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\"The future is sh*t: the literal kind. For most of human history we've been, well, disinclined to take a closer look at our body's natural product-the complex antihero of this story-save for gleaning some prophecy of our own health. But if we were to take more than a passing look at our poop, we would spy a veritable cornucopia of possibilities. We would see potent medicine, sustainable power, and natural fertilizer to restore the world's depleted lands. We would spy a time capsule of evidence for understanding past lives and murderous ends. We would glimpse effective ways of measuring and improving human health from the cradle to the grave, early warnings of community outbreaks like Covid-19, and new means of identifying environmental harm-and then reversing it. Flush is both an urgent exploration of the world's single most squandered natural resource, and a cri de coeur (or cri de colon?) for the vast, hidden value in our \"waste.\" Award-winning journalist and microbiologist Bryn Nelson, PhD, leads readers through the colon and beyond with infectious enthusiasm, helping to usher in a necessary mental shift that could restore our balance with the rest of the planet and save us from ourselves. Unlocking poop's enormous potential will require us to overcome our shame and disgust and embrace our role as the producers and architects of a more circular economy in which lowly byproducts become our species' salvation. Locked within you is a medicine cabinet, a biogas pipeline, a glass of drinking water, a mound of fuel briquettes; it's time to open the doors (carefully!). A dose of medicine, a glass of water, a gallon of rocket fuel, an acre of soil: sometimes hope arrives in surprising packages\"-- Provided by publisher.

Centenarians have a decreased susceptibility to ageing-associated illnesses, chronic inflammation and infectious diseases 1 – 3 . Here we show that centenarians have a distinct gut microbiome that is enriched in microorganisms that are capable of generating unique secondary bile acids, including various isoforms of lithocholic acid (LCA): iso-, 3-oxo-, allo-, 3-oxoallo- and isoallolithocholic acid. Among these bile acids, the biosynthetic pathway for isoalloLCA had not been described previously. By screening 68 bacterial isolates from the faecal microbiota of a centenarian, we identified Odoribacteraceae strains as effective producers of isoalloLCA both in vitro and in vivo. Furthermore, we found that the enzymes 5α-reductase (5AR) and 3β-hydroxysteroid dehydrogenase (3β-HSDH) were responsible for the production of isoalloLCA. IsoalloLCA exerted potent antimicrobial effects against Gram-positive (but not Gram-negative) multidrug-resistant pathogens, including Clostridioides difficile and Enterococcus faecium . These findings suggest that the metabolism of specific bile acids may be involved in reducing the risk of infection with pathobionts, thereby potentially contributing to the maintenance of intestinal homeostasis. The microbiota of centenarians (aged 100 years and older) comprise gut microorganisms that are capable of generating unique secondary bile acids, including isoallolithocholic acid, a bile acid with potent antimicrobial effects against Gram-positive—but not Gram-negative—multidrug-resistant pathogens.

Background Different dietary approaches, such as gluten and casein free diets, or the use of probiotics and prebiotics have been suggested in autistic spectrum disorders in order to reduce gastrointestinal (GI) disturbances. GI symptoms are of particular interest in this population due to prevalence and correlation with the severity of behavioural traits. Nowadays, there is lack of strong evidence about the effect of dietary interventions on these problems, particularly prebiotics. Therefore, we assessed the impact of exclusion diets and a 6-week Bimuno® galactooligosaccharide (B-GOS®) prebiotic intervention in 30 autistic children. Results The results showed that children on exclusion diets reported significantly lower scores of abdominal pain and bowel movement, as well as lower abundance of Bifidobacterium spp. and Veillonellaceae family, but higher presence of Faecalibacterium prausnitzii and Bacteroides spp. In addition, significant correlations were found between bacterial populations and faecal amino acids in this group, compared to children following an unrestricted diet. Following B-GOS® intervention, we observed improvements in anti-social behaviour, significant increase of Lachnospiraceae family, and significant changes in faecal and urine metabolites. Conclusions To our knowledge, this is the first study where the effect of exclusion diets and prebiotics has been evaluated in autism, showing potential beneficial effects. A combined dietary approach resulted in significant changes in gut microbiota composition and metabolism suggesting that multiple interventions might be more relevant for the improvement of these aspects as well as psychological traits. Trial registration NCT02720900 ; registered in November 2015.

