Insights into Gut Dysbiosis: Inflammatory Diseases, Obesity, and Restoration Approaches.

The gut microbiota is one of the most critical factors in human health. It involves numerous physiological processes impacting host health, mainly via immune system modulation. A balanced microbiome contributes to the gut's barrier function, preventing the invasion of pathogens and maintaining the integrity of the gut lining. Dysbiosis, or an imbalance in the gut microbiome's composition and function, disrupts essential processes and contributes to various diseases. This narrative review summarizes key findings related to the gut microbiota in modern multifactorial inflammatory conditions such as ulcerative colitis or Crohn's disease. It addresses the challenges posed by antibiotic-driven dysbiosis, particularly in the context of C. difficile infections, and the development of novel therapies like fecal microbiota transplantation and biotherapeutic drugs to combat these infections. An emphasis is given to restoration of the healthy gut microbiome through dietary interventions, probiotics, prebiotics, and novel approaches for managing gut-related diseases.

Shifts in the gut microbiota of sea urchin Diadema antillarum associated with the 2022 disease outbreak.

Introduction: In recent decades, Caribbean coral reefs have lost many vital marine species due to diseases. The well-documented mass mortality event of the long-spined black sea urchin Diadema antillarum in the early 1980s stands out among these collapses. This die-off killed over 90% of D. antillarum changing the reefscape from coral to algal-dominated. Nearly 40 years later, D. antillarum populations have yet to recover. In early 2022, a new mortality event of D. antillarum was reported along the Caribbean, including Puerto Rico. Methods: This study identifies the gut microbiota changes associated with the D. antillarum during this mortality event. It contrasts them with the bacterial composition of gut samples from healthy individuals collected in 2019 by using 16S rRNA sequencing analyses. Results: Notably, the die-off group's core microbiome resembled bacteria commonly found in the human skin and gut, suggesting potential anthropogenic contamination and wastewater pollution as contributing factors to the 2022 dysbiosis. The animals collected in 2022, especially those with signs of disease, lacked keystone taxa normally found in Diadema including Photobacterium and Propionigenium. Discussion: The association between human microbes and disease stages in the long-spined urchin D. antillarum, especially in relation to anthropogenic contamination, highlights a complex interplay between environmental stressors and marine health. While these microbes might not be the direct cause of death in this species of sea urchins, their presence and proliferation can indicate underlying issues, such as immune depletion due to pollution, habitat destruction, or climate change, that ultimately compromise the health of these marine organisms.

Vaginal Microbiota and HPV in Latin America: A Narrative Review.

With the expansion of human microbiome studies in the last 15 years, we have realized the immense implications of microbes in human health. The human holobiont is now accepted, given the commensal relationships with bacteria, fungi, parasites, viruses, and human cells. The cervicovaginal microbiota is a specific case within the human microbiome where diversity is lower to maintain a chemical barrier of protection against infections. This narrative review focuses on the vaginal microbiome. It summarizes key findings on how native bacteria protect women from disease or predispose them to damaging inflammatory processes with an emphasis on the role of HPV infections in Latin America, one of the world's regions with the highest cervical cancer prevalence.

Ecological competition in the oral mycobiome of Hispanic adults living in Puerto Rico associates with periodontitis.

Background: Fungi are a major component of the human microbiome that only recently received attention. The imbalance of indigenous fungal communities and environmental fungi present in the oral cavity may have a role in oral dysbiosis, which could exacerbate oral inflammatory diseases. Methods: We performed a cross-sectional study and recruited 88 participants aged 21 to 49 from sexually transmitted infection clinics in Puerto Rico. A full-mouth periodontal examination following the NHANES protocol defined periodontal severity (CDC/AAP). ITS2 (fungal) genes were amplified and sequenced for mycobiota characterization of yeast and environmental fungi. Environmental outdoor spore levels were measured daily by the American Academy of Allergy Asthma and Immunology San Juan station and defined by quartiles as spore scores. Results: Our data indicate polymicrobial colonization of yeast and environmental fungi in the oral cavity. Dominant taxa associated with periodontal disease included Saccharomyces cerevisiae, Rigidoporus vinctus, and Aspergillus penicilloides, while Candida albicans were found to be ubiquitous. Fungal aerosols were found to impact the oral cavity biofilm, likely due to competition and neutralization by inhaled outdoor and indoor fungal spores. Conclusion: To our knowledge, this is the first report showcasing the ecological competition of measured outdoor environmental fungi with the human oral mycobiota.

