Microbiome structure of a wild Drosophila community along tropical elevational gradients and comparison to laboratory lines

While the biogeography of free-living microbial communities is well-studied, community turnover along environmental gradients in host-associated communities is not well understood. In particular, patterns of host-microbiome diversity along elevational gradients remain largely uncharacterized. Because elevational gradients may serve as natural proxies for climate change, understanding these temperature-influenced patterns can inform our understanding of the threats facing hosts and their microbes in a warming world. In this study, we analysed microbiomes from pupae & adults of four Drosophila species native to Australian tropical rainforests. We sampled wild individuals at high and low elevation along two mountain gradients, to determine natural diversity patterns, and sampled laboratory-reared individuals from isofemale lines established from the same localities, to see if any natural patterns would be retained in the lab. In both environments, we controlled for diet to help elucidate other deterministic patterns of microbiome composition. Microbiome community composition differed radically between laboratory-reared and field-caught flies but did not significantly differ across elevation. We found some notable taxonomic differences in Drosophila microbiomes between different species and elevations. We also found similar microbiome composition from both types of provided food, and we therefore suggest the significant differences in richness are the products of environments with different bacterial species pools. We conclude that elevational differences in temperature are not a major factor in determining Drosophila microbiome composition and we caution against determining microbiome composition from lab-only specimens, particularly long-term cultures.

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Single-colony sequencing reveals microbe-by-microbiome phylosymbiosis between the cyanobacterium Microcystis and its associated bacteria

Microbiome ◽

10.1186/s40168-021-01140-8 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Olga M. Pérez-Carrascal ◽

Nicolas Tromas ◽

Yves Terrat ◽

Elisa Moreno ◽

Alessandra Giani ◽

...

Keyword(s):

Genetic Diversity ◽

Heterotrophic Bacteria ◽

Bacterial Species ◽

Colony Growth ◽

Genomic Diversity ◽

Gene Copy ◽

Metagenomic Sequencing ◽

Associated Bacteria ◽

Microbiome Composition

Abstract Background Cyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria—their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies—including cyanobacteria and associated bacterial genomes—isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. Results We identified 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in only two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter. These phylogenetically associated genera could enrich the metabolic repertoire of Microcystis, for example by encoding the biosynthesis of complementary carotenoid molecules. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting. Conclusions We have introduced a method for culture-free isolation of single colonies from nature followed by metagenomic sequencing, which could be applied to other types of microbes. Together, our results expand the known genetic diversity of both Microcystis and its microbiome in natural settings, and support their long-term, specific, and potentially beneficial associations.

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Single-colony sequencing reveals phylosymbiosis, co-phylogeny, and horizontal gene transfer between the cyanobacterium Microcystis and its microbiome

10.1101/2020.11.17.386995 ◽

2020 ◽

Author(s):

Olga M. Pérez-Carrascal ◽

Nicolas Tromas ◽

Yves Terrat ◽

Elisa Moreno ◽

Alessandra Giani ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Heterotrophic Bacteria ◽

Bacterial Species ◽

Carotenoid Biosynthesis ◽

Colony Growth ◽

Genomic Diversity ◽

Gene Copy ◽

Microbiome Composition

AbstractCyanobacteria from the genus Microcystis can form large mucilaginous colonies with attached heterotrophic bacteria – their microbiome. However, the nature of the relationship between Microcystis and its microbiome remains unclear. Is it a long-term, evolutionarily stable association? Which partners benefit? Here we report the genomic diversity of 109 individual Microcystis colonies – including cyanobacteria and associated bacterial genomes – isolated in situ and without culture from Lake Champlain, Canada and Pampulha Reservoir, Brazil. We found 14 distinct Microcystis genotypes from Canada, of which only two have been previously reported, and four genotypes specific to Brazil. Microcystis genetic diversity was much greater between than within colonies, consistent with colony growth by clonal expansion rather than aggregation of Microcystis cells. We also identified 72 bacterial species in the microbiome. Each Microcystis genotype had a distinct microbiome composition, and more closely-related genotypes had more similar microbiomes. This pattern of phylosymbiosis could be explained by co-phylogeny in two out of the nine most prevalent associated bacterial genera, Roseomonas and Rhodobacter, suggesting long-term evolutionary associations. Roseomonas and Rhodobacter genomes encode functions which could complement the metabolic repertoire of Microcystis, such as cobalamin and carotenoid biosynthesis, and nitrogen fixation. In contrast, other colony-associated bacteria showed weaker signals of co-phylogeny, but stronger evidence of horizontal gene transfer with Microcystis. These observations suggest that acquired genes are more likely to be retained in both partners (Microcystis and members of its microbiome) when they are loosely associated, whereas one gene copy is sufficient when the association is physically tight and evolutionarily long-lasting.

