Hand bacterial communities vary across two different human populations

This study utilized pyrosequencing-based phylogenetic library results to assess bacterial communities on the hands of women in Tanzania and compared these communities with bacteria assemblages on the hands of US women. Bacterial population profiles and phylogenetically based ordinate analysis demonstrated that the bacterial communities on hands were more similar for selected populations within a country than between the two countries considered. Organisms that have commonly been identified in prior human skin microbiome studies, including members of the Propionibacteriaceae, Staphylococcaceae and Streptococceacea families, were highly abundant on US hands and drove the clustering of US hand microbial communities into a distinct group. The most abundant bacterial taxa on Tanzanian hands were the soil-associated Rhodobacteraceae and Nocardioidaceae. These results help to expand human microbiome results beyond US and European populations, and the identification and abundance of soil-associated bacteria on Tanzanian hands demonstrated the important role of the environment in shaping the microbial communities on human hands.

Download Full-text

Bottom-up ecology of the human microbiome: from metagenomes to metabolomes

10.1101/060673 ◽

2016 ◽

Cited By ~ 2

Author(s):

Daniel R. Garza ◽

Marcel C. Van Verk ◽

Martijn A. Huynen ◽

Bas E. Dutilh

Keyword(s):

High Resolution ◽

Microbial Communities ◽

Human Skin ◽

Human Microbiome ◽

Skin Microbiome ◽

Body Site ◽

Essential Factor ◽

Metabolomics Data ◽

Bottom Up ◽

Site Specific

AbstractThe environmental metabolome is a dominant and essential factor shaping microbial communities. Thus, we hypothesized that metagenomic datasets could reveal the quantitative metabolic status of a given sample. Using a newly developed bottom-up ecology algorithm, we predicted high-resolution metabolomes of hundreds of metagenomic datasets from the human microbiome, revealing body-site specific metabolomes consistent with known metabolomics data, and suggesting that common cosmetics ingredients are some of the major metabolites shaping the human skin microbiome.

Download Full-text

Host dietary specialization and neutral assembly shape gut bacterial communities of wild dragonflies

10.1101/357996 ◽

2018 ◽

Cited By ~ 1

Author(s):

Rittik Deb ◽

Ashwin Nair ◽

Deepa Agashe

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Host Species ◽

Bacterial Communities ◽

Gut Contents ◽

Spatial And Temporal Variation ◽

Dietary Specialization ◽

Wild Host ◽

Dragonfly Species

ABSTRACTHost-associated gut microbial communities can have large impacts on host ecology and evolution, and are typically shaped by host taxonomy and diet. Different host species often harbor distinct microbial communities, potentially because (1) host dietary specialization determines microbial colonization, (2) host-specific selection acts on diet-acquired microbiota, and (3) a combination of both processes. While the first possibility involves passive community structuring, the other two may arise from a functional association and should produce stable microbial communities. However, these alternatives have rarely been tested in wild host populations. We used 16S rRNA amplicon sequencing to characterize the gut bacterial communities of six dragonfly species collected across multiple seasons and locations. We found that variation in bacterial community composition was predominantly explained by sampling season and location, and secondarily by host species. To distinguish the role of host dietary specialization and host-imposed selection, we used insect-specific primers to identify prey in the gut contents of three focal dragonfly species. We found that these dragonflies – considered to be generalist predators – consumed distinct prey, with seasonal diet variation. Together, the patterns of host dietary specialization and spatial and temporal variation suggest a strong role of passive processes in shaping the gut bacterial community. Indeed, the abundance and distribution of ~76% of the bacterial community members were consistent with neutral community assembly. Our results contradict the pervasive expectation that host-imposed selection shapes gut microbial communities, and highlight the importance of joint analyses of variation in host diet and gut microbial communities of natural host populations.

Download Full-text

Postmortem succession of gut microbial communities in deceased human subjects

PeerJ ◽

10.7717/peerj.3437 ◽

2017 ◽

Vol 5 ◽

pp. e3437 ◽

Cited By ~ 35

Author(s):

Jennifer M. DeBruyn ◽

Kathleen A. Hauther

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Human Subjects ◽

Human Microbiome ◽

Amplicon Sequencing ◽

Postmortem Changes ◽

Rrna Gene ◽

Human Gut ◽

Decomposition Processes ◽

Over Time

The human microbiome has demonstrated an importance for the health and functioning in living individuals. However, the fate of the microbiome after death is less understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs = − 0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.

