Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions

AbstractGut microbiomes were analyzed by 16S rRNA gene metabarcoding for polar bears (Ursus maritimus) from the southern Beaufort Sea (SB), where sea ice loss has led to increased use of land-based food resources by bears, and from East Greenland (EG), where persistent sea ice has allowed hunting of ice-associated prey nearly year-round. SB polar bears showed a higher number of total (940 vs. 742) and unique (387 vs. 189) amplicon sequence variants and higher inter-individual variation compared to EG polar bears. Gut microbiome composition differed significantly between the two subpopulations and among sex/age classes, likely driven by diet variation and ontogenetic shifts in the gut microbiome. Dietary tracer analysis using fatty acid signatures for SB polar bears showed that diet explained more intrapopulation variation in gut microbiome composition and diversity than other tested variables, i.e., sex/age class, body condition, and capture year. Substantial differences in the SB gut microbiome relative to EG polar bears, and associations between SB gut microbiome and diet, suggest that the shifting foraging habits of SB polar bears tied to sea ice loss may be altering their gut microbiome, with potential consequences for nutrition and physiology.

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The effects of captivity on the microbiome of the endangered Comal Springs riffle beetle (Heterelmis comalensis)

FEMS Microbiology Letters ◽

10.1093/femsle/fnab121 ◽

2021 ◽

Vol 368 (17) ◽

Author(s):

Zachary Mays ◽

Amelia Hunter ◽

Lindsay Glass Campbell ◽

Camila Carlos-Shanley

Keyword(s):

16S Rrna ◽

Gut Microbiome ◽

Amplicon Sequencing ◽

Conservation Education ◽

Rrna Gene ◽

Sequence Variants ◽

Microbiome Composition ◽

Intrinsic Factors ◽

Captive Populations ◽

The 16S Rrna Gene

Abstract The gut microbiome is affected by host intrinsic factors, diet and environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 amplicon sequence variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.

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A comparison of wild and captive Comal Springs riffle beetle (Heterelmis comalensis) microbiomes

10.1101/2021.07.12.452104 ◽

2021 ◽

Author(s):

Zachary Mays ◽

Camila Carlos-Shanley ◽

Lindsay Glass Campbell ◽

Amelia Hunter

Keyword(s):

16S Rrna ◽

Gut Microbiome ◽

Amplicon Sequencing ◽

Conservation Education ◽

Rrna Gene ◽

Sequence Variants ◽

Microbiome Composition ◽

Intrinsic Factors ◽

Captive Populations ◽

The 16S Rrna Gene

The gut microbiome is affected by host intrinsic factors, diet, environment, and strongly linked to host's health. Although fluctuations of microbiome composition are normal, some are due to changes in host environmental conditions. When species are moved into captive environments for conservation, education, or rehabilitation, these new conditions can influence a change in gut microbiome composition. Here, we compared the microbiomes of wild and captive Comal Springs riffle beetles (Heterelmis comalensis) by using amplicon sequencing of the 16S rRNA gene. We found that the microbiome of captive beetles was more diverse than wild beetle microbiomes. We identified 24 Amplicon Sequence Variants (ASVs) with relative abundances significantly different between the wild and captive beetles. Many of the ASVs overrepresented in captive beetle microbiomes belong to taxa linked to nitrogen-rich environments. This is one of the first studies comparing the effects of captivity on the microbiome of an endangered insect species. Our findings provide valuable information for future applications in the management of captive populations of H. comalensis.

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Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽

10.3390/md18060298 ◽

2020 ◽

Vol 18 (6) ◽

pp. 298

Author(s):

Alison E. Murray ◽

Nicole E. Avalon ◽

Lucas Bishop ◽

Karen W. Davenport ◽

Erwan Delage ◽

...

Keyword(s):

Marine Invertebrate ◽

Bioactive Compound ◽

Rrna Gene ◽

Sequence Variants ◽

Specific Sequence ◽

Core Microbiome ◽

Microbiome Composition ◽

The Core ◽

Synoicum Adareanum ◽

Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

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Conservation status of polar bears ( Ursus maritimus ) in relation to projected sea-ice declines

Biology Letters ◽

10.1098/rsbl.2016.0556 ◽

2016 ◽

Vol 12 (12) ◽

pp. 20160556 ◽

Cited By ~ 31

Author(s):

Eric V. Regehr ◽

Kristin L. Laidre ◽

H. Resit Akçakaya ◽

Steven C. Amstrup ◽

Todd C. Atwood ◽

...

