomics amplicon (16S rRNA and ITS) sequencing to identify the microbial communities at the taxonomic level. We identified 34 genera with 200 microbial species yet described in kombucha. The dominance of organic acid producing microorganisms Acetobacter, Komagataeibacter and Starmerella are healthy for the human gut and their glucose metabolising activities have a putative role in preventing conditions such as diabetes and obesity. Kombucha contains high protein (3.31 µg/mL), high phenolic content (290.4 mg/100 mL) and low sugars (glucose: 1.87 g/L; sucrose 1.11 g/L; fructose: 0.05 g/L) as compared to green tea. The broad microbial diversity with proven health benefits for the human gut suggests kombucha is a powerful probiotic. These findings are important to improve the commercial value of kombucha and uncover the immense prospects for health benefits.

scholarly journals New View on Dietary Fiber Selection for Predictable Shifts in Gut Microbiota

mBio ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
T. M. Cantu-Jungles ◽  
B. R. Hamaker
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Dietary Fiber ◽  
Physical Characteristics ◽  
Dietary Fibers ◽  
Human Gut ◽  
Microbial Composition ◽  
Human Gut Microbiota ◽  
Selection For ◽  
Fiber Selection

ABSTRACT Dietary fibers can be utilized to shape the human gut microbiota. However, the outcomes from most dietary fibers currently used as prebiotics are a result of competition between microbes with overlapping abilities to utilize these fibers. Thus, divergent fiber responses are observed across individuals harboring distinct microbial communities. Here, we propose that dietary fibers can be classified hierarchically according to their specificity toward gut microbes. Highly specific fibers harbor chemical and physical characteristics that allow them to be utilized by only a narrow group of bacteria within the gut, reducing competition for that substrate. The use of such fibers as prebiotics targeted to specific microbes would result in predictable shifts independent of the background microbial composition.

scholarly journals Multi-scale ecological filters shape the crayfish microbiome

2016 ◽  
Author(s):  
James Skelton ◽  
Kevin M Geyer ◽  
Jay T Lennon ◽  
Robert P Creed ◽  
Bryan L Brown
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Local Environment ◽  
Host Tissue ◽  
In Situ Experiment ◽  
Microbial Composition ◽  
Ecological Processes ◽  
Multi Scale ◽  
Microbiome Assembly ◽  
Ecological Filters

Communities of symbiotic microbes obtained from the environment are an integral component of animal fitness and ecology. Thus a general and practical understanding of the processes that drive microbiome assembly and structure are paramount to understanding animal ecology, health, and evolution. We conceptualized a series of ecological filters that operate at the environment, host, and host tissue levels during microbiome assembly and discuss key ecological processes that structure animal microbiomes at each level. We conducted a survey of crayfish across four sites within the contiguous range of the of stream-inhabiting crayfish Cambarus sciotensis in western Virginia, USA, to characterize multiscale variation in the crayfish microbiome. We also conducted an in situ experiment to assess local drivers of microbial diversity on the closely related Cambarus chasmodactylus. We used a combination of DNA fingerprinting and next-generation sequencing to characterize microbiome diversity and composition from crayfish carapaces and gills to identify key filters affecting microbiome structure. Field survey showed that local environment and host tissues interact to create patterns of microbial diversity and composition, but the strongest effects on microbial community structure were observed at the level of host tissue. Our field experiment confirmed strong effects of host tissue, and also showed that a metazoan ectosymbiont which feeds on biofilms (Annelida; Branchiobdellida) had significant effects on microbial composition of the host carapace. Crayfish carapaces were colonized by diverse and taxonomically even microbial communities that were similar to, and correlated with, microbial communities of the ambient environment. Conversely, crayfish gills were colonized by less diverse communities and dominated by two families of bacteria with potentially significant functional roles: Comamonadaceae and Chitinophagaceae. Our results suggest that microbial assembly of the carapace is driven by external biotic and abiotic processes, whereas assembly on the gills appears to be coupled to host biology that favors interactions with few specific taxa. Our work shows how multi-scale studies of symbiont community assembly provide valuable insights into how the animal microbiome is structured under conditions of natural complexity and help identify other symbiont taxa, i.e., the branchiobdellidans, that may further influence microbiome assembly and structure.

