scholarly journals Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa

2021 ◽  
Author(s):  
Andrei Bombin ◽  
Jonathan D. Mosley ◽  
Shun Yan ◽  
Sergei Bombin ◽  
Jane F. Ferguson
Keyword(s):  
Bacterial Communities ◽  
Community Dynamics ◽  
Fecal Microbiota ◽  
Health Concern ◽  
Cardiometabolic Health ◽  
Strong Correlations ◽  
Microbiome Composition ◽  
Bacterial Community Dynamics ◽  
Obesity Status ◽  
Rdna Sequencing

Obesity is an increasing global health concern and is associated with a broad range of morbidities. The gut microbiota are increasingly recognized as important contributors to obesity and cardiometabolic health. This study aimed to characterize oral and gut microbial communities, and evaluate host:microbiota interactions between clinical obesity classifications. We performed 16S rDNA sequencing on fecal and salivary samples, global metabolomics profiling on plasma and stool samples, and dietary profiling in 135 healthy individuals. We grouped individuals by obesity status, based on body mass index (BMI), including lean (BMI 18-24.9), overweight (BMI 25-29.9), or obese (BMI ≥30). We analyzed differences in microbiome composition, community inter-relationships, and predicted microbial function by obesity status. We found that salivary bacterial communities of lean and obese individuals were compositionally and phylogenetically distinct. An increase in obesity status was positively associated with strong correlations between bacterial taxa, particularly with bacterial groups implicated in metabolic disorders including Fretibacterium, and Tannerella. Consumption of sweeteners, especially xylitol, significantly influenced compositional and phylogenetic diversities of salivary and fecal bacterial communities. In addition, obesity groups exhibited differences in predicted bacterial metabolic activity, which was correlated with host's metabolite concentrations. Overall, obesity was associated with distinct changes in bacterial community dynamics, particularly in saliva. Consideration of microbiome community structure, and inclusion of salivary samples may improve our ability to understand pathways linking microbiota to obesity and cardiometabolic disease.

scholarly journals Bacterial community dynamics during embryonic and larval development of three confamilial echinoids

2018 ◽  
Author(s):  
Tyler J. Carrier ◽  
Adam M. Reitzel
Keyword(s):  
Bacterial Community ◽  
Larval Development ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Marine Invertebrates ◽  
Sea Urchins ◽  
Larval Feeding ◽  
Bacterial Community Dynamics ◽  
Future Work ◽  
Embryonic And Larval Development

ABSTRACTDevelopment of some animals is influenced by and, in some cases, dependent on the associated microbiota. The timing of when associated bacterial communities are established during the development of marine invertebrates and their subsequent dynamics across stages are known for only a few species. Here, we compare the bacterial communities of three confamilial echinoids from egg to juvenile using sequence-based approaches. Bacterial communities are established on unfertilized eggs and change gradually during embryonic and larval development. Despite the differences amongst these pre-metamorphic stages, approximately thirty-percent of OTUs identified in association with unfertilized egg were present in the juveniles. During embryonic development, host-associated communities diverged from the environmental microbiota but later converged following the onset of larval feeding. Taken together, the data presented here support the hypothesis that bacterial communities are established prior to fertilization and community composition shifts gradually thereafter, all while remaining distinct from the environment. Future work will need to determine the relative influence of the host and bacteria-bacteria interactions in shaping the associated bacterial community to determine the potential functional importance of bacteria during the development of larval sea urchins and benthic marine invertebrates more broadly.

scholarly journals Mice Microbiota Composition Changes by Inulin Feeding with a Long Fasting Period under a Two-Meals-Per-Day Schedule

Nutrients ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2802 ◽  
Author(s):  
Sasaki ◽  
Miyakawa ◽  
Watanabe ◽  
Nakayama ◽  
Lyu ◽  
...  
Keyword(s):  
Short Chain Fatty Acids ◽  
Fecal Microbiota ◽  
Water Soluble ◽  
Soluble Dietary Fiber ◽  
Fasting Period ◽  
Microbiome Composition ◽  
Rdna Sequencing ◽  
Timing Effects ◽  
The Difference ◽  
Composition Changes

Water-soluble dietary fiber is known to modulate fecal microbiota. Although there are a few reports investigating the effects of fiber intake timing on metabolism, there are none on the effect of intake timing on microbiota. Therefore, in this study, we examined the timing effects of inulin-containing food on fecal microbiota. Mice were housed under conditions with a two-meals-per-day schedule, with a long fasting period in the morning and a short fasting period in the evening. Then, 10–14 days after inulin intake, cecal content and feces were collected, and cecal pH and short-chain fatty acids (SCFAs) were measured. The microbiome was determined using 16S rDNA sequencing. Inulin feeding in the morning rather than the evening decreased the cecal pH, increased SCFAs, and changed the microbiome composition. These data suggest that inulin is more easily digested by fecal microbiota during the active period than the inactive period. Furthermore, to confirm the effect of fasting length, mice were housed under a one-meal-per-day schedule. When the duration of fasting was equal, the difference between morning and evening nearly disappeared. Thus, our study demonstrates that consuming inulin at breakfast, which is generally after a longer fasting period, has a greater effect on the microbiota.

