Fecal Microbiota of Toxigenic Clostridioides difficile-Associated Diarrhea

Lactobacillus-derived indole derivatives ameliorate intestinal barrier damage in rat pups with complementary food administration

The consumption of complementary foods can bring about diarrhea and intestinal barrier dysfunction in infants. In this study, three different Lactobacillus strains combined with L-tryptophan (Trp) were administered to rat pups with complementary foods. Complementary food feeding caused inflammatory cell infiltration, crypt structure irregularity and goblet cell reduction in the colon tissues of the rat pups. However, the oral administration of Trp combined with Lactiplantibacillus plantarum DPUL-S164 or Limosilactobacillus reuteri DPUL-M94 significantly restored the pathological changes in the colon tissues and inhibited the expression of pro-inflammatory cytokines in the colon and ileum of the rat pups. M94 or S164 combined with Trp intervention could promote the expression of cell differentiation genes and tight junction proteins, and restore the intestinal barrier damage caused by complementary foods in rat pups by activating the aryl hydrocarbon receptors (AhR) and nuclear factor erythroid 2-related factor 2 (Nrf2) pathway. In addition, the indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), or indole-3-carbaldehyde (I3C) level in the cecal contents of the rat pups increased after intervention of Trp combined with S164 or M94, which may account for the amelioration of intestinal barrier damage in rat pups administered with complementary foods. Furthermore, S164 or M94 combined with Trp intervention up-regulated the relative abundance of f_Lactobacillaceae, f_Akkermansiaceae, g_Lactobacillus, and g_Akkermansia in the intestinal tract of the rat pups. In conclusion, S164 or M94 combined with Trp intervention can ameliorate complementary food-induced intestinal barrier damage and gut flora disorder in rat pups by producing ILA, IPA, or I3C, which are AhR ligands.

Gut microbiome changes in mouse, Mongolian gerbil, and hamster models following Clostridioides difficile challenge

Introduction

Clostridioides difficile infection (CDI), as well as its etiology and pathogenesis, have been extensively investigated. However, the absence of suitable CDI animal models that reflect CDI symptoms and the associated gut microbiome changes in humans has limited research progress in this field. Thus, we aimed to investigate whether Mongolian gerbils, which present a range of human pathological conditions, can been used in studies on CDI. Methods: In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

Methods

In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

Results

The results obtained showed that C. difficile colonized the gastrointestinal tracts of the three rodents, and after the C. difficile challenge, C57BL/6J mice did not manifest CDI symptoms and their intestines showed no significant pathological changes. However, the hamsters showed explosive intestinal bleeding and inflammation and the Mongolian gerbils presented diarrhea as well as increased infiltration of inflammatory cells, mucus secretion, and epithelial cell shedding in their intestinal tissue. Further, intestinal microbiome analysis revealed significant differences with respect to intestinal flora abundance and diversity. Specifically, after C. difficile challenge, the Firmicutes/Bacteroidetes ratio decreased for C57BL/6J mice, but increased significantly for Mongolian gerbils and hamsters. Furthermore, the abundance of Proteobacteria increased in all three models, especially in hamsters, while that of Verrucomicrobia only increased significantly in C57BL/6J mice and Mongolian gerbils. Our results also indicated that differences in the relative abundances of Lactobacillaceae and Akkermansia were primarily responsible for the observed differences in response to C. difficile challenge.

Conclusion

Based on the observed responses to C. difficile challenge, we concluded for the first time that the Mongolian gerbil could be used as an animal model for CDI. Additionally, the taxa identified in this study may be used as biomarkers for further studies on CDI and to improve understanding regarding changes in gut microbiome in CDI-related diseases.

Shengjiang Xiexin decoction mitigates murine Clostridium difficile infection through modulation of the gut microbiota and bile acid metabolism

ETHNOPHARMACOLOGICAL RELEVANCE

The overuse of antibiotics has resulted in Clostridium difficile infection (CDI) as a significant global public health concern. Studies have shown that imbalances in gut microbiota and metabolism play a vital role in the onset of CDI. Shengjiang Xiexin decoction (SJT), a traditional Chinese medicinal formula widely employed in the treatment of gastrointestinal ailments, demonstrates effectiveness in addressing murine CDI. However, the precise mechanistic role of SJT in CDI treatment remains uncertain, particularly regarding its impact on gut microbiota and intestinal metabolism. Thus, further investigation is imperative to shed light on these mechanisms.

AIM OF THE STUDY

This study aims to thoroughly investigate the therapeutic potential of SJT in the treatment of CDI, while also examining its impact on the intricate interplay between gut microbiota and bile acid metabolism. By employing a mouse model, we aspire to uncover novel insights that could pave the way for the development of more effective strategies in combating CDI.

MATERIALS AND METHODS

We developed a mouse model for CDI and assessed SJT's potential as a therapeutic agent through pharmacological analyses. Our study employed high-throughput sequencing of 16S rRNA to identify changes in gut microbiota composition and untargeted metabolomics analysis to evaluate SJT's intervention on intestinal metabolism. We also conducted targeted analysis of bile acid metabolism to examine the specific effects of SJT. Finally, the growth-inhibitory effect of SJT on C. difficile was confirmed through ex vivo cultivation of the pathogen using cecal contents, supporting its potential role in treating CDI by modulating gut microbiota and bile acid metabolism.

