The use of wastewater for irrigation and animal manure as fertilizer can cause transmission of intestinal pathogens, conditions frequently observed in lowand middle-income countries (LMICs). Here, we tested the ability of Salmonella to grow in the faecal matter. We inoculated freshly isolated Salmonella strains (from chickens) in chicken faecal matter and incubated for 1 to 12 days, under aerobic and anaerobic conditions. We found that both Salmonella and Escherichia coli multiplied massively in faecal matter outside a host and significantly higher in aerobic conditions. Our results have critical implications in waste management, as we demonstrate that aerobic treatments may not be the best to reduce the number of Salmonella in the environment.

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Obesity is defi ned as abnormal or excessive body fat accumulation that may have negative effects on health. Healthy diet induces a balance of gut microbiota, helping in turn to combat this metabolic disorder. Amaranth is well known because of its benefi cial properties on health, but its effects on microbiota profi le are still unknown. The aim of this study was to analyse the changes of gut microbiota in diet-induced obese mice due to amaranth protein consumption and to compare them with the changes due to soybean protein intake. Male C57BL/6 mice were fed for 8 weeks with regular (RD) or high-fat (HF) diet, without or with complementation with amaranth or soybean protein isolates. Morphological changes in caecum ultrathin sections were measured after hematoxylin/eosin staining. Microbiota was isolated from the caecum and 16S rRNA gene was sequenced. Caecal Short Chain Fatty Acids (SCFAs) were quantifi ed by gas chromatography. The consumption of soybean protein induced the ectopic deposition of fat in the whole intestine while amaranth proteins increased caecal crypt depth and calceiform cells number sustaining its benefi cial effect on health. The count of Ruminococcacea family bacteria was increased in mice fed with HF diet, but amaranth proteins intake reduced its abundance. In turn, Lachnospiraceae bacteria abundance decreased in mice fed the Control-HF and amaranth HF diets, but increased in mice fed the soybean diets. In mice fed the RD diets, amaranth induced the abundance of Prevotellaceae, an acetate-producing bacteria. Study results indicate that the modulation of caecal microbiota could be one of the mechanisms by which amaranth exerts its benefi cial effects on health.

The gastrointestinal tract (GIT) constitutes a complex and diverse ecosystem. Escherichia coli is one of the most frequently studied and characterized species in the gut ecosystem. Nevertheless, there has been little research to determine their diversity and population dynamics in the intestines of children over time. Many intestinal E. coli lineages carry antimicrobial resistance and virulence genes, which have implications in disease and public health. In this one-year prospective study, a fresh fecal sample was obtained from 30 children longitudinally for one year (n = 82 fecal samples). From each stool sample, five Escherichia coli colonies were randomly selected to characterize their genotype and phenotypic antimicrobial resistance pattern (n = 405 E. coli isolates). We found that the most numerically dominant E. coli lineages in children’s intestines were transient colonizers, and phenotypic antimicrobial resistance varied significantly over time, however, ST131 a multi-drug resistant pathogen, and 3 additional STs persisted in a child’s intestine for 3 months or more.IMPORTANCEThe length of residency and numeric dominance of antimicrobial-resistant E. coli may affect the extent to which an isolate contributes to the dissemination of antimicrobial resistance. We studied the persistence of numerically dominant and antimicrobial-resistant lineages of E. coli in the human intestine and found that E. coli lineages in the gut of children change rapidly over time.

Probiotic bacteria are frequently used to treat intestinal diseases or to improve health; however, little is known about the evolutionary changes of these bacteria during probiotic manufacture and the bacterial ability to colonize the intestine. It has been observed that when bacteria adapt to a new environment, they lose some traits required to thrive in the original niche. In this study, a strain of Lactobacillus reuteri was isolated from mouse duodenum and subjected to 150 serial passes in milk to simulate the industrial propagation of probiotic bacteria. The strains adapted to milk outperformed their ancestor when grown in milk; we also showed evidence of reduced intestinal colonization of milk‐adapted strains. Whole‐genome sequencing showed that bacterial adaptation to milk selects mutants with altered metabolic functions.