Temporal Bacterial Community Dynamics Vary Among Ulcerative Colitis Patients After Fecal Microbiota Transplantation

2013 ◽  
Vol 108 (10) ◽  
pp. 1620-1630 ◽  
Author(s):  
Sieglinde Angelberger ◽  
Walter Reinisch ◽  
Athanasios Makristathis ◽  
Cornelia Lichtenberger ◽  
Clemens Dejaco ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Bacterial Community ◽  
Community Dynamics ◽  
Fecal Microbiota Transplantation ◽  
Fecal Microbiota ◽  
Bacterial Community Dynamics

scholarly journals Effects of a Simulated Acute Oil Spillage on Bacterial Communities from Arctic and Antarctic Marine Sediments

2019 ◽  
Vol 7 (12) ◽  
pp. 632 ◽  
Author(s):  
Carmen Rizzo ◽  
Roberta Malavenda ◽  
Berna Gerçe ◽  
Maria Papale ◽  
Christoph Syldatk ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Oil Spill ◽  
Incubation Time ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Hydrocarbon Mixture ◽  
Cold Temperatures ◽  
Hydrocarbon Pollution ◽  
Bacterial Community Dynamics ◽  
Oil Spillage

Background: The bacterial community responses to oil spill events are key elements to predict the fate of hydrocarbon pollution in receiving aquatic environments. In polar systems, cold temperatures and low irradiance levels can limit the effectiveness of contamination removal processes. In this study, the effects of a simulated acute oil spillage on bacterial communities from polar sediments were investigated, by assessing the role of hydrocarbon mixture, incubation time and source bacterial community in selecting oil-degrading bacterial phylotypes. Methods: The bacterial hydrocarbon degradation was evaluated by gas chromatography. Flow cytometric and fingerprinting profiles were used to assess the bacterial community dynamics over the experimental incubation time. Results: Direct responses to the simulated oil spill event were found from both Arctic and Antarctic settings, with recurrent bacterial community traits and diversity profiles, especially in crude oil enrichment. Along with the dominance of Pseudomonas spp., members of the well-known hydrocarbon degraders Granulosicoccus spp. and Cycloclasticus spp. were retrieved from both sediments. Conclusions: Our findings indicated that polar bacterial populations are able to respond to the detrimental effects of simulated hydrocarbon pollution, by developing into a more specialized active oil degrading community.

Bacterial community dynamics across developmental stages of fungal fruiting bodies

2020 ◽  
Vol 96 (10) ◽  
Author(s):  
Daniyal Gohar ◽  
Mari Pent ◽  
Kadri Põldmaa ◽  
Mohammad Bahram
Keyword(s):  
Bacterial Community ◽  
Fruiting Body ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Developmental Stages ◽  
Body Parts ◽  
Fruiting Bodies ◽  
Bacterial Community Dynamics ◽  
Host Development

ABSTRACT Increasing evidence suggest that bacteria form diverse communities in various eukaryotic hosts, including fungi. However, little is known about their succession and the functional potential at different host development stages. Here we examined the effect of fruiting body parts and developmental stages on the structure and potential function of fungus-associated bacterial communities. Using high-throughput sequencing, we characterized bacterial communities and their associated potential functions in fruiting bodies from ten genera belonging to four major mushroom-forming orders and three different developmental stages of a model host species Cantharellus cibarius. Our results demonstrate that bacterial community structure differs between internal and external parts of the fruiting body but not between inner tissues. The structure of the bacterial communities showed significant variation across fruiting body developmental stages. We provide evidence that certain functional groups, such as those related to nitrogen fixation, persist in fruiting bodies during the maturation, but are replaced by putative parasites/pathogens afterwards. These data suggest that bacterial communities inhabiting fungal fruiting bodies may play important roles in their growth and development.

scholarly journals Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes

mSphere ◽  
2017 ◽  
Vol 2 (3) ◽  
Author(s):  
Alexandra M. Linz ◽  
Benjamin C. Crary ◽  
Ashley Shade ◽  
Sarah Owens ◽  
Jack A. Gilbert ◽  
...  
Keyword(s):  
Time Series ◽  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Environmental Gradients ◽  
Bacterial Community Composition ◽  
Bacterial Community Dynamics ◽  
Long Time ◽  
Bog Lakes

