Gut Microbiome Analysis Identifies Potential Etiological Factors in Acute Gastroenteritis

Lactobacillus paracasei ZFM54 alters the metabolomic profiles of yogurt and the co-fermented yogurt improves the gut microecology of human adults

Gut microbiota imbalance could lead to various diseases, making it important to optimize the structure of the gut flora in adults. Lactobacillus paracasei ZFM54 is a bacteriocin- and folic acid-producing Lactobacillus strain. Herein, L. paracasei ZFM54 was used as the potentially probiotic bacterium to ferment milk together with a yogurt starter. We optimized the fermentation conditions, and the obtained yogurts were then subjected to volatile and nonvolatile metabolome analysis, showing that L. paracasei ZFM54 can not only improve the acidity, water holding capacity and live lactic acid bacteria counts, but also improve many volatile acid contents and increase some beneficial nonvolatile metabolites, such as N-ethyl glycine and l-lysine, endowing the yogurt with more flavor and better function. The regulatory effects of the co-fermented yogurt on the intestinal microecology of volunteers were investigated by 16S rRNA sequencing and short-chain fatty acid (SCFA) analysis after consuming the yogurt for a 2-wk period, showing a better effect to increase the relative abundance of beneficial bacteria such as Ruminococcus and Alistipes, decrease harmful bacteria (Escherichia-Shigella and Enterobacter), and enhance the production of SCFA (acetate, propionate, and butyric acid) compared with the control yogurt. We found that L. paracasei ZFM54 can significantly improve the health benefits of yogurt, laying the foundation for its commercial application in improving gut microbiota.

In vitro fecal fermentation of acylated porous Canna edulis starch and corresponding stabilized Pickering emulsions

In this study, acylated porous Canna edulis starch with varying degrees of substitution (DS) were prepared and employed for stabilizing Pickering emulsions. Subsequently, the fermentation characteristics of them were investigated. Enzymatically produced porous starch (PS) was esterified with acetic, propionic, butyric, or valeric anhydrides, yielding acetylated (PSA-0.116), propionylated (PSP-0.163), butyrylated (PSB-0.304), and valerylated PS (PSV-0.462) with different DS. Scanning electron microscopy revealed the presence of pores and surface micro-particles in the modified PS, confirming successful esterification through characteristic peaks in 1H NMR and a CO peak at 1736 cm-1 in the FT-IR spectrum. With increasing DS, starch exhibited reduced crystallinity (PSV, 26.61 %), elevated resistant starch content (PSV, 91.63 %), and a higher contact angle (PSV, 87.13°). Acylated PS particles effectively stabilized Pickering emulsions. Pickering emulsions stabilized by acylated PS with higher DS exhibited higher emulsification index and smaller droplet sizes. In vitro fermentation of acylated PS and corresponding stabilized Pickering emulsions fostered short-chain fatty acid production, boosted the relative abundance of beneficial bacteria (Bifidobacterium, Prevotella, etc.) while inhibited the growth of harmful bacteria (Escherichia-Shigella, Comamonas, etc.), maintaining the intestinal microbiota balance. These findings support the potential applications of acylated PS and corresponding stabilized Pickering emulsions in functional foods and drug delivery.

Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People

The gut microbiome is one of the main factors affecting human health. It has been proven that probiotics can regulate the metabolism in the host body. A large number of people use probiotics not as medicines, but as a prophylactic supplement. The aim of our study was to evaluate the effect of lactic acid bacteria on the gut microbiome of healthy people using the V3 region of the 16S rRNA gene. Our study showed changes in the generic composition in the gut of healthy people when taking the supplement. There was an increase in the members responsible for the production of short-chain fatty acids in the gut of the host (Blautia, Fusicatenibacter, Eubacterium hallii group, Ruminococcus), as well as bacteria that improve intestinal homeostasis (Dorea and Barnesiella). There was also a decrease in the abundance of bacteria in the genera Catenibacterium, Hungatella, Escherichia-Shigella, and Pseudomonas, associated with an unhealthy profile of the human gut microbiome. An increase in members of the phylum Actinobacteriota was also observed, which has a positive effect on the host organism. Our results indicate that short-term prophylactic use of lactic acid bacteria-based supplements can be effective, as it contributes to a beneficial effect on the gut microbiome of healthy people.

Fine-scale geographic difference of the endangered Big-headed Turtle (Platysternon megacephalum) fecal microbiota, and comparison with the syntopic Beale's Eyed Turtle (Sacalia bealei)

BACKGROUND

Studies have elucidated the importance of gut microbiota for an organism, but we are still learning about the important influencing factors. Several factors have been identified in helping shape the microbiome of a host, and in this study we focus on two factors-geography and host. We characterize the fecal microbiota of the Big-headed Turtle (Platysternon megacephalum) and compare across a relatively fine geographic scale (three populations within an 8-km radius) and between two syntopic hosts (P. megacephalum and Sacalia bealei). Both species are endangered, which limits the number of samples we include in the study. Despite this limitation, these data serve as baseline data for healthy, wild fecal microbiotas of two endangered turtle species to aid in conservation management.

RESULTS

For geography, the beta diversity of fecal microbiota differed between the most distant sites. The genus Citrobacter significantly differs between sites, which may indicate a difference in food availability, environmental microbiota, or both. Also, we identify the common core microbiome for Platysternon across Hong Kong as the shared taxa across the three sites. Additionally, beta diversity differs between host species. Since the two species are from the same site and encounter the same environmental microbiota, we infer that there is a host effect on the fecal microbiota, such as diet or the recruitment of host-adapted bacteria. Lastly, functional analyses found metabolism pathways (KEGG level 1) to be the most common, and pathways (KEGG level 3) to be statistically significant between sites, but statistically indistinguishable between species at the same site.

CONCLUSIONS

We find that fecal microbiota can significantly differ at a fine geographic scale and between syntopic hosts. Also, the function of fecal microbiota seems to be strongly affected by geographic site, rather than species. This study characterizes the identity and function of the fecal microbiota of two endangered turtle species, from what is likely their last remaining wild populations. These data of healthy, wild fecal microbiota will serve as a baseline for comparison and contribute to the conservation of these two endangered species.

