Role of the microbiome in human development.

The host-microbiome supraorganism appears to have coevolved and the unperturbed microbial component of the dyad renders host health sustainable. This coevolution has likely shaped evolving phenotypes in all life forms on this predominantly microbial planet. The microbiota seems to exert effects on the next generation from gestation, via maternal microbiota and immune responses. The microbiota ecosystems develop, restricted to their epithelial niches by the host immune system, concomitantly with the host chronological development, providing early modulation of physiological host development and functions for nutrition, immunity and resistance to pathogens at all ages. Here, we review the role of the microbiome in human development, including evolutionary considerations, and the maternal/fetal relationships, contributions to nutrition and growth. We also discuss what constitutes a healthy microbiota, how antimicrobial modern practices are impacting the human microbiota, the associations between microbiota perturbations, host responses and diseases rocketing in urban societies and potential for future restoration

Positive selection on a bacterial oncoprotein associated with gastric cancer

<p>Background</p> <p><it>Helicobacter pylori </it>is a vertically inherited gut commensal that is carcinogenic if it possesses the <it>cag</it> pathogenicity island (<it>cag </it>PaI); infection with <it>H.pylori </it>is the major risk factor for gastric cancer, the second leading cause of death from cancer worldwide (WHO). The <it>cag </it>PaI locus encodes the <it>cagA </it>gene, whose protein product is injected into stomach epithelial cells via a Type IV secretion system, also encoded by the <it>cag </it>PaI. Once there, the cagA protein binds to various cellular proteins, resulting in dysregulation of cell division and carcinogenesis. For this reason, cagA may be described as an oncoprotein. A clear understanding of the mechanism of action of cagA and its benefit to the bacteria is lacking.</p> <p>Results</p> <p>Here, we reveal that the <it>cagA </it>gene displays strong signatures of positive selection in bacteria isolated from amerindian populations, using the Ka/Ks ratio. Weaker signatures are also detected in the gene from bacteria isolated from asian populations, using the Ka/Ks ratio and the more sensitive branches-sites model of the PAML package. When the <it>cagA </it>gene isolated from amerindian populations was examined in more detail it was found that the region under positive selection contains the EPIYA domains, which are known to modulate the carcinogenicity of the gene. This means that the carcinogenicity modulating region of the gene is undergoing adaptation. The results are discussed in relation to the high incidences of stomach cancer in some latin american and asian populations.</p> <p>Conclusion</p> <p>Positive selection on cagA indicates antagonistic coevolution between host and bacteria, which appears paradoxical given that cagA is detrimental to the human host upon which the bacteria depends. This suggests several non-exclusive possibilities; that gastric cancer has not been a major selective pressure on human populations, that cagA has an undetermined benefit to the human host, or that horizontal transmission of <it>H.pylori </it>between hosts has been more important in the evolution of <it>H.pylori </it>than previously recognized, reducing the selective pressure to lower the pathogenicity of the bacteria. The different patterns of adaptation of the gene in different human populations indicates that there are population specific differences in the human gut environment - due either to differences in host genetics or diet and other lifestyle features.</p

Should we modulate the neonatal microbiome and what should be the goal?

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Antimicrobial prophylaxis administration after umbilical cord clamping in cesarean section and the risk of surgical site infection: a cohort study with 55,901 patients.

BACKGROUND The World Health Organization (WHO) recommends administration of surgical antimicrobial prophylaxis (SAP) in cesarean section prior to incision to prevent surgical site infections (SSI). This study aimed to determine whether SAP administration following cord clamping confers an increased SSI risk to the mother. METHODS Study design: Cohort. SETTING 75 participating Swiss hospitals, from 2009 to 2018. PARTICIPANTS A total of 55,901 patients were analyzed. MAIN OUTCOME MEASURES We assessed the association between SAP administration relative to incision and clamping and the SSI rate, using generalized linear multilevel models, adjusted for patient characteristics, procedural variables, and health-care system factors. RESULTS SAP was administered before incision in 26'405 patients (47.2%) and after clamping in 29,496 patients (52.8%). Overall 846 SSIs were documented, of which 379 (1.6% [95% CI, 1.4-1.8%]) occurred before incision and 449 (1.7% [1.5-1.9%]) after clamping (p = 0.759). The adjusted odds ratio for SAP administration after clamping was not significantly associated with an increased SSI rate (1.14, 95% CI 0.96-1.36; p = 0.144) when compared to before incision. Supplementary and subgroup analyses supported these main results. CONCLUSIONS This study did not confirm an increased SSI risk for the mother in cesarean section if SAP is given after umbilical cord clamping compared to before incision

A randomized controlled trial of the effects of whole grains versus refined grains diets on the microbiome in pregnancy

Dietary whole grain consumption has been postulated to have metabolic benefits. The purpose of this study was to compare a pregnancy diet containing 75% of total carbohydrates as refined grains with a diet of 75% of total carbohydrates as whole grains for pregnancy outcomes and effects on the microbiome. Gestational weight gain, glucose tolerance and newborn outcomes were measured on 248 enrolled compliant women from whom a subset of 103 women consented to give 108 vaginal and 109 anal swabs. The data presented here are limited to the patients from whom the vaginal and anal swabs were obtained in order to study the microbiome. A microbiome—16SrRNA survey—was characterized in these samples. Samples and measurements were obtained at the first obstetrical visit, before beginning a prescribed diet (T1—baseline) and after 17–32\ua0weeks on the prescribed diet (T3). Food frequency questionnaires and total plasma alkylresorcinols were used as a measure of whole grain consumption. There were no dietary differences in maternal weight gain, birth weight, or glucose tolerance test. Mothers consuming the whole grains diet showed a trend of gestational decrease in vaginal bacterial alpha diversity, with increasing Lactobacillus-dominance. No significant difference was observed for the anal microbiome. The results suggest that diet modulations of the vaginal microbiome during gestation may have important implications for maternal and neonatal health and in the intergenerational transfer of maternal microbiome. Trial registration: ClinicalTrials.gov Identifier: NCT03232762