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Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.2193 ◽

2021 ◽

Vol 288 (1965) ◽

Author(s):

Rupert Mazzucco ◽

Christian Schlötterer

Keyword(s):

Drosophila Melanogaster ◽

Longitudinal Studies ◽

Microbiome Composition ◽

Temperature Regimes ◽

Microbiome Diversity ◽

The Family ◽

Single Host ◽

Post Hoc ◽

Genome Dataset

The influence of the microbiome on its host is well-documented, but the interplay of its members is not yet well-understood. Even for simple microbiomes, the interaction among members of the microbiome is difficult to study. Longitudinal studies provide a promising approach to studying such interactions through the temporal covariation of different taxonomic units. By contrast to most longitudinal studies, which span only a single host generation, we here present a post hoc analysis of a whole-genome dataset of 81 samples that follows microbiome composition for up to 180 host generations, which cover nearly 10 years. The microbiome diversity remained rather stable in replicated Drosophila melanogaster populations exposed to two different temperature regimes. The composition changed, however, systematically across replicates of the two temperature regimes. Significant associations between families, mostly specific to one temperature regime, indicate functional interdependence of different microbiome components. These associations also involve moderately abundant families, which emphasizes their functional importance, and highlights the importance of looking beyond the common constituents of the Drosophila microbiome.

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Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth

Microbiome ◽

10.1186/s40168-020-00959-x ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Alexander Mahnert ◽

Cyprien Verseux ◽

Petra Schwendner ◽

Kaisa Koskinen ◽

Christina Kumpitsch ◽

...

Keyword(s):

Quantitative Information ◽

Rrna Gene ◽

Skin Microbiome ◽

Microbiome Composition ◽

Microbial Monitoring ◽

Gene Profiles ◽

Abiotic Surfaces ◽

Future Space ◽

Microbiome Diversity

Abstract Background Human health is closely interconnected with its microbiome. Resilient microbiomes in, on, and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein, we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a 1 year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars. Results Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance, and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crew members were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crew members within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility. Conclusions This study highlights main routes of microbial transfer, interaction of the crew, and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors.

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Taxonomic signatures of cause-specific mortality risk in human gut microbiome

Nature Communications ◽

10.1038/s41467-021-22962-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Aaro Salosensaari ◽

Ville Laitinen ◽

Aki S. Havulinna ◽

Guillaume Meric ◽

Susan Cheng ◽

...

Keyword(s):

Mortality Risk ◽

Gut Microbiome ◽

Human Gut ◽

Cross Sectional ◽

Microbiome Composition ◽

Human Gut Microbiome ◽

Non Invasive ◽

Sequencing Technologies

AbstractThe collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

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Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation

Communications Biology ◽

10.1038/s42003-021-01741-x ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Travis T. Sims ◽

Molly B. El Alam ◽

Tatiana V. Karpinets ◽

Stephanie Dorta-Estremera ◽

Venkatesh L. Hegde ◽

...

Keyword(s):

Cervical Cancer ◽

Radiation Therapy ◽

Gut Microbiota ◽

Cancer Patients ◽

Gut Microbiome ◽

Compositional Variation ◽

Short Term ◽

Microbiome Diversity ◽

Term Survivor

AbstractDiversity of the gut microbiome is associated with higher response rates for cancer patients receiving immunotherapy but has not been investigated in patients receiving radiation therapy. Additionally, current studies investigating the gut microbiome and outcomes in cancer patients may not have adjusted for established risk factors. Here, we sought to determine if diversity and composition of the gut microbiome was independently associated with survival in cervical cancer patients receiving chemoradiation. Our study demonstrates that the diversity of gut microbiota is associated with a favorable response to chemoradiation. Additionally, compositional variation among patients correlated with short term and long-term survival. Short term survivor fecal samples were significantly enriched in Porphyromonas, Porphyromonadaceae, and Dialister, whereas long term survivor samples were significantly enriched in Escherichia Shigella, Enterobacteriaceae, and Enterobacteriales. Moreover, analysis of immune cells from cervical tumor brush samples by flow cytometry revealed that patients with a high microbiome diversity had increased tumor infiltration of CD4+ lymphocytes as well as activated subsets of CD4 cells expressing ki67+ and CD69+ over the course of radiation therapy. Modulation of the gut microbiota before chemoradiation might provide an alternative way to enhance treatment efficacy and improve treatment outcomes in cervical cancer patients.

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Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

FEMS Microbiology Ecology ◽

10.1093/femsec/fiaa022 ◽

2020 ◽

Vol 96 (3) ◽

Cited By ~ 2

Author(s):

Gavin J Fenske ◽

Sudeep Ghimire ◽

Linto Antony ◽

Jane Christopher-Hennings ◽

Joy Scaria

Keyword(s):

Bacterial Communities ◽

Bacterial Species ◽

Shotgun Metagenomics ◽

Culture Techniques ◽

Microbiome Composition ◽

Culture Independent ◽

Health And Disease ◽

The Media ◽

And Function ◽

Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

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Long-term CO2 fertilization increases vegetation productivity and has little effect on hydrological partitioning in tropical rainforests

Journal of Geophysical Research Biogeosciences ◽

10.1002/2016jg003475 ◽

2016 ◽

Vol 121 (8) ◽

pp. 2125-2140 ◽

Cited By ~ 42

Author(s):

Yuting Yang ◽

Randall J. Donohue ◽

Tim R. McVicar ◽

Michael L. Roderick ◽

Hylke E. Beck

Keyword(s):