scholarly journals Multi-scale ecological filters shape the crayfish microbiome

2016 ◽  
Author(s):  
James Skelton ◽  
Kevin M Geyer ◽  
Jay T Lennon ◽  
Robert P Creed ◽  
Bryan L Brown
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Local Environment ◽  
Host Tissue ◽  
In Situ Experiment ◽  
Microbial Composition ◽  
Ecological Processes ◽  
Multi Scale ◽  
Microbiome Assembly ◽  
Ecological Filters

Communities of symbiotic microbes obtained from the environment are an integral component of animal fitness and ecology. Thus a general and practical understanding of the processes that drive microbiome assembly and structure are paramount to understanding animal ecology, health, and evolution. We conceptualized a series of ecological filters that operate at the environment, host, and host tissue levels during microbiome assembly and discuss key ecological processes that structure animal microbiomes at each level. We conducted a survey of crayfish across four sites within the contiguous range of the of stream-inhabiting crayfish Cambarus sciotensis in western Virginia, USA, to characterize multiscale variation in the crayfish microbiome. We also conducted an in situ experiment to assess local drivers of microbial diversity on the closely related Cambarus chasmodactylus. We used a combination of DNA fingerprinting and next-generation sequencing to characterize microbiome diversity and composition from crayfish carapaces and gills to identify key filters affecting microbiome structure. Field survey showed that local environment and host tissues interact to create patterns of microbial diversity and composition, but the strongest effects on microbial community structure were observed at the level of host tissue. Our field experiment confirmed strong effects of host tissue, and also showed that a metazoan ectosymbiont which feeds on biofilms (Annelida; Branchiobdellida) had significant effects on microbial composition of the host carapace. Crayfish carapaces were colonized by diverse and taxonomically even microbial communities that were similar to, and correlated with, microbial communities of the ambient environment. Conversely, crayfish gills were colonized by less diverse communities and dominated by two families of bacteria with potentially significant functional roles: Comamonadaceae and Chitinophagaceae. Our results suggest that microbial assembly of the carapace is driven by external biotic and abiotic processes, whereas assembly on the gills appears to be coupled to host biology that favors interactions with few specific taxa. Our work shows how multi-scale studies of symbiont community assembly provide valuable insights into how the animal microbiome is structured under conditions of natural complexity and help identify other symbiont taxa, i.e., the branchiobdellidans, that may further influence microbiome assembly and structure.

scholarly journals Halophytes Increase Rhizosphere Microbial Diversity And Network Complexity In Inland Saline Ecosystem

2021 ◽  
Author(s):  
Liping Qiu ◽  
Weibo Kong ◽  
Hansong Zhu ◽  
Qian Zhang ◽  
Samiran Banerjee ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Microbial Communities ◽  
Environmental Problem ◽  
Terrestrial Ecosystems ◽  
Salt Tolerant ◽  
Microbial Composition ◽  
Microbial Network ◽  
Global Environmental ◽  
Relationship Of ◽  
The Relationship

Abstract Background: Salinization is an important global environmental problem influencing sustainable development of terrestrial ecosystems. Salt-tolerant halophytes are often used as a promising approach to remedy the saline soils. Yet, how halophytes affect rhizosphere microbial diversity, and microbes’ association and functions in saline ecosystems remains unclear, restricting our ability to assess plant fitness to salt stress and to remediate saline ecosystems. Herein, we examined bacterial and fungal diversities, compositions, and co-occurrence networks in the rhizospheres of six halophytes and bulk soils in a semiarid inland saline ecosystem. We also established the relationship of microbial structure and network complexity to microbial functions.Results: The microbial communities in rhizospheres were more diverse and complex than those the bulk soils. The connections of taxa in the rhizosphere microbial communities increased with fungi-fungi and bacteria-fungi connections and fungal diversity, but decreased with bacteria-bacteria connections and bacterial diversity. The proportion of the fungi-related central connections were larger in the rhizospheres (13-73%) than the bulk soils (3%). Additionally, fungi accounted for 27-63% of the keystone taxa identified in the microbial co-occurrence networks present in the rhizospheres, whereas the keystone taxa identified in the bulk soils were all bacteria/archaea. Moreover, microbial activity and residues were significantly higher in the halophyte rhizospheres than the bulk soils, and were significantly correlated with microbial composition and co-occurrence network complexity.Conclusions: These results indicated that halophytes shaped rhizosphere microbiomes and increased microbial diversity and network complexity in inland saline ecosystem, while fungi enhanced rhizosphere microbiota associations. The increased microbial network complexity contributed to the higher microbial functions in rhizosphere soils.