Exploring the interplay between running exercises, microbial diversity, and tryptophan metabolism along the microbiota-gut-brain axis.

The emergent recognition of the gut-brain axis connection has shed light on the role of the microbiota in modulating the gut-brain axis's functions. Several microbial metabolites, such as serotonin, kynurenine, tryptamine, indole, and their derivatives originating from tryptophan metabolism have been implicated in influencing this axis. In our study, we aimed to investigate the impact of running exercises on microbial tryptophan metabolism using a mouse model. We conducted a multi-omics analysis to obtain a comprehensive insight into the changes in tryptophan metabolism along the microbiota-gut-brain axis induced by running exercises. The analyses integrated multiple components, such as tryptophan changes and metabolite levels in the gut, blood, hippocampus, and brainstem. Fecal microbiota analysis aimed to examine the composition and diversity of the gut microbiota, and taxon-function analysis explored the associations between specific microbial taxa and functional activities in tryptophan metabolism. Our findings revealed significant alterations in tryptophan metabolism across multiple sites, including the gut, blood, hippocampus, and brainstem. The outcomes indicate a shift in microbiota diversity and tryptophan metabolizing capabilities within the running group, linked to increased tryptophan transportation to the hippocampus and brainstem through circulation. Moreover, the symbiotic association between Romboutsia and A. muciniphila indicated their potential contribution to modifying the gut microenvironment and influencing tryptophan transport to the hippocampus and brainstem. These findings have potential applications for developing microbiota-based approaches in the context of exercise for neurological diseases, especially on mental health and overall well-being.

Inflammatory cytokines and a diverse cervicovaginal microbiota associate with cervical dysplasia in a cohort of Hispanics living in Puerto Rico.

Cervical cancer (CC) is women's fourth most common cancer worldwide. A worrying increase in CC rates in Hispanics suggests that besides Human papillomavirus infections, there may be other cofactors included in the epithelial microenvironment that could play a role in promoting the disease. We hypothesized that the cervical microbiome and the epithelial microenvironment favoring inflammation is conducive to disease progression in a group of Hispanics attending gynecology clinics in Puerto Rico. Few studies have focused on the joint microbiota and cytokine profile response in Hispanics outside the US, especially regarding the development of precancerous lesions. We aimed to investigate the relationship between the cervicovaginal microbiome and inflammation in Hispanic women living in PR while considering cervical dysplasia and HPV genotype risk. Cervical samples collected from 91 participants coming to gynecology clinics in San Juan, underwent 16S rRNA genes (V4 region) profiling, and cytokines were measured using Luminex MAGPIX technology. Cytokines were grouped as inflammatory (IL-1ß, TNFα, IFNγ, IL-6), anti-inflammatory (IL- 4, IL-10, TGFß1), and traffic-associated (IL-8, MIP1a, MCP1, IP10). They were related to microbes via an inflammation scoring index based on the quartile and tercile distribution of the cytokine's concentration. We found significant differences in the diversity and composition of the microbiota according to HPV type according to carcinogenic risk, cervical disease, and cytokine abundance. Community State Types (CSTs) represents a profile of microbial communities observed within the vaginal microbiome ecological niche, and Lactobacillus-depleted CST IV had ~ 90% dominance in participants with high-grade squamous intraepithelial lesions and high-risk HPV. The increasing concentration of pro-inflammatory cytokines was associated with a decrease in L. crispatus. In contrast, dysbiosis-associated bacteria such as Gardnerella, Prevotella, Atopobium concomitantly increased with pro-inflammatory cytokines. Our study highlights that the cervical microbiota of Hispanics living in Puerto Rico is composed mostly of diverse CST profiles with decreased Lactobacillus and is associated with a higher pro-inflammatory environment. The joint host-microbe interaction analyses via cytokine and microbiota profiling have very good translational potential.

The cervical microbiota of Hispanics living in Puerto Rico is nonoptimal regardless of HPV status.