Keyword(s):

Sea Ice ◽

Polar Bear ◽

Extinction Risk ◽

Conservation Status ◽

Iucn Red List ◽

Arctic Sea Ice ◽

Polar Bears ◽

Near Term ◽

Conservation Assessments ◽

Global Population

Loss of Arctic sea ice owing to climate change is the primary threat to polar bears throughout their range. We evaluated the potential response of polar bears to sea-ice declines by (i) calculating generation length (GL) for the species, which determines the timeframe for conservation assessments; (ii) developing a standardized sea-ice metric representing important habitat; and (iii) using statistical models and computer simulation to project changes in the global population under three approaches relating polar bear abundance to sea ice. Mean GL was 11.5 years. Ice-covered days declined in all subpopulation areas during 1979–2014 (median −1.26 days year −1 ). The estimated probabilities that reductions in the mean global population size of polar bears will be greater than 30%, 50% and 80% over three generations (35–41 years) were 0.71 (range 0.20–0.95), 0.07 (range 0–0.35) and less than 0.01 (range 0–0.02), respectively. According to IUCN Red List reduction thresholds, which provide a common measure of extinction risk across taxa, these results are consistent with listing the species as vulnerable. Our findings support the potential for large declines in polar bear numbers owing to sea-ice loss, and highlight near-term uncertainty in statistical projections as well as the sensitivity of projections to different plausible assumptions.

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Abstract 18: Gut Microbiome Modifies the Protective Effects of a Mediterranean Dietary Pattern Against Diabetes Mellitus in US Hispanics/ Latinos: The Hispanic Community Health Study/ Study of Latinos (HCHS/SOL)

Circulation ◽

10.1161/circ.141.suppl_1.18 ◽

2020 ◽

Vol 141 (Suppl_1) ◽

Cited By ~ 1

Author(s):

Dong Wang ◽

Qibin Qi ◽

Zheng Wang ◽

Mykhaylo Usyk ◽

Daniela Sotres-Alvarez ◽

...

Keyword(s):

Diabetes Mellitus ◽

Relative Abundance ◽

Gut Microbiome ◽

16S Rrna Gene Sequencing ◽

Health Study ◽

Rrna Gene ◽

Inverse Association ◽

Protective Effects ◽

Acid Fermentation ◽

Microbiome Composition

Introduction: Little is known about whether the effect of a healthy diet on diabetes mellitus (DM) is modified by the gut microbiome in human. Hypothesis: We hypothesize that the gut microbiome modifies the inverse association between the Mediterranean diet (MedDiet) and risk of DM. Methods: This study included 543 DM cases, 805 with impaired glucose tolerance (IGT) and 394 with normal glucose regulation (NGR) in adults 23-83yrs old from the HCHS/SOL. Fecal samples were profiled using 16s rRNA gene sequencing. We applied QIIME 2 to cluster sequences into OTUs and assign taxonomies, and PICRUSt to predict metagenomic gene functions. Adherence to the MedDiet was evaluated by a MedDiet index using the average of two 24-hr dietary recalls. We applied MaAsLin2 to quantify associations between the MedDiet index and microbial features with adjustment for confounding factors listed in the caption of Fig. 1. Results: MedDiet was associated with phylogenetically diverse, rare, and abundant gut microbes (Fig. 1a). For example, a higher MedDiet index was associated with a higher relative abundance of Faecalibacterium Prausnitzii [FDR-adjusted p (q) =0.002], but a lower relative abundance of Collinsella aerofaciens ( q =0.009). We found that several microbial functions related to plant-derived polysaccharide degradation such as fructuronate reductase ( q =0.02), and short-chain fatty acid fermentation such as butyryl-CoA dehydrogenase ( q =0.002) were enriched in participants with higher MedDiet index. We found that the inverse association between MedDiet and risk of DM was more pronounced in participants with greater abundance of Prevotella copri , but weaker in participants whose gut microbial communities were dominated by Bacteroides ( P interaction =0.02 for IGT/DM vs NGR, Fig. 1b). Conclusions: Adherence to the MedDiet is associated with diverse gut microorganisms and microbial functions. The inverse association between MedDiet and risk of DM might be modified by gut microbiome composition. 1

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Changes in the Intestinal Microbiome during a Multispecies Probiotic Intervention in Compensated Cirrhosis

Nutrients ◽

10.3390/nu12061874 ◽

2020 ◽

Vol 12 (6) ◽

pp. 1874 ◽

Cited By ~ 1

Author(s):

Angela Horvath ◽

Marija Durdevic ◽

Bettina Leber ◽

Katharina di Vora ◽

Florian Rainer ◽

...