scholarly journals Microbiome divergence across four major Indian riverine water ecosystems impacted by anthropogenic contamination: A comparative metagenomic analysis

2020 ◽  
Author(s):  
Raj Kumar Regar ◽  
Mohan Kamthan ◽  
Vivek Kumar gaur ◽  
Satyendra Pratap Singh ◽  
Seema Mishra ◽  
...  
Keyword(s):  
Trace Elements ◽  
Microbial Diversity ◽  
Microbial Communities ◽  
Anthropogenic Activities ◽  
Large Population ◽  
Anthropogenic Contamination ◽  
Carbon Utilization ◽  
Microbial Composition ◽  
Bacterial Phyla ◽  
Functional Potential

Abstract Background Indian rivers are a major source of livelihood as river water is used for drinking, agriculture, and religious purposes to a large population. In this study, we report comparative microbial structures and functional potential of four major rivers of India, namely Ganga, Narmada, Cauvery, and Gomti. Comparative microbiome study of these geographically distinct rivers was performed using the samples collected from the source to the downstream sites of each river. We employed metagenomic approach to comprehensively determine the taxonomic and functional potential of river microbiome. Results In this study, we report the pollution influences on microbial composition and functional potential of four distantly located rivers. Results revealed significant microbial diversity in contaminated locations as compared to the upstream samples. A total number of 37 bacterial phyla were detected out of which Proteobacteria, Actinobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia were abundant. Microbial diversity in respect to anthropogenic activities revealed the prevalence of Acidobacteria, Actinobacteria, Verrucomicrobia, Firmicutes, and Nitrospirae phyla, whereas a decline in Proteobacteria and Bacteroides. Virulent and temperate bacteriophages were found high in Ganga when compared to others. Interestingly, the abundance of bacteriophage decreased with increasing pollution load in the river Ganga, unlike in other rivers. The carbon utilization studies indicated a correlation with functional genes occurred in metal contaminated sites. Ganga water has relatively higher trace elements at pristine-upstream than in the Narmada and Cauvery, indicating its origin from Himalayan rocky mountains and also both Ganga and Cauvery rivers found to harbour a large number of metal resistance genes. Conclusion Our findings indicate a correlation between pollution and the microbiome composition. The insights obtained suggest the role of high abundance of microbial communities with implications for human health and demonstrate the functional capabilities contributed by the microbial communities. Among the four rivers studied, the distinctiveness of Ganga in comparison to others, particularly upstream of Ganga revealed a highly dynamic microbial structure. Bhagirathi and Alaknanda confluence to form Ganga, the microbiome revealed that Alaknanda has the foremost contribution to Ganga with respect to microbial community, bacteriophages, and the type of trace elements and heavy metals detected.