The cervicovaginal microbiota is influenced by host physiology, immunology, lifestyle, and ethnicity. We hypothesized that there would be differences in the cervicovaginal microbiota among pregnant, nonpregnant, and menopausal women living in Puerto Rico (PR) with and without human papillomavirus (HPV) infection and cervical cancer. We specifically wanted to determine if the microbiota is associated with variations in cervical cytology. A total of 294 women, including reproductive-age nonpregnant (N = 196), pregnant (N = 37), and menopausal (N = 61) women, were enrolled. The cervicovaginal bacteria were characterized by 16S rRNA amplicon sequencing, the HPV was genotyped with SPF10-LiPA, and cervical cytology was quantified. High-risk HPV (HR-HPV, 67.3%) was prevalent, including genotypes not covered by the 9vt HPV vaccine. Cervical lesions (34%) were also common. The cervical microbiota was dominated by Lactobacillus iners. Pregnant women in the second and third trimesters exhibited a decrease in diversity and abundance of microbes associated with bacterial vaginosis. Women in menopause had greater alpha diversity, a greater proportion of facultative and strictly anaerobic bacteria, and higher cervicovaginal pH than premenopausal women. Cervical lesions were associated with greater alpha diversity. However, no significant associations between the microbiota and HPV infection (HR or LR-HPV types) were found. The cervicovaginal microbiota of women living in Puerto Rican were either dominated by L. iners or diverse microbial communities regardless of a woman's physiological stage. We postulate that the microbiota and the high prevalence of HR-HPV increase the risk of cervical lesions among women living in PR. IMPORTANCE In the enclosed manuscript, we provide the first in-depth characterization of the cervicovaginal microbiota of Hispanic women living in Puerto Rico (PR), using a 16S rRNA approach, and include women of different physiological stages. Surprisingly we found that high-risk HPV was ubiquitous with a prevalence of 67.3%, including types not covered by the 9vt HPV vaccine. We also found highly diverse microbial communities across women groups-with a reduction in pregnant women, but dominated by nonoptimal Lactobacillus iners. Additionally, we found vaginosis-associated bacteria as Dialister spp., Gardnerella spp., Clostridium, or Prevotella among most women. We believe this is a relevant and timely article expanding knowledge on the cervicovaginal microbiome of PR women, where we postulate that these highly diverse communities are conducive to cervical disease.

The Epibiotic Microbiota of Wild Caribbean Sea Urchin Spines Is Species Specific.

Caribbean sea urchins are marine invertebrates that have experienced a decline over the years. Studies on sea urchins have focused primarily on the microbiome of the coelomic fluid or the gut microbiota. In this study, the epibiota community associated with four wild Caribbean sea urchin species, Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum, was characterized for the first time. Using 57 sea urchin animal samples, we evaluated the influence of animal species, trophic niches, and geographical location on the composition of the epibiotic microbiota. We found significant differences in the bacterial biota among species and trophic niches, but not among geographical locations. L. variegatus exhibited the highest alpha diversity with high dominance of Fusobacteria, Planctomycetes, and Cyanobacteria, whereas T. ventricosus and D. antillarum were dominated by Firmicutes. T. ventricosus inhabiting the seagrass biotope dominated by Thalassia testudinum meadows had mostly Endozoicomonas. In contrast, samples located in the reef (dominated by corals and other reef builders) had a higher abundance of Kistimonas and Photobacterium. Our findings confirm that the epibiotic microbiota is species-specific, but also niche-dependent, revealing the trophic networks emerging from the organic matter being recycled in the seagrass and reef niches. As echinoids are important grazers of benthic communities, their microbiota will likely influence ecosystem processes.

Bacterial composition along the digestive tract of the Horned Screamer (Anhima cornuta), a tropical herbivorous bird.