Enteric α-Defensin Contributes to Recovery of Radiation-Induced Intestinal Injury by Modulating Gut Microbiota and Fecal Metabolites

The effect of ionizing radiation on the gastrointestinal tract is a common complication of abdominal and pelvic radiotherapy. However, the pathological features of radiation enteropathy and its effective medical intervention regimen is still a global challenge. Here, we explored the role and mechanism of enteric alpha-defensins (EαDs) in protecting against radiation enteropathy. To address this, we utilized EαDs-deficiency mice, in which the matrix metallopeptidase 7 to activate Paneth cell α-defensins was knockout (KO) mice, and the complementary wild-type (WT) control mice for this study. Remarkably, the KO mice were more susceptible to 5.0 Gy total-body irradiation, resulting in worse clinic scores and lower survival rate, compared with the wild-type mice. Histological examination indicated that the KO mice were subjected to slow recovery of intestinal villus and mucosa function, characterized by the reduced expression of TFF3, Glut1 and Muc2. In addition, compared with the wild-type controls, the KO mice experienced serious inflammation response in intestinal tissue, indicated by the remarkably increased expression level of IL-1β, IL-6 and IL-12. Using high-throughput sequencing analysis, we found that the intestinal bacterial community of the KO mice was more prone to dysbiosis than that of the WT mice, with significantly increased abundance of opportunistic pathogenic bacteria, such as Streptococcus sp. and Escherichia-Shigella sp., whereas remarkably decreased probiotics harboring Lactobacillus sp., Desulfovibrio sp. etc. Fecal metabolomics analysis indicated that the relative abundance of 31 metabolites arose significantly different between WT and KO mice on day 10 after radiation exposure. A subset of differential metabolites to regulate host metabolism and immunity, such as acetic acid, acetate, butanoic acid, was negatively correlated with the alteration of gut microbiota in the irradiated KO mice. This study provides new insight into EαDs contribution to the recovery of radiation-induced intestinal damage, and suggests a potential novel target to prevent the adverse effects of radiotherapy.

Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods

Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.

White feces syndrome in Penaeus vannamei is potentially an Enterocytozoon hepatopenaei (EHP) associated pathobiome origin of Vibrio spp

White feces syndrome (WFS) is a commercially important disease in Penaeus vannamei (whiteleg shrimp) farming. The aetiology beyond the white or golden white midgut with mediocre growth performance producing a floating mass of white fecal strings in WFS-affected shrimp farms remains uncharted. To give WFS a perception of pathobiome, healthy P. vannamei shrimps were subjected to an enteric microsporidian Enterocytozoon hepatopenaei (EHP) infection along with Vibrio harveyi and V. alginolyticus in different combinations. Immune responses in haemolymph (total haemocyte count (THC), prophenoloxidase activity (proPO), respiratory burst activity (RBA), superoxide dismutase activity (SOD) and catalase activity (CAT)), plasma biochemical changes (aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase (ALP)) and digestive enzymes activity (alpha-amylase (AMY), lipase (LIP) and protease (PRO)) were assessed in the challenged shrimps at 5, 10 and 15 days post-infection (dpi). The microbial interactions between the EHP and Vibrio spp. have led to the formation of WFS in the challenged shrimps. The histological sections of the hepatopancreas revealed the presence of EHP along with colonized bacterial masses, leading to the formation of aggregated transformed microvilli (ATM) structures and increased sloughing of lipid vacuoles into the tubule lumen. A significantly decreased THC and increased proPO levels, dysregulated antioxidant system, prominent hepatic damage, reduced energy metabolism and higher lipid production were the key records supporting that EHP-associated WFS in P. vannamei is due to the pathobiome.

Consumption of Solnul™ Resistant Potato Starch Produces a Prebiotic Effect in a Randomized, Placebo-Controlled Clinical Trial

The effects of resistant starch at high doses have been well-characterized, but the potential prebiotic effects of resistant starch at doses comparable to oligosaccharide prebiotics have not been evaluated. A three-arm randomized, double-blind, placebo-controlled clinical trial was conducted to evaluate the effect of 3.5 g and 7 g daily doses of Solnul^™ resistant potato starch (RPS) on beneficial populations of gut bacteria and stool consistency after a 4-week period. The relative abundance of Bifidobacterium and Akkermansia was determined by employing 16Sv4 sequencing of stool samples. To assess the effect of RPS on laxation and bowel movements, stools were recorded and scored using the Bristol Stool Form Scale. Participants consuming 3.5 g/day of RPS experienced significantly greater changes in Bifidobacterium and Akkermansia compared to the placebo after 4 weeks. The number of diarrhea- and constipation-associated bowel movements were both significantly lower in the 3.5 g RPS arm compared to the placebo group. Participants consuming 7 g of RPS responded similarly to those in the 3.5 g arm. Our analyses demonstrate that Solnul^™ RPS has a prebiotic effect when consumed for 4 weeks at the 3.5 g per day dose, stimulating increases in beneficial health-associated bacteria and reducing diarrhea- and constipation-associated bowel movements when compared to the placebo group.

Altered Faecal Microbiota Composition and Structure of Ghanaian Children with Acute Gastroenteritis

Acute gastroenteritis (AGE) is a disease of global public health importance. Recent studies show that children with AGE have an altered gut microbiota relative to non-AGE controls. Yet, how the gut microbiota differs in Ghanaian children with and without AGE remains unclear. Here, we explore the 16S rRNA gene-based faecal microbiota profiles of Ghanaian children five years of age and younger, comprising 57 AGE cases and 50 healthy controls. We found that AGE cases were associated with lower microbial diversity and altered microbial sequence profiles relative to the controls. The faecal microbiota of AGE cases was enriched for disease-associated bacterial genera, including Enterococcus, Streptococcus, and Staphylococcus. In contrast, the faecal microbiota of controls was enriched for potentially beneficial genera, including Faecalibacterium, Prevotella, Ruminococcus, and Bacteroides. Lastly, distinct microbial correlation network characteristics were observed between AGE cases and controls, thereby supporting broad differences in faecal microbiota structure. Altogether, we show that the faecal microbiota of Ghanaian children with AGE differ from controls and are enriched for bacterial genera increasingly associated with diseases.

Bifidobacterium longum subsp. infantis FJSYZ1M3 ameliorates DSS-induced colitis by maintaining the intestinal barrier, regulating inflammatory cytokines, and modifying gut microbiota

B. longum subsp. infantis is a subspecies of Bifidobacterium longum, and very few strains are shown to have immunomodulatory effects. In the present study, the improvement of dextran sulphate sodium (DSS)-induced colitis by four B. longum subsp. infantis strains was compared. The results showed that B. longum subsp. infantis FJSYZ1M3 could significantly decrease disease activity index (DAI), inhibit weight loss and colon shortening, and attenuate colon tissue damage in DSS-induced colitis mice. And B. longum subsp. infantis FJSYZ1M3 intervention improved the integrity of intestinal tight junctions, relieved mucus layer damage and inhibited epithelial cell apoptosis, thereby maintaining the intestinal barrier. Additionally, B. longum subsp. infantis FJSYZ1M3 significantly affected the levels of inflammatory cytokines IL-6, IL-1β, and IL-10 in the colon, thus relieving inflammation in colitis mice. Furthermore, B. longum subsp. infantis FJSYZ1M3 could ameliorate gut microbiota disturbance caused by DSS exposure and increase the level of butyric acid in cecal contents. In general, these findings suggested that B. longum subsp. infantis FJSYZ1M3 alleviated DSS-induced colitis by maintaining the intestinal barrier, regulating inflammatory cytokines, and modifying the gut microbiota.

Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status

Background

Patients with chronic constipation (CC) show altered gut microbial composition.

Objectives

To compare the fecal microbiota with different constipation subtypes and to identify potential influencing factors.

Design

This is a prospective cohort study.

Methods

The stool samples of 53 individuals with CC and 31 healthy individuals were analyzed using 16S rRNA sequencing. The associations between microbiota composition and colorectal physiology, lifestyle factors, and psychological distress were analyzed.