scholarly journals Microbiota identified from preserved Anopheles

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Bianca E Silva ◽  
Zvifadzo Matsena Zingoni ◽  
Lizette L. Koekemoer ◽  
Yael L. Dahan-Moss
Keyword(s):  
Microbial Diversity ◽  
Vector Competence ◽  
Mosquito Species ◽  
Anopheles Funestus ◽  
Cost Effective ◽  
Diversity Indices ◽  
Malaria Vectors ◽  
Microbial Composition ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background Mosquito species from the Anopheles gambiae complex and the Anopheles funestus group are dominant African malaria vectors. Mosquito microbiota play vital roles in physiology and vector competence. Recent research has focused on investigating the mosquito microbiota, especially in wild populations. Wild mosquitoes are preserved and transported to a laboratory for analyses. Thus far, microbial characterization post-preservation has been investigated in only Aedes vexans and Culex pipiens. Investigating the efficacy of cost-effective preservatives has also been limited to AllProtect reagent, ethanol and nucleic acid preservation buffer. This study characterized the microbiota of African Anopheles vectors: Anopheles arabiensis (member of the An. gambiae complex) and An. funestus (member of the An. funestus group), preserved on silica desiccant and RNAlater® solution. Methods Microbial composition and diversity were characterized using culture-dependent (midgut dissections, culturomics, MALDI-TOF MS) and culture-independent techniques (abdominal dissections, DNA extraction, next-generation sequencing) from laboratory (colonized) and field-collected mosquitoes. Colonized mosquitoes were either fresh (non-preserved) or preserved for 4 and 12 weeks on silica or in RNAlater®. Microbiota were also characterized from field-collected An. arabiensis preserved on silica for 8, 12 and 16 weeks. Results Elizabethkingia anophelis and Serratia oryzae were common between both vector species, while Enterobacter cloacae and Staphylococcus epidermidis were specific to females and males, respectively. Microbial diversity was not influenced by sex, condition (fresh or preserved), preservative, or preservation time-period; however, the type of bacterial identification technique affected all microbial diversity indices. Conclusions This study broadly characterized the microbiota of An. arabiensis and An. funestus. Silica- and RNAlater®-preservation were appropriate when paired with culture-dependent and culture-independent techniques, respectively. These results broaden the selection of cost-effective methods available for handling vector samples for downstream microbial analyses.

scholarly journals Influence of pig farming on human Gut Microbiota: role of airborne microbial communities

Gut Microbes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 1-13
Author(s):  
Julia Moor ◽  
Tsering Wüthrich ◽  
Suzanne Aebi ◽  
Nadezda Mostacci ◽  
Gudrun Overesch ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Communities ◽  
Human Gut ◽  
Human Gut Microbiota ◽  
Pig Farming

scholarly journals Evaluation of acidogenesis products’ effect on biogas production performed with metagenomics and isotopic approaches

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Anna Detman ◽  
Michał Bucha ◽  
Laura Treu ◽  
Aleksandra Chojnacka ◽  
Łukasz Pleśniak ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Methane Production ◽  
Bacterial Species ◽  
Stable Carbon Isotope ◽  
Anaerobic Sludge ◽  
Methane Formation ◽  
Microbial Composition ◽  
Fermentation Products ◽  
Core Microbiome ◽  
Specific Species

Abstract Background During the acetogenic step of anaerobic digestion, the products of acidogenesis are oxidized to substrates for methanogenesis: hydrogen, carbon dioxide and acetate. Acetogenesis and methanogenesis are highly interconnected processes due to the syntrophic associations between acetogenic bacteria and hydrogenotrophic methanogens, allowing the whole process to become thermodynamically favorable. The aim of this study is to determine the influence of the dominant acidic products on the metabolic pathways of methane formation and to find a core microbiome and substrate-specific species in a mixed biogas-producing system. Results Four methane-producing microbial communities were fed with artificial media having one dominant component, respectively, lactate, butyrate, propionate and acetate, for 896 days in 3.5-L Up-flow Anaerobic Sludge Blanket (UASB) bioreactors. All the microbial communities showed moderately different methane production and utilization of the substrates. Analyses of stable carbon isotope composition of the fermentation gas and the substrates showed differences in average values of δ13C(CH4) and δ13C(CO2) revealing that acetate and lactate strongly favored the acetotrophic pathway, while butyrate and propionate favored the hydrogenotrophic pathway of methane formation. Genome-centric metagenomic analysis recovered 234 Metagenome Assembled Genomes (MAGs), including 31 archaeal and 203 bacterial species, mostly unknown and uncultivable. MAGs accounted for 54%–67% of the entire microbial community (depending on the bioreactor) and evidenced that the microbiome is extremely complex in terms of the number of species. The core microbiome was composed of Methanothrix soehngenii (the most abundant), Methanoculleus sp., unknown Bacteroidales and Spirochaetaceae. Relative abundance analysis of all the samples revealed microbes having substrate preferences. Substrate-specific species were mostly unknown and not predominant in the microbial communities. Conclusions In this experimental system, the dominant fermentation products subjected to methanogenesis moderately modified the final effect of bioreactor performance. At the molecular level, a different contribution of acetotrophic and hydrogenotrophic pathways for methane production, a very high level of new species recovered, and a moderate variability in microbial composition depending on substrate availability were evidenced. Propionate was not a factor ceasing methane production. All these findings are relevant because lactate, acetate, propionate and butyrate are the universal products of acidogenesis, regardless of feedstock.