Access to safe drinking-water is a fundamental requirement for good health and is also a human right. Global access to safe drinking-water is monitored by WHO and UNICEF using as an indicator \"use of an improved source,\" which does not account for water quality measurements. Our objectives were to determine whether water from \"improved\" sources is less likely to contain fecal contamination than \"unimproved\" sources and to assess the extent to which contamination varies by source type and setting. Studies in Chinese, English, French, Portuguese, and Spanish were identified from online databases, including PubMed and Web of Science, and grey literature. Studies in low- and middle-income countries published between 1990 and August 2013 that assessed drinking-water for the presence of Escherichia coli or thermotolerant coliforms (TTC) were included provided they associated results with a particular source type. In total 319 studies were included, reporting on 96,737 water samples. The odds of contamination within a given study were considerably lower for \"improved\" sources than \"unimproved\" sources (odds ratio [OR] = 0.15 [0.10-0.21], I2 = 80.3% [72.9-85.6]). However over a quarter of samples from improved sources contained fecal contamination in 38% of 191 studies. Water sources in low-income countries (OR = 2.37 [1.52-3.71]; p<0.001) and rural areas (OR = 2.37 [1.47-3.81] p<0.001) were more likely to be contaminated. Studies rarely reported stored water quality or sanitary risks and few achieved robust random selection. Safety may be overestimated due to infrequent water sampling and deterioration in quality prior to consumption. Access to an \"improved source\" provides a measure of sanitary protection but does not ensure water is free of fecal contamination nor is it consistent between source types or settings. International estimates therefore greatly overstate use of safe drinking-water and do not fully reflect disparities in access. An enhanced monitoring strategy would combine indicators of sanitary protection with measures of water quality.

Consuming diets rich in plant versus animal products changes the microbes found in the human gut within days, with important implications for our health and evolution. Diet can rapidly alter gut microbiome Diet influences the structure and function of the gut microbiota in the long term, but it is not clear how rapidly the microbiota is affected by short-term dietary change. Peter Turnbaugh and colleagues studied the effect of transition to a diet consisting entirely of either animal products or plant products on the composition and function of the human gut microbiota. They find that the community changes rapidly, within a single day, overwhelming the pre-existing inter-individual differences in microbiota composition to recapitulate expected patterns of composition and metabolic function for carnivorous and herbivorous mammals. The animal-based diet was associated with higher levels of bile-tolerant microorganisms, including the bacterium Bilophila wadsworthia , which has previously been linked to inflammatory bowel disease. The authors also detected intact foodborne fungi, bacteria and viruses in the distal gut. Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut 1 , 2 , 3 , 4 , 5 , but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms ( Alistipes , Bilophila and Bacteroides ) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides ( Roseburia , Eubacterium rectale and Ruminococcus bromii ). Microbial activity mirrored differences between herbivorous and carnivorous mammals 2 , reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease 6 . In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

Human intestinal parasitosis and microsporidiosis are a global health concern, mostly in endemic areas but should not be neglected elsewhere. Recent nationwide epidemiological data are scarce, especially from primary health care and developed countries. Diagnosis by molecular tools are increasing and several commercial gastrointestinal panel assays including protozoans and/or helminths are now available. These news tools improve the knowledge into real human parasite epidemiology. This study provides an epidemiological update on intestinal parasites found in primary health care in France and Luxembourg. Two thousand fifty-six stools from primary health care patients were analyzed for the presence of intestinal parasites (IPs) during two different seasons of 2022, the winter and the summer, corresponding to more than 1500 patients from all over France and Luxembourg. Parasite detection was performed combining standard microscopy (merthiolate-iodine-formaldehyde and Bailenger concentration procedures) with two molecular panel assays (AMPLIQUICK Fecal Pretreatment, AMPLIQUICK Protozoans and AMPLIQUICK Helminths, BIOSYNEX, France). The prevalence of IPs in primary care patients reached 33.2%. Blastocystis sp. and Dientamoeba fragilis were the most frequently detected parasites in 20.5% and 13.1% of patients, respectively. Coinfection with two or more parasites was detected in 9.9% of patients. For some parasites, patterns according to gender, age, geography or season have been observed. The high prevalence of pathogenic IPs (about 7%) underlines the importance of investigating gastrointestinal disorders through parasite examination, even in developed countries. The detection of parasites, pathogenic or not, remains a marker of the faecal-oral route of transmission and results should be interpreted accordingly. Parasites molecular characterization give new insights and should encourage further research as industrialized countries are not exempt of parasitic circulation and a better survey is necessary.