RESULTS

In pharmacological studies, SJT was found to effectively reduce the levels of A&B toxins and alleviate colonic inflammation in CDI mice. Mechanistically, SJT demonstrated a mild increase in the abundance and diversity of the gut microbiota. However, its most significant impact was observed in the substantial improvement of the structural composition of the gut microbiota. Specifically, SJT decreased the abundance of gut Polymorphs and Firmicutes while restoring the proportions of family Trichophyton and Bacteroides_S24-7 spp (P < 0.001). Moreover, SJT not only decreased the levels of primary bile acids but also elevated the levels of secondary bile acids. Notably, it enhanced the conversion of taurocholic acid (TCA) to deoxycholic acid (DCA), leading to a balanced bile acid metabolism. Finally, cecal contents of SJT-treated mice showed a significant reduction in the growth of C. difficile, underscoring the therapeutic potential of SJT via modulation of gut microbiota and bile acid metabolism.

CONCLUSION

SJT demonstrates remarkable efficacy in treating CDI in mice by not only effectively combating the infection but also restoring the intricate balance of gut microbiota and bile acid metabolism. Furthermore, promising indications suggest that SJT may have the potential to prevent CDI recurrence. These findings underscore the comprehensive therapeutic value of SJT in managing CDI. Moving forward, we plan to transition from the laboratory to clinical settings to conduct further studies, validating our conclusions on SJT's efficacy.

Decentralized ORP Measurements for Gut Redox Status Monitoring: Toward Personalized Gut Microbiota Balance

Gut microbiome targeting has emerged as a new generation of personalized medicine and a potential wellness and disease driver. Specifically, the gut redox balance plays a key role in shaping the gut microbiota and its link with the host, immune system, and disease evolution. In this sense, precise and personalized nutrition has proven synergy and capability to modulate the gut microbiome environment through the formulation of dietary interventions, such as vitamin support. Accordingly, there are urgent demands for simple and effective analytical platforms for understanding the relationship between the tailored vitamin administration and the gut microbiota balance by rapid noninvasive on-the-spot oxidation/reduction potential monitoring for frequent and close surveillance of the gut redox status and targeting by personalized nutrition interventions. Herein, we present a disposable potentiometric sensor chip and a homemade multiwell potentiometric array to address the interplay of vitamin levels with the oxidation/reduction potential in human feces and saliva. The potentiometric ORP sensing platforms have been successfully validated and scaled up for the setup of a multiapplication prototype for cross-talk-free simple screening of many specimens. The interpersonal variability of the gut microbiota environment illustrates the potential of feces and saliva samples for noninvasive, frequent, and decentralized monitoring of the gut redox status to support timely human microbiota surveillance and guide precise dietary intervention toward restoring and promoting personalized gut redox balance.

Ferrostatin-1 mitigates ionizing radiation-induced intestinal injuries by inhibiting apoptosis and ferroptosis: an in vitro and in vivo study

PURPOSE

Intestinal injuries caused by ionizing radiation (IR) are a major complication of radiotherapy. Ferrostatin-1 (Fer-1) exerts antioxidant and anti-inflammatory effects. We investigated the influence of Fer-1 on IR-induced intestinal damage and explored the possible mechanisms.

MATERIALS AND METHODS

IEC-6 cells were administrated with Fer-1 for 30 min and subsequently subjected to 9.0 Gy-irradiation. Flow cytometry, qPCR, and WB were used to detect changes. For in vivo experiments, Fer-1 was given intraperitoneally to mice at 1 h before and 24 h after 9.0 Gy total body irradiation (TBI) respectively. Three days after TBI, the small intestines were isolated for analysis. The diversity and composition of the gut microbiota were analyzed by 16S rRNA gene sequencing.

RESULTS

In vitro, Fer-1 protected IEC-6 cells from IR injury by reducing the production of ROS and inhibiting both ferroptosis and apoptosis. In vivo, Fer-1 enhanced the survival rates of mice subjected to lethal doses of IR and restored intestinal structure and physiological function. Further investigation showed that Fer-1 protected IEC-6 cells and mice by inhibiting the p53-mediated apoptosis signaling pathway and restoring the gut-microbe balance.

CONCLUSION

This study confirms that Fer-1 protects intestinal injuries through suppressing apoptosis and ferroptosis.

Lower gut dysbiosis and mortality in acute critical illness: a systematic review and meta-analysis

BACKGROUND

The human gastrointestinal tract harbours a complex multi-kingdom community known as the microbiome. Dysbiosis refers to its disruption and is reportedly extreme in acute critical illness yet its clinical implications are unresolved. The review systematically evaluates the association between gut dysbiosis and clinical outcomes of patients early in critical illness.

METHODS

Following PRISMA guidelines, a prospectively registered search was undertaken of MEDLINE and Cochrane databases for observational studies undertaking metagenomic sequencing of the lower gastrointestinal tract of critically ill adults and children within 72 h of admission. Eligible studies reported an alpha diversity metric and one or more of the primary outcome, in-hospital mortality, or secondary clinical outcomes. After aggregate data were requested, meta-analysis was performed for four studies with in-hospital mortality stratified to high or low Shannon index.

