Fecal Microbes Research Articles

Revealing potential mechanisms of native and non-native snail coexistence through fecal microbiomes and dietary compositions

Understanding how animals coexist within an ecosystem is essential for the conservation of biodiversity. In China, large populations of a non-native snail Rumina decollata (a highly invasive species reported by various other countries) coexist with two native snail species (Acusta ravida and Euphaedusa aculus). However, the potential mechanisms that facilitate this non-native and native snail coexistence remain uncertain. Here, we analyzed the fecal microbiomes and dietary compositions of R. decollata, A. ravida, and E. aculus to elucidate the mechanisms that drive the cohabitation of non-native and native species in Nanjing, China. It was found that the composition of the E. aculus fecal microbiome was similar to that of R. decollata, while it was significantly different from that of A. ravida. Furthermore, R. decollata preyed on E. aculus and had similar plant food compositions like A. ravida. These results indicated that the fecal microbiomes of snails may be adaptable to variable environmental conditions, while being minimally influenced by host genetics. R. decollata integrated a portion of the fecal microbes of E. aculus by preying on them. Our findings highlighted that the coexistence of R. decollata with native snails may have been due to abundant environmental resources, which negated the emergence of strong competition. However, the specific dietary changes of R. decollata and their propagation still need to be continuously monitored to better understand the long-term effects of R. decollata on ecosystems. This research provides a new understanding toward the prevention of invasive species and biodiversity conservation.

Fecal Microbiome Composition Correlates with Pathologic Complete Response in Patients with Operable Esophageal Cancer Treated with Combined Chemoradiotherapy and Immunotherapy.

Background: Preclinical and clinical data indicate that chemoradiotherapy (CRT) in combination with checkpoint inhibitors may prime an anti-tumor immunological response in esophageal cancer. However, responses to neoadjuvant therapy can vary widely and the key biomarkers to determine response remain poorly understood. The fecal microbiome is a novel and potentially modifiable biomarker of immunotherapy response, and both fecal and tumor microbes have been found to associate with outcomes in esophageal cancer. Methods: Fecal and tumor samples were collected from patients with stage II-III resectable esophageal or gastroesophageal junction carcinoma treated with neoadjuvant immune checkpoint inhibitors (ICIs) plus CRT prior to surgical resection. Microbiome profiles were analyzed by 16S rRNA amplicon sequencing and taxonomic data were integrated with fecal metabolite analysis to assess microbial function. Results: The fecal microbiome of patients with pathological complete response (PCR) grouped in distinct clusters compared to patients with residual viable tumor (RVT) by Bray-Curtis diversity metric. Integrated taxonomic and metabolomic analysis of fecal samples identified a sphingolipid and primary bile acid as enriched in the PCR, the levels of which correlated with several bacterial species: Roseburis inulinivorans, Ruminococcus callidus, and Fusicantenibacter saccharivorans. Analysis of the tumor microbiome profiles identified several bacterial genera previously associated with esophageal tumors, including Streptococcus and Veillonella. Conclusions: These results further characterize the fecal and tumor microbiome of patients with operable esophageal cancer and identify specific microbes and metabolites that may help elucidate how microbes contribute to tumor response with neoadjuvant CRT combined with ICI.

Cultured fecal microbial community and its impact as fecal microbiota transplantation treatment in mice gut inflammation

The fecal microbiome is identical to the gut microbial communities and provides an easy access to the gut microbiome. Therefore, fecal microbial transplantation (FMT) strategies have been used to alter dysbiotic gut microbiomes with healthy fecal microbiota, successfully alleviating various metabolic disorders, such as obesity, type 2 diabetes, and inflammatory bowel disease (IBD). However, the success of FMT treatment is donor-dependent and variations in gut microbes cannot be avoided. This problem may be overcome by using a cultured fecal microbiome. In this study, a human fecal microbiome was cultured using five different media; growth in brain heart infusion (BHI) media resulted in the highest microbial community cell count. The microbiome (16S rRNA) data demonstrated that the cultured microbial communities were similar to that of the original fecal sample. Therefore, the BHI-cultured fecal microbiome was selected for cultured FMT (cFMT). Furthermore, a dextran sodium sulfate (DSS)-induced mice-IBD model was used to confirm the impact of cFMT. Results showed that cFMT effectively alleviated IBD-associated symptoms, including improved gut permeability, restoration of the inflamed gut epithelium, decreased expression of pro-inflammatory cytokines (IFN-γ, TNF-α, IL-1, IL-6, IL-12, and IL-17), and increased expression of anti-inflammatory cytokines (IL-4 and IL-10). Thus, study’s findings suggest that cFMT can be a potential alternative to nFMT.Key points• In vitro fecal microbial communities were grown in a batch culture using five different media.• Fecal microbial transplantation was performed on DSS-treated mice using cultured and normal fecal microbes.• Cultured fecal microbes effectively alleviated IBD-associated symptoms.Graphical