Viral diversity and life cycles are poorly understood in the human gut and other body habitats. Phages and their encoded functions may provide informative signatures of a human microbiota and of microbial community responses to various disturbances, and may indicate whether community health or dysfunction is manifest after apparent recovery from a disease or therapeutic intervention. Here we report sequencing of the viromes (metagenomes) of virus-like particles isolated from faecal samples collected from healthy adult female monozygotic twins and their mothers at three time points over a one-year period. We compared these data sets with data sets of sequenced bacterial 16S ribosomal RNA genes and total-faecal-community DNA. Co-twins and their mothers share a significantly greater degree of similarity in their faecal bacterial communities than do unrelated individuals. In contrast, viromes are unique to individuals regardless of their degree of genetic relatedness. Despite remarkable interpersonal variations in viromes and their encoded functions, intrapersonal diversity is very low, with >95% of virotypes retained over the period surveyed, and with viromes dominated by a few temperate phages that exhibit remarkable genetic stability. These results indicate that a predatory viral–microbial dynamic, manifest in a number of other characterized environmental ecosystems, is notably absent in the very distal intestine. Variations in the gut virome The microbial component of the human gut microbiota has been the focus of much research interest recently. Now another layer of complexity is added in the form of the first viral metagenome, determined from virus-like particles isolated from faecal samples of four sets of identical twins and their mothers. A previous study showed that co-twins and their mothers share a significantly greater degree of similarity in their faecal bacterial communities than do unrelated individuals. By contrast, the viromes are found to be unique to individuals, regardless of their degree of genetic relatedness. And in each individual, there was little change in the viromes during the one-year span of the study. The microbial content of the human gut has been the focus of much research interest recently. Now another layer of complexity has been added: the viral content of the gut. Virus-like particles were isolated from faecal samples from four sets of identical twins and their mothers, at three time points over a one-year period. The viromes (metagenomes) of these particles were then sequenced. The results show that there is high interpersonal variation in viromes, but that intrapersonal diversity was very low over this time period.

By exploring the phageome in mice, antibiotic treatment is shown to lead to enrichment of phage-encoded genes that are related to antibiotic resistance. Gut bacteria top-up their antibiotic resistance from a phage-gene reservoir Phages naturally coexist in abundance with their bacterial hosts in the mammalian gut. Antibiotic treatment can negatively affect the gut environment and cause immune and metabolic deficiencies. Previously the disruption of intestinal homeostasis has been studied mainly at the level of bacterial species, but here James Collins and colleagues use comparative metagenomics to profile gut phage populations following antibiotic treatment in mice. They find that exposure to ciprofloxacin or ampicillin enriches phage-encoded genes related to antibiotic resistance. Furthermore, phages from antibiotic-treated mice are able to increase resistance in an aerobically cultured naive microbiota. These results suggest that antibiotic treatment increases the frequency of phage integration and stimulates broad host range, which promotes a functional reservoir that is both genetically diverse and highly accessible to gut bacteria. The mammalian gut ecosystem has considerable influence on host physiology 1 , 2 , 3 , 4 , but the mechanisms that sustain this complex environment in the face of different stresses remain obscure. Perturbations to the gut ecosystem, such as through antibiotic treatment or diet, are at present interpreted at the level of bacterial phylogeny 5 , 6 , 7 . Less is known about the contributions of the abundant population of phages to this ecological network. Here we explore the phageome as a potential genetic reservoir for bacterial adaptation by sequencing murine faecal phage populations following antibiotic perturbation. We show that antibiotic treatment leads to the enrichment of phage-encoded genes that confer resistance via disparate mechanisms to the administered drug, as well as genes that confer resistance to antibiotics unrelated to the administered drug, and we demonstrate experimentally that phages from treated mice provide aerobically cultured naive microbiota with increased resistance. Systems-wide analyses uncovered post-treatment phage-encoded processes related to host colonization and growth adaptation, indicating that the phageome becomes broadly enriched for functionally beneficial genes under stress-related conditions. We also show that antibiotic treatment expands the interactions between phage and bacterial species, leading to a more highly connected phage–bacterial network for gene exchange. Our work implicates the phageome in the emergence of multidrug resistance, and indicates that the adaptive capacity of the phageome may represent a community-based mechanism for protecting the gut microflora, preserving its functional robustness during antibiotic stress.