RESULTS

The search identified 26 studies for systematic review and 4 had suitable data for meta-analysis. No effect of alpha diversity was seen on in-hospital mortality after binary transformation of Shannon index (odds ratio 0.52, CI 0.12-4.98, I² = 0.64) however certainty of evidence is low. Pathogen dominance and commensal depletion were each more frequently associated with in-hospital mortality, adverse clinical and ecological sequelae, particularly overabundance of Enterococcus.

CONCLUSIONS

There is a paucity of large, rigorous observational studies in this population. Globally, alpha diversity was dynamically reduced in early ICU admission in adults and children and was not associated with in-hospital mortality. The abundance of taxa such as Enterococcus spp. appears to offer greater predictive capacity for important clinical and ecological outcomes.

Gut microbiome alterations in ICU patients with enteral nutrition-related diarrhea

Enteral Nutrition-related Diarrhea (END) is an extremely common complication in Intensive Care Unit (ICU) patients. However, it is currently unclear whether the patient’s gut microbiota is disturbed. Our study aimed to explore the characteristics of gut microbiota changes in END patients. We divided ICU patients into no-END group (n = 7) and END group (n = 7) according to whether they had END, then stool samples were collected separately. The V3-V4 region of stool bacterial 16S rRNA gene was amplified by PCR and sequenced on an Illumina MiSeq PE300 platform. Microbiome data obtained by quality control were analyzed, including microbial community composition, diversity and gene function prediction.The results showed that the dominant gut microbiota in ICU patients who were given total enteral nutrition were Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Verrucomicrobia. Bacterial richness and diversity in END patients were all significantly lower than those in no-END patients. In addition, END caused significant changes in bacterial composition. LEfSe found 34 biomarkers represented by Bacteroidetes and Subdoligranulum in the no-END group as well as 11 biomarkers represented by Enterococcus and Klebsiella in the END group. Finally, through PICRUST function prediction, we found that diarrhea led to abnormal changes in numerous KEGG pathways mainly related to immunity and metabolism. In short, ICU patients with END have severe gut dysbiosis, and our study provides a reliable experimental basis for the patient’s microbiota therapy.

Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection

Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.

Restored intestinal integrity, nutrients transporters, energy metabolism, antioxidative capacity and decreased harmful microbiota were associated with IUGR piglet's catch-up growth before weanling

BACKGROUND

Intrauterine growth restriction (IUGR) is a major inducer of higher morbidity and mortality in the pig industry and catch-up growth (CUG) before weanling could significantly restore this negative influence. But there was limited knowledge about the underlying mechanism of CUG occurrence.

METHODS

Eighty litters of newborn piglets were divided into normal birth weight (NBW) and IUGR groups according to birth weight. At 26 d, those piglets with IUGR but over average body weight of eighty litters of weaned piglets were considered as CUG, and the piglets with IUGR still below average body weight were considered as NCUG. This study was conducted to systemically compare the intestinal difference among NBW, CUG and NCUG weaned piglets considering the crucial role of the intestine for piglet growth.

RESULTS

The results indicated that the mRNA expression of nutrients (amino acids, glucose, and fatty acids) transporters, and mitochondrial electron transport chain (ETC) I were upregulated in CUG piglets' gut with improved morphology compared with those NCUG, as well as the ratio of P-AMPK/AMPK protein expression which is the indicator of energy metabolism. Meanwhile, CUG piglet's gut showed higher antioxidative capacity with increased SOD and GSH-Px activity, decreased MDA levels, as well as higher mRNA expressions of Nrf2, Keap1, SOD, and GSH-Px. Furthermore, inflammatory parameters including TNF-α, IL-1β, IL-6, and IL-12 factors, and the activation of MAPK and NF-κB signaling pathways were significantly elevated in the NCUG intestine, while the protein expression of ZO-1, Occludin and Claudin-1 was reduced. The alpha diversity of fecal microbiota was higher in CUG piglets in contrast with NCUG piglets, and the increased beneficial bacteria and decreased pathogenic bacteria was also observed in CUG piglets.

CONCLUSIONS

CUG piglet's intestine showed comprehensive restoration including higher nutrients transport, energy metabolism, antioxidant capacity, and intestinal physical barrier, while lower oxidative stress, inflammatory response, and pathogenic microbiota.

Gut microbiota in burned patients with Clostridioides difficile infection

BACKGROUND

The survival rate of patients with severe burn is positively associated with increasing the incidence of the Clostridioides difficile (C. difficile) infection (CDI). The surviving rate of severe burn patients now has an improved but the incidence of Clostridioides difficile (C. difficile) infection (CDI) has been continues increasing during recent two decades. This study assessed the molecular typing and phenotypic characterization isolates of C. difficile in burn patients with diarrhea, as well as environmental and skin infections with C. difficile spores at a referral burn hospital in Isfahan, Iran. It mainly aimed to evaluate the dominant bacterial structure in the gut microbiome of burned subjects with and without CDI.

METHODS

In general, 309 samples were collected from 189 burned patients with hospital-acquired diarrhea and 120 swabs were collected from the healthcare workers' dominant hands, different sites of patients' skin, and medical tools. In addition, C. difficile isolates were characterized considering the existence of antibiotic resistance and toxin genes. Clinical cultures with identification of organisms and antibiotic susceptibility were done. C. difficle isolates were then genotyped and compared to clinical outcomes. Finally, the clinical characteristics of the participants were gathered through their records, and the bacterial targets of the gut microbiome were detected using quantitative real-time polymerase chain reaction (PCR).

RESULTS

Based on the findings, 51 C. difficile isolates were detected from 189 severe burn patients hospitalized in the hospital. Further, PCR amplification tcdB and tcdA showed 23 isolates (12.2%) as toxigenic. Overall, 18.3% (22/120) of skin and environment samples demonstrated a positive result for C. difficile colonization. A low concentration of metronidazole and vancomycin (MIC90, 0.5, and 1.2 mg/L) inhibited all toxigenic C. difficile strains. Moreover, these isolates represented the highest rates of resistance to moxifloxacin and clindamycin (MIC90, 0.5, and 1.6 mg/L). A significantly reduced abundance of Clostridium spp., Bacteroidetes, and Bifidobacterium and an increase in the quantity of Firmicutes was observed in the gastrointestinal microbiome of burn patients (P < 0.01). Burn patients with CDI showed a significant decrease in Faecalibacterium prausnitzii (F. prausnitzii) while higher Akkermansia muciniphila (A. muciniphila) loads in comparison with healthy controls (P < 0.001 and P < 0.05). Contrarily, burned cases displayed increased levels of opportunistic pathogenic bacteria including the members of Enterococcus spp. and Escherichia coli (P < 0.05).

CONCLUSIONS

Despite appropriate infection control strategies in the burn intensive care unit, CDI remains prevalent in severe burn patients. Eventually, the overgrowth of A. muciniphila and the decreased abundance of F. prausnitzii in burn cases with CDI could be potential predictive microbiome biomarkers in burned patients.

MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis

MOTIVATION

Microbiota analyses have important implications for health and science. These analyses make use of 16S/18S rRNA gene sequencing to identify taxa and predict species diversity. However, most available tools for analyzing microbiota data require adept programming skills and in-depth statistical knowledge for proper implementation. While long-read amplicon sequencing can lead to more accurate taxa predictions and is quickly becoming more common, practitioners have no easily accessible tools with which to perform their analyses.

RESULTS

We present MOCHI, a GUI tool for microbiota amplicon sequencing analysis. MOCHI preprocesses sequences, assigns taxonomy, identifies different abundant species and predicts species diversity and function. It takes either taxonomic count table or FASTQ of partial 16S/18S rRNA or full-length 16S rRNA gene as input. It performs analyses in real time and visualizes data in both tabular and graphical formats.

AVAILABILITY AND IMPLEMENTATION

MOCHI can be installed to run locally or accessed as a web tool at https://mochi.life.nctu.edu.tw.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Effects of Dietary Bopu Powder Supplementation on Serum Antioxidant Capacity, Egg Quality, and Intestinal Microbiota of Laying Hens

The purpose of this study was to investigate the effects of dietary Bopu powder supplementation on the serum antioxidant capacity, serum biochemical indices, egg quality, and intestinal microbiota. Six hundred and forty-eight 33-week-old Lohmann Brown commercial laying hens were randomly allocated into six groups and fed a basal diet supplemented with 0, 25, 50, 100, 200, and 400 mg/kg Bopu powder for 8 weeks, denoted BP0, BP25, BP50, BP100, BP200, and BP400, respectively. The results showed that dietary Bopu powder supplementation reduced serum cholesterol concentrations (linear, p < 0.01) while increasing serum globulin and albumin concentrations (linear, p < 0.05). Furthermore, the BP50 and BP100 groups had greater serum catalase and glutathione peroxidase activity (p < 0.05). The egg Haugh Units were considerably higher in BP25 and BP50 (p < 0.05), and eggshell thickness was higher in BP25, BP200, and BP400 (p < 0.05) when compared to BP0. Dietary treatment with Bopu powder at doses ranging from 25–100 mg/kg improved glutathione peroxidase and catalase activities while decreasing malondialdehyde concentrations in the yolk (p < 0.05). The addition of Bopu powder increased the diversity of microbiota and the relative abundance of Bacteroidota in the gut. For instance, dietary Bopu powder supplementation of 25–50 mg/kg significantly raised the relative abundance of Enterococcus, Bacteroides, and Fusobacterium in the foregut. Supplementing the diet with 50–100 mg/kg of Bopu powder improved the relative abundance of Lactobacillus in the hindgut. In conclusion, dietary Bopu powder supplementation enhanced the abundance of beneficial bacteria in the foregut of laying hens and improved egg quality and antioxidant capacity. Furthermore, in the laying hen diet, the optimal dosage of Bopu powder additive was 25–50 mg/kg.

Gut Microbiota Composition Associated with Clostridioides difficile Colonization and Infection

Clostridioides difficile is an anaerobic Gram-positive and spore-forming bacterium. The majority of C. difficile strains produce two toxins, A and B, associated with the development of acute diarrhea and/or colitis. In this review, two situations are distinguished: C. difficile infection (CDI) and asymptomatic colonization (AC). The main objective of this review is to explore the available data related to the link between the gut microbiota and the development of CDI. The secondary aim is to provide more information on why some people colonized with toxigenic C. difficile develop an infection while others show no signs of disease. Several factors, such as the use of antibiotics and proton pump inhibitors, hospitalization, and age, predispose individuals to C. difficile colonization and/or C. difficile infection. The gut microbiota of people with AC showed decreased abundances of Prevotella, Alistipes, Bacteroides, Bifidobacterium, Dorea, Coprococcus, and Roseburia. The gut microbiota of people suffering from CDI showed reductions in the abundances of Lachnospiraceae, Ruminococcaceae, Blautia spp., Prevotella spp., Dialister spp., Bifidobacterium spp., Roseburia spp., Anaerostipes spp., Faecalibacterium spp. and Coprococcus spp., in comparison with healthy people. Furthermore, increases in the abundances of Enterococcaceae and Enterococcus were associated with C. difficile infection.

The development of live biotherapeutics against Clostridioides difficile infection towards reconstituting gut microbiota

Clostridioides difficile is the most prevalent pathogen of nosocomial diarrhea. In the United States, over 450,000 cases of C. difficile infection (CDI), responsible for more than 29,000 deaths, are reported annually in recent years. Because of the emergence of hypervirulent strains and strains less susceptible to vancomycin and fidaxomicin, new therapeutics other than antibiotics are urgently needed. The gut microbiome serves as one of the first-line defenses against C. difficile colonization. The use of antibiotics causes gut microbiota dysbiosis and shifts the status from colonization resistance to infection. Hence, novel CDI biotherapeutics capable of reconstituting normal gut microbiota have become a focus of drug development in this field.

Effects of Electroacupuncture on the Gut Microbiome in Cisplatin-Induced Premature Ovarian Failure Mice

Growing evidence showed that the gut microbiota was associated with premature ovarian failure (POF). Many clinical types of research had shown that electroacupuncture was effective in the treatment of POF. However, there was little research on regulating the gut microbiome of POF mice by electroacupuncture. Therefore, this study attempted to verify whether electroacupuncture could regulate the gut microbiome in POF mice. POF mice were established by being injected intraperitoneally with cisplatin (2 mg/kg) for 2 weeks. Guanyuan (CV4) and Sanyinjiao (SP6) were selected in the electroacupuncture-at-the-acupoints group (EA group). Nonacupoints around CV4 and SP6 were selected in the electroacupuncture-at-the-nonacupoints group (EN group). The EA group and EN group were treated for 3 weeks. The ovarian function was evaluated by histopathological and molecular assays. Meanwhile, the gut microbiome of all mice was detected by 16S rDNA sequencing. The results showed that EA could restore the estrous cycle and reduce the number of atresia follicles in POF mice. The levels of serum follicle-stimulating hormone and luteinizing hormone were decreased by EA. As well, the levels of serum estradiol, anti-Mullerian hormone, and β-glucuronidase were increased by EA. The relative expressions of PI3K, AKT, and mTOR were increased to promote the proliferation of ovarian cells in the EA group. According to the results of 16S rDNA sequencing, the abundance and diversity of the gut microbiome could be regulated by EA. The relative abundance of beneficial bacteria was increased by EA. The KEGG pathway analysis showed that the gut microbiome associated with the estrogen signaling pathway, oocyte maturation, and PI3K-AKT signaling pathway was regulated by EA.

Gut Dysbiosis and Clostridioides difficile Infection in Neonates and Adults

In this review, we focus on gut microbiota profiles in infants and adults colonized (CDC) or infected (CDI) with Clostridioides difficile. After a short update on CDI epidemiology and pathology, we present the gut dysbiosis profiles associated with CDI in adults and infants, as well as the role of dysbiosis in C. difficile spores germination and multiplication. Both molecular and culturomic studies agree on a significant decrease of gut microbiota diversity and resilience in CDI, depletion of Firmicutes, Bacteroidetes, and Actinobacteria phyla and a high abundance of Proteobacteria, associated with low butyrogenic and high lactic acid-bacteria levels. In symptomatic cases, microbiota deviations are associated with high levels of inflammatory markers, such as calprotectin. In infants, colonization with Bifidobacteria that trigger a local anti-inflammatory response and abundance of Ruminococcus, together with lack of receptors for clostridial toxins and immunological factors (e.g., C. difficile toxins neutralizing antibodies) might explain the lack of clinical symptoms. Gut dysbiosis amelioration through administration of “biotics” or non-toxigenic C. difficile preparations and fecal microbiota transplantation proved to be very useful for the management of CDI.