Download Full-text

From Structure to Function: the Ecology of Host-Associated Microbial Communities

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00014-10 ◽

2010 ◽

Vol 74 (3) ◽

pp. 453-476 ◽

Cited By ~ 229

Author(s):

Courtney J. Robinson ◽

Brendan J. M. Bohannan ◽

Vincent B. Young

Keyword(s):

Community Structure ◽

Microbial Communities ◽

Human Microbiome ◽

Structure And Function ◽

Future Directions ◽

Human Microbiota ◽

Health And Disease ◽

Indigenous Microbiota ◽

And Function

SUMMARY In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota.

Download Full-text

Postmortem succession of gut microbial communities in human cadavers

10.7287/peerj.preprints.2777 ◽

2017 ◽

Author(s):

Jennifer M DeBruyn ◽

Kathleen A Hauther

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Human Microbiome ◽

Amplicon Sequencing ◽

Multiple Regression Model ◽

Postmortem Changes ◽

Rrna Gene ◽

Decomposition Processes ◽

Human Cadavers ◽

Over Time

The human microbiome has demonstrated importance for health and functioning in living individuals. However the fate of the microbiome after death is poorly understood. In addition to a better understanding of microbe-mediated decomposition processes, postmortem succession of human-associated microbial communities has been suggested as a possible forensic tool for estimating time since death, or postmortem interval (PMI). The objective of our study was to document postmortem changes in human gut bacterial communities. Gut microflora were repeatedly sampled from the caeca of cadavers as they decayed under natural environmental conditions. 16S rRNA gene amplicon sequencing revealed that over time, bacterial richness significantly increased (rs = 0.449) while diversity decreased (rs = -0.701). The composition of gut bacterial communities changed in a similar manner over time towards a common decay community. OTUs belonging to Bacteroidales (Bacteroides, Parabacteroides) significantly declined while Clostridiales (Clostridium, Anaerosphaera) and the fly-associated Gammaproteobacteria Ignatzschineria and Wohlfahrtiimonas increased. A best fit multiple regression model, which included five OTUs, improved the ability to predict PMI (R2 = 0.824; p < 0.001). Our examination of human caeca microflora in decomposing cadavers adds to the growing literature on postmortem microbial communities, which will ultimately contribute to a better understanding of decomposition processes.

Download Full-text

The Skin Microbiome in Atopic Dermatitis and Its Relationship to Emollients

Journal of Cutaneous Medicine and Surgery ◽

10.1177/1203475415605498 ◽

2015 ◽

Vol 20 (1) ◽

pp. 21-28 ◽

Cited By ~ 13

Author(s):

Charles W. Lynde ◽

Anneke Andriessen ◽

Vince Bertucci ◽

Catherine McCuaig ◽

Sandy Skotnicki ◽

...

Keyword(s):

Atopic Dermatitis ◽

Bacterial Diversity ◽

Bacterial Communities ◽

Expert Panel ◽

Treatment Strategies ◽

Skin Microbiome ◽

Microbiome Diversity ◽

Atopic Skin ◽

Clinical Dermatology

Background: Human-associated bacterial communities on the skin, skin microbiome, likely play a central role in development of immunity and protection from pathogens. In atopic patients, the skin bacterial diversity is smaller than in healthy subjects. Objective: To review treatment strategies for atopic dermatitis in Canada, taking the skin microbiome concept into account. Methods: An expert panel of 8 Canadian dermatologists explored the role of skin microbiome in clinical dermatology, specifically looking at atopic dermatitis. Results: The panel reached consensus on the following: (1) In atopic patients, the skin microbiome of lesional atopic skin is different from nonlesional skin in adjacent areas. (2) Worsening atopic dermatitis and smaller bacterial diversity are strongly associated. (3) Application of emollients containing antioxidant and antibacterial components may increase microbiome diversity in atopic skin. Conclusion: The skin microbiome may be the next frontier in preventive health and may impact the approach to atopic dermatitis treatment.

Download Full-text

Floral organs act as environmental filters and interact with pollinators to structure the yellow monkeyflower (Mimulus guttatus) floral microbiome

10.1101/721647 ◽

2019 ◽

Cited By ~ 1

Author(s):

María Rebolleda Gómez ◽

Tia-Lynn Ashman

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Abiotic Factors ◽

Geographic Distance ◽

Mimulus Guttatus ◽

Environmental Filters ◽

Floral Organs ◽

Environmental Selection ◽

Plant Pollinator

AbstractAssembly of microbial communities is the result of neutral and selective processes. However, the relative importance of these processes is still debated. Microbial communities of flowers, in particular, have gained recent attention because of their potential impact to plant fitness and plant-pollinator interactions. However, the role of selection and dispersal in the assembly of these communities remains poorly understood. We evaluated the role of pollinator-mediated dispersal on the contribution of neutral and selective processes in the assembly of floral microbiomes of the yellow monkeyflower (Mimulus guttatus). We sampled floral organs from flowers in the presence and absence of pollinators within five different serpentine seeps in CA and obtained 16S amplicon data on the epiphytic bacterial communities. Consistent with strong micro-environment selection within flowers we observed significant differences in community composition across floral organs and only a small effect of geographic distance. Pollinator exposure affected the contribution of environmental selection and depended on the rate and “intimacy” of interactions with flower visitors. This study provides evidence of the importance of dispersal and within-flower heterogeneity in shaping epiphytic bacterial communities of flowers, and highlights the complex interplay between pollinator behavior, environmental selection and additional abiotic factors in shaping the epiphytic bacterial communities of flowers.

Download Full-text

Identification and Diversity of Bacterial Communities Associated with the Venom Glands of the Fire Ant, Solenopsis invicta Buren (Hymenoptera: Formicidae)

10.21203/rs.3.rs-43900/v1 ◽

2020 ◽

Author(s):

Fan Yang ◽

Jinyong Yu ◽

Siqi Chen ◽

Dongdong Ning ◽

Babar Hassan ◽

...

Keyword(s):

Bacterial Communities ◽

Solenopsis Invicta ◽

Fire Ant ◽

Diversity Analysis ◽

Associated Bacteria ◽

Solenopsis Invicta Buren ◽

Venom Glands ◽

Microbe Interactions ◽

Insight Into

Abstract Background Ant-microbe interactions that naturally occur in the venom microenvironment remain mostly unknown. To best of our knowledge, no research exists that shows the identity and diversity of bacterial communities in the fires ants, and what adaptive advantages that venom-associated microbes might offer to their hosts or that hosts might provide to venom-associated bacteria. This study assessed the diversity and identity of bacteria associated with the venom glands of Solenopsis invicta and compared this community with the bacterial communities of two other stinging ants, Solenopsis geminata and Diacamma rugosum. Results The major phylum associated with the venom glands of S. invicta (workers, alates, and queens) and S. geminata (workers) was Proteobacteria, while Firmicutes were abundant in the venom glands of D. rugosum (workers). Tenericutes were also more abundant in the venom glands of S. invicta queens than in those of workers and alates. The relative abundance of Spiroplasma in S. geminata was significantly higher than those in D. rugosum and S. invicta. A microbial diversity analysis of venom glands of worker ants of Solenopsis species showed that the relative abundances of Bacillus and Lactococcus were higher in Guangxi S. invicta workers than in workers collected from Guangzhou. However, the abundance of Lactococcus in workers of D. rugosum was higher than those in workers of S. geminata from Guangxi and S. invicta collected from Guangzhou. Conclusions This study provides the first insight into the microbiota in the venom glands of S. invicta, S. geminata, and D. rugosum, which might contribute to a more comprehensive view of the role of bacteria in the synthesis or degradation of active venom components in the host. We hypothesized that the differences in bacterial communities of three ant species could be due to the local adaptation of insects along with the coevolution of bacteria and hosts.

Download Full-text

A core microbiota of the plant-earthworm interaction conserved across soils

10.1101/571240 ◽

2019 ◽

Author(s):

Samuel Jacquiod ◽

Ruben Puga-Freitas ◽

Aymé Spor ◽

Arnaud Mounier ◽

Cécile Monard ◽

...

Keyword(s):

Microbial Communities ◽

Bacterial Communities ◽

Core Network ◽

Core Microbiota ◽

Soil Bacterial Communities ◽

Community Theory ◽

Source Sink ◽

New Framework ◽

Endogeic Earthworms

AbstractMicroorganisms participate in most crucial soil functions and services benefiting human activities, such as biogeochemical cycles, bioremediation and food production. Their activity happens essentially in hotspots created by major soil macroorganisms, like rhizosphere and cast shaped by plants and earthworms respectively1. While effects of individual macroorganism on soil microbes are documented, no studies attempted to decipher how the mosaic of microhabitats built by multiple macroorganisms and their interaction determine the structure of microbial communities. Here we show a joint shaping of soil bacterial communities by these two macroorganisms, with a prevalent role of plants over earthworms. In a controlled microcosm experiment with three contrasted soils and meticulous microhabitat sampling, we found that the simultaneous presence of barley and endogeic earthworms resulted in non-additive effects on cast and rhizosphere bacterial communities. Using a source-sink approach derived from the meta-community theory2,3, we found specific cast and rhizospherecore microbiota4,5of the plant-eartworm interaction, detected in all soils only when both macroorganisms are present. We also evidenced acore networkof the plant-earthworm interaction, with cosmopolitan OTUs correlated both in cast and rhizosphere of all soils. Our study provides a new framework to explore aboveground-belowground interactions through the prism of microbial communities. This multiple-macroorganisms shaping of bacterial communities also affects fungi and archaea, while being strongly influenced by soil type. Further functional investigations are needed to understand how thesecore microbiotaandcore networkcontribute to the modulation of plant adaptive response to local abiotic and biotic conditions.

Download Full-text

Skin bacterial communities of neotropical treefrogs vary with local environmental conditions at the time of sampling

PeerJ ◽

10.7717/peerj.7044 ◽

2019 ◽

Vol 7 ◽

pp. e7044 ◽

Cited By ~ 5

Author(s):

Angie Estrada ◽

Myra C. Hughey ◽

Daniel Medina ◽

Eria A. Rebollar ◽

Jenifer B. Walke ◽

...

Keyword(s):

Bacterial Community ◽

Temporal Variation ◽

Microbial Communities ◽

Relative Abundance ◽

Bacterial Communities ◽

Community Diversity ◽

Amphibian Conservation ◽

Rrna Gene ◽

Skin Microbiome ◽

Amphibian Skin

The amphibian skin microbiome has been the focus of recent studies aiming to better understand the role of these microbial symbionts in host defense against disease. However, host-associated microbial communities are complex and dynamic, and changes in their composition and structure can influence their function. Understanding temporal variation of bacterial communities on amphibian skin is critical for establishing baselines from which to improve the development of mitigation techniques based on probiotic therapy and provides long-term host protection in a changing environment. Here, we investigated whether microbial communities on amphibian skin change over time at a single site. To examine this, we collected skin swabs from two pond-breeding species of treefrogs, Agalychnis callidryas and Dendropsophus ebraccatus, over 4 years at a single lowland tropical pond in Panamá. Relative abundance of operational taxonomic units (OTUs) based on 16S rRNA gene amplicon sequencing was used to determine bacterial community diversity on the skin of both treefrog species. We found significant variation in bacterial community structure across long and short-term time scales. Skin bacterial communities differed across years on both species and between seasons and sampling days only in D. ebraccatus. Importantly, bacterial community structures across days were as variable as year level comparisons. The differences in bacterial community were driven primarily by differences in relative abundance of key OTUs and explained by rainfall at the time of sampling. These findings suggest that skin-associated microbiomes are highly variable across time, and that for tropical lowland sites, rainfall is a good predictor of variability. However, more research is necessary to elucidate the significance of temporal variation in bacterial skin communities and their maintenance for amphibian conservation efforts.

Download Full-text