Results

In all, 31 patients with CC were classified as having slow-transit constipation, and 22 were classified under normal-transit constipation. The relative abundance of Bacteroidaceae was lower, and the relative abundance of Peptostreptococcaceae, Christensenellaceae, and Clostridiaceae was higher in slow-transit than in normal-transit group. In all, 28 and 25 patients with CC had dyssynergic defecation (DD) and non-DD, respectively. The relative abundance of Bacteroidaceae and Ruminococcaceae was higher in DD than in non-DD. Rectal defecation pressure was negatively correlated with the relative abundance of Prevotellaceae and Ruminococcaceae but positively correlated with that of Bifidobacteriaceae in CC patients. Multiple linear regression analysis suggested that depression was a positive predictor of Lachnospiraceae relative abundance, and sleep quality was an independent predictor of decreased relative abundance of Prevotellaceae.

Conclusion

Patients with different CC subtypes showed different characteristics of dysbiosis. Depression and poor sleep were the main factors that affected the intestinal microbiota of patients with CC.

Plain language summary

Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status Patients with chronic constipation (CC) show altered gut microbial composition. Previous studies in CC are limited by lacking of subtype stratification, which is reflected in the lack of agreement in findings across the large number of microbiome studies. We analyzed stool microbiome of 53 CC patients and 31 healthy individuals using 16S rRNA sequencing. We found that the relative abundance of Bacteroidaceae was lower, and the relative abundance of Peptostreptococcaceae, Christensenellaceae, and Clostridiaceae was higher in slow-transit than in normal-transit CC patients. The relative abundance of Bacteroidaceae and Ruminococcaceae was higher in dyssynergic defecation (DD) than in non-DD patients with CC. In addition, depression was a positive predictor of Lachnospiraceae relative abundance, and sleep quality was an independent predictor of decreased relative abundance of Prevotellaceae in all CC patients. This study emphasizes patients with different CC subtypes have different characteristics of dysbiosis. Depression and poor sleep may be the main factors that affect the intestinal microbiota of patients with CC.

The gut microbiome of wild American marten in the Upper Peninsula of Michigan

Carnivores are ecologically important and sensitive to habitat loss and anthropogenic disruption. Here we measured trophic level and gut bacterial composition as proxies of carnivore ecological status across the Upper Peninsula, Michigan, for wild American marten (Martes americana; hereafter marten). In contrast to studies that have focused on omnivorous and herbivorous species, we find that marten, like other carnivore species without a cecum, are dominated by Firmicutes (52.35%) and Proteobacteria (45.31%) but lack Bacteroidetes. Additionally, a majority of the 12 major bacterial genera (occurring at ≥1%) are known hydrogen producers, suggesting these taxa may contribute to host energy requirements through fermentative production of acetate. Our study suggests that live trapping and harvest methods yield similar marten gut microbiome data. In addition, preserving undisturbed forest likely impacts marten ecology by measurably increasing marten trophic level and altering the gut microbiome. Our study underscores the utility of the gut microbiome as a tool to monitor the ecological status of wild carnivore populations.

Prevalence of Aeromonas spp. Infection in Pediatric Patients Hospitalized with Gastroenteritis in Latvia between 2020 and 2021

Purpose: Aeromonas species are emerging human enteric pathogens. However, there is no systematic analysis of Aeromonas infection in the pediatric population in Latvia. The aim of the study was to describe potential sources, prevalence of infection, associated virulence factors and antimicrobial resistance of Aeromonas spp. isolated from fecal samples. Methods: Stool samples (n = 1360) were obtained from the Children’s Clinical University Hospital between 2020 and 2021. The target population was pediatric patients, 0 to 18 years of age, with a preliminary diagnosis of gastroenteritis. Identification was performed by Maldi-TOF, antimicrobial resistance by Vitek2 and 9 virulence factors by polymerase chain reaction (PCR). Results: Aeromonas spp. were isolated in 50 stool samples; positive findings made up 3.6% of all study cases and included four species: A. hydrophila, A. caviae, A. veronii, and A. eucrenophila. In 42% of the samples, Aeromonas spp. appeared alongside the other significant pathogens: Campylobacter jejuni, Salmonella Enteritidis, Salmonella Typhimurium, Yersinia enterocolitica, norovirus, adenovirus, and rotavirus. The study population positive for Aeromonas spp. infection contained 28 male (56%) and 22 female (44%) patients; median age was 4.56 years. The most common symptoms were: diarrhea, blood in stool, vomiting, abdominal pain, and fever. Aside from expected natural resistance, no significant antibacterial resistance was detected. The presence of multiple virulence genes was noticed in all isolates. No statistically significant correlation was found between the virulence patterns, bacterial species, and the intensity of clinical symptoms. Discussion: According to the clinical data and the results of this study Aeromonas spp. has an important role in pediatric practice and requires appropriate attention and monitoring.

Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity

Gut microbes significantly impact animal health, yet research on the gut microbiota of most birds, especially raptors, is lacking. This study investigated the effects of dietary and environmental changes on the composition and abundance of gut microbiota in 17 rescued common kestrels (Falco tinnunculus) through 16S rRNA gene high-throughput sequencing of microorganisms in the feces of the birds. Firmicutes (relative abundance, 43.63%), Proteobacteria (37.26%), Actinobacteria (7.31%), and Bacteroidetes (5.48%) were the dominant phyla in the gut microbiota of the common kestrels. A comparison of the gut microbiota before and after captivity revealed that community composition and abundance of the common kestrel gut microbiota differed among different living conditions including diet and environment. At the phylum level, the abundance of Firmicutes was higher (P < 0.05), and that of Proteobacteria was lower (P < 0.05), after captivity (54.62 and 27.16%, respectively) compared with before captivity (33.67 and 46.41%, respectively), but no significant differences were found among other phyla. At the genus level, the abundance of Lactobacillus was higher (P < 0.05) after captivity (15.77%) compared with the abundance before captivity (5.02%). Hierarchical clustering and principal component analyses showed that common kestrels in different living conditions exhibited differences (P < 0.05) in gut microbiota at phylum and genus levels. Functional prediction of gene sequences using PICRUSt2 further revealed that pathways related to glucose metabolism and amino acid metabolism were enhanced (P < 0.05) after captivity. Collectively, the findings from this study demonstrated that the relative abundance of specific microbes in the gut of the rescued common kestrels either increased or decreased, and that dietary and environment changes might be the predominant factors affecting the gut microbiota of these birds during rescue or captivity.

Impact analysis of hydraulic loading rate on constructed wetland: Insight into the response of bulk substrate and root-associated microbiota

Constructed wetland (CW) is an environment-friendly and low-cost technology for nutrients removal from domestic wastewater. For a well-tuned CW, hydraulic loading rate (HLR) is one of the critical factors, particularly under the challenging circumstance of more frequent heavy rainfall events brought by global warming. In this study, a comprehensive investigation was conducted to explore the influence of different HLRs on the CW's bulk substrate and root-associated microbiota aiming to yield new insight for CW management from a hybrid perspective of environmental microbiology and engineering science. The response of the microbial community and associated nutrients removal performance under different HLR settings were analyzed after a one-year operation. Results showed that the bulk substrate and rhizosphere genera involved in desulfurization and denitrification, such as Ferritrophicum, Sulfurimonas, and Sulfurisoma, were enriched in the higher HLR condition and associated with the higher total nitrogen (TN) and nitrate nitrogen (NO₃^--N) removal compared to the lower HLR condition. Co-occurrence network analysis demonstrated a more complex network under the higher HLR condition. Besides, it was observed that more stochastic in microbial assembly under the higher HLR condition. Surprisingly, zoonotic pathogens were observed and showed a greater prevalence under the higher HLR condition, indicating the potential correlation between HLR and pathogen intrusion. Collectively, this study revealed that the microbiota could be significantly altered under different HLR conditions, thereby resulting in differences in nutrients removal performance.