The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation

Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis associated diseases, such as Clostridioides difficile infection (CDI) and inflammatory bowel disease (IBD). The engraftment of donor bacteria is essential for the effectiveness of FMT, which to some extent depends on the matching of donors and recipients. However, how different types of donor-derived bacteria affect FMT efficacy has not been fully dissected. We recruited two longitudinal IBD cohorts of 103 FMT recipients and further analyzed 1,280 microbiota datasets from 14 public CDI and IBD studies to uncover the effect of donor-derived microbiota in recipients. We found that two enterotypes, RCPT/E and RCPT/B (dominated by Enterobacteriaceae and Bacteroides, respectively), consistently exist in both CDI and IBD patients. Based on a time-course-based multi-cohort analysis of FMT fecal samples, we observed the interplay between recipient and donor-derived microbiota during FMT, in which the FMT outcome was significantly associated with the enterotype and microbiota distance between donor and recipient after FMT. We proposed a new measurement, the ratio of colonizers to residents after FMT (C2R), to quantify the engraftment of donor-derived bacteria in the recipients, and then constructed an enterotype-based statistical model for donor-recipient matching, which was validated by both cross-validation and an additional IBD FMT cohort (n = 42). We believe that with the accumulation of FMT multi-omics datasets, machine learning-based methods will be helpful for rational donor selection for improving efficacy and precision FMT practices.

Fecal microbiota transplantation as therapy for recurrent Clostridioides difficile infection is associated with amelioration of delirium and accompanied by changes in fecal microbiota and the metabolome

Recurrent Clostridioides difficile infection (rCDI) is a frustrating condition that may affect a person's quality of life for months. Microbiome-based therapy such as fecal microbiota transplantation (FMT) has been effective for the treatment of rCDI by correcting the imbalance of the gut microbiota. Appropriate antibiotic treatment is recommended for at least two recurrences before offering FMT. Here, we report the case of a 92-year-old woman who experienced five recurrences of Clostridioides difficile infection (CDI) (six episodes in total) complicated by dementia and delirium, both of which were dramatically improved by FMT, which was associated with alterations in fecal microbiota and the metabolome. Analyses of whole microbial communities and metabolomic analyses were performed on stool specimens collected from the patient on the first episode, the third episode, the day of FMT (before FMT), and 2, 8, and 23 weeks after the FMT and from the donor. The patient had various fecal dysbioses on the first and third episodes and on the day of FMT. Two weeks after FMT, diversity of the gut bacteriome as well as the virome increased dramatically and was reflected in a positive clinical outcome for this patient. Metabolomic analysis revealed that short-chain fatty acids, which have been reported to be associated with improved memory function, were increased after FMT.

Strain-Specific Identification and In Vivo Immunomodulatory Activity of Heat-Killed Latilactobacillus sakei K040706

We previously reported that the immunostimulatory activity of heat-killed Latilactobacillus sakei K040706 in macrophages and cyclophosphamide (CTX)-treated mice. However, identification of heat-killed L. sakei K040706 (heat-killed LS06) using a validated method is not yet reported. Further, the underlying molecular mechanisms for its immunostimulatory effects in CTX-induced immunosuppressed mice remain unknown. In this study, we developed strain-specific genetic markers to detect heat-killed L. sakei LS06. The lower detection limit of the validated primer set was 2.1 × 10⁵ colony forming units (CFU)/mL for the heat-killed LS06 assay. Moreover, oral administration of heat-killed LS06 (10⁸ or 10⁹ CFU/day, p.o.) effectively improved the body loss, thymus index, natural killer cell activity, granzyme B production, and T and B cell proliferation in CTX-treated mice. In addition, heat-killed LS06 enhanced CTX-reduced immune-related cytokine (interferon-γ, interleukin (IL)-2, and IL-12) production and mRNA expression. Heat-killed LS06 also recovered CTX-altered microbiota composition, including the phylum levels of Bacteroidetes, Firmicutes, and Proteobacteria and the family levels of Muribaculaceae, Prevotellaceae, Tannerellaceae, Christensenellaceae, Gracilibacteraceae, and Hungateiclostridiaceae. In conclusion, since heat-killed L. sakei K040706 ameliorated CTX-induced immunosuppression and modulated gut microbiota composition, they have the potential to be used in functional foods for immune regulation.

Alteration of Intestinal Microbiota Composition in Oral Sensitized C3H/HeJ Mice Is Associated With Changes in Dendritic Cells and T Cells in Mesenteric Lymph Nodes

This research aimed to investigate the allergic reaction of C3H/HeJ mice after sensitization with ovalbumin (OVA) without any adjuvant and to analyze the association between intestinal microbiota and allergy-related immune cells in mesenteric lymph nodes (MLN). The allergic responses of C3H/HeJ mice orally sensitized with OVA were evaluated, and immune cell subsets in spleen and MLN and cytokines were also detected. The intestinal bacterial community structure was analyzed, followed by Spearman correlation analysis between changed gut microbiota species and allergic parameters. Sensitization induced a noticeable allergic response to the gavage of OVA without adjuvant. Increased levels of Th2, IL-4, CD103⁺CD86⁺ DC, and MHCII⁺CD86⁺ DC and decreased levels of Th1, Treg, IFN-γ, TGF-β1, and CD11C⁺CD103⁺ DC were observed in allergic mice. Furthermore, families of Lachnospiraceae, Clostridiaceae_1, Ruminococcaceae, and peprostreptococcaceae, all of which belonging to the order Clostridiales, were positively related to Treg and CD11C⁺CD103⁺ DC, while they were negatively related to an allergic reaction, levels of Th2, CD103⁺CD86⁺ DC, and MHCII⁺CD86⁺ DC in MLN. The family of norank_o_Mollicutes_RF39 belonging to the order Mollicutes_RF39 was similarly correlated with allergic reaction and immune cells in MLN of mice. To sum up, allergic reactions and intestinal flora disturbances could be induced by OVA oral administration alone. The orders of Clostridiales and Mollicutes_RF39 in intestinal flora are positively correlated with levels of Treg and CD11C⁺CD103⁺ DC in MLN of mice.

Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection

The role of gut microbiota in the establishment and development of Clostridioides difficile infection (CDI) has been widely discussed. Studies showed the impact of CDI on bacterial communities and the importance of some genera and species in recovering from and preventing infection. However, most studies have overlooked important components of the intestinal ecosystem, such as eukaryotes and archaea. We investigated the bacterial, archaea, and eukaryotic intestinal microbiota of patients with health-care-facility- or community-onset (HCFO and CO, respectively) diarrhea who were positive or negative for CDI. The CDI-positive groups (CO/+, HCFO/+) showed an increase in microorganisms belonging to Bacteroidetes, Firmicutes, Proteobacteria, Ascomycota, and Opalinata compared with the CDI-negative groups (CO/-, HCFO/-). Patients with intrahospital-acquired diarrhea (HCFO/+, HCFO/-) showed a marked decrease in bacteria beneficial to the intestine, and there was evidence of increased Archaea and Candida and Malassezia species compared with the CO groups (CO/+, CO/-). Characteristic microbiota biomarkers were established for each group. Finally, correlations between bacteria and eukaryotes indicated interactions among the different kingdoms making up the intestinal ecosystem. We showed the impact of CDI on microbiota and how it varies with where the infection is acquired, being intrahospital-acquired diarrhea one of the most influential factors in the modulation of bacterial, archaea, and eukaryotic populations. We also highlight interactions between the different kingdoms of the intestinal ecosystem, which need to be evaluated to improve our understanding of CDI pathophysiology.

Fecal Bacterial Microbiota of Healthy Free-Ranging, Healthy Corralled, and Chronic Diarrheic Corralled Rhesus Macaques (Macaca mulatta)

A clinical challenge to nearly every primate facility in North America is chronic idiopathic diarrhea (CID), the pathogenesis of which has yet to be fully elucidated. However, wild macaques appear resistant to CID, a trend that we observed in the free-ranging population of the Caribbean Primate Research Center. The gastrointestinal microbiota has been shown to have a significant role in the pathogenesis of disease and in maintaining normal health and development of the gut. In humans, chronic diarrhea is associated with alteration of the gut microbiota, which has lower bacterial diversity than does the microbiota of healthy humans. The current study was designed to describe and compare the fecal bacterial microbiota of healthy corralled, CID corralled, and healthy, free-ranging macaques. Fresh fecal samples were collected from healthy corralled (HC; n = 30) and CID (n = 27) rhesus macaques and from healthy macaques from our free-ranging colony (HF; n = 43). We excluded macaques that had received antibiotics during the preceding 60 d (90 d for healthy animals). Bacterial DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced and compared with known databases. The relative abundance of Proteobacteria was higher in CID animals than HC animals, but otherwise few differences were found between these 2 groups. HF macaques were differentially enriched with Christensenellaceae and Helicobacter, which are highly associated with a 'healthy' gut in humans, as compared to corralled animals, whereas CID animals were enriched with Proteobacteria, which are associated with dysbiosis in other species. These results indicate that environment has a greater influence than health status on the gut microbiota. Furthermore, the current data provided targets for future studies on potential clinical interventions, such as probiotics and fecal transplants.

Updating changes in human gut microbial communities associated with Clostridioides difficile infection

Clostridioides difficile is the causative agent of antibiotic-associated diarrhea, a worldwide public health problem. Different factors can promote the progression of C. difficile infection (CDI), mainly altered intestinal microbiota composition. Microbial species belonging to different domains (i.e., bacteria, archaea, eukaryotes, and even viruses) are synergistically and antagonistically associated with CDI. This review was aimed at updating changes regarding CDI-related human microbiota composition using recent data and an integral approach that included the different microorganism domains. The three domains of life contribute to intestinal microbiota homeostasis at different levels in which relationships among microorganisms could explain the wide range of clinical manifestations. A holistic understanding of intestinal ecosystem functioning will facilitate identifying new predictive factors for infection and developing better treatment and new diagnostic tools, thereby reducing this disease's morbidity and mortality.

Short-term high-dose gavage of hydroxychloroquine changes gut microbiota but not the intestinal integrity and immunological responses in mice

Aims

Hydroxychloroquine (HCQ), a widely used antimalarial drug, is proposed to treat coronavirus disease 2019 (COVID-19). However, no report is currently available regarding the direct effects of HCQ on gut microbiota, which is associated with the outcomes of elderly patients with COVID-19. Here, we first investigated the effects of HCQ on intestinal microecology in mice.