Keyword(s):

Gut Microbiome ◽

Controlled Trial ◽

16S Rrna Gene Sequencing ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Microbiome Composition ◽

Beneficial Effects ◽

Compensated Cirrhosis ◽

Gut Barrier Function ◽

Probiotic Treatment

Probiotics have been used in trials to therapeutically modulate the gut microbiome and have shown beneficial effects in cirrhosis. However, their effect on the microbiome of cirrhosis patients is not fully understood yet. Here, we tested the effects of a multispecies probiotic on microbiome composition in compensated cirrhosis. The gut microbiome composition of 58 patients with compensated cirrhosis from a randomized controlled trial who received a daily dose of multispecies probiotics or placebo for six months was analysed by 16S rRNA gene sequencing. Microbiome composition of patients who received probiotics was enriched with probiotic strains and the abundance of Faecalibacterium prausnitzii, Syntrophococcus sucromutans, Bacteroides vulgatus, Alistipes shahii and a Prevotella species was increased in the probiotic group compared to the placebo group. Patients who had microbiome changes in response to probiotic treatment also showed a significant increase in neopterin and a significant decrease in faecal zonulin levels after intervention, which was not observed in placebo-treated patients or patients with unchanged microbiome compositions. In conclusion, multispecies probiotics may enrich the microbiome of compensated cirrhotic patients with probiotic bacteria during a six-month intervention and beneficially change the residential microbiome and gut barrier function.

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Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition

BMC Microbiology ◽

10.1186/s12866-020-02017-w ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

O. H. Oduaran ◽

F. B. Tamburini ◽

V. Sahibdeen ◽

R. Brewster ◽

F. X. Gómez-Olivé ◽

...

Keyword(s):

South African ◽

Gut Microbiome ◽

Geographical Location ◽

16S Rrna Gene Sequencing ◽

Overweight And Obesity ◽

Future Research ◽

Epidemiological Transition ◽

Rrna Gene ◽

Microbiome Composition ◽

Targeted Interventions

Abstract Background Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. Results We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = − 4.7). Conclusions Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.

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Unusual Predation Attempts of Polar Bears on Ringed Seals in the Southern Beaufort Sea: Possible Significance of Changing Spring Ice Conditions

ARCTIC ◽

10.14430/arctic3 ◽

2009 ◽

Vol 61 (1) ◽

pp. 14 ◽

Cited By ~ 33

Author(s):

Ian Stirling ◽

Evan Richardson ◽

Gregory W. Thiemann ◽

Andrew E. Derocher

Keyword(s):

Sea Ice ◽

Polar Bear ◽

Foraging Behaviour ◽

Open Water ◽

Beaufort Sea ◽

Polar Bears ◽

Ringed Seals ◽

Decadal Scale ◽

Underlying Causes ◽

Ice Conditions

In April and May 2003 through 2006, unusually rough and rafted sea ice extended for several tens of kilometres offshore in the southeastern Beaufort Sea from about Atkinson Point to the Alaska border. Hunting success of polar bears (Ursus maritimus) seeking seals was low despite extensive searching for prey. It is unknown whether seals were less abundant in comparison to other years or less accessible because they maintained breathing holes below rafted ice rather than snowdrifts, or whether some other factor was involved. However, we found 13 sites where polar bears had clawed holes through rafted ice in attempts to capture ringed seals (Phoca hispida) in 2005 through 2006 and another site during an additional research project in 2007. Ice thickness at the 12 sites that we measured averaged 41 cm. These observations, along with cannibalized and starved polar bears found on the sea ice in the same general area in the springs of 2004 through 2006, suggest that during those years, polar bears in the southern Beaufort Sea were nutritionally stressed. Searches made farther north during the same period and using the same methods produced no similar observations near Banks Island or in Amundsen Gulf. A possible underlying ecological explanation is a decadal-scale downturn in seal populations. But a more likely explanation is major changes in the sea-ice and marine environment resulting from record amounts and duration of open water in the Beaufort and Chukchi seas, possibly influenced by climate warming. Because the underlying causes of observed changes in polar bear body condition and foraging behaviour are unknown, further study is warranted.

