Comparative prevalence of Oxalobacter formigenes in three human populations.

There has been increasing interest in the human anaerobic colonic bacterium Oxalobacter formigenes because of its ability to metabolize oxalate, and its potential contribution to protection from calcium oxalate kidney stones. Prior studies examining the prevalence of this organism have focused on subjects in developed countries and on adults. Now using O. formigenes-specific PCR, we have compared the prevalence of these organisms among subjects in two remote areas in which modern medical practices have hardly been present with a USA group of mothers and their infants for the first three years of life. Among the Amerindians of the Yanomami-Sanema and Yekwana ethnic groups in Venezuela and the Hadza in Tanzania, O. formigenes was detected in 60-80% of the adult subjects, higher than found in adults from USA in this and prior studies. In young children, the prevalence was much lower in USA than in either tribal village. These data extend our understanding of the epidemiology of O. formigenes carriage, and are consistent with the hypothesis that the rising incidence of kidney stones is associated with the progressive loss of O. formigenes colonization in populations that have been highly impacted by modern medical practices.

Publisher Correction: Complex virome in feces from Amerindian children in isolated Amazonian villages.

In the original version of this Article, the affiliation details for Eric Delwart were incorrectly given as 'Blood Systems Research Institute, San Francisco, CA 94118, USA and Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela'. The correct affiliations are 'Blood Systems Research Institute, San Francisco, CA 94118, USA and Department of Laboratory Medicine, University of California at San Francisco, San Francisco, CA 94118, USA'. This has been corrected in both the PDF and HTML versions of the Article.

Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village.

People living traditional lifestyles have higher gut microbiota diversity than urban subjects. We hypothesized that shifting lifestyles from an urban environment to a traditional rainforest village would lead to changes in the microbiota of visitors, which would become more similar to the microbiota of villagers. Here, we characterized at different time points the microbiota of 7 urban visitors (5 adults and 2 children) staying in a rainforest Amerindian village for 16 days and compared them with a reference collection of samples from age-matched local villagers. We performed a 16S rRNA gene survey of samples from multiple body sites (including fecal, oral, nasal, and skin samples) using Illumina MiSeq sequencing. The main factor segregating the microbiotas of each body site was the human group (i.e., visitors versus villagers), with the visitor microbiota tending to have lower alpha diversity; the lowered alpha diversity was statistically significant in the microbiota of skin and in the children's fecal and oral microbiota. During the rainforest period, all visitors experienced microbiota changes within their personal cloud of variation. For all body sites, the microbiota conformations in the visitor children better matched the microbiota conformations in villagers of the same age than did those of the visitor adults, which showed a lower "microbiota age" than the microbiota of the villagers. The results suggest higher stability in the adult microbiota, with the less resilient children's microbiota responding more to dietary changes.IMPORTANCE Despite the limitations of a small study, our results evidence higher resilience of the gut microbiota with respect to dietary manipulation in adults than in children and urge further studies to understand the extent of microbiota plasticity in response to dietary changes and the mechanisms underlying microbiota resilience. These studies are relevant to the potential of future human pre- and probiotics in preventing or curing microbiota-associated diseases.

Complex virome in feces from Amerindian children in isolated Amazonian villages.

The number of viruses circulating in small isolated human populations may be reduced by viral extinctions and rare introductions. Here we used viral metagenomics to characterize the eukaryotic virome in feces from healthy children from a large urban center and from three Amerindian villages with minimal outside contact. Numerous human enteric viruses, mainly from the Picornaviridae and Caliciviridae families, were sequenced from each of the sites. Multiple children from the same villages shed closely related viruses reflecting frequent transmission clusters. Feces of isolated villagers also contained multiple viral genomes of unknown cellular origin from the Picornavirales order and CRESS-DNA group and higher levels of nematode and protozoan DNA. Despite cultural and geographic isolation, the diversity of enteric human viruses was therefore not reduced in these Amazonian villages. Frequent viral introductions and/or increased susceptibility to enteric infections may account for the complex fecal virome of Amerindian children in isolated villages.

The microbiome of uncontacted Amerindians.

Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.

Hidatidosis poliquística autóctona en dos pacientes Yanomami en el Alto Orinoco, Amazonas, Venezuela / Polycystic hydatid disease in two patients indigenous Yanomami in the Upper Orinoco, Amazonas, Venezuela

La infección por Echinococcus sp. es hipoendémica en Venezuela. Sólo cuatro casos de hidatidosis autóctona por E. vogeli han sido reportados, tres de ellos en la región de la Guayana venezolana. En Febrero del año 2009 se realizó el diagnóstico clínico-sero-epidemiológico de hidatidosis poliquística en una paciente femenina de la etnia Yanomami, procedente de Parima B, Alto Orinoco, en la Amazonía venezolana. Se resolvió con tratamiento médico y quirúrgico por laparoscopia y se evidenció en el quiste la presencia de ganchos rostelares compatibles con E. vogeli. En Abril del 2009 en una segunda paciente Yanomami de igual procedencia, se le diagnosticó hidatidosis por E. vogeli siendo operada exitosamente por cirugía laparoscópica asistida por robot. Dos casos humanos en una misma población y la presencia de factores de riesgo como la tenencia de perros domésticos y la comunicación por informantes indígenas del hallazgo de quistes en hígados de animales de cacería (Cuniculus paca o lapa y Dasyprocta sp. o picure), hacen pensar en transmisión activa en la cuenca del Alto Orinoco y en zonas selváticas de la Guayana venezolana. El presente, es el primer registro de casos de hidatidosis poliquística en indígenas de la etnia Yanomami.

Infection by Echinococcus sp. is hypoendemic in Venezuela. Only four cases of autochthonous E. vogeli hydatidosis have been reported, including three in the Venezuelan region of Guayana. In February 2009, based on epidemiological data, signs and symptoms and serological tests, a female patient of the Yanomami ethnic group, was diagnosed with a polycystic hydatid disease in Parima B, Alto Orinoco, in the Venezuelan Amazon. Rostellar hooks compatible with E. vogeli were found in the cyst. It was resolved with medical and surgical treatment by laparoscopy. A second Yanomami patient from the same location was diagnosed with E. vogeli hydatidosis in April 2009, being successfully operated with robot-assisted laparoscopy. Two human cases in the same population and the presence of risk factors such as domestic dog ownership and findings of cysts in livers of hunted animals (such as Cuniculus and Dasyprocta sp.) reported by indigenous informants, suggest active transmission in the Upper Orinoco basin and forested areas of the Venezuelan Guayana. These are the first reported cases of polycystic hydatid disease of the Yanomami ethnic group.