Faecal microbiota transplantation associated adverse events

Abstract Faecal microbiota transplantation (FMT) aims to restore intestinal microbiota balance with the objective of normalising its composition and achieve therapeutic benefits. The procedure involves the administration of fresh or frozen faecal microbes from a healthy donor into the recipient’s gastrointestinal tract with the intent to restore the proper structure and functionality of the recipient’s intestinal microbial community. Evidence showing the positive effects of FMT is abundant, however, less attention has been devoted to FMT-associated adverse events, especially in relation to liver diseases. Based on literature review, studies and reports regarding FMT-associated adverse events since the beginning of FMT use, have been analysed. The review covering the period 2010-2022 was undertaken in accordance with the PRISMA guidelines. Studies conducted on the patient population suffering from various types and forms of liver disease have proven the possible effectiveness of the FMT method and reported moderate adverse events (nausea, constipation, flatulence). Severe adverse events occurring in relation to FMT were also noted. No safety issues or infection signals associated with FMT were observed in studies performed within the population suffering from cirrhosis. The present review of scientific reports, publications and literature reviews describes the adverse events reported in the literature. Faecal microbiota transplants are associated with adverse events classified as mild, moderate and severe, among others, diarrhoea, fever, infections or death. There is a need to implement a donor screening programme and personalised transplantation methods. Further research is recommended to assess and monitor FMT efficacy, benefits and risks.

Abstract 42: Fecal Microbiota Transplantation Decreases Autoantibody Production and Lowers Blood Pressure in an Experimental Model of Autoimmune Disease

Systemic lupus erythematosus (SLE) is a chronic multisystem autoimmune disorder that disproportionately affects women. It is characterized by a breach of immunological self-tolerance and the expansion of autoreactive T and B lymphocytes, leading to the production of autoantibodies. Autoantibody production leads to downstream chronic inflammation resulting in high rates of hypertension, renal injury, and cardiovascular disease. Gut dysbiosis is associated with many autoimmune diseases, including SLE. In the present study, we hypothesized that gut dysbiosis in SLE may play a role in the development of immune system dysfunction and hypertension in an experimental model of SLE, and that fecal microbiota transplantation (FMT) with microbes from control mice may improve these parameters. To test this hypothesis, we treated 26-week-old female control (NZW, n=10) and SLE (NZBWF1, n=9) mice with broad spectrum antibiotics in drinking water for one week to deplete the existing microbiota. Subsequently, mice were given 0.1 mL of fecal microbes from either control or SLE mice via oral gavage two times per week for four weeks in the following groups (n=9-10 mice/group): Control-vehicle, Control-SLE microbes, SLE-vehicle, SLE-Control microbes. Changes in the gut microbiome after FMT were assessed by metagenomic sequencing of fecal pellets from all four groups. Mean arterial pressure (MAP, mmHg) was higher in SLE mice compared to control mice (Control: 112±3 vs. SLE: 140±2 mmHg, p<0.0001). SLE mice that received FMT with control microbes had lower blood pressure (SLE-FMT: 126±4 mmHg, p=0.03). While there were no changes in circulating and splenic B cell percentages, SLE mice had significantly higher percentages of CD11b + CD11c + autoimmune-associated B cells compared to control mice (Control: 0.41±0.04% vs. SLE: 1.2±0.1%, p=0.0006), which were significantly decreased in SLE-FMT mice (SLE-FMT: 0.76±0.1%, p=0.02). Circulating autoantibodies were also measured at the conclusion of the study. Anti-dsDNA IgG was elevated in SLE mice compared to control (Control: 149±38 vs. SLE: 527±114 kU/mL, p=0.02), and were significantly lower in SLE mice treated with control microbes (SLE-Control microbes: 126±4 mmHg, p=0.03). These data suggest that gut microbiota present in NZBWF1 mice contribute to the accumulation of activated B cells and increased autoantibody production, which are known pathogenic factors in the development of hypertension in SLE.