A comparative study of the fecal microbiota of gray seal pups and yearlings - a marine mammal sentinel species

Gray seals (Halichoerus grypus) can act as sentinel species reflecting the condition of the environment they inhabit. Our previous research identified strains of pathogenic Campylobacter and Salmonella, originating from both human and agricultural animal hosts, on rectal swabs from live gray seal (H. grypus) pups and yearlings on the Isle of May, Scotland, UK. We examined rectal swabs from the same pup (n = 90) and yearling (n = 19) gray seals to gain further understanding into the effects of age-related changes (pup vs. yearling) and three different natal terrestrial habitats on seal pup fecal microbiota. DNA was extracted from a subset of rectal swabs (pups n = 23, yearlings n = 9) using an optimized procedure, and the V4 region of the 16S ribosomal RNA gene was sequenced to identify each individual's microbiota. Diversity in pup samples was lower (3.92 ± 0.19) than yearlings (4.66 ± 0.39) although not significant at the p = 0.05 level (p = 0.062) but differences in the composition of the microbiota were (p < 0.001). Similarly, differences between the composition of the microbiota from pups from three different terrestrial habitats (Pilgrim's Haven [PH], Rona Rocks [RR], and Tarbet Slope [TS]) were highly significant (p < 0.001). Pairwise tests showed significant differences between all three habitats: PH versus TS (p = 0.019), PH versus RR (p = 0.042) and TS versus RR (p = 0.020). This preliminary study suggests a general trend, that seal microbiomes are modified by both age and, in pups, different terrestrial habitats. Furthermore, knowledge of the microbiota species present has the potential to be used in determining the environmental quality index.

Experimental colonization with Blastocystis ST4 is associated with protective immune responses and modulation of gut microbiome in a DSS-induced colitis mouse model

Background

Blastocystis is a common gut protistan parasite in humans and animals worldwide, but its interrelationship with the host gut microbiota and mucosal immune responses remains poorly understood. Different murine models of Blastocystis colonization were used to examine the effect of a common Blastocystis subtype (ST4) on host gut microbial community and adaptive immune system.

Results

Blastocystis ST4-colonized normal healthy mice and Rag1^−/− mice asymptomatically and was able to alter the microbial community composition, mainly leading to increases in the proportion of Clostridia vadinBB60 group and Lachnospiraceae NK4A136 group, respectively. Blastocystis ST4 colonization promoted T helper 2 (Th2) response defined by interleukin (IL)-5 and IL-13 cytokine production, and T regulatory (Treg) induction from colonic lamina propria in normal healthy mice. Additionally, we observed that Blastocystis ST4 colonization can maintain the stability of bacterial community composition and induce Th2 and Treg immune responses to promote faster recovery from experimentally induced colitis. Furthermore, fecal microbiota transplantation of Blastocystis ST4-altered gut microbiome to colitis mice reduced the severity of colitis, which was associated with increased production of short-chain fat acids (SCFAs) and anti-inflammatory cytokine IL-10.

Conclusions

The data confirm our hypothesis that Blastocystis ST4 is a beneficial commensal, and the beneficial effects of Blastocystis ST4 colonization is mediated through modulating of the host gut bacterial composition, SCFAs production, and Th2 and Treg responses in different murine colonization models.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00018-022-04271-9.

Meta-analysis defines predominant shared microbial responses in various diseases and a specific inflammatory bowel disease signal

BACKGROUND

Gut microbial alteration is implicated in inflammatory bowel disease but is noted in other diseases. Systematic comparison to define similarities and specificities is hampered since most studies focus on a single disease.

RESULTS

We develop a pipeline to compare between disease cohorts starting from the raw V4 16S amplicon sequence variants. Including 12,838 subjects, from 59 disease cohorts, we demonstrate a predominant shared signature across diseases, indicating a common bacterial response to different diseases. We show that classifiers trained on one disease cohort predict relatively well other diseases due to this shared signal, and hence, caution should be taken when using such classifiers in real-world scenarios, where diseases are intermixed. Based on this common signature across a large array of diseases, we develop a universal dysbiosis index that successfully differentiates between cases and controls across various diseases and can be used for prioritizing fecal donors and samples with lower disease probability. Finally, we identify a set of IBD-specific bacteria, which can direct mechanistic studies and design of IBD-specific microbial interventions.

CONCLUSIONS

A robust non-specific general response of the gut microbiome is detected in a large array of diseases. Disease classifiers may confuse between different diseases due to this shared microbial response. Our universal dysbiosis index can be used as a tool to prioritize fecal samples and donors. Finally, the IBD-specific taxa may indicate a more direct association to gut inflammation and disease pathogenesis, and those can be further used as biomarkers and as future targets for interventions.

The Cutting Edge of Gastroenteritis: Advances in Understanding of Enteric Infection

ABSTRACT

In recent years, multiple advances have been made in the care, diagnosis, and mechanistic understanding of acute gastroenteritis (AGE). In this review, we discuss the current state of the art of diagnosis and management, as well as how changes in practice can improve care and decrease costs. We will discuss present study demonstrating the effect of AGE on the microbiome and how that may be linked to secondary effects or long-term changes. We will explore the use of novel technologies to further our capacity to understand how gastrointestinal infections occur and promulgate. Finally, will discuss advances in our understanding of how gastrointestinal infections capacitate other changes such as post-viral motility or other post viral intestinal dysfunction.

Bacterial Gut Microbiota and Infections During Early Childhood

Gut microbiota composition during the first years of life is variable, dynamic and influenced by both prenatal and postnatal factors, such as maternal antibiotics administered during labor, delivery mode, maternal diet, breastfeeding, and/or antibiotic consumption during infancy. Furthermore, the microbiota displays bidirectional interactions with infectious agents, either through direct microbiota-microorganism interactions or indirectly through various stimuli of the host immune system. Here we review these interactions during childhood until 5 years of life, focusing on bacterial microbiota, the most common gastrointestinal and respiratory infections and two well characterized gastrointestinal diseases related to dysbiosis (necrotizing enterocolitis and Clostridioides difficile infection). To date, most peer-reviewed studies on the bacterial microbiota in childhood have been cross-sectional and have reported patterns of gut dysbiosis during infections as compared to healthy controls; prospective studies suggest that most children progressively return to a "healthy microbiota status" following infection. Animal models and/or studies focusing on specific preventive and therapeutic interventions, such as probiotic administration and fecal transplantation, support the role of the bacterial gut microbiota in modulating both enteric and respiratory infections. A more in depth understanding of the mechanisms involved in the establishment and maintenance of the early bacterial microbiota, focusing on specific components of the microbiota-immunity-infectious agent axis is necessary in order to better define potential preventive or therapeutic tools against significant infections in children.