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Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content

Microbial Ecology ◽

10.1007/s00248-021-01944-z ◽

2021 ◽

Author(s):

Artur Trzebny ◽

Anna Slodkowicz-Kowalska ◽

Johanna Björkroth ◽

Miroslawa Dabert

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Gut Microbiome ◽

Bacterial Communities ◽

Bacterial Species ◽

Rrna Gene ◽

Microbial Composition ◽

Microbiome Composition ◽

Microsporidian Infection ◽

Functional Content

AbstractThe animal gut microbiota consist of many different microorganisms, mainly bacteria, but archaea, fungi, protozoans, and viruses may also be present. This complex and dynamic community of microorganisms may change during parasitic infection. In the present study, we investigated the effect of the presence of microsporidians on the composition of the mosquito gut microbiota and linked some microbiome taxa and functionalities to infections caused by these parasites. We characterised bacterial communities of 188 mosquito females, of which 108 were positive for microsporidian DNA. To assess how bacterial communities change during microsporidian infection, microbiome structures were identified using 16S rRNA microbial profiling. In total, we identified 46 families and four higher taxa, of which Comamonadaceae, Enterobacteriaceae, Flavobacteriaceae and Pseudomonadaceae were the most abundant mosquito-associated bacterial families. Our data suggest that the mosquito gut microbial composition varies among host species. In addition, we found a correlation between the microbiome composition and the presence of microsporidians. The prediction of metagenome functional content from the 16S rRNA gene sequencing suggests that microsporidian infection is characterised by some bacterial species capable of specific metabolic functions, especially the biosynthesis of ansamycins and vancomycin antibiotics and the pentose phosphate pathway. Moreover, we detected a positive correlation between the presence of microsporidian DNA and bacteria belonging to Spiroplasmataceae and Leuconostocaceae, each represented by a single species, Spiroplasma sp. PL03 and Weissella cf. viridescens, respectively. Additionally, W. cf. viridescens was observed only in microsporidian-infected mosquitoes. More extensive research, including intensive and varied host sampling, as well as determination of metabolic activities based on quantitative methods, should be carried out to confirm our results.

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Long-Distance Movement of a Female Polar Bear from Canada to Russia

ARCTIC ◽

10.14430/arctic4641 ◽

2017 ◽

Vol 70 (2) ◽

pp. 121 ◽

Cited By ~ 3

Author(s):

Amy C. Johnson ◽

Jodie D. Pongracz ◽

Andrew E. Derocher

Keyword(s):

Home Range ◽

Sea Ice ◽

Polar Bear ◽

Brownian Bridge ◽

Polar Bears ◽

Minimum Convex Polygon ◽

Long Distance ◽

Movement Model ◽

Female Polar Bear ◽

Long Distance Movement

Polar bears (Ursus maritimus) display fidelity to large geographic regions, and their movements are influenced by sea ice distribution. Polar bear subpopulations are moderately distinct from one another, and long-distance movements between subpopulations are rare. We describe and analyze the movements of a female polar bear tracked by satellite telemetry from spring 2009 for 798 days. This female traveled an exceptionally long distance (totaling 11 686 km) from the sea ice off the Yukon Territory, Canada (Southern Beaufort Sea subpopulation) to Wrangel Island, Russia (Chukchi Sea subpopulation). In comparison to other polar bears in this study, this bear traveled farther, moved faster, and had a much larger home range in the first year. Furthermore, the calculation of the home range size by two different methods demonstrated that the commonly used minimum convex polygon method overestimated the home range compared to the less biased Brownian bridge movement model. This female’s long-distance movement was unusual and provides additional evidence for gene flow between subpopulations. Monitoring polar bear movements is useful to track such events, which is especially important at present because sea ice loss due to climate change can affect subpopulation boundaries and influence management.

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