Background: The Horned Screamer (Anhima cornuta) is an herbivorous bird that inhabits wetlands of the South American tropical region. We hypothesize that due to its herbivorous niche, its digestive tract compartments may have bacteria specialized in fermenting complex plant carbohydrates. To test this hypothesis, we compared the bacterial communities along the gastrointestinal tract (GIT) of a Horned Screamer captured in Venezuela. Methods: Samples were taken from tissues and content of the proventriculus and the small intestine (considered for this study as upper GIT), and the large intestine and cecum (lower GIT). The bacterial community was characterized by sequencing the V4 region of the 16S rRNA gene. Bioinformatic analysis was performed using QIIME, QIITA and Microbiome Analyst. The association between microbial taxonomy and function was analyzed using their Greengenes OTU IDs and a custom KEGG BRITE hierarchical tree and visualized with BURRITO. Results: The Screamer's gastrointestinal microbiota was composed by seven phyla being Firmicutes and Bacteroidetes the most predominant. The dominant taxa in the upper GIT were Helicobacter, Vibrio, Enterobacter, Acinetobacter and Staphylococcus. The dominant taxa in the lower GIT were Oribacterium, Blautia, Roseburia, Ruminococcus, Desulfovibrio, Intestinimonas, Marvinbryantia and Parabacteroides. Complete degradation of cellulose to the end-products acetate, propanoate, butanoate and acetoacetate was found in the upper and lower GIT without significant differences. Conclusion: Our study confirmed changes in bacterial community composition throughout the GIT of the Horned Screamer primarily associated with the production of metabolic end-products of carbohydrate digestion essential for the fermentation of the herbivorous diet.

Assessment of Vibrio populations in a transect of Rhizophora mangle in Punta Galeta, Panamá: culture-dependent analyses reveal biotechnological applications.

Introduction: Rhizophora mangle is considered an ecological niche for microorganisms with potentially novel and complex degrading enzymes. Objective: To characterize Vibrio populations using culture-dependent methods, using samples collected from sediments and water along a red mangrove transect composed of three sites. Methods: Strains were characterized according to their distribution, capacity to degrade of organic matter and other environmental parameters. Additionally the sequence diversity was assessed using 16S rRNA sequencing. Results: Bacterial densities were strongly associated with temperature and salinity. A total of 87 good-quality sequences representing the isolates from the three sites, were binned into eight OTUs (Operational taxonomic units). Taxonomic assignment indicated that the dominant members were Vibrionaceae. Beta diversity analyses showed that bacterial communities clustered by sample source rather than spatial distribution, and that alpha diversity was found to be higher in water than in sediment. Three percent of the strains from water samples could degrade carboxyl-methyl cellulose with the smallest enzymatic indexes compared to 4 % of the strains from sediment samples that showed the highest enzymatic indexes. Two strains identified as Vibrio agarivorans degraded cellulose and agarose, producing the highest enzymatic indexes. Conclusions: We found higher bacterial densities and diversity in the bacterial communities of the water samples compared to the sediment, with different OTUs including those similar to Ferrimonas, Providencia, or Shewanella which were not isolated in the sediment. Vibrio OTUs were shown to degrade cellulose in both sample types. The results of this study highlight the importance of red mangroves as Vibrio habitats and as reservoirs of potential enzyme sources with biotechnological applications.

Introducción: Rhizophora mangle se considera un nicho para microorganismos con enzimas degradantes potencialmente novedosas y complejas. Objetivo: Caracterizar poblaciones de Vibrio con métodos dependientes de cultivo, provenientes de muestras de sedimentos y de agua recolectadas a lo largo de un transecto de R. mangle compuesto por tres sitios. Métodos: Las cepas se caracterizaron según su distribución, diversidad, degradación de materia orgánica y parámetros ambientales. Resultados: Las densidades bacterianas estuvieron fuertemente asociadas con la temperatura y la salinidad. Un total de 87 secuencias de buena calidad que representan los aislamientos de los tres sitios se agruparon en 8 OTUs (Unidad taxonómica operativa). La asignación taxonómica indicó que los miembros dominantes eran Vibrionaceae. Los análisis de diversidad beta mostraron que las comunidades bacterianas se agruparon por fuente de la muestra en lugar de distribución espacial, y se encontró que la diversidad alfa era mayor en el agua que en los sedimentos. El 3 % de las cepas de muestras de agua fueron capaces de degradar carboxi-metilcelulosa con índices enzimáticos más bajos en comparación con el 4 % de las cepas de muestras de sedimentos que mostraron los índices enzimáticos más altos. Dos cepas identificadas como Vibrio agarivorans degradaron celulosa y agarosa, produciendo los índices enzimáticos más altos. Conclusiones: Encontramos mayor densidad bacteriana y diversidad en comunidades bacterianas de muestras de agua que en las de sedimento, con diferentes OTUs, incluyendo aquellos similares a Ferrimonas, Providencia, o Shewanella, que no fueron aislados en el sedimento. OTUs de Vibrio degradaron celulosa en ambos tipos de muestras. Los resultados del estudio resaltan la importancia de mangle rojo como habitat de Vibrio y reservorio de fuentes potenciales de enzimas con aplicaciones biotecnológicas.