Links between environment, diet, and the hunter-gatherer microbiome

The study of traditional populations provides a view of human-associated microbes unperturbed by industrialization, as well as a window into the microbiota that co-evolved with humans. Here we discuss our recent work characterizing the microbiota from the Hadza hunter-gatherers of Tanzania. We found seasonal shifts in bacterial taxa, diversity, and carbohydrate utilization by the microbiota. When compared to the microbiota composition from other populations around the world, the Hadza microbiota shares bacterial families with other traditional societies that are rare or absent from microbiotas of industrialized nations. We present additional observations from the Hadza microbiota and their lifestyle and environment, including microbes detected on hands, water, and animal sources, how the microbiota varies with sex and age, and the short-term effects of introducing agricultural products into the diet. In the context of our previously published findings and of these additional observations, we discuss a path forward for future work

Oximetry and neonatal examination for the detection of critical congenital heart disease: a systematic review and meta-analysis

Background: Undiagnosed congenital heart disease in the prenatal stage can occur in approximately 5 to 15 out of 1000 live births; more than a quarter of these will have critical congenital heart disease (CCHD). Late postnatal diagnosis is associated with a worse prognosis during childhood, and there is evidence that a standardized measurement of oxygen saturation in the newborn by cutaneous oximetry is an optimal method for the detection of CCHD. We conducted a systematic review of the literature and meta-analysis comparing the operational characteristics of oximetry and physical examination for the detection of CCHD. Methods: A systematic review of the literature was conducted on the following databases including published studies between 2002 and 2017, with no language restrictions: Pubmed, Science Direct, Ovid, Scopus and EBSCO, with the following keywords: oximetry screening, critical congenital heart disease, newborn OR oximetry screening heart defects, congenital, specificity, sensitivity, physical examination. Results: A total of 419 articles were found, from which 69 were selected based on their titles and abstracts. After quality assessment, five articles were chosen for extraction of data according to inclusion criteria; data were analyzed on a sample of 404,735 newborns in the five included studies. The following values were found, corresponding to the operational characteristics of oximetry in combination with the physical examination: sensitivity: 0.92 (CI 95%, 0.87-0.95), specificity: 0.98 (CI 95%, 0.89-1.00), for physical examination alone sensitivity: 0.53 (CI 95%, 0.28-0.78) and specificity: 0.99 (CI 95%, 0.97-1.00). Conclusions: Evidence found in different articles suggests that pulse oximetry in addition to neonatal physical examination presents optimal operative characteristics that make it an adequate screening test for detection of CCHD in newborns, above all this is essential in low and middle-income settings where technology medical support is not entirely available

Cervicovaginal Fungi and Bacteria Associated With Cervical Intraepithelial Neoplasia and High-Risk Human Papillomavirus Infections in a Hispanic Population

The human cervicovaginal microbiota resides at an interface between the host and the environment and may affect susceptibility to disease. Puerto Rican women have high human papillomavirus (HPV) infection and cervical cancer rates. We hypothesized that the population structure of the cervicovaginal bacterial and fungal biota changed with cervical squamous intraepithelial lesions and HPV infections. DNA was extracted from cervix, introitus, and anal sites of 62 patients attending high-risk San Juan clinics. The 16S rRNA V4 region and ITS-2 fungal regions were amplified and sequenced using Illumina technology. HPV genotyping was determined by reverse hybridization with the HPV SPF10-LiPA25 kit. HPV prevalence was 84% of which ∼44% subjects were infected with high-risk HPV, ∼35% were co-infected with as many as 9 HPV types and ∼5% were infected with exclusively low-risk HPV types. HPV diversity did not change with cervical dysplasia. Cervical bacteria were more diverse in patients with CIN3 pre-cancerous lesions. We found enrichment of Atopobium vaginae and Gardnerella vaginalis in patients with CIN3 lesions. We found no significant bacterial biomarkers associated with HPV infections. Fungal diversity was significantly higher in cervical samples with high-risk HPV and introitus samples of patients with Atypical Squamous Cells of Undetermined Significance (ASCUS). Fungal biomarker signatures for vagina and cervix include Sporidiobolaceae and Sacharomyces for ASCUS, and Malassezia for high-risk HPV infections. Our combined data suggests that specific cervicovaginal bacterial and fungal populations are related to the host epithelial microenvironment, and could play roles in cervical dysplasia

Allometry and Ecology of the Bilaterian Gut Microbiome.

Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (Bilateria) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction.IMPORTANCEThe intestinal microbiome of animals is essential for health, contributing to digestion of foods, proper immune development, inhibition of pathogen colonization, and catabolism of xenobiotic compounds. How these communities assemble and persist is just beginning to be investigated. Here we interrogated a set of gut samples from a wide range of animals to investigate the roles of selection and random processes in microbial community construction. We show that the numbers of bacterial species increased with the weight of host organisms, paralleling findings from studies of island biogeography. Communities in larger organisms tended to be more anaerobic, suggesting one mechanism for niche diversification. Nonselective processes enable specific predictions for community structure, but our samples did not match the predictions of the neutral model. Thus, these findings highlight the importance of niche selection in community construction and suggest mechanisms of niche diversification

A communal catalogue reveals Earth's multiscale microbial diversity

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.Peer reviewe