scholarly journals Dissimilarity of microbial diversity of pond water, shrimp intestine and sediment in Aquamimicry system

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Shenzheng Zeng ◽  
Sukontorn Khoruamkid ◽  
Warinphorn Kongpakdee ◽  
Dongdong Wei ◽  
Lingfei Yu ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Well Being ◽  
Pacific White Shrimp ◽  
Shrimp Farming ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Shrimp Culture ◽  
Water And Sediment ◽  
Surrounding Environment ◽  
Shrimp Production

Abstract The Pacific white shrimp, with the largest production in shrimp industry, has suffered from multiple severe viral and bacterial diseases, which calls for a more reliable and environmentally friendly system to promote shrimp culture. The “Aquamimicry system”, mimicking the nature of aquatic ecosystems for the well-being of aquatic animals, has effectively increased shrimp production and been adapted in many countries. However, the microbial communities in the shrimp intestine and surrounding environment that act as an essential component in Aquamimicry remain largely unknown. In this study, the microbial composition and diversity alteration in shrimp intestine, surrounding water and sediment at different culture stages were investigated by high throughput sequencing of 16S rRNA gene, obtaining 13,562 operational taxonomic units (OTUs). Results showed that the microbial communities in shrimp intestine and surrounding environment were significantly distinct from each other, and 23 distinguished taxa for each habitat were further characterized. The microbial communities differed significantly at different culture stages, confirmed by a great number of OTUs dramatically altered during the culture period. A small part of these altered OTUs were shared between shrimp intestine and surrounding environment, suggesting that the microbial alteration of intestine was not consistent with that of water and sediment. Regarding the high production of Aquamimicry farm used as a case in this study, the dissimilarity between intestinal and surrounding microbiota might be considered as a potential indicator for healthy status of shrimp farming, which provided hints on the appropriate culture practices to improve shrimp production.

scholarly journals Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients

2021 ◽  
Author(s):  
Yueqiong Ni ◽  
Zoltan Lohinai ◽  
Yoshitaro Heshiki ◽  
Balazs Dome ◽  
Judit Moldvay ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Gut Microbiota ◽  
Cancer Patients ◽  
Gut Microbiome ◽  
Human Gut ◽  
Microbial Composition ◽  
Shotgun Metagenomics ◽  
Lung Cancer Patients ◽  
Microbial Species ◽  
Functional Pathways

AbstractCachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. The etiology of cachexia is poorly understood, and limited treatment options exist. Here, we investigated the role of the human gut microbiome in cachexia by integrating shotgun metagenomics and plasma metabolomics of 31 lung cancer patients. The cachexia group showed significant differences in the gut microbial composition, functional pathways of the metagenome, and the related plasma metabolites compared to non-cachectic patients. Branched-chain amino acids (BCAAs), methylhistamine, and vitamins were significantly depleted in the plasma of cachexia patients, which was also reflected in the depletion of relevant gut microbiota functional pathways. The enrichment of BCAAs and 3-oxocholic acid in non-cachectic patients were positively correlated with gut microbial species Prevotella copri and Lactobacillus gasseri, respectively. Furthermore, the gut microbiota capacity for lipopolysaccharides biosynthesis was significantly enriched in cachectic patients. The involvement of the gut microbiome in cachexia was further observed in a high-performance machine learning model using solely gut microbial features. Our study demonstrates the links between cachectic host metabolism and specific gut microbial species and functions in a clinical setting, suggesting that the gut microbiota could have an influence on cachexia with possible therapeutic applications.

Sign in / Sign up

Export Citation Format

Share Document