Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population.

The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.

COVID-19: Rethinking the nature of viruses.

In this brief essay, we combine biological, historical, philosophical and anthropological perspectives to ask anew the question about the nature of the virus. How should we understand Sars-CoV-2 and why does it matter? The argument we present is that the virus undermines any neat distinction between the natural and the human-made, the biological and the social. Rather, to understand the virus and the pandemic we need to understand both as intimately connected to our own social and historical condition. What started as a reflection on the nature of the virus thus turns into a reflection on the human condition as refracted in this pandemic or an anthropology of the virus.

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations.

BACKGROUND: Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out. RESULTS: Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis. CONCLUSIONS: Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.

Allergy narratives in Italy: 'naturalness' in the social construction of medical pluralism.

Based on an ethnographic study conducted in both biomedical and complementary and alternative medicine settings in north Italy, I explore how people and practitioners make sense of allergy and how patients utilize plural healing options. Despite a wide range of medical modalities, people categorize and use medicine according to whether they are 'natural' or 'not-natural,' thus dissolving any potential confusion between diverse therapies. I analyze how the concept of naturalness relates to allergy and medical pluralism. Nature is perceived as opposed to pollution, the first associated with a reassuring and idealized past and the latter to a modernity riddled with uncertainties. Participants associated a diverse set of meanings with nature, permitting them the syncretism of different medical modalities. Medical pluralism in the study area is an uneven platform for discussion and experimentation, the outcome of historical and cultural context and local entanglements of power.

Conflicting sensory relationships. Encounters with allergic people.

Increasingly, people employ the term 'allergy' to define various pathological conditions, although the biomedical community lacks a consensus on a definition of the term. It has become a widespread and convenient label for diverse conditions, often going beyond biomedical diagnosis. The aim of this paper is to explore how allergic people narrate their illness experiences, focusing specifically on the relationship between words, senses and bodies. This paper is based on an ethnographic study in a medium-sized north Italian city conducted from 2004 to 2008, starting in a public hospital Allergy Unit, and then developing through snowball recruitment and referral methods. Interviews were conducted with 37 allergic people, four allergologists and four nurses. Allergic people's narratives constantly drew upon two main concepts: weakness and pollution. These are interpreted as sensorial dimensions expressing a conflicting relationship with the outside environment. It is argued that in times of marked individualism and social transformations, bodily states are of fundamental importance and the mobilisation of sensory concepts is an attempt to give order and meaning to a world that is perceived as constituted by threatening aspects, polluted and out of order.