Evaluation of the effects of black pepper extract on the growth performance of grower pigs

This study aimed to evaluate the effects of black pepper (BP) extract on growth performance, nutrient digestibility, serum total protein, blood urea nitrogen (BUN), creatinine, counts of Lactobacillus and Escherichia coli (E. Coli), back fat thickness, lean meat percentage (LMP), and fecal gas emission in grower pigs. A total of 160 crossbred grower pigs [(Landrace × Yorkshire) × Duroc] with an average initial body weight (BW) of 25.31 ± 1.29 kg were used in a 42-day feeding trial. Pigs were randomly assigned to four experimental treatments. The basal diet was composed of soybeans and corn to meet or exceed the NRC (2012) recommendations. The dietary treatments included: basic diet, basic diet + 0.025 %, 0.05 %, and 0.1 % BP extract. There were eight replicates per treatment, each comprising five pigs (three gilts and two barrows). All data were subjected to statistical analysis using general linear model procedures (SAS 2001, SAS Institute Inc., Cary, NC, USA), with the pen serving as the experimental unit. The results indicated a linear improvement in BW and average daily gain of pigs during days 1–28, 28–42, and the overall period with increasing levels of BP extract in the diet. The apparent total tract digestibility (ATTD) of crude protein (CP) and lean meat percentage (LMP) increased linearly with BP treatment at the end of the experiment (p < 0.05). In addition, total protein, BUN, and creatinine levels were not affected by the BP extract (p > 0.05). Some fecal microbes, such as Lactobacillus and E. coli, did not change considerably when pigs were fed BP extract (p > 0.05). No apparent response to faecal gas emission of NH3, total mercaptans, or H2S was observed in relation to the BP extract in the pig diet (p < 0.05). Dietary supplementation with 0.1 % BP extract improved growth performance by increasing the ATTD of CP and improving LMP without adverse effects in grower pigs.

Differences in Milk Fatty Acids Profile of Two Breeds of Water Buffaloes Explained by Their Gastrointestinal Microbiota.

This experiment investigated gastrointestinal microbes' role in milk fatty acid differences between Murrah and Nili-Ravi buffaloes. After 30 days of a basal diet, rumen microbial diversity was similar, but Murrah buffaloes had greater partially unsaturated fatty acids like C18:2c9t11. Rumen bacteria like Acetobacter, Ruminococcus, and Prevotellaceae_YAB2003_group correlated positively with milk fatty acids C22:5n-6 and C18:3 in Murrah. Fecal microbial beta diversity differed, with UCG-005 and Prevolla positively correlated with C18:2c9t11 and C22:5n-6. The greater quantity of milk fatty acids C18:3, C18:2c9t11, and C22:5n-6 in Murrah milk was linked to rumen and fecal microbes. This suggests that gastrointestinal microbes like Acetobacter, Ruminococcus, and UCG_005 regulate milk fatty acid concentrations in buffaloes.

Improved diet-based nutritional interventions can improve childhood obesity with the synergistic regulation of gut microbiota.

Childhood obesity is a crucial public health concern worldwide. Dietary intervention is the most common intervention for the treatment of obesity. Therefore, we tested an improved diet-based nutritional interventions to improve the childhood obesity and its gut microbiota. Thirty obese children received a 12-week intervention with the adjust-energy-restricted dietary pattern (A-CRD). Body composition was measured by bioelectrical impedance (Inbody S10) and faecal microbes were profiled by sequencing 16S rRNA. Compared to the NTB group (at 0 week), the NTA group (at 12 weeks) had a significantly greater decrease in body weight, body mass index (BMI) and percent body fat (PBF) ( P < 0.001, respectively), whereas skeletal muscle mass (SMM) and fat free mass (FFM) were not statistically significantly different ( P > 0.05). The gut microbiota was found significantly different between the NTB and NTA groups based on alpha and beta diversity. Bifidobacterium, Blautia, and Streptococcus was significantly increased, whereas Bacteroides and Megamonas was significantly decreased in the NTA group ( P < 0.05, respectively). Meanwhile, NTA group significantly increased the ability to produce short-chain fatty acids (SCFAs; e.g. acetic acid/total dietary energy) and changed he predictive metabolic functional features of the microbiota communities ( P < 0.05, respectively) than the NTB group. In conclusion, A-CRD can significantly improve childhood obesity, and the underlying mechanism may be its effect on gut microbiota and metabolism. Therefore, the diet-based nutrition intervention targeting gut microbiota will be more effective management of body weight and prevention of obesity. Chinese Clinical Trial Register: ChiCTR2300074571.