ABSTRACT Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series. Bacteria play a key role in freshwater biogeochemical cycling, but long-term trends in freshwater bacterial community composition and dynamics are not yet well characterized. We used a multiyear time series of 16S rRNA gene amplicon sequencing data from eight bog lakes to census the freshwater bacterial community and observe annual and seasonal trends in abundance. The sites that we studied encompassed a range of water column mixing frequencies, which we hypothesized would be associated with trends in alpha and beta diversity. Each lake and layer contained a distinct bacterial community, with distinct levels of richness and indicator taxa that likely reflected the environmental conditions of each lake type sampled, including Actinobacteria in polymictic lakes (i.e., lakes with multiple mixing events per year), Methylophilales in dimictic lakes (lakes with two mixing events per year, usually in spring and fall), and “Candidatus Omnitrophica” in meromictic lakes (lakes with no recorded mixing events). The community present during each year at each site was also surprisingly unique. Despite unexpected interannual variability in community composition, we detected a core community of taxa found in all lakes and layers, including Actinobacteria tribe acI-B2 and Betaprotobacteria lineage PnecC. Although trends in abundance did not repeat annually, each freshwater lineage within the communities had a consistent lifestyle, defined by persistence, abundance, and variability. The results of our analysis emphasize the importance of long-term multisite observations, as analyzing only a single year of data or one lake would not have allowed us to describe the dynamics and composition of these freshwater bacterial communities to the extent presented here. IMPORTANCE Lakes are excellent systems for investigating bacterial community dynamics because they have clear boundaries and strong environmental gradients. The results of our research demonstrate that bacterial community composition varies by year, a finding which likely applies to other ecosystems and has implications for study design and interpretation. Understanding the drivers and controls of bacterial communities on long time scales would improve both our knowledge of fundamental properties of bacterial communities and our ability to predict community states. In this specific ecosystem, bog lakes play a disproportionately large role in global carbon cycling, and the information presented here may ultimately help refine carbon budgets for these lakes. Finally, all data and code in this study are publicly available. We hope that this will serve as a resource for anyone seeking to answer their own microbial ecology questions using a multiyear time series.

scholarly journals Inter-phylum negative interactions affect soil bacterial community dynamics and functions during soybean development under long-term nitrogen fertilization

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Chunfang Zhang ◽  
Shuo Jiao ◽  
Duntao Shu ◽  
Gehong Wei
Keyword(s):  
Bacterial Community ◽  
Nitrogen Fertilization ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Community Dynamics ◽  
Temporal Variations ◽  
Interspecies Interactions ◽  
Bacterial Community Dynamics ◽  
Nitrogen Inputs ◽  
Negative Interactions

AbstractUnderstanding interspecies interactions is essential to predict the response of microbial communities to exogenous perturbation. Herein, rhizospheric and bulk soils were collected from five developmental stages of soybean, which grew in soils receiving 16-year nitrogen inputs. Bacterial communities and functional profiles were examined using high-throughput sequencing and quantitative PCR, respectively. The objective of this study was to identify the key bacterial interactions that influenced community dynamics and functions. We found that the stages of soybean development outcompeted nitrogen fertilization management in shaping bacterial community structure, while fertilization treatments significantly shaped the abundance distribution of nitrogen functional genes. Temporal variations in bacterial abundances increased in bulk soils, especially at the stage of soybean branching, which helps to infer underlying negative interspecies interactions. Members of Cyanobacteria and Actinobacteria actively engaged in inter-phylum negative interactions in bulk soils and soybean rhizosphere, respectively. Furthermore, the negative interactions between nitrogen-fixing functional groups and the reduction of nifH gene abundance were coupled during soybean development, which may help to explain the linkages between population dynamics and functions. Overall, these findings highlight the importance of inter-phylum negative interactions in shaping the correlation patterns of bacterial communities and in determining soil functional potential.

scholarly journals Seasonal Variation Imparts The Endophytic Bacterial Community Dynamics in Mango Plants and Its Hemiparasites

2021 ◽  
Author(s):  
Rajsekhar Adhikary ◽  
Sukhendu Mandal ◽  
Vivekananda Mandal
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Community Dynamics ◽  
Mangifera Indica ◽  
Alpha Diversity ◽  
Diversity Indices ◽  
Rrna Gene ◽  
Flowering Season ◽  
Bacterial Community Dynamics ◽  
Endophytic Community

