Specific Bacterial Genera Research Articles

Akkermansia muciniphila in the small intestine improves liver fibrosis in a murine liver cirrhosis model

Recent evidence indicates that liver cirrhosis (LC) is a reversible condition, but there is no established intervention against liver fibrosis. Although the gut microbiota is considered involved in the pathogenesis of LC, the underlying mechanisms remain unclear. Although the antibiotic, rifaximin (RFX), is effective for hepatic encephalopathy (HE) with LC, the impact of RFX on intestinal bacteria is unknown. We investigated the bacterial compositions along the GI tract under RFX treatment using a murine LC model. RFX improved liver fibrosis and hyperammonemia and altered the bacterial composition in the small intestine. The efficacy of RFX was associated with increases in specific bacterial genera, including Akkermansia. Administration of a commensal strain of Akkermansiamuciniphila improved liver fibrosis and hyperammonemia with changing bacterial composition in the small intestine. This study proposed a new concept “small intestine-liver axis” in the pathophysiology of LC and oral A. muciniphila administration is a promising microbial intervention.

The Beneficial Effects of Lacticaseibacillus paracasei subsp. paracasei DSM 27449 in a Letrozole-Induced Polycystic Ovary Syndrome Rat Model.

Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder affecting women of reproductive age globally. Emerging evidence suggests that the dysregulation of microRNAs (miRNAs) and gut dysbiosis are linked to the development of PCOS. In this study, the effects of Lacticaseibacillus paracasei subsp. paracasei DSM 27449 (DSM 27449) were investigated in a rat model of PCOS induced by letrozole. The administration of DSM 27449 resulted in improved ovarian function, reduced cystic follicles, and lower serum testosterone levels. Alterations in miRNA expressions and increased levels of the pro-apoptotic protein Bax in ovarian tissues were observed in PCOS-like rats. Notably, the administration of DSM 27449 restored the expression of miRNAs, including miR-30a-5p, miR-93-5p, and miR-223-3p, leading to enhanced ovarian function through the downregulation of Bax expressions in ovarian tissues. Additionally, 16S rRNA sequencing showed changes in the gut microbiome composition after letrozole induction. The strong correlation between specific bacterial genera and PCOS-related parameters suggested that the modulation of the gut microbiome by DSM 27449 was associated with the improvement of PCOS symptoms. These findings demonstrate the beneficial effects of DSM 27449 in ameliorating PCOS symptoms in letrozole-induced PCOS-like rats, suggesting that DSM 27449 may serve as a beneficial dietary supplement with the therapeutic potential for alleviating PCOS.

Microbial Allies in Plastic Degradation: Specific bacterial genera as universal plastic-degraders in various environments

Microbiological degradation of polymers offers a promising approach for mitigating environmental plastic pollution. This study (i) elucidated the diversity and structure of bacterial microbiomes from distinct environments (landfill soil, sewage sludge, and river water) characterized by specific physicochemical parameters, and (ii) utilized environment-derived microbial cultures enriched with microplastics (MPs) to investigate the degradation of polymers and identify culturable bacterial strains contributing to the plastisphere. We found that alpha diversity was notably higher in river water (∼20%) compared to landfill soil and sewage sludge. Dominant phyla included Pseudomonadota in sewage sludge (39.1%) and water (23.7%), while Actinomycetota prevailed in soil (38.5%). A multistage experiment, involving successive subcultures of environmental microbiomes exposed to polypropylene (PP), polyvinyl chloride (PVC), polycarbonate (PC), and polylactic acid (PLA), facilitated the assessment of MPs degradation processes. Analysis of carbonyl indices CIs and FTIR spectra revealed substantial structural changes in the treatment PVC-landfill soil, as well as in PLA- and PC-sludge enriched cultures. Further, using enriched cultures as a source of microorganisms, the study obtained 17 strains of plastic degraders from landfill soil, 14 from sewage sludge, and 6 from river water. Remarkably, similar bacterial genera were isolated across environmental microbiomes regardless of the MPs substrate used in enriched cultures. Among the 37 identified strains, Pseudomonadota predominated (64.86%) and were accompanied by Bacteroidota (16.22%), Actinomycetota (13.51%), and Bacillota (5.41%). This study highlights the complex relationship between microbiome diversity and the biodegradation efficiency of plastics, showing the potential for using microbial communities in the plastic pollution management.

Impact of including two types of destoned olive cakes in pigs' diets on fecal bacterial composition and study of the relationship between fecal microbiota, feed efficiency, gut fermentation, and gaseous emissions.

The microbial population in the pig's gastrointestinal tract can be influenced by incorporating fibrous by-products into the diets. This study investigated the impact of including two types of dried olive cake (OC) in pigs' diets on fecal bacterial composition. The correlation between fecal microbiota and growth performance, nutrient digestibility, gut fermentation pattern and slