The microbiome of captive hamadryas baboon

AbstractHamadryas baboon is a highly social primate that lives in complex multilevel societies exhibiting a wide range of group behaviors akin to humans. Here, we report the comprehensive 16s rRNA gene analyses of group-living baboon microbiota across different body sites. Additionally, we compared the baboon and human microbiome of the oral cavity, gut and vagina. Our analyses show that the baboon microbiome is distinct from the human and baboon cohabitants share similar microbial profiles in multiple body sites. The oral, gut and vagina shared more bacterial ASVs in group-living baboons than in humans. The shared ASVs in baboons had significantly positive correlations, suggesting a potential bacterial exchange throughout the body. No significant differences in baboon gut microbiome composition within the maternity line and between maternity lines were detected, suggesting that the offspring acquire their gut microbiota primarily through bacterial exchange among cohabitants. Besides, Lactobacillus was not so predominant in baboon vagina as in the human vagina but was the most abundant genus in baboon gut. These data and findings can form the basis of future microbiome studies in baboons and be used as a reference to research where the microbiome is expected to impact human modeling with baboons.

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Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

Animals ◽

10.3390/ani11010004 ◽

2020 ◽

Vol 11 (1) ◽

pp. 4

Author(s):

Giulietta Minozzi ◽

Filippo Biscarini ◽

Emanuela Dalla Costa ◽

Matteo Chincarini ◽

Nicola Ferri ◽

...

Keyword(s):

Animal Health ◽

Control Group ◽

P Value ◽

Rrna Gene ◽

Microbial Composition ◽

Core Microbiome ◽

Fecal Microbiome ◽

Microbiome Composition ◽

The Core ◽

Wide Range

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition.

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Abstract 321: A High-Salt Diet Alters the Composition of Intestinal Microbiota in Mice

Hypertension ◽

10.1161/hyp.64.suppl_1.321 ◽

2014 ◽

Vol 64 (suppl_1) ◽

Author(s):

Nicola Wilck ◽

Scott Olesen ◽

Mariana Matus ◽

Andras Balogh ◽

Ralf Dechend ◽

...

Keyword(s):

Gut Microbiome ◽

The Body ◽

High Salt ◽

Rrna Gene ◽

High Salt Diet ◽

Salt Diet ◽

Microbiome Composition ◽

High Salt Intake ◽

Number Of Patients ◽

Jensen Shannon Divergence

Objective: High-salt intake is associated with cardiovascular disease and hypertension. A substantial number of patients are sensitive to salt, but environmental factors influencing this phenomenon are poorly understood. The gut microbiome has not been considered in the context of salt and hypertension research to date. It is known to respond to fluctuations in lifestyle and diet, and is increasingly recognized as an important factor which influences host health and disease. Using next generation sequencing methods we aimed to determine the effect of a high-salt diet on gut microbiome composition. Methods and Results: Male C57BL6/J mice, 10 weeks of age, were individually housed and either subjected to a purified normal salt (0.5% sodium) or high-salt diet (4% sodium + 1% in drinking water) ad libitum for 14 days. Feces was collected on days 0 and 14 of the diets. DNA was extracted from feces, the V4 region of the 16S rRNA gene amplified with PCR. Samples were multiplexed and sequenced with MiSeq. Reads were quality controlled and operational taxonomic units (OTUs) were called by comparison to the Greengenes database. The high-salt diet created a distinct gut microbiome composition compared to the normal-salt diet (analysis of Jensen-Shannon divergence). Whereas normal diet’s gut microbiome is composed mostly of OTUs from the Bacteroidetes phylum (70% of reads), high-salt diet causes a shift in relative abundance to other phyla (increased Firmicutes:Bacteroidetes ratio). Moreover, the genus Allobaculum significantly spikes after high-salt feeding. Both phenomena have recently been implicated in obesity studies. Conclusion: An increase in dietary sodium chloride alters the gut microbiome composition. Our findings indicate new perspectives on how salt impacts the body.

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pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis

Bioinformatics ◽

10.1093/bioinformatics/btz120 ◽

2019 ◽

Vol 35 (19) ◽

pp. 3567-3575 ◽

Cited By ~ 4

Author(s):

Anna M Plantinga ◽

Jun Chen ◽

Robert R Jenq ◽

Michael C Wu

Keyword(s):

Statistical Power ◽

Human Microbiome ◽

R Package ◽

Supplementary Information ◽

Microbiome Composition ◽

Type 1 Error ◽

Wide Range ◽

Subject Variability ◽

Ordination Analysis

Abstract Motivation The human microbiome is notoriously variable across individuals, with a wide range of ‘healthy’ microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confounding and to increase statistical power by reducing large inter-subject variability. Statistical methods for analyzing such datasets are scarce. Results We introduce a paired UniFrac dissimilarity that summarizes within-individual (or within-pair) shifts in microbiome composition and then compares these compositional shifts across individuals (or pairs). This dissimilarity depends on a novel transformation of relative abundances, which we then extend to more than two time points and incorporate into several phylogenetic and non-phylogenetic dissimilarities. The data transformation and resulting dissimilarities may be used in a wide variety of downstream analyses, including ordination analysis and distance-based hypothesis testing. Simulations demonstrate that tests based on these dissimilarities retain appropriate type 1 error and high power. We apply the method in two real datasets. Availability and implementation The R package pldist is available on GitHub at https://github.com/aplantin/pldist. Supplementary information Supplementary data are available at Bioinformatics online.

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The vagino-cervical microbiome as a woman’s life history

10.1101/533588 ◽

2019 ◽

Cited By ~ 2

Author(s):

Zhuye Jie ◽

Chen Chen ◽

Lilan Hao ◽

Fei Li ◽

Liu Tian ◽

...

Keyword(s):

Sexual Behaviors ◽

Reproductive Tract ◽

Human Microbiome ◽

Human Microbiome Project ◽

Amplicon Sequencing ◽

Female Reproductive Tract ◽

Reproductive Age ◽

Rrna Gene ◽

Microbiome Composition ◽

Major Factors

The gut microbiome has been the center of attention for human commensal microbiome studies. The vaginal microbiome is also densely populated with bacteria, viruses and fungi, and the presence of microorganisms beyond the cervix is increasingly reported in non-infectious conditions1–3. Due to the over 90% of human sequences in female reproductive tract samples3,4, metagenomic information has been very limited. 16S rRNA gene amplicon sequencing studies have identified community types in the vaginal microbiota, and observed its dynamic changes due to menstrual cycles and sexual behaviors in small cohorts5,6. Here we perform metagenomic shotgun sequencing on cervical samples from 516 women of reproductive age (more than 10-fold of the Human Microbiome Project (HMP)4), and dissect major factors, especially pregnancy and delivery histories and contraception methods on the microbiome composition. Features of other body sites, such as mood fluctuations and facial speckles could potentially be deduced from the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota in the female reproductive tract and imply disease susceptibilities that may be relieved by behavioural changes.

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Creating the Wind

Latin American and Latinx Visual Culture ◽

10.1525/lavc.2020.2.4.14 ◽

2020 ◽

Vol 2 (4) ◽

pp. 14-31

Author(s):

Élodie Dupey García

Keyword(s):

Indigenous Communities ◽

The Body ◽

Historical Sources ◽

Natural Behavior ◽

Sensory Experiences ◽

Identity And Agency ◽

Wide Range ◽

Late Postclassic ◽

Comparative Examination ◽

Meteorological Phenomenon

This article explores how the Nahua of late Postclassic Mesoamerica (1200–1521 CE) created living and material embodiments of their wind god constructed on the basis of sensory experiences that shaped their conception of this divinized meteorological phenomenon. In this process, they employed chromatic and design devices, based on a wide range of natural elements, to add several layers of meaning to the human, painted, and sculpted supports dressed in the god’s insignia. Through a comparative examination of pre-Columbian visual production—especially codices and sculptures—historical sources mainly written in Nahuatl during the viceregal period, and ethnographic data on indigenous communities in modern Mexico, my analysis targets the body paint and shell jewelry of the anthropomorphic “images” of the wind god, along with the Feathered Serpent and the monkey-inspired embodiments of the deity. This study identifies the centrality of other human senses beyond sight in the conception of the wind god and the making of its earthly manifestations. Constructing these deity “images” was tantamount to creating the wind because they were intended to be visual replicas of the wind’s natural behavior. At the same time, they referred to the identity and agency of the wind god in myths and rituals.

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Host reproductive cycle influences the pouch microbiota of wild southern hairy-nosed wombats (Lasiorhinus latifrons)

Animal Microbiome ◽

10.1186/s42523-021-00074-8 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Sesilje Weiss ◽

David Taggart ◽

Ian Smith ◽

Kristofer M. Helgen ◽

Raphael Eisenhofer

Keyword(s):

Microbial Community ◽

Reproductive Cycle ◽

Tammar Wallaby ◽

The Body ◽

Rrna Gene ◽

Microbial Composition ◽

Birth Canal ◽

Gram Positive Bacteria ◽

Rigorous Framework ◽

The 16S Rrna Gene

Abstract Background Marsupials are born much earlier than placental mammals, with most crawling from the birth canal to the protective marsupium (pouch) to further their development. However, little is known about the microbiology of the pouch and how it changes throughout a marsupial’s reproductive cycle. Here, using stringent controls, we characterized the microbial composition of multiple body sites from 26 wild Southern Hairy-nosed Wombats (SHNWs), including pouch samples from animals at different reproductive stages. Results Using qPCR of the 16S rRNA gene we detected a microbial community in the SHNW pouch. We observed significant differences in microbial composition and diversity between the body sites tested, as well as between pouch samples from different reproductive stages. The pouches of reproductively active females had drastically lower microbial diversity (mean ASV richness 19 ± 8) compared to reproductively inactive females (mean ASV richness 941 ± 393) and were dominated by gram positive bacteria from the Actinobacteriota phylum (81.7–90.6%), with the dominant families classified as Brevibacteriaceae, Corynebacteriaceae, Microbacteriaceae, and Dietziaceae. Three of the five most abundant sequences identified in reproductively active pouches had closest matches to microbes previously isolated from tammar wallaby pouches. Conclusions This study represents the first contamination-controlled investigation into the marsupial pouch microbiota, and sets a rigorous framework for future pouch microbiota studies. Our results indicate that SHNW pouches contain communities of microorganisms that are substantially altered by the host reproductive cycle. We recommend further investigation into the roles that pouch microorganisms may play in marsupial reproductive health and joey survival.

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Development and Validation of a New Scoring Tool to Evaluate the Clinical Evolution of Adult Patients with Nonsegmental Vitiligo

Dermatology ◽

10.1159/000511890 ◽

2021 ◽

pp. 1-9

Author(s):

María Luisa Peralta-Pedrero ◽

Denisse Herrera-Bringas ◽

Karla Samantha Torres-González ◽

Martha Alejandra Morales-Sánchez ◽

Fermín Jurado Santa-Cruz ◽

...

Keyword(s):

Body Surface ◽

Task Force ◽

Intraclass Correlation ◽

The Body ◽

Response To Treatment ◽

Similar Response ◽

Clinical Evolution ◽

Wide Range ◽

Patient Reported ◽

Extreme Groups

Background: Vitiligo has an unpredictable course and a variable response to treatment. Furthermore, the improvement of some vitiligo lesions cannot be considered a guarantee of a similar response to the other lesions. Instruments for patient-reported outcome measures (PROM) can be an alternative to measure complex constructions such as clinical evolution. Objective: The aim of this study was to validate a PROM that allows to measure the clinical evolution of patients with nonsegmental vitiligo in a simple but standardized way that serves to gather information for a better understanding of the disease. Methods: The instrument was created through expert consensus and patient participation. For the validation study, a prospective cohort design was performed. The body surface area affected was measured with the Vitiligo Extension Score (VES), the extension, the stage, and the spread by the evaluation of the Vitiligo European Task Force assessment (VETFa). Reliability was determined with test-retest, construct validity through hypothesis testing, discriminative capacity with extreme groups, and response capacity by comparing initial and final measurements. Results: Eighteen semi-structured interviews and 7 cognitive interviews were conducted, and 4 dermatologists were consulted. The instrument Clinical Evolution-Vitiligo (CV-6) was answered by 119 patients with a minimum of primary schooling. A wide range was observed in the affected body surface; incident and prevalent cases were included. The average time to answer the CV-6 was 3.08 ± 0.58 min. In the test-retest (n = 53), an intraclass correlation coefficient was obtained: 0.896 (95% CI 0.82–0.94; p < 0.001). In extreme groups, the mean score was 2 (2–3) and 5 (4–6); p < 0.001. The initial CV-6 score was different from the final one and the change was verified with VES and VETFa (p < 0.05, n = 92). Conclusions: The CV-6 instrument allows patient collaboration, it is simple and brief, and it makes it easier for the doctor to focus attention on injuries that present changes at the time of medical consultation.