Dracocephalum moldavica L. Extract Ameliorates Hypertension Through Modulating the Interaction Between miRNAs and Gut Microbiota in 2K1C Rats

Aim: To investigate the therapeutic effects of Dracocephalum moldavica L. extract (DME) against hypertension and elucidate the underlying molecular mechanism. Method: A two-kidney one-clip (2K1C) model was established in male Wistar rats, and DME or saline was administered via oral gavage for 4 weeks. Subsequently, the blood pressure was monitored. Fecal microRNAs (miRNAs), gut microbes, and host metabolites were evaluated through miRNA sequencing, 16S rRNA gene sequencing, and serum metabolomics analysis, respectively. Results: DME administration attenuated 2K1C-induced hypertension in rats. Additionally, DME alleviated the dysregulation of miRNA expression and gut microbiota dysbiosis in 2K1C rats. The correlation analysis confirmed the association of the differentially expressed miRNAs with gut microbes. Furthermore, non-targeted metabolomics analysis revealed different metabolic profiles in the serum of 2K1C rats compared to control rats. Interestingly, the changes in those serum metabolites were partially attenuated by DME. The metabolite enrichment analysis demonstrated that the differentially expressed metabolites were mainly involved in three metabolic pathways (Arachidonic acid metabolism, TCA cycle, and Alanine, aspartate and glutamate metabolism). Conclusion: DME can be suggested as an effective intervention in the prevention of hypertension through modulating the miRNAs, gut microbiota, and host metabolites. Our findings may give new insights regarding the treatment of hypertension.

The Impact of Pit Latrines on the Pollution of Groundwater in the District of Rwamagana, Rwanda

The composition and condition of a water body change over time and across different locations due to internal and external factors. In many rural and peri- urban communities in Rwamagana, the lack of treated water has increased reliance on groundwater for various household and community needs. Groundwater sources are essential for meeting the water demand in these regions. An investigation was carried out in the Rwamagana district of the eastern province of Rwanda to evaluate the influence of pit latrines on groundwater quality. The research examined the water quality of four boreholes with hand pumps and 18 improved springs located near pit latrines. The evaluation specifically looked at total coliforms (TC), electrical conductivity (EC), turbidity, and pH. The proximity of the pit latrines to the boreholes or springs was considered in order to determine the presence of fecal coliforms in the groundwater, with the goal of establishing a minimum safe distance between the pit latrines and water sources. The physicochemical indicators of the water samples met the drinking water quality criteria set by the World Health Organization (WHO). However, the levels of biological contaminants exceeded the WHO's drinking water quality standards. The highest coliform counts detected in the study were 99cfu/100ml of water. The research findings suggest a clear relationship between fecal microbes from pit latrines and their impact on groundwater quality, with the contamination effect extending up to 322.4m for improved springs and 266.2m for boreholes with hand pumps.

Detection and comparison of tumor cell-associated microbiota from different compartments of colorectal cancer.

Intratumoral microbes play an important role in the development of colorectal cancer (CRC). However, studying intratumoral microbes in CRC faces technical challenges, as tumor microbe communities are often contaminated by fecal microbes due to the structure of the gut folds and villi. The present study aimed to develop a new method for isolating tumor cell-associated microbiota and comparing microbial populations from different compartments. The distribution of intestinal bacteria was detected using immunohistochemistry combined with 5R-16s rRNA gene sequencing to explore the effects of the sampling site and number of washes on the detection of microbiota. The 5R-16s rRNA gene sequencing was performed using 44 samples from 11 patients with CRC, including CRC tumor tissues (TT), normal tissues adjacent to CRC (NT), tumor cells (TC), and normal cells (NC). TC and NC were obtained from the TT and NT using an enzymatic digestion method. The microbiota and their potential functions in the four groups were analyzed and compared to determine the differential microbiota related to CRC. Bacteria were mainly distributed in the feces covering intestinal tissues and in the epithelial cells and macrophages within the tissues. Different sampling sites and number of washes led to detection of different microbiota distributions. Although the cleaning method could be controlled, sampling sites varied and led to different microbiota distributions. The phyla of Firmicutes and Bacteroidetes were highly abundant in the conventionally used tissue samples, whereas Proteobacteria was the most abundant phyla in the cell samples isolated with the new method (i.e., after cell enzymatic hydrolysis). Detection of CRC cell-associated microbiota using a cell enzymatic digestion method showed that some bacteria, such as Fusobacterium, Eikenella, Shewanella, and Listeria, were more abundant in TT than NT, whereas the abundance of Akkermansia was lower in TT than NT. The tumor/normal ratios of some bacteria, such as Gemella, Escherichia, Shigella, and Blautia, were different between the cell and tissue samples. The cell enzymatic digestion method reduced fecal bacterial contamination, enabling low biomass intratumoral microbiota to be detected and allowing prediction of bacterial distributions.

