scholarly journals Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered tropical birds

2021 ◽  
Author(s):  
Maria Sara Costantini ◽  
Matthew C I Medeiros ◽  
Lisa H Crampton ◽  
Floyd A. Reed
Keyword(s):  
Endangered Species ◽  
Gut Microbiome ◽  
Environmental Changes ◽  
Critically Endangered ◽  
Sampling Location ◽  
Human Populations ◽  
Rrna Gene ◽  
Population Declines ◽  
Important Species ◽  
Hawaiian Honeycreepers

The gut microbiome of an animal has a strong influence on the health, fitness, and behavior of its host, and is thus a critical component of the animal itself. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats have caused widespread population declines of Hawaiian honeycreepers (subfamily Carduelinae). These threats, and the environmental changes that result, can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, no previous study has explored the natural patterns of the gut microbiome of a honeycreeper species in the wild. This project used amplicon-based sequencing of the 16S rRNA gene to characterize the gut microbiome of two critically endangered species of Hawaiian honeycreepers. The two species differed significantly in both alpha and beta diversity. Intraspecific variation of the gut microbiome among individual birds was a major factor. However, small but significant differences also exist between sampling location and sexes. This baseline knowledge will help inform management decisions for these honeycreeper species both in their native habitats and in captivity.

scholarly journals Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12291
Author(s):  
Maria S. Costantini ◽  
Matthew C.I. Medeiros ◽  
Lisa H. Crampton ◽  
Floyd A. Reed
Keyword(s):  
Gut Microbiome ◽  
Beta Diversity ◽  
Captive Breeding ◽  
Critically Endangered ◽  
Sampling Location ◽  
Human Populations ◽  
Rrna Gene ◽  
Important Species ◽  
Fecal Samples ◽  
Hawaiian Honeycreepers

Background The gut microbiome of animals is an important component that has strong influence on the health, fitness, and behavior of its host. Most research in the microbiome field has focused on human populations and commercially important species. However, researchers are now considering the link between endangered species conservation and the microbiome. In Hawaiʻi, several threats (e.g., avian malaria and habitat loss) have caused widespread population declines of Hawaiian honeycreepers (subfamily: Carduelinae). These threats can have a significant effect on the avian gut microbiome and may even lead to disruption of microbial function. However, the gut microbiome of honeycreeper in the wild has yet to be explored. Methods We collected 13 and 42 fecal samples, respectively, from two critically endangered honeycreeper species, the ʻakikiki (Oreomystis bairdi) and the ʻakekeʻe (Loxops caeruleirostris). The 16S rRNA gene was sequenced and processed though a MOTHUR-based bioinformatics pipeline. Bacterial ASVs were identified using the DADA2 program and bacterial community analyses, including alpha and beta diversity measures, were conducted using R packages Phyloseq and vegan. Results A total of 8,958 bacterial ASVs were identified from the fecal samples. Intraspecific differences in the gut microbiome among individual birds explained most of the variation present in the dataset, however differences between species did exist. Both species had distinct microbiomes with minimal overlap in beta diversity. ‘Akikiki had a more diverse microbiome compared to ‘akekeʻe. Additionally, small but stastically significant differences in beta diversity also exist between sampling location and sexes in ʻakikiki. Conclusion ʻAkikiki and ʻakekeʻe are currently the focus of captive breeding efforts and plans to translocate the two species to other islands are underway. This baseline knowledge will help inform management decisions for these honeycreeper species in their native habitats, on other islands, and in captivity.

scholarly journals Sewage Reflects the Microbiomes of Human Populations

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
Ryan J. Newton ◽  
Sandra L. McLellan ◽  
Deborah K. Dila ◽  
Joseph H. Vineis ◽  
Hilary G. Morrison ◽  
...  
Keyword(s):  
Microbial Community ◽  
Gut Microbiome ◽  
Marker Gene ◽  
Population Variation ◽  
Human Populations ◽  
Rrna Gene ◽  
Community Structures ◽  
Data Set ◽  
Stool Samples ◽  
Number Of Individuals

ABSTRACT Molecular characterizations of the gut microbiome from individual human stool samples have identified community patterns that correlate with age, disease, diet, and other human characteristics, but resources for marker gene studies that consider microbiome trends among human populations scale with the number of individuals sampled from each population. As an alternative strategy for sampling populations, we examined whether sewage accurately reflects the microbial community of a mixture of stool samples. We used oligotyping of high-throughput 16S rRNA gene sequence data to compare the bacterial distribution in a stool data set to a sewage influent data set from 71 U.S. cities. On average, only 15% of sewage sample sequence reads were attributed to human fecal origin, but sewage recaptured most (97%) human fecal oligotypes. The most common oligotypes in stool matched the most common and abundant in sewage. After informatically separating sequences of human fecal origin, sewage samples exhibited ~3× greater diversity than stool samples. Comparisons among municipal sewage communities revealed the ubiquitous and abundant occurrence of 27 human fecal oligotypes, representing an apparent core set of organisms in U.S. populations. The fecal community variability among U.S. populations was significantly lower than among individuals. It clustered into three primary community structures distinguished by oligotypes from either: Bacteroidaceae, Prevotellaceae, or Lachnospiraceae/Ruminococcaceae. These distribution patterns reflected human population variation and predicted whether samples represented lean or obese populations with 81 to 89% accuracy. Our findings demonstrate that sewage represents the fecal microbial community of human populations and captures population-level traits of the human microbiome. IMPORTANCE The gut microbiota serves important functions in healthy humans. Numerous projects aim to define a healthy gut microbiome and its association with health states. However, financial considerations and privacy concerns limit the number of individuals who can be screened. By analyzing sewage from 71 cities, we demonstrate that geographically distributed U.S. populations share a small set of bacteria whose members represent various common community states within U.S. adults. Cities were differentiated by their sewage bacterial communities, and the community structures were good predictors of a city's estimated level of obesity. Our approach demonstrates the use of sewage as a means to sample the fecal microbiota from millions of people and its potential to elucidate microbiome patterns associated with human demographics.

scholarly journals Integrating remote sensing and phytosociology of the Atlantic Forest to map a small continental island in southeastern Brazil: subsidies to protect the habitat of critically endangered species

Rodriguésia ◽  
2018 ◽  
Vol 69 (4) ◽  
pp. 2081-2092
Author(s):  
Bruno Coutinho Kurtz ◽  
Adriana Melo Magalhães ◽  
Vinícius da Silva Seabra ◽  
Monika Richter ◽  
Elisa Araujo Penna Caris
Keyword(s):  
Remote Sensing ◽  
Endangered Species ◽  
Atlantic Forest ◽  
In Situ Conservation ◽  
Critically Endangered ◽  
Southeastern Brazil ◽  
Local Conditions ◽  
Important Species ◽  
Bare Rock ◽  
Critically Endangered Species

Abstract Queimada Grande (QGI) is a small, legally protected island off the southeastern coast of Brazil that harbors two endemic and critically endangered herpetofauna species: the Golden Lancehead viper (Bothrops insularis) and a hylid frog (Scinax peixotoi); its vegetation, however, has been little studied. We integrated remote sensing and phytosociology of the Atlantic Forest on QGI to characterize the habitat of those two species and support their in situ conservation. QGI retains a mosaic of Atlantic Forest, rock outcrop and anthropogenic vegetation, including invasive alien species, and bare rock surfaces. Mature Atlantic Forest, the preferential habitat of B. insularis and S. peixotoi, currently covers ~28 ha (~50%) of QGI and shows very low tree richness and an oligarchic structure. The most important species are Guapira opposita, Rudgea minor and Aspidosperma australe. Anthropogenic formations cover ~9% of the island and do not seem to have expanded in recent years. Based on local conditions, we recommend permanent monitoring of QGI and the use of local tree species in projects to restore the habitat of those two endangered species.

scholarly journals Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Robert C. Kaplan ◽  
Zheng Wang ◽  
Mykhaylo Usyk ◽  
Daniela Sotres-Alvarez ◽  
Martha L. Daviglus ◽  
...  
Keyword(s):  
Community Health ◽  
Gut Microbiome ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Shannon Index ◽  
Health Study ◽  
Rrna Gene ◽  
Cross Sectional ◽  
Hispanic Community ◽  
The Usa

Abstract Background Hispanics living in the USA may have unrecognized potential birthplace and lifestyle influences on the gut microbiome. We report a cross-sectional analysis of 1674 participants from four centers of the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), aged 18 to 74 years old at recruitment. Results Amplicon sequencing of 16S rRNA gene V4 and fungal ITS1 fragments from self-collected stool samples indicate that the host microbiome is determined by sociodemographic and migration-related variables. Those who relocate from Latin America to the USA at an early age have reductions in Prevotella to Bacteroides ratios that persist across the life course. Shannon index of alpha diversity in fungi and bacteria is low in those who relocate to the USA in early life. In contrast, those who relocate to the USA during adulthood, over 45 years old, have high bacterial and fungal diversity and high Prevotella to Bacteroides ratios, compared to USA-born and childhood arrivals. Low bacterial diversity is associated in turn with obesity. Contrasting with prior studies, our study of the Latino population shows increasing Prevotella to Bacteroides ratio with greater obesity. Taxa within Acidaminococcus, Megasphaera, Ruminococcaceae, Coriobacteriaceae, Clostridiales, Christensenellaceae, YS2 (Cyanobacteria), and Victivallaceae are significantly associated with both obesity and earlier exposure to the USA, while Oscillospira and Anaerotruncus show paradoxical associations with both obesity and late-life introduction to the USA. Conclusions Our analysis of the gut microbiome of Latinos demonstrates unique features that might be responsible for health disparities affecting Hispanics living in the USA.

scholarly journals Retinitis pigmentosa is associated with shifts in the gut microbiome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Oksana Kutsyr ◽  
Lucía Maestre-Carballa ◽  
Mónica Lluesma-Gomez ◽  
Manuel Martinez-Garcia ◽  
Nicolás Cuenca ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Gut Microbiome ◽  
Functional Decline ◽  
Retinal Disease ◽  
Photoreceptor Cells ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Alpha And Beta Diversity ◽  
Potential Biomarker