Evaluation of Bacterial Diversity and Evolutionary Dynamics of Gut Bifidobacterium longum Isolates Obtained from Older Individuals in Hubei Province, China

Bifidobacterium longum predominates in the human gut throughout the life span, from birth to old age, and could alter the intestinal microbial population and immune function in the elderly. We investigated the intestinal bacterial diversity in the elderly, and further evaluated the genetic diversity and population structure of B. longum. The results revealed a distinct difference in gut bacterial populations between the elderly from Xiangyang and its neighboring region, Enshi city. A total of 62 bifidobacterial strains were isolated, 30 of which were found to be B. longum. The multilocus sequence typing (MLST) analysis also revealed that 437 B. longum isolates from diverse regions worldwide, including the 30 isolated in this study, could be classified into 341 sequence types (STs). They could be further clustered into 10 clonal complexes and 127 singleton STs, indicating a highly genetic diversity among B. longum isolates. Two putative clone complexes (CCs) containing the isolates from Xiangyang were found to be geographically specific, and a 213-bp recombination fragment was detected. Phylogenetic trees divided these 437 isolates into three lineages, corresponding to the three subspecies of B. longum. It is noteworthy that two isolates from the elderly were identified to be B. longum subsp. suis, while the others were B. longum subsp. longum. Together, our study characterized the intestinal bacterial diversity and evolution of B. longum in the elderly, and it could contribute to further studies on the genotyping and discrimination of B. longum.

IMPORTANCEBifidobacterium longum are common inhabitants of the human gut throughout the life span, and have been associated with health-promoting effects, yet little is known about the genotype profile and evolution of these isolates. Our study showed that there was significant difference in gut bacterial community and abundance of B. longum between the elderly from two neighboring cities. Furthermore, the possible geographically specific STs, CCs, and intraspecies recombination fragment were found among the B. longum isolates from elderly.

Experimental reproduction of White Feces Syndrome in whiteleg shrimp, Penaeus vannamei

White Feces Syndrome (WFS) is an emergent disease of penaeid shrimp (Penaeus monodon and P. vannamei) that is identified by the presence of floating white fecal strings on pond water in grow-out ponds. Although the clinical manifestations of WFS are well defined, the underling etiology remains obscure. WFS has been associated with several enteric pathogens, including Enterocytozoon hepatopenaei (EHP). The association is based on studies that found areas where WFS has been reported, the prevalence and severity of EHP infection are high. In this study, we describe an experimental reproduction of WFS in P. vannamei pre-infected with EHP and challenged with a unique isolate of Vibrio parahaemolyticus isolated from the gastrointestinal tract of a shrimp displaying WFS. Upon laboratory challenge, shrimp displaying white fecal strings and white discoloration of the gastrointestinal tract were analyzed by histopathology, in-situ hybridization and quantitative PCR. Histological analysis confirmed the lesions of EHP and septic hepatopancreatic necrosis in the hepatopancreas of shrimp exposed to both pathogens. Quantitative PCR showed shrimp infected with both EHP and V. parahaemolyticus had a significantly higher load of EHP compared to shrimp infected with EHP alone. This is the first demonstration of experimental reproduction of WFS under laboratory conditions when animals are infected with EHP and V. parahaemolyticus concurrently. The data revealed a synergistic relation between EHP and V. parahaemolyticus isolate that led to the manifestation of WFS. We propose the gross signs of WFS can be used as an indicator of the presence of EHP infection in association with a particular strain of an enteric Vibrio spp. in countries where EHP is endemic.

Composition of Eukaryotic Viruses and Bacteriophages in Individuals with Acute Gastroenteritis

Metagenomics based on the next-generation sequencing (NGS) technique is a target-independent assay that enables the simultaneous detection and genomic characterization of all viruses present in a sample. There is a limited amount of data about the virome of individuals with gastroenteritis (GI). In this study, the enteric virome of 250 individuals (92% were children under 5 years old) with GI living in the northeastern and northern regions of Brazil was characterized. Fecal samples were subjected to NGS, and the metagenomic analysis of virus-like particles (VLPs) identified 11 viral DNA families and 12 viral RNA families. As expected, the highest percentage of viral sequences detected were those commonly associated with GI, including rotavirus, adenovirus, norovirus (94.8%, 82% and 71.2%, respectively). The most common co-occurrences, in a single individual, were the combinations of rotavirus-adenovirus, rotavirus-norovirus, and norovirus-adenovirus (78%, 69%, and 62%, respectively). In the same way, common fecal-emerging human viruses were also detected, such as parechovirus, bocaporvirus, cosavirus, picobirnavirus, cardiovirus, salivirus, and Aichivirus. In addition, viruses that infect plants, nematodes, fungi, protists, animals, and arthropods could be identified. A large number of unclassified viral contigs were also identified. We show that the metagenomics approach is a powerful and promising tool for the detection and characterization of different viruses in clinical GI samples.

The role of gut and genital microbiota and the estrobolome in endometriosis, infertility and chronic pelvic pain

BACKGROUND

Endometriosis is a chronic, burdensome condition that is historically understudied. Consequently, there is a lack of understanding of the etiology of the disease and its associated symptoms, including infertility and chronic pelvic pain (CPP). Endometriosis development is influenced by estrogen metabolism and inflammation, which are modulated by several factors including the microbiome and the estrobolome (the collection of genes encoding estrogen-metabolizing enzymes in the gut microbiome). Therefore, there is increasing interest in understanding the role of microbiota in endometriosis etiology.

OBJECTIVE AND RATIONALE

To date, there is no cure for endometriosis and treatment options often are ineffective. This manuscript will review the potential relationship between the microbiome and endometriosis, infertility and CPP and highlight the available data on the microbiome in relation to endometriosis and its related symptoms. The overarching goal of this manuscript is to inform future microbiome research that will lead to a deeper understanding of the etiology of the disease and possible diagnostic modalities and treatments. The potential impact of the microbiome on estrogen regulation modulated by the estrobolome, as well as inflammation and other endometriosis-promoting mechanisms within the genital tract, will be reviewed. The methodological limitations of microbiome-related studies will be critically assessed to provide improved guidelines for future microbiome and clinical studies.

SEARCH METHODS

PubMed databases were searched using the following keywords: endometriosis AND microbiome, infertility AND microbiome, pelvic pain AND microbiome, IVF (in-vitro fertilization) AND microbiome, endometriosis AND infertility. Clinical and preclinical animal trials that were eligible for review, and related to microbiome and endometriosis, infertility or CPP were included. All available manuscripts were published in 2002-2021.