Explainable machine learning model for identifying key gut microbes and metabolites biomarkers associated with myasthenia gravis

Diagnostic markers for myasthenia gravis (MG) are limited; thus, innovative approaches are required for supportive diagnosis and personalized care. Gut microbes are associated with MG pathogenesis; however, few studies have adopted machine learning (ML) to identify the associations among MG, gut microbiota, and metabolites. In this study, we developed an explainable ML model to predict biomarkers for MG diagnosis. We enrolled 19 MG patients and 10 non-MG individuals. Stool samples were collected and microbiome assessment was performed using 16S rRNA sequencing. Untargeted metabolic profiling was conducted to identify fecal amplicon significant variants (ASVs) and metabolites. We developed an explainable ML model in which the top ASVs and metabolites are combined to identify the best predictive performance. This model uses the SHapley Additive exPlanations method to generate both global and personalized explanations. Fecal microbe–metabolite composition differed significantly between groups. The key bacterial families were Lachnospiraceae and Ruminococcaceae, and the top three features were Lachnospiraceae, inosine, and methylhistidine. An ML model trained with the top 1 % ASVs and top 15 % metabolites combined outperformed all other models. Personalized explanations revealed different patterns of microbe–metabolite contributions in patients with MG. The integration of the microbiota-metabolite features and the development of an explainable ML framework can accurately identify MG and provide personalized explanations, revealing the associations between gut microbiota, metabolites, and MG. An online calculator employing this algorithm was developed that provides a streamlined interface for MG diagnosis screening and conducting personalized evaluations.

Scenario-based assessment of fecal pathogen sources affecting bathing water quality: novel treatment options to reduce norovirus and Campylobacter infection risks.

Wastewater discharge and runoff waters are significant sources of human and animal fecal microbes in surface waters. Human-derived fecal contamination of water is generally estimated to pose a greater risk to human health than animal fecal contamination, but animals may serve as reservoirs of zoonotic pathogens. In this study, quantitative microbial risk assessment (QMRA) tools were used to evaluate the hygienic impact of sewage effluents and runoff water from municipalities and animal farms on surface and bathing waters. The human-specific microbial source tracking (MST) marker HF183 was used to evaluate the dilution of fecal pathogens originating from the sewage effluent discharge to the downstream watershed. As novel risk management options, the efficiency of UV-LED disinfection and wetland treatment as well as biochar filtration was tested on-site for the contamination sources. According to the dilution pattern of the MST marker HF183, microbes from wastewater were diluted (2.3-3.7 log10) in the receiving waters. The scenario-based QMRA revealed, that the health risks posed by exposure to human-specific norovirus GII and zoonotic Campylobacter jejuni during the bathing events were evaluated. The risk for gastroenteritis was found to be elevated during wastewater contamination events, where especially norovirus GII infection risk increased (1-15 cases per day among 50 bathers) compared with the business as usual (BAU) situation (1 case per day). The noted C. jejuni infection risk was associated with animal farm contamination (1 case per day, versus 0.2-0.6 cases during BAU). Tertiary treatment of wastewater with wetland treatment and UV-LED disinfection effectively reduced the waterborne gastroenteritis risks associated with bathing. Based on the experiences from this study, a QMRA-based approach for health risk evaluations at bathing sites can be useful and is recommended for bathing site risk assessments in the future. In case of low pathogen numbers at the exposure sites, the MST marker HF183 could be used as a pathogen dilution coefficient for the watershed under evaluation. The full-scale implementation of novel tertiary treatment options at wastewater treatment plants (WWTPs) as well as on-site runoff water treatment options should be considered for infection risk management at locations where scenario-based QMRA implies elevated infection risks.

Abstract 6676: Microbiome modification impacts PSCA directed chimeric antigen receptor (CAR) T cell therapy for prostate cancer

Abstract Background: There is growing evidence that responsiveness to immunotherapy is influenced by the composition of a patient’s gut microbiota. Recent analysis identified strong correlations between abundance of gut microbial species and positive response to immune based therapies in cancer patients. Further, enrichment of commensal microbes can promote immunostimulatory effects, immune based anti-tumor responses, and increased cytotoxic T cell abundance within the TME. Conversely, the presence of gut microbes known to cause inflammatory states in gut tissues may be correlated to negative immunotherapy outcomes or toxicities. To this end, we aimed to evaluate the impact of microbiome manipulation on gut microbe diversity, systemic immunity, local TME, and PSCA-targeted chimeric antigen receptor (CAR) T cell therapy in our established syngeneic prostate cancer mouse model. Methods: In an immune competent mouse model of PSCA+ prostate cancer developed in our lab, we sequentially modified the gut microbiome using antibiotic clearance followed by distinct human derived fecal matter transfers (CPI-FMT, HD-FMT, or No-FMT). Simultaneously, we treated microbiome modified tumor bearing mice with PSCA-targeting CAR T cells and measured differences in anti-tumor efficacy and survival. To provide mechanistic insight, we performed longitudinal whole genome sequencing (WGS) of fecal matter microbes and RNA sequencing on spleen and tissues following FMT administration. Results: In our model, a unique checkpoint inhibitor (CPI) treated patient derived human FMT (CPI-FMT) improved PSCA-CAR anti-tumor responses relative to healthy donor (HD-FMT) or No-FMT treatment controls. CPI-FMT administration also significantly improved overall survival in CAR T cell and non-targeting T cell control treated mice. Temporal analysis of microbes present in the gut following CPI-FMT and HD-FMT treatment show CPI-FMT treated mice exhibit favorable maintenance of gut microbe species richness and significant increase in microbiota diversity. We identify CPI-FMT provides an enrichment of specific microbes associated with preservation of gut homeostasis and improved immune response. RNA sequencing analysis on tumor tissues show differential transcription of immune related pathways following FMT which may influence immune and CAR T cell function. Conclusions: We show that our mouse prostate cancer model is sensitive microbiome modulation and can significantly impact PSCA-CAR T cell directed anti-tumor responses. Temporal WGS analysis of gut fecal matter reveal enrichment suggest specific species abundances which may promote gut homeostasis over dysbiosis or inflammatory states and may account for improved CAR T cell response. We aim to further develop this model to interrogate candidate targeted microbiome modifiers which may impact mechanisms which promote CAR T cell and immune function. Citation Format: John Paul Murad, Lea Christian, Yukiko Yamaguchi, Lupita Lopez, Ching Ouyang, Hirokazu Sato, Bryce Jarman, Sean Stromberg, Stephen J. Forman, Stephen Van Dien, Stephanie Culler, Saul J. Priceman. Microbiome modification impacts PSCA directed chimeric antigen receptor (CAR) T cell therapy for prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6676.

Sanitation in urban areas may limit the spread of antimicrobial resistance via flies.

Synanthropic filth flies are common where sanitation is poor and fecal wastes are accessible to them. These flies have been proposed as mechanical vectors for the localized transport of fecal microbes including antimicrobial resistant (AMR) organisms and associated antimicrobial resistance genes (ARGs), increasing exposure risks. We evaluated whether an onsite sanitation intervention in Maputo, Mozambique reduced the concentration of enteric bacteria and the frequency of detection of ARGs carried by flies collected in household compounds of low-income neighborhoods. Additionally, we assessed the phenotypic resistance profile of Enterobacteriaceae isolates recovered from flies during the pre-intervention phase. After fly enumeration at study compounds, quantitative polymerase chain reaction was used to quantify an enteric 16S rRNA gene (i.e., specific to a cluster of phylotypes corresponding to 5% of the human fecal microflora), 28 ARGs, and Kirby Bauer Disk Diffusion of Enterobacteriaceae isolates was utilized to assess resistance to eleven clinically relevant antibiotics. The intervention was associated with a 1.5 log10 reduction (95% confidence interval: -0.73, -2.3) in the concentration of the enteric 16S gene and a 31% reduction (adjusted prevalence ratio = 0.69, [0.52, 0.92]) in the mean number of ARGs per fly compared to a control group with poor sanitation. This protective effect was consistent across the six ARG classes that we detected. Enterobacteriaceae isolates-only from the pre-intervention phase-were resistant to a mean of 3.4 antibiotics out of the eleven assessed. Improving onsite sanitation infrastructure in low-income informal settlements may help reduce fly-mediated transmission of enteric bacteria and the ARGs carried by them.