AbstractThe gut microbiome is known to influence the pathogenesis and progression of neurodegenerative diseases. However, there has been relatively little focus upon the implications of the gut microbiome in retinal diseases such as retinitis pigmentosa (RP). Here, we investigated changes in gut microbiome composition linked to RP, by assessing both retinal degeneration and gut microbiome in the rd10 mouse model of RP as compared to control C57BL/6J mice. In rd10 mice, retinal responsiveness to flashlight stimuli and visual acuity were deteriorated with respect to observed in age-matched control mice. This functional decline in dystrophic animals was accompanied by photoreceptor loss, morphologic anomalies in photoreceptor cells and retinal reactive gliosis. Furthermore, 16S rRNA gene amplicon sequencing data showed a microbial gut dysbiosis with differences in alpha and beta diversity at the genera, species and amplicon sequence variants (ASV) levels between dystrophic and control mice. Remarkably, four fairly common ASV in healthy gut microbiome belonging to Rikenella spp., Muribaculaceace spp., Prevotellaceae UCG-001 spp., and Bacilli spp. were absent in the gut microbiome of retinal disease mice, while Bacteroides caecimuris was significantly enriched in mice with RP. The results indicate that retinal degenerative changes in RP are linked to relevant gut microbiome changes. The findings suggest that microbiome shifting could be considered as potential biomarker and therapeutic target for retinal degenerative diseases.

scholarly journals Gut Microbiome in a Russian Cohort of Pre- and Post-Cholecystectomy Female Patients

2021 ◽  
Vol 11 (4) ◽  
pp. 294
Author(s):  
Irina Grigor’eva ◽  
Tatiana Romanova ◽  
Natalia Naumova ◽  
Tatiana Alikina ◽  
Alexey Kuznetsov ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Relative Abundance ◽  
Gut Microbiome ◽  
Gallstone Disease ◽  
Illumina Miseq ◽  
Rrna Gene ◽  
Bacterial Phyla ◽  
Female Patients ◽  
Composition And Structure ◽  
Before And After

The last decade saw extensive studies of the human gut microbiome and its relationship to specific diseases, including gallstone disease (GSD). The information about the gut microbiome in GSD-afflicted Russian patients is scarce, despite the increasing GSD incidence worldwide. Although the gut microbiota was described in some GSD cohorts, little is known regarding the gut microbiome before and after cholecystectomy (CCE). By using Illumina MiSeq sequencing of 16S rRNA gene amplicons, we inventoried the fecal bacteriobiome composition and structure in GSD-afflicted females, seeking to reveal associations with age, BMI and some blood biochemistry. Overall, 11 bacterial phyla were identified, containing 916 operational taxonomic units (OTUs). The fecal bacteriobiome was dominated by Firmicutes (66% relative abundance), followed by Bacteroidetes (19%), Actinobacteria (8%) and Proteobacteria (4%) phyla. Most (97%) of the OTUs were minor or rare species with ≤1% relative abundance. Prevotella and Enterocossus were linked to blood bilirubin. Some taxa had differential pre- and post-CCE abundance, despite the very short time (1–3 days) elapsed after CCE. The detailed description of the bacteriobiome in pre-CCE female patients suggests bacterial foci for further research to elucidate the gut microbiota and GSD relationship and has potentially important biological and medical implications regarding gut bacteria involvement in the increased GSD incidence rate in females.

scholarly journals Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

2020 ◽  
Author(s):  
Rachel J Sorensen ◽  
James S Drouillard ◽  
Teresa L Douthit ◽  
Qinghong Ran ◽  
Douglas G Marthaler ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Volatile Fatty Acids ◽  
Random Effect ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Β Diversity ◽  
Fermentation Parameters

Abstract The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split plot design run as a crossover in 2 periods. Whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. Main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, all possible interactions and random effect of horse. Alpha and β diversity were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05) whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total volatile fatty acid (VFA) concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared to cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared to the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared to cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

Where have all the sawfishes gone? Perspectives on declines of these Critically Endangered species in Sri Lanka

2021 ◽  
Author(s):  
Akshay Tanna ◽  
Daniel Fernando ◽  
Ramajeyam Gobiraj ◽  
Buddhi M. Pathirana ◽  
Sahan Thilakaratna ◽  
...  
Keyword(s):  
Sri Lanka ◽  
Endangered Species ◽  
Critically Endangered ◽  
Critically Endangered Species

scholarly journals Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Esteban Góngora ◽  
Kyle H. Elliott ◽  
Lyle Whyte
Keyword(s):  
Gut Microbiome ◽  
Sulfur Isotopes ◽  
Trophic Position ◽  
Isotope Analysis ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Uria Lomvia ◽  
Fecal Microbiome ◽  
Prey Specialization ◽  
Rrna Gene Sequencing

AbstractThe role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

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