Main methods

Fifteen female C57BL/6J mice were randomly divided into two groups: HCQ group (n = 10) and control group (n = 5). Mice in the HCQ group were administered with HCQ at dose of 100 mg/kg by gavage daily for 14 days. The feces of mice were collected before and on the 7th and 14th days after HCQ challenge, and then analyzed by 16S rRNA amplicon sequencing. At the end of the experiment, the hematology, serum biochemistry and cytokines were determined, respectively. The mRNA expression of tight junction proteins in colonic tissues were also studied by RT-PCR.

Key findings

HCQ challenge had no effects on the counts of white blood cells, the levels of serum cytokines, and the gene expression of tight junction proteins in colon. HCQ also did not increase the content of serum d-lactate in mice. Notably, HCQ significantly decreased the diversity of gut microbiota, increased the relative abundance of phylum Bacteroidetes whereas decreased that of Firmicutes.

Significance

Short-term high dose HCQ challenge changes gut microbiota but not the intestinal integrity and immunological responses in mice. Special attention should be paid to the effects of HCQ on intestinal microecology in future clinical use.

Intestinal Microbiota in Elderly Inpatients with Clostridioides difficile Infection

Purpose

The incidence of Clostridioides difficile infection (CDI) has been reported as 10-fold higher among the elderly population than in young adults. The aim of this study was to compare the targeted bacteria population in the fecal microbiota in two groups of hospitalized elderly, categorized according to CDI and non-CDI.

Patient and Methods

In this case–control study, 84 fecal samples of the 28 patients with CDI and 56 non-CDI patients (>65 years) were studied. C. difficile isolates were characterized by anaerobic culture and multiplex PCR. Quantitative PCR was used to analyze the bacterial elements.

Results

CDI group differed significantly for a prolonged hospital stay, previous surgery, residence in nursing home and exposure to a range of antibiotics including quinolone, clindamycin and cephalosporin. CDI group had significantly fewer members of Bacteroides spp., Clostridium cluster IV, Bifidobacterium spp., Faecalibacterium prausnitzii, and Prevotella spp. in their fecal microbiota than the control group (P < 0.05). The abundances of Akkermansia muciniphila, Lactobacillus spp., Escherichia coli and Klebsiella spp. were higher in group CDI compared with the control group (P < 0.05).

Conclusion

CDI status is associated with the abundance of some bacterial populations. In this study, an increase in Akkermansia muciniphila, Lactobacillus spp., and Enterobacteriaceae genus was highlighted in CDI patients. A reduction in butyrate-producing bacteria was found in CDI patients. The differences in the composition of fecal microbiota can help to understand how antimicrobial agents impact on gut homeostasis and lead to loss of colonization resistance to C. difficile.

Effect of Debaryomyces hansenii combined with Qiweibaizhu powder extract on the gut microbiota of antibiotic-treated mice with diarrhea

The aim of this study was to investigate the effects of an extract of Qiweibaizhu powder combined with Debaryomyces hansenii on the gut microbiota of antibiotic-treated mice with diarrhea. Mice were gavaged with a mixture of gentamycin sulfate and cefradine to induce diarrhea. After diarrhea was observed, 25% dose of ultra-micro Qiweibaizhu powder extract combined with 25% dose of Debaryomyces hansenii (QCD) was gavaged to mice with diarrhea. DNA of intestinal contents in mice was extracted for 16S rRNA gene sequence analysis by high-throughput sequencing following treatment finished. The results showed that the QCD increased the species richness and diversity, but did not recover the diversity to the original level. Antibiotics and QCD significantly altered the composition of gut microbiota at different taxonomic levels. At the genus level, the relative abundance of Bacteroidales S24-7 group_unidentified and Bacteroides returned to baseline after QCD treatment. Additionally, QCD suppressed the growth of Oscillospira and Ruminococcus, and promoted the proliferation of Erysipelotrichaceae_norank and Blautia compared with the healthy and diarrheal mice. Our results indicated that QCD modulated the diversity and composition of the gut microbiota in antibiotic-treated mice with diarrhea. The synergistic effect between Qiweibaizhu powder extract and Debaryomyces hansenii may be related to Bifidobacterium and Bacteroidales S24-7 group_unidentified.

[Bioinformatics of next generation sequencing in clinical microbiology diagnosis]

Massive parallel sequencing (High-Throughput Sequencing [HTS]) allows to read millions or billions of DNA sequences or fragments (reads) in parallel and is revolutionizing microbiology research, moving from laboratory methods to computed-assisted analyses, with the compelling use of Bioinformatics. The time and cost reduction in studies on the microbiota, microbiome and metagenome, allows to rapidly progress in diagnosis, taxonomy, epidemiology, comparative genomics, virulence, discovery of genes or variants of interest and the association of microorganisms with traditionally considered non-microbial diseases. In this review, the terminology, the sequencing technologies and their applications are described for microbial analysis using open-source bioinformatics software, analysis pipelines, databases and web platforms that allow a user-friendly bioinformatics approach affordable by the clinical microbiologist and infectious disease practitioners.