OUTCOMES

In total, 28 clinical and 6 animal studies were included in the review. In both human and animal studies, bacteria were enriched in endometriosis groups, although there was no clear consensus on specific microbiota compositions that were associated with endometriosis, and no studies included infertility or CPP with endometriosis. However, bacterial vaginosis-associated bacteria and Lactobacillus depletion in the cervicovaginal microbiome were associated with endometriosis and infertility in the majority (23/28) of studies. Interpretation of endometrial studies is limited owing to a variety of methodological factors, discussed in this review. In addition, metadata outlining antibiotic usage, age, race/ethnicity, menopausal status and timing of sample collection in relation to diagnosis of endometriosis was not consistently reported. Animal studies (6/6) support a bidirectional relationship between the gut microbiota and endometriosis onset and progression.

WIDER IMPLICATIONS

There is evidence that a dysbiotic gut or genital microbiota is associated with multiple gynecologic conditions, with mounting data supporting an association between the microbiome and endometriosis and infertility. These microbiomes likely play a role in the gut-brain axis, which further supports a putative association with the spectrum of symptoms associated with endometriosis, including infertility and CPP. Collectively, this review highlights the demand for more rigorous and transparent methodology and controls, consistency across the field, and inclusion of key demographic and clinical characteristics of disease and comparison participants. Rigorous study designs will allow for a better understanding of the potential role of the microbiome in endometriosis etiology and the relationship to other disorders of the female reproductive tract.

Cross-Sectional Study on the Gut Microbiome of Parkinson's Disease Patients in Central China

Gastrointestinal dysfunction plays an important role in the occurrence and development of Parkinson's disease (PD). This study investigates the composition of the gut microbiome using shotgun metagenomic sequencing in PD patients in central China. Fecal samples from 39 PD patients (PD group) and the corresponding 39 healthy spouses of the patients (SP) were collected for shotgun metagenomics sequencing. Results showed a significantly altered microbial composition in the PD patients. Bilophila wadsworthia enrichment was found in the gut microbiome of PD patients, which has not been reported in previous studies. The random forest (RF) model, which identifies differences in microbiomes, reliably discriminated patients with PD from controls; the area under the receiver operating characteristic curve was 0.803. Further analysis of the microbiome and clinical symptoms showed that Klebsiella and Parasutterella were positively correlated with the duration and severity of PD, whereas hydrogen-generating Prevotella was negatively correlated with disease severity. The Cluster of Orthologous Groups of protein database, the KEGG Orthology database, and the carbohydrate-active enzymes of gene-category analysis showed that branched-chain amino acid-related proteins were significantly increased, and GH43 was significantly reduced in the PD group. Functional analysis of the metagenome confirmed differences in microbiome metabolism in the PD group related to short-chain fatty acid precursor metabolism.

Long-term changes in the gut microbiota after triple therapy, sequential therapy, bismuth quadruple therapy and concomitant therapy for Helicobacter pylori eradication in Chinese children

BACKGROUND

We previously reported that the administration of 14-day standard triple therapy (TT), sequential therapy (ST), bismuth-based quadruple therapy (BT), and concomitant therapy (CT) as the first-line therapy for Helicobacter pylori infection in Chinese children achieved eradication rates of 74.1%, 69.5%, 89.8%, and 84.6%, respectively. In this follow-up study, we further evaluated the short- and long-term effects of the four regimens on the gut microbiota in these children.

METHODS

We prospectively recruited treatment-naïve children with H. pylori infection. Fecal samples were collected at week 0, 2, 6, and 52, and alterations in the gut microbiota were analyzed by 16S rRNA gene sequencing.

RESULTS

Sixty-three patients participated in this study (16 with TT, 15 with ST, 16 with BT and 16 with CT). At week 2, the alpha diversity (Shannon and Chao 1 index) was significantly reduced in the TT (p = 0.008, p < 0.001), ST (p < 0.001, p < 0.001), BT (p < 0.001, p < 0.001) and CT groups (p < 0.001, p < 0.001). Some changes persisted in the ST, BT, and CT groups at week 6, and all were restored (expect p = 0.02 with Chao 1 index in the CT group) at week 52. The beta diversity was significantly changed in the BT (p = 0.001) and CT groups (p = 0.001) 2 weeks post-eradication and restored 1 year after therapy. Immediately after therapy, the relative abundance of Proteobacteria was strikingly increased in the ST (p = 0.005), BT (p < 0.001) and CT groups (p < 0.001), and the genus-level analysis showed that the abundances of 23.1%, 43.3%, 78.6%, and 78% of the bacterial genera in the TT, ST, BT, and CT groups were significantly changed. All these changes returned to almost the pre-eradication level 1 year post-eradication.

CONCLUSION

Eradication of H. pylori infection can lead to transient dysbiosis of gut microbiota, and these changes almost recovered 1 year post-eradication, which indicates the long-term safety of H. pylori therapy.

Review: Effect of Gut Microbiota and Its Metabolite SCFAs on Radiation-Induced Intestinal Injury

Gut microbiota is regarded as the second human genome and forgotten organ, which is symbiotic with the human host and cannot live and exist alone. The gut microbiota performs multiple physiological functions and plays a pivotal role in host health and intestinal homeostasis. However, the gut microbiota can always be affected by various factors and among them, it is radiotherapy that results in gut microbiota ¹²dysbiosis and it is often embodied in a decrease in the abundance and diversity of gut microbiota, an increase in harmful bacteria and a decrease in beneficial bacteria, thereby affecting many disease states, especially intestine diseases. Furthermore, gut microbiota can produce a variety of metabolites, among which short-chain fatty acids (SCFAs) are one of the most abundant and important metabolites. More importantly, SCFAs can be identified as second messengers to promote signal transduction and affect the occurrence and development of diseases. Radiotherapy can lead to the alterations of SCFAs-producing bacteria and cause changes in SCFAs, which is associated with a variety of diseases such as radiation-induced intestinal injury. However, the specific mechanism of its occurrence is not yet clear. Therefore, this review intends to emphasize the alterations of gut microbiota after radiotherapy and highlight the alterations of SCFAs-producing bacteria and SCFAs to explore the mechanisms of radiation-induced intestinal injury from the perspective of gut microbiota and its metabolite SCFAs.

Stool pattern is associated with not only the prevalence of tumorigenic bacteria isolated from fecal matter but also plasma and fecal fatty acids in healthy Japanese adults

BACKGROUND

Colibactin-producing Escherichia coli containing polyketide synthase (pks⁺ E. coli) has been shown to be involved in colorectal cancer (CRC) development through gut microbiota analysis in animal models. Stool status has been associated with potentially adverse gut microbiome profiles from fecal analysis in adults. We examined the association between stool patterns and the prevalence of pks⁺ E. coli isolated from microbiota in fecal samples of 224 healthy Japanese individuals.

RESULTS

Stool patterns were determined through factorial analysis using a previously validated questionnaire that included stool frequency, volume, color, shape, and odor. Factor scores were classified into tertiles. The prevalence of pks⁺ E. coli was determined by using specific primers for pks⁺ E. coli in fecal samples. Plasma and fecal fatty acids were measured via gas chromatography-mass spectrometry. The prevalence of pks⁺ E. coli was 26.8%. Three stool patterns identified by factorial analysis accounted for 70.1% of all patterns seen (factor 1: lower frequency, darker color, and harder shape; factor 2: higher volume and softer shape; and factor 3: darker color and stronger odor). Multivariable-adjusted odds ratios (95% confidence intervals) of the prevalence of pks⁺ E. coli for the highest versus the lowest third of the factor 1 score was 3.16 (1.38 to 7.24; P for trend = 0.006). This stool pattern exhibited a significant positive correlation with fecal isobutyrate, isovalerate, valerate, and hexanoate but showed a significant negative correlation with plasma eicosenoic acid and α-linoleic acid, as well as fecal propionate and succinate. No other stool patterns were significant.