Abstract Assessment of bacterial community dynamics helps to estimate the endophytic community structure and ecological behaviour imposed by them. Such community composition is essential to understand the molecular interplay that lies between them and the host plants. The present study aims to explore the endophytic bacterial communities and their dynamics in the pre-flowering and post-flowering seasons in the horticulturally important Mango (Mangifera indica L.) and its hemiparasites Loranthus sp., and Macrosolen sp. through a metagenomic approach using the sequence of V3 region of 16S rRNA gene. Bacillus was found to be the most abundant genera, followed by Acinetobacter, and Corynebacterium, which belong to the phyla Firmicutes, Proteobacteria, and Actinobacteria. It has been found that during the post-flowering season, twigs and leaves of mango have lower endophytic bacterial loads. Furthermore, the alpha-diversity indices of the representative genera were highest in Loranthus sp. during the post-flowering seasons of mango. The ecological, taxonomic, and complex correlation studies unravelled that the hemiparasites act as the potent reservoirs of endophytic community throughout the year, and during favourable conditions, these bacterial communities disseminate to the mango plant.

scholarly journals Proanthocyanidin-enriched cranberry extract induces resilient bacterial community dynamics in a gnotobiotic mouse model

2021 ◽  
Author(s):  
Catherine C. Neto ◽  
Benedikt M. Mortzfeld ◽  
John R. Turbitt ◽  
Shakti K. Bhattarai ◽  
Vladimir Yeliseyev ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Mouse Model ◽  
Community Dynamics ◽  
Water Soluble ◽  
Long Term Effects ◽  
Intestinal Mucus ◽  
Bacterial Community Dynamics ◽  
Rdna Sequencing ◽  
Anti Inflammatory ◽  
Pre Treatment

AbstractCranberry consumption has numerous health benefits, with experimental reports showing its anti-inflammatory and anti-tumor properties. Importantly, microbiome research has demonstrated that the gastrointestinal bacterial community modulates host immunity, raising the question whether the cranberry-derived effect may be related to its ability to modulate the microbiome. Only a few studies have investigated the effect of cranberry products on the microbiome to date. Especially because cranberry is rich in dietary fibers, we do not know the extent of microbiome modulation that is caused solely by polyphenols, particularly proanthocyanidins (PACs). Since previous work has only focused on the long-term effects of cranberry extracts, in this study we investigated the effect of a water-soluble, polyphenol-rich cranberry juice extract (CJE) on the short-term dynamics of human-derived bacterial community in a gnotobiotic mouse model. CJE characterization revealed a high enrichment in PACs (57% PACs), the highest ever utilized in a microbiome study. In a 37-day experiment with a 10-day CJE intervention and 14-day recovery time, we profiled the microbiota via 16 rDNA sequencing and applied diverse time-series analytics methods to identify individual bacterial responses. We show that daily administration of CJE induces distinct dynamical patterns in bacterial abundances during and after treatment before recovering resiliently to pre-treatment levels. Specifically, we observed an increase of the immunomodulatory mucin degrading Akkermansia muciniphila after treatment, suggesting intestinal mucus accumulation due to CJE. Interestingly, this expansion coincided with an increase in the abundance of butyrate-producing Clostridia, a group of microbes known to promote numerous adaptive and innate anti-inflammatory phenotypes.

Seasonal changes and the unexpected impact of environmental disturbance on skin bacteria of individual amphibians in a natural habitat

2020 ◽  
Author(s):  
Jenifer B Walke ◽  
Matthew H Becker ◽  
Arianna Krinos ◽  
Elizabeth A B Chang ◽  
Celina Santiago ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Bacterial Communities ◽  
Seasonal Changes ◽  
Community Dynamics ◽  
Natural Habitat ◽  
Rrna Gene ◽  
Skin Bacteria ◽  
Bacterial Community Dynamics ◽  
Metabolite Profiles ◽  
Over Time

Abstract Amphibians host diverse skin bacteria that have a role in pathogen defense, but these skin communities could change over time and impact this function. Here, we monitored individual Eastern red-spotted newts (Notophthalmus viridescens; N = 17) for two years in a field pond enclosure and assessed the effects of season and disturbance on skin bacterial community dynamics. We created disturbances by adding additional pond substrate to the enclosure at two timepoints. We planned to sample the skin bacterial community and metabolite profiles of each newt every six weeks; we ultimately sampled eight individuals at least six times. We used 16S rRNA gene amplicon sequencing to characterize the bacterial communities and HPLC-MS for metabolite profiling. We found that disturbance had a dramatic effect on skin bacterial communities and metabolite profiles, while season had an effect only using select metrics. There were seven core bacterial taxa (97% OTUs) that were found on all newts in all seasons, pre- and post-disturbance. Lastly, there was a correlation between bacterial and metabolite profiles post-disturbance, which was not observed pre-disturbance. This longitudinal study suggests that environmental disturbances can have lasting effects on skin bacterial communities that overwhelm seasonal changes, although the core bacteria remain relatively consistent over time.

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