Oral microbiota and periodontitis severity among Hispanic adults.

Background: Periodontitis, one of the most common bacterial infections characterized by chronic inflammation, is also known to be a risk factor for chronic conditions, including cardiovascular disease and cancer. This inflammation is driven by an altered microbiota with an increase in pathogenic bacteria. We evaluated the association between oral microbiota and periodontitis severity in high-risk Hispanics. Method: This cross-sectional study recruited 134 sexually active participants aged 21 to 49 years old from STI Clinics in Puerto Rico. A periodontal examination, saliva collection, and an interviewer-administered questionnaire were performed. Periodontal severity was categorized as: having no disease, mild, and moderate/severe and BOP and tooth loos was noted. Saliva samples were collected for genomic DNA extraction, downstream 16S rDNA amplification sequencing, and bioinformatics analyses. Results: The structure, composition, and diversity of bacterial communities differed significantly according to periodontal severity. The richness and overall diversity also differed between participants without periodontitis and participants with some level of periodontal disease. A higher abundance of Prevotella, Veillonella, or Treponema was attributed to periodontal disease and Aggregatibacter to severe bleeding on probing, while Neisseria was found in higher abundance in healthy participants, decreasing its levels with drinking, smoking, and oral sex practices. Conclusions: Our findings indicate that dysbiosis occurs as periodontal disease progresses, and both alcohol consumption and smoking habits pose risk factors for oral dysbiosis. These results are of public health and clinical impact, as several bacteria identified could serve in the future as biomarkers for periodontitis and oral cancer risk.

The Bacterial and Fungal Gut Microbiota of the Greater Wax Moth, Galleria mellonella L. Consuming Polyethylene and Polystyrene.

Plastic production has been increasing exponentially in the last 60 years, but plastic disposal is out of control, resulting in the pollution of all ecosystems on Earth. Finding alternative environmentally sustainable choices, such as biodegradation by insects and their associated gut microbiota, is crucial, however we have only begun to characterize these ecosystems. Some bacteria and one fungus have been previously identified in the gut of Greater Wax Moth larvae (Galleria mellonella L., Lepidoptera, Pyralidae) located mainly in the Northern hemisphere. The aim of this study was to describe changes in the gut microbiota associated with the consumption of polyethylene and polystyrene by the Greater Wax Moth in Argentina, considering both bacteria and fungi. Larvae were fed polyethylene, polystyrene and beeswax as control for 7 days. Next generation sequencing revealed changes in the bacterial gut microbiome of the wax moth larvae at the phyla and genus levels, with an increase in two Pseudomonas strains. The fungal communities showed no differences in composition between diets, only changing in relative abundance. This is the first report of both bacterial and fungal communities associated with a plastivore insect. The results are promising and call for more studies concerning a potential multi-kingdom synergy in the plastic biodegradation process.

Sex and educational attainment differences in HPV knowledge and vaccination awareness among unvaccinated-sexually active adults in Puerto Rico.

Human papillomavirus (HPV) knowledge and HPV vaccination uptake remain suboptimal. We assessed sex and educational attainment differences in HPV knowledge and vaccine awareness. Data from a cross-sectional study (2018-2021) in Puerto Rico among adults aged 21-49 was analyzed (n = 278). Adequate knowledge was defined as a score of ≥70% of correct responses on a 13-item knowledge scale. Multivariable logistic regression was used to assess the association of sex (men vs. women) and education (high school or less vs. more than high school) categories with adequate HPV knowledge and vaccine awareness. Adequate HPV knowledge was higher among women (53%) and men (46%) with more than high school and was lower among women (46%) and men (27%) with high school or less. For HPV vaccine awareness, similar results were observed. Women (OR = 3.0 ; 95%CI = 1.4-6.2) and men (OR = 2.3 , 95%CI = 1.1-4.8) with more than high school and women with high school or less (OR = 2.3 , 95%CI = 1.0-5.2) were more likely to have adequate HPV vaccine knowledge than men with high-school or less education. Heightened HPV vaccine awareness was also seen among more educated women and men and women with similar lower education when compared to men with ≤ high school. Men and individuals with lower educational attainment were more likely to have inadequate HPV knowledge and vaccine awareness. HPV vaccine-oriented educational interventions should target these high-risk groups.

The Gut Microbiome May Help Address Mental Health Disparities in Hispanics: A Narrative Review.

The gut-brain axis is the biological connection between the enteric and the central nervous systems. Given the expansion of the microbial sciences with the new human microbiome field facilitated by the decrease in sequencing costs, we now know more about the role of gut microbiota in human health. In this short review, particular focus is given to the gut-brain axis and its role in psychiatric diseases such as anxiety and depression. Additionally, factors that contribute to changes in the gut-brain axis, including the gut microbiome, nutrition, the host's genome, and ethnic difference, are highlighted. Emphasis is given to the lack of studies on Hispanic populations, despite the fact this ethnic group has a higher prevalence of anxiety and depression in the US.

Hurricane María drives increased indoor proliferation of filamentous fungi in San Juan, Puerto Rico: a two-year culture-based approach.

Extensive flooding caused by Hurricane María in Puerto Rico (PR) created favorable conditions for indoor growth of filamentous fungi. These conditions represent a public health concern as contamination by environmental fungi is associated with a higher prevalence of inflammatory respiratory conditions. This work compares culturable fungal spore communities present in homes that sustained water damage after Hurricane María to those present in dry, non-flooded homes. We collected air samples from 50 houses in a neighborhood in San Juan, PR, 12 and 22 months after Hurricane María. Self-reported data was used to classify the homes as flooded, water-damage or dry non-flooded. Fungi abundances, composition and diversity were analyzed by culturing on two media. Our results showed no significant differences in indoor fungal concentrations (CFU/m3) one year after the Hurricane in both culture media studied (MEA and G25N). During the second sampling period fungal levels were 2.7 times higher in previously flooded homes (Median = 758) when compared to dry homes (Median = 283), (p-value < 0.005). Fungal profiles showed enrichment of Aspergillus species inside flooded homes compared to outdoor samples during the first sampling period (FDR-adjusted p-value = 0.05). In contrast, 22 months after the storm, indoor fungal composition consisted primarily of non-sporulated fungi, most likely basidiospores, which are characteristic of the outdoor air in PR. Together, this data highlights that homes that suffered water damage not only have higher indoor proliferation of filamentous fungi, but their indoor fungal populations change over time following the Hurricane. Ultimately, after nearly two years, indoor and outdoor fungal communities converged in this sample of naturally ventilated homes.

Soy and Frequent Dairy Consumption with Subsequent Equol Production Reveals Decreased Gut Health in a Cohort of Healthy Puerto Rican Women.

The U.S. Hispanic female population has one of the highest breast cancer (BC) incidence and mortality rates, while BC is the leading cause of cancer death in Puerto Rican women. Certain foods may predispose to carcinogenesis. Our previous studies indicate that consuming combined soy isoflavones (genistein, daidzein, and glycitein) promotes tumor metastasis possibly through increased protein synthesis activated by equol, a secondary dietary metabolite. Equol is a bacterial metabolite produced in about 20-60% of the population that harbor and exhibit specific gut microbiota capable of producing it from daidzein. The aim of the current study was to investigate the prevalence of equol production in Puerto Rican women and identify the equol producing microbiota in this understudied population. Herein, we conducted a cross-sectional characterization of equol production in a clinically based sample of eighty healthy 25-50 year old Puerto Rican women. Urine samples were collected and evaluated by GCMS for the presence of soy isoflavones and metabolites to determine the ratio of equol producers to equol non-producers. Furthermore, fecal samples were collected for gut microbiota characterization on a subset of women using next generation sequencing (NGS). We report that 25% of the participants were classified as equol producers. Importantly, the gut microbiota from equol non-producers demonstrated a higher diversity. Our results suggest that healthy women with soy and high dairy consumption with subsequent equol production may result in gut dysbiosis by having reduced quantities (diversity) of healthy bacterial biomarkers, which might be associated to increased diseased outcomes (e.g., cancer, and other diseases).

Changes in the vaginal microbiota across a gradient of urbanization.

The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations. Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity. To test this hypothesis, we characterized the vaginal microbiota in the cervicovaginal and introital sites in sexually active Amerindians (N = 82) spanning urbanization, and in urban mestizos (N = 29), in the Venezuelan Amazonas. HPV status was also considered. Sampling was performed in an urban gradient from remote villages to a town, and women were individually classified by the degree of urbanization (low, medium, and high). Amerindian cervicovaginal and introital microbiota diversity were not associated with major changes in urbanization or ethnicity. There was a non-significant trend of increased diversity with urbanization, with a few taxa found overrepresented in urban Amerindians (Brevibacterium linens and Peptoniphilus lacrimalis) or mestizos (Mobiluncus mulieris and Prevotella sp.). Among all women, cervicovaginal and introital samples clustered, respectively, in four and two community state types (CSTs), where most profiles were dominated by Lactobacillus iners, Gardnerella vaginalis or were highly diverse profiles. HPV status did not associate with microbial diversity. In conclusion, no association was found between urban level and the vaginal microbiome in Amerindian women, and little difference was found between ethnicities. L. iners and high diversity profiles, associated with vaginal health outcomes, prevail in these populations.

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla.

Plant-associated microbial communities have diverse phenotypic effects on their hosts that are only beginning to be revealed. We hypothesized that morpho-physiological variations in the tropical tree Tabebuia heterophylla, observed on different geological substrates, arise in part due to microbial processes in the rhizosphere. We characterized the microbiota of the rhizosphere and soil communities associated with T. heterophylla trees in high and low altitude sites (with varying temperature and precipitation) of volcanic, karst and serpentine geologies across Puerto Rico. We sampled 6 areas across the island in three geological materials including volcanic, serpentine and karst soils. Collection was done in 2 elevations (>450m and 0-300m high), that included 3 trees for each site and 4 replicate soil samples per tree of both bulk and rhizosphere. Genomic DNA was extracted from 144 samples, and 16S rRNA V4 sequencing was performed on the Illumina MiSeq platform. Proteobacteria, Actinobacteria, and Verrucomicrobia were the most dominant phyla, and microbiomes clustered by geological substrate and elevation. Volcanic samples were enriched in Verrucomicrobia; karst was dominated by nitrogen-fixing Proteobacteria, and serpentine sites harbored the most diverse communities, with dominant Cyanobacteria. Sites with similar climates but differing geologies showed significant differences on rhizobiota diversity and composition demonstrating the importance of geology in shaping the rhizosphere microbiota, with implications for the plant's phenotype. Our study sheds light on the combined role of geology and climate in the rhizosphere microbial consortia, likely contributing to the phenotypic plasticity of the trees.

A Protocol for the Multi-Omic Integration of Cervical Microbiota and Urine Metabolomics to Understand Human Papillomavirus (HPV)-Driven Dysbiosis.

The multi-omic integration of microbiota data with metabolomics has gained popularity. This protocol is based on a human multi-omics study, integrating cervicovaginal microbiota, HPV status and neoplasia, with urinary metabolites. Indeed, to understand the biology of the infections and to develop adequate interventions for cervical cancer prevention, studies are needed to characterize in detail the cervical microbiota and understand the systemic metabolome. This article is a detailed protocol for the multi-omic integration of cervical microbiota and urine metabolome to shed light on the systemic effects of cervical dysbioses associated with Human Papillomavirus (HPV) infections. This methods article suggests detailed sample collection and laboratory processes of metabolomics, DNA extraction for microbiota, HPV typing, and the bioinformatic analyses of the data, both to characterize the metabolome, the microbiota, and joint multi-omic analyses, useful for the development of new point-of-care diagnostic tests based on these approaches.