CONCLUSIONS

These results suggest that stool patterns may be useful in the evaluation of the presence of tumorigenic bacteria and fecal fatty acids through self-monitoring of stool status without the requirement for specialist technology or skill. Furthermore, it may provide valuable insight about effective strategies for the early discovery of CRC.

New insights into the interactions between Blastocystis, the gut microbiota, and host immunity

The human gut microbiota is a diverse and complex ecosystem that is involved in beneficial physiological functions as well as disease pathogenesis. Blastocystis is a common protistan parasite and is increasingly recognized as an important component of the gut microbiota. The correlations between Blastocystis and other communities of intestinal microbiota have been investigated, and, to a lesser extent, the role of this parasite in maintaining the host immunological homeostasis. Despite recent studies suggesting that Blastocystis decreases the abundance of beneficial bacteria, most reports indicate that Blastocystis is a common component of the healthy gut microbiome. This review covers recent finding on the potential interactions between Blastocystis and the gut microbiota communities and its roles in regulating host immune responses.

Long-term changes in the gut microbiota after 14-day bismuth quadruple therapy in penicillin-allergic children

BACKGROUND

Penicillin-allergic children who are infected with Helicobacter pylori constitute a relatively common subgroup. We aimed to study the short-term and long-term effects of bismuth quadruple therapy on gut microbiota in penicillin-allergic children.

METHODS

We prospectively recruited treatment-naive children with H pylori infection and H pylori-negative asymptomatic children as healthy controls. Patients received 14-day bismuth quadruple therapy consisting of omeprazole, clarithromycin, metronidazole, and bismuth. Fecal samples were collected at weeks 0, 2, 6, and 52. Alterations in the gut microbiota were analyzed by 16S rRNA gene sequencing.

RESULTS

Twenty-two subjects (14 gastritis patients, 8 duodenal ulcer patients) and 23 controls participated in this study. At week 2, alpha diversity was reduced in both gastritis (P < .05) and ulcer (except P = .16 with Chao 1 index) patients compared with baseline. Some changes persisted at week 6, and all were restored at week 52. Beta diversity was significantly altered 2 weeks after treatment in the gastritis and duodenal ulcer groups (P = .001, P = .002, respectively) and restored at weeks 6 and 52. The mean relative abundance of Bacteroidetes (P < .001, P = .005, respectively) decreased and that of Proteobacteria increased (P < .001, P = .03, respectively). All alterations recovered at week 6 and 52. In both the gastritis and ulcer groups at week 2, some beneficial bacteria were decreased including Bacteroides (P < .001 and P = .003), Faecalibacterium (P < .001 and P = .02), Phascolarctobacterium (P = .002 and P = .004), Roseburia ( P < .001 and P = .13), Bifidobacterium (P = .08 and P = .04), and Blautia (P < .001 and P = .002). Some detrimental bacteria were increased including Escherichia-Shigella (P < .001 and P = .19), Klebsiella (P < .001, and P = .09), Enterococcus (P < .001 and P = .007), and Streptococcus (P = .002 and P = .004). The changes returned to almost the pre-eradication level 1 year after therapy.

CONCLUSION

Bismuth quadruple therapy causes short-term dysbiosis of the gut microbiota. Most changes recovered 1-year post-eradication, indicating the long-term safety of H pylori therapy.

Obesity Measures and Dietary Parameters as Predictors of Gut Microbiota Phyla in Healthy Individuals

The dynamics and diversity of human gut microbiota that can remarkably influence the wellbeing and health of the host are constantly changing through the host’s lifetime in response to various factors. The aim of the present study was to determine a set of parameters that could have a major impact on classifying subjects into a single cluster regarding gut bacteria composition. Therefore, a set of demographical, environmental, and clinical data of healthy adults aged 25–50 years (117 female and 83 men) was collected. Fecal microbiota composition was characterized using Illumina MiSeq 16S rRNA gene amplicon sequencing. Hierarchical clustering was performed to analyze the microbiota data set, and a supervised machine learning model (SVM; Support Vector Machines) was applied for classification. Seventy variables from collected data were included in machine learning analysis. The agglomerative clustering algorithm suggested the presence of four distinct community types of most abundant bacterial phyla. Each cluster harbored a statistically significant different proportion of bacterial phyla. Regarding prediction, the most important features classifying subjects into clusters were measures of obesity (waist to hip ratio, BMI, and visceral fat index), total body water, blood pressure, energy intake, total fat, olive oil intake, total fiber intake, and water intake. In conclusion, the SVM model was shown as a valuable tool to classify healthy individuals based on their gut microbiota composition.

Critical Network Structures and Medical Ecology Mechanisms Underlying Human Microbiome-Associated Diseases

A fundamental problem in studies on human microbiome-associated diseases (MADs) is to understand the relationships between microbiome structures and health status of hosts. For example, species diversity metrics have been routinely evaluated in virtually all studies on MADs, yet a recent meta-analysis revealed that, in only approximately one-third of the cases, diversity and diseases were related. In this study, we ask whether Hubbell's neutral theory (supplemented with the normalized stochasticity ratio [NSR]) or critical microbiome network structures may offer better alternatives. Whereas neutral theory and NSR focus on stochastic processes, we use core/periphery and high-salience skeleton networks to evaluate deterministic, asymmetrical niche effects, assuming that all species or their interactions were not “born” equal and focusing on non-neutral, critical network structures. We found that properties of critical network structures are more indicative of disease effects. Finally, seven findings (mechanisms, interpretations, and postulations) regarding medical ecology mechanisms underlying MADs were summarized.

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Seven findings (mechanisms/interpretations/postulations) of medical ecology proposed

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Critical network structures more indicative of disease effects than ecology metrics

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One-third seems ceiling of diversity-disease relations, half to two-thirds of network structures

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Super resilience (unexplained one-third to half gap) is likely attributed to host genome

Microbiota- and Radiotherapy-Induced Gastrointestinal Side-Effects (MARS) Study: A Large Pilot Study of the Microbiome in Acute and Late-Radiation Enteropathy

PURPOSE

Radiotherapy is important in managing pelvic cancers. However, radiation enteropathy may occur and can be dose limiting. The gut microbiota may contribute to the pathogenesis of radiation enteropathy. We hypothesized that the microbiome differs between patients with and without radiation enteropathy.Experimental Design: Three cohorts of patients (n = 134) were recruited. The early cohort (n = 32) was followed sequentially up to 12 months post-radiotherapy to assess early radiation enteropathy. Linear mixed models were used to assess microbiota dynamics. The late cohort (n = 87) was assessed cross-sectionally to assess late radiation enteropathy. The colonoscopy cohort compared the intestinal mucosa microenvironment in patients with radiation enteropathy (cases, n = 9) with healthy controls (controls, n = 6). Fecal samples were obtained from all cohorts. In the colonoscopy cohort, intestinal mucosa samples were taken. Metataxonomics (16S rRNA gene) and imputed metataxonomics (Piphillin) were used to characterize the microbiome. Clinician- and patient-reported outcomes were used for clinical characterization.