Maternal probiotic Lactocaseibacillus rhamnosus HN001 treatment alters postpartum anxiety, cortical monoamines, and the gut microbiome

Peripartum mood and anxiety disorders (PMADs) affect 15–20% of peripartum women and are well known to disrupt infant caregiving. A recent study in humans reported that anxiety and depressive symptoms were alleviated by peripartum treatment with the probiotic, Lactocaseibacillus rhamnosus HN001. The current study determined the effects of chronic Lactocaseibacillus rhamnosus HN001 (HN001) treatment on postpartum affective and caregiving behaviors in a laboratory rodent model. Female rats were given probiotic overnight in their drinking water, or untreated water, from the first day of pregnancy through postpartum day 10. To determine whether the HN001 effects were influenced by a background of stress, half the females underwent chronic variable pregnancy stress and the other half remained undisturbed. The results revealed that, even without pregnancy stress, HN001 reduced postpartum anxiety-related behavior, increased variability in behavioral fragmentation when dams interacted with pups, increased time away from pups, and decreased prefrontal cortex norepinephrine (NE), dopamine (DA) and serotonin (5-HT). Probiotic plus stress consistently reduced the latency to float in the forced swim test, increased DA and 5-HT turnovers in the prefrontal cortex, increased hippocampal NE, and reduced hypothalamic DA. Fecal microbe alpha and beta diversities were lower postpartum than prepartum, which was prevented by the probiotic treatment and/or stress. Across the entire sample lower postpartum anxiety behavior was associated with lower fecal Bacteroides dorei. This study reveals novel information about how L. rhamnosus HN001 influences postpartum behavior and microbiota-gut-brain physiology in female laboratory rats, with implications for probiotic supplement use by pregnant and postpartum women.

Resistance role of Lactobacillus sp. and Lactococcus sp. to copper ions in healthy children’s intestinal microorganisms

Heavy metal exposure is closely associated with gut microbe function and tolerance. However, intestinal microbe responses in children to different copper ion (Cu2+) concentrations have not yet been clarified. Here, in vitro cultivation systems were established for fecal microbe control and Cu2+-treated groups in healthy children. 16S rDNA high-throughput sequencing, meta-transcriptomics and metabolomics were used here to identify toxicity resistance mechanisms at microbiome levels. The results showed that Lactobacillus sp. and Lactococcus sp. exerted protective effects against Cu2+ toxicity, but these effects were limited by Cu2+ concentration. When the Cu2+ concentration was ≥ 4 mg/L, the abundance of Lactobacillus sp. and Lactococcus sp. significantly decreased, and the pathways of antioxidant activity and detoxification processes were enriched at 2 mg/L Cu2+, and beneficial metabolites accumulated. However, at high concentrations of Cu2+ (≥4 mg/L), the abundance of potential pathogen increased, and was accompanied by a downregulation of genes in metabolism and detoxification pathways, which meant that the balance of gut microbiota was disrupted and toxicity resistance decreased. From these observations, we identified some probiotics that are tolerant to heavy metal Cu2+, and warn that only when the concentration limit of Cu2+ in food is 2 mg/L, then a balanced gut microbiota can be guaranteed in children, thereby providing protection for their health.

Large intestinal nutritional and physicochemical parameters from different dog sizes reshape canine microbiota structure and functions in vitro

ABSTRACT Different dog sizes are associated with variations in large intestinal physiology including gut microbiota, which plays a key role in animal health. This study aims to evaluate, using the CANIM-ARCOL (Canine Mucosal Artificial Colon), the relative importance of gut microbes versus physicochemical and nutritional parameters of the canine colonic environment in shaping microbiota structure and functions. CANIM-ARCOL was set up to reproduce nutrient availability, bile acid profiles, colonic pH, and transit time from small, medium, or large dogs according to in vivo data, while bioreactors were all inoculated with a fecal sample collected from medium size dogs (n = 2). Applying different dog size parameters resulted in a positive association between size and gas or SCFA production, as well as distinct microbiota profiles as revealed by 16S Metabarcoding. Comparisons with in vivo data from canine stools and previous in vitro results obtained when CANIM-ARCOL was inoculated with fecal samples from three dog sizes revealed that environmental colonic parameters were sufficient to drive microbiota functions. However, size-related fecal microbes were necessary to accurately reproduce in vitro the colonic ecosystem of small, medium, and large dogs. For the first time, this study provides mechanistic insights on which parameters from colonic ecosystem mainly drive canine microbiota in relation to dog size. The CANIM-ARCOL can be used as a relevant in vitro platform to unravel interactions between food or pharma compounds and canine colonic microbiota, under different dog size conditions. The potential of the model will be extended soon to diseased situations (e.g. chronic enteropathies or obesity).