Intestinal commensal bacteria can inhibit dense colonization of the gut by vancomycin-resistant Enterococcus faecium (VRE), a leading cause of hospital-acquired infections 1 , 2 . A four-strained consortium of commensal bacteria that contains Blautia producta BP SCSK can reverse antibiotic-induced susceptibility to VRE infection 3 . Here we show that BP SCSK reduces growth of VRE by secreting a lantibiotic that is similar to the nisin-A produced by Lactococcus lactis . Although the growth of VRE is inhibited by BP SCSK and L. lactis in vitro, only BP SCSK colonizes the colon and reduces VRE density in vivo. In comparison to nisin-A, the BP SCSK lantibiotic has reduced activity against intestinal commensal bacteria. In patients at high risk of VRE infection, high abundance of the lantibiotic gene is associated with reduced density of E. faecium . In germ-free mice transplanted with patient-derived faeces, resistance to VRE colonization correlates with abundance of the lantibiotic gene. Lantibiotic-producing commensal strains of the gastrointestinal tract reduce colonization by VRE and represent potential probiotic agents to re-establish resistance to VRE. The gut commensal Blautia producta secretes a lantibiotic that reduces colonization of the gut by the major pathogen vancomycin-resistant Enterococcus faecium , and transplantation of microbiota with high abundance of the lantibiotic gene enhances resistance to colonization in mice.

This study documents the introduction process of eight unrelated captive male Asian elephants in a free-contact management setting in Laos, utilizing a two-phase introduction process comprising limited tactile contact followed by full physical introduction. Behavioral data were collected using all-occurrence and focal-animal sampling, while fecal samples were analyzed for glucocorticoid (fGCM) and androgen (fAM) metabolite concentrations to assess physiological responses. Results indicated a prevalence of affiliative over aggressive or submissive behaviors throughout both introduction phases, supporting the idea that unrelated males can create social bonds without excessive aggression in captive settings. Affiliative behaviors declined over time during the limited tactile contact phase, then stabilized during physical introductions. Aggressive and submissive behaviors were consistently low throughout the study. Individual variations in behavior were observed, highlighting the importance of considering temperament in elephant introductions. No significant differences were found in fGCM concentrations before or after social introductions among the males, suggesting that the process did not cause substantial physiological stress. Only one male exhibited decreased fAM concentrations after social interactions, which could indicate testosterone suppression from more dominant males. During the limited contact period, aggressive interactions were positively associated with fGCM concentrations, whereas a longer duration since first introduction was associated with a decrease. In the physical introduction step, the number of days since the first introduction positively predicted an increase in fGCM concentrations, while the fAM concentration before social interactions negatively predicted fGCM. In addition, age was significantly positively predictive of fAM concentrations. These findings challenge traditional views on male elephant sociality under captive conditions and suggest that, with proper management, forming all-male groups can be a viable option for conservation and ex situ management programs. This study emphasizes the importance of gradual introduction processes, individual monitoring, and long-term behavioral observations in the successful introduction of unrelated captive male Asian elephants.