RESULTS

In the acute cohort, we observed a trend for higher preradiotherapy diversity in patients with no self-reported symptoms (P = 0.09). Dynamically, diversity decreased less over time in patients with rising radiation enteropathy (P = 0.05). A consistent association between low bacterial diversity and late radiation enteropathy was also observed, albeit nonsignificantly. Higher counts of Clostridium IV, Roseburia, and Phascolarctobacterium significantly associated with radiation enteropathy. Homeostatic intestinal mucosa cytokines related to microbiota regulation and intestinal wall maintenance were significantly reduced in radiation enteropathy [IL7 (P = 0.05), IL12/IL23p40 (P = 0.03), IL15 (P = 0.05), and IL16 (P = 0.009)]. IL15 inversely correlated with counts of Roseburia and Propionibacterium.

CONCLUSIONS

The microbiota presents opportunities to predict, prevent, or treat radiation enteropathy. We report the largest clinical study to date into associations of the microbiota with acute and late radiation enteropathy. An altered microbiota associates with early and late radiation enteropathy, with clinical implications for risk assessment, prevention, and treatment of radiation-induced side-effects.See related commentary by Lam et al., p. 6280.

Association Between Repeated Episodes of Gastroenteritis and Mental Health Problems in Childhood and Adolescence

OBJECTIVE

The Avon Longitudinal Study of Parents and Children (ALSPAC) and Maternal Adversity, Vulnerability and Neurodevelopment (MAVAN) cohorts were used to determine whether repeated exposure to gastroenteritis in early life could predict risk for psychiatric problems in childhood and in ALSPAC adolescents. We determined whether inflammatory biomarkers moderated the association between repeated gastroenteritis and mental health in adolescents from ALSPAC.

METHOD

Episodes of gastroenteritis from birth to 30 and 36 months were reported by mothers. Psychological problems were assessed using the total difficulties and subscale scores on the Revised Rutter Parent Scale for Preschool Children at 42 months and the Strengths and Difficulties Questionnaire (SDQ) at 81 months in ALSPAC. Presence of psychiatric disorders at 15.5 years was assessed using the Development and Well-Being Assessment (DAWBA) in ALSPAC. In the MAVAN replication cohort, total difficulties were assessed on the SDQ at 60 and 72 months. Serum interleukin-6 (IL-6) and C-reactive protein (CRP) at 9.5 years and CRP at 15.5 years were measured in ALSPAC participants.

RESULTS

Repeated gastroenteritis associated with the total difficulties score in ALSPAC and MAVAN children. The β values were small, indicating that the clinical relevance of these findings requires further investigation. Repeated gastroenteritis was significantly associated with an increased prevalence of externalizing disorders at age 15.5 years, but odds ratios were small. CRP or IL-6 at 9.5 years or CRP at 15.5 years did not significantly moderate the association between repeated gastroenteritis and prevalence of psychiatric disorders.

CONCLUSION

Identifying factors associated with vulnerability to psychopathology is key to early identification of individuals at risk.

Meta-taxonomic analysis of prokaryotic and eukaryotic gut flora in stool samples from visceral leishmaniasis cases and endemic controls in Bihar State India

Visceral leishmaniasis (VL) caused by Leishmania donovani remains of public health concern in rural India. Those at risk of VL are also at risk of other neglected tropical diseases (NTDs) including soil transmitted helminths. Intestinal helminths are potent regulators of host immune responses sometimes mediated through cross-talk with gut microbiota. We evaluate a meta-taxonomic approach to determine the composition of prokaryotic and eukaryotic gut microflora using amplicon-based sequencing of 16S ribosomal RNA (16S rRNA) and 18S rRNA gene regions. The most abundant bacterial taxa identified in faecal samples from Bihar State India were Prevotella (37.1%), Faecalibacterium (11.3%), Escherichia-Shigella (9.1%), Alloprevotella (4.5%), Bacteroides (4.1%), Ruminococcaceae UCG-002 (1.6%), and Bifidobacterium (1.5%). Eukaryotic taxa identified (excluding plant genera) included Blastocystis (57.9%; Order: Stramenopiles), Dientamoeba (12.1%; Family: Tritrichomonadea), Pentatrichomonas (10.1%; Family: Trichomonodea), Entamoeba (3.5%; Family: Entamoebida), Ascaridida (0.8%; Family: Chromodorea; concordant with Ascaris by microscopy), Rhabditida (0.8%; Family: Chromodorea; concordant with Strongyloides), and Cyclophyllidea (0.2%; Order: Eucestoda; concordant with Hymenolepis). Overall alpha (Shannon's, Faith's and Pielou's indices) and beta (Bray-Curtis dissimilarity statistic; weighted UniFrac distances) diversity of taxa did not differ significantly by age, sex, geographic subdistrict, or VL case (N = 23) versus endemic control (EC; N = 23) status. However, taxon-specific associations occurred: (i) Ruminococcaceae UCG- 014 and Gastranaerophilales_uncultured bacterium were enriched in EC compared to VL cases; (ii) Pentatrichomonas was more abundant in VL cases than in EC, whereas the reverse occurred for Entamoeba. Across the cohort, high Escherichia-Shigella was associated with reduced bacterial diversity, while high Blastocystis was associated with high bacterial diversity and low Escherichia-Shigella. Individuals with high Blastocystis had low Bacteroidaceae and high Clostridiales vadin BB60 whereas the reverse held true for low Blastocystis. This scoping study provides useful baseline data upon which to develop a broader analysis of pathogenic enteric microflora and their influence on gut microbial health and NTDs generally.

Phthalate exposure alters gut microbiota composition and IgM vaccine response in human newborns

Postnatal exposure to di-(2-ethylhexyl) phthalate (DEHP), a common plasticizer, is associated with allergy development in childhood, suggesting that DEHP exposure may dysregulate immune response in infants. We investigated whether DEHP exposure in newborns through medical treatment affected the gut microbiota pattern and vaccine response, which are both related to immune development. In this prospective cohort study from May 1, 2016 through July 31, 2017, newborns with respiratory distress who were given intravenous infusions (IVs) were enrolled as the DEHP group, and newborns who did not receive IVs were enrolled as the control group. We excluded patients with perinatal maternal probiotics, vaginal delivery, antibiotic treatment, and exclusive human milk or formula feeding. Of 118 infants, urinary phthalate metabolite analysis revealed that the calculated DEHP concentrations of the newborns treated with IVs (n = 15) were higher than those in the control group (n = 10) (p = 0.0001). DEHP exposure altered bacterial communities both in composition and diversity, particularly decreases in Rothia sp. and Bifidobacterium longum in the DEHP group. Furthermore, DEHP exposure significantly enhanced anti-HBsAg-IgM responses in the DEHP group (p = 0.013). Early-life DEHP exposure alter gut microbiota of newborns and may change their immune responses in later life.