Construction and validation of a machine learning model for the diagnosis of juvenile idiopathic arthritis based on fecal microbiota.

Human gut microbiota has been shown to be significantly associated with various inflammatory diseases. Therefore, this study aimed to develop an excellent auxiliary tool for the diagnosis of juvenile idiopathic arthritis (JIA) based on fecal microbial biomarkers. The fecal metagenomic sequencing data associated with JIA were extracted from NCBI, and the sequencing data were transformed into the relative abundance of microorganisms by professional data cleaning (KneadData, Trimmomatic and Bowtie2) and comparison software (Kraken2 and Bracken). After that, the fecal microbes with high abundance were extracted for subsequent analysis. The extracted fecal microbes were further screened by least absolute shrinkage and selection operator (LASSO) regression, and the selected fecal microbe biomarkers were used for model training. In this study, we constructed six different machine learning (ML) models, and then selected the best model for constructing a JIA diagnostic tool by comparing the performance of the models based on a combined consideration of area under receiver operating characteristic curve (AUC), accuracy, specificity, F1 score, calibration curves and clinical decision curves. In addition, to further explain the model, Permutation Importance analysis and Shapley Additive Explanations (SHAP) were performed to understand the contribution of each biomarker in the prediction process. A total of 231 individuals were included in this study, including 203 JIA patients and Non-JIA individuals. In the analysis of diversity at the genus level, the alpha diversity represented by Shannon value was not significantly different between the two groups, while the belt diversity was slightly different. After selection by LASSO regression, 10 fecal microbe biomarkers were selected for model training. By comparing six different models, the XGB model showed the best performance, which average AUC, accuracy and F1 score were 0.976, 0.914 and 0.952, respectively, thus being used to construct the final JIA diagnosis model. A JIA diagnosis model based on XGB algorithm was constructed with excellent performance, which may assist physicians in early detection of JIA patients and improve the prognosis of JIA patients.

Dietary supplementation of phytoncide and soybean oil increases milk conjugated linoleic acid and depresses methane emissions in Holstein dairy cows

The objective of this study was to determine whether adding phytoncide oil (PO) and soybean oil (SBO) to the dairy cow diet could increase milk conjugated linoleic acid (CLA) and depress methane (CH4) emissions in Holstein dairy cows. Rumen fermentation was conducted at four levels of SBO (0, 1, 2, and 4%, on DM basis) and two levels of PO (0 and 0.1%, on DM basis) with in vitro experiment. To evaluate blood parameters, fecal microbe population, milk yield and fatty acid compositions, and CH4 production, in vivo experiment was conducted using 38 Holstein dairy cows divided into two groups of control (fed TMR) and treatment (fed TMR with 0.1% PO and 2% SBO as DM basis). In the in vitro study (Experiment 1), PO or SBO did not affect rumen pH. However, SBO tended to decrease ruminal ammonia-N (p = 0.099). Additionally, PO or SBO significantly decreased total gas production (p = 0.041 and p = 0.034, respectively). Both PO and SBO significantly decreased CH4 production (p < 0.05). In addition, PO significantly increased both CLA isomers (c9, t11 and t10, c12 CLA) (p < 0.001). Collectively, 0.1% PO and 2% SBO were selected resulting in most effectively improved CLA and decreased CH4 production. In the in vivo study (Experiment 2), 0.1% PO with 2% SBO (PSO) did not affect complete blood count. However, it decreased blood urea nitrogen and magnesium levels in blood (p = 0.021 and p = 0.01, respectively). PSO treatment decreased pathogenic microbes (p < 0.05). It increased milk yield (p = 0.017) but decreased percentage of milk fat (p = 0.013) and MUN level (p < 0.01). In addition, PSO treatment increased both the concentration of CLA and PUFA in milk fat (p < 0.01). Finally, it decreased CH4 emissions from dairy cows. These results provide compelling evidence that a diet supplemented with PSO can simultaneously increase CLA concentration and decrease CH4 production with no influence on the amount of milk fat (kg/day) in Holstein dairy cows.