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Hydromechanics of low-Reynolds-number flow. Part 2. Singularity method for Stokes flows

Journal of Fluid Mechanics ◽

10.1017/s0022112075000614 ◽

1975 ◽

Vol 67 (4) ◽

pp. 787-815 ◽

Cited By ~ 300

Author(s):

Allen T. Chwang ◽

T. Yao-Tsu Wu

Keyword(s):

Exact Solutions ◽

Stokes Flow ◽

Fundamental Solutions ◽

The Body ◽

Circular Cylinders ◽

Geometrical Parameters ◽

Flow Problems ◽

Singularity Method ◽

Wide Range ◽

Body Shapes

The present study further explores the fundamental singular solutions for Stokes flow that can be useful for constructing solutions over a wide range of free-stream profiles and body shapes. The primary singularity is the Stokeslet, which is associated with a singular point force embedded in a Stokes flow. From its derivatives other fundamental singularities can be obtained, including rotlets, stresslets, potential doublets and higher-order poles derived from them. For treating interior Stokes-flow problems new fundamental solutions are introduced; they include the Stokeson and its derivatives, called the roton and stresson.These fundamental singularities are employed here to construct exact solutions to a number of exterior and interior Stokes-flow problems for several specific body shapes translating and rotating in a viscous fluid which may itself be providing a primary flow. The different primary flows considered here include the uniform stream, shear flows, parabolic profiles and extensional flows (hyper-bolic profiles), while the body shapes cover prolate spheroids, spheres and circular cylinders. The salient features of these exact solutions (all obtained in closed form) regarding the types of singularities required for the construction of a solution in each specific case, their distribution densities and the range of validity of the solution, which may depend on the characteristic Reynolds numbers and governing geometrical parameters, are discussed.

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Phenotypic Characterisation for Growth and Nut Characteristics Revealed the Extent of Genetic Diversity in Wild Macadamia Germplasm

Agriculture ◽

10.3390/agriculture11070680 ◽

2021 ◽

Vol 11 (7) ◽

pp. 680

Author(s):

Thuy T. P. Mai ◽

Craig M. Hardner ◽

Mobashwer M. Alam ◽

Robert J. Henry ◽

Bruce L. Topp

Keyword(s):

Genetic Diversity ◽

Growth Traits ◽

Principal Component ◽

Conservation Strategies ◽

Wild Germplasm ◽

Phenotypic Characterisation ◽

Wide Range ◽

Genetic And Environmental Factors ◽

Positive Correlations ◽

Wild Accessions

Macadamia is a recently domesticated Australian native nut crop, and a large proportion of its wild germplasm is unexploited. Aiming to explore the existing diversity, 247 wild accessions from four species and inter-specific hybrids were phenotyped. A wide range of variation was found in growth and nut traits. Broad-sense heritability of traits were moderate (0.43–0.64), which suggested that both genetic and environmental factors are equally important for the variability of the traits. Correlations among the growth traits were significantly positive (0.49–0.76). There were significant positive correlations among the nut traits except for kernel recovery. The association between kernel recovery and shell thickness was highly significant and negative. Principal component analysis of the traits separated representative species groups. Accessions from Macadamia integrifolia Maiden and Betche, M. tetraphylla L.A.S. Johnson, and admixtures were clustered into one group and those of M. ternifolia F. Muell were separated into another group. In both M. integrifolia and M. tetraphylla groups, variation within site was greater than across sites, which suggested that the conservation strategies should concentrate on increased sampling within sites to capture wide genetic diversity. This study provides a background on the utilisation of wild germplasm as a genetic resource to be used in breeding programs and the direction for gene pool conservation.

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Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome

Scientific Reports ◽

10.1038/s41598-021-83875-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhen Han ◽

Peter S. Thuy-Boun ◽

Wayne Pfeiffer ◽

Vincent F. Vartabedian ◽

Ali Torkamani ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Human Microbiome ◽

Host Immunity ◽

Rrna Gene ◽

Metabolic Labeling ◽

Selective Labeling ◽

Fecal Microbiome ◽

Acetylneuraminic Acid ◽

Intestinal Mucus ◽

Microbial Systems

AbstractN-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.

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