Tropical Rainforests ◽

Co2 Fertilization ◽

Vegetation Productivity

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Nestling telomere shortening, but not telomere length, reflects developmental stress and predicts survival in wild birds

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.3287 ◽

2014 ◽

Vol 281 (1785) ◽

pp. 20133287 ◽

Cited By ~ 130

Author(s):

Jelle J. Boonekamp ◽

G. A. Mulder ◽

H. Martijn Salomons ◽

Cor Dijkstra ◽

Simon Verhulst

Keyword(s):

Telomere Length ◽

Brood Size ◽

Developmental Stress ◽

Free Living ◽

Telomere Shortening ◽

Developmental Effects ◽

Fitness Consequences ◽

Developmental Conditions ◽

Fledgling Mass

Developmental stressors often have long-term fitness consequences, but linking offspring traits to fitness prospects has remained a challenge. Telomere length predicts mortality in adult birds, and may provide a link between developmental conditions and fitness prospects. Here, we examine the effects of manipulated brood size on growth, telomere dynamics and post-fledging survival in free-living jackdaws. Nestlings in enlarged broods achieved lower mass and lost 21% more telomere repeats relative to nestlings in reduced broods, showing that developmental stress accelerates telomere shortening. Adult telomere length was positively correlated with their telomere length as nestling ( r = 0.83). Thus, an advantage of long telomeres in nestlings is carried through to adulthood. Nestling telomere shortening predicted post-fledging survival and recruitment independent of manipulation and fledgling mass. This effect was strong, with a threefold difference in recruitment probability over the telomere shortening range. By contrast, absolute telomere length was neither affected by brood size manipulation nor related to survival. We conclude that telomere loss, but not absolute telomere length, links developmental conditions to subsequent survival and suggest that telomere shortening may provide a key to unravelling the physiological causes of developmental effects on fitness.

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Distinct dietary alpha-linolenic acid-dependent shifts in the fecal microbiome composition suppresses aging-associated inflammatory responses and thrombus formation

European Heart Journal ◽

10.1093/ehjci/ehaa946.3773 ◽

2020 ◽

Vol 41 (Supplement_2) ◽

Author(s):

S.S Saeedi Saravi ◽

N.R Bonetti ◽

G.G Camici ◽

T.F Luscher ◽

J.H Beer

Keyword(s):

Platelet Aggregation ◽

Shear Flow ◽

Plasma Levels ◽

Inflammatory Responses ◽

Thrombus Formation ◽

Funding Source ◽

High Shear ◽

Fecal Microbiome ◽

Microbiome Composition

Abstract Background Aging is associated with alterations in the fecal microbiome composition. The microbiota-derived trimethylamine-N-oxide (TMAO) correlates with arterial thrombotic events, e.g. myocardial infarction and stroke, the leading causes of mortality worldwide. The omega-3 fatty acid (n-3 FA) α-linolenic acid (ALA) has been shown to be protective against thrombosis and associated pathologies. Therefore, we hypothesized that long-term dietary ALA supplementation protects against the aging-associated microbiome dysbiosis, and reduces inflammatory and thrombotic responses. Methods 24 week-old male C57BL/6 mice were fed either a high ALA (7.3g%) or low ALA (0.03g%) diet for 12 months. We examined the compositional changes of fecal microbiota of the animals treated with high vs. low ALA via 16S rRNA gene sequencing. The plasma levels of TMAO and its precursors choline and betaine, and LPS were measured by ELISA. Additionally, the platelet aggregation in response to thrombin, and thrombus formation on collagen under high-shear flow conditions of 3000/sec (to mimic blood flow in stenosed arteries) were investigated. Results Genomic analyses showed that the abundance of Phylum Proteobacteria and the family of desulfovibrio were reduced 71.72% and 51.73% in the aged high ALA-treated mice (p<0.01 and p<0.001, resp.) that may result in decrease in TAMO production and the subsequent inflammatory responses. However, microbial diversity of Bacteroidetes or Fermicutes and Bacteroidetes/Fermicutes ratio did not demonstrate a significant change between high vs. low ALA groups. Interestingly, the dietary intake of high ALA increased the abundance of Lachnospiraceae (p<0.01) that may exert anti-inflammatory effects. Importantly, high ALA significantly decreased the plasma levels of TMAO (p<0.01) and its precursor choline (P<0.05), but not betaine. The pro-inflammatory cytokine TNF-α showed a significant reduction (p<0.05), whereas plasma IL-1β did not change significantly following high ALA supplementation. An increased thrombus formation on collagen under high-shear flow (36.34%, p<0.01) and thrombin-induced platelet aggregation (31.31%, p<0.05) were found in the aged mice. Conclusion These studies demonstrate that an ALA-rich diet induces beneficial bacterial shifts in the aging-associated fecal microbiome that may lead to the suppression of inflammatory and thrombotic responses. Hence, long-term dietary ALA supplementation may be exploited as a nutritional antithrombotic strategy in the aging. Microbiome-Thrombosis-Aging Funding Acknowledgement Type of funding source: Foundation. Main funding source(s): Swiss National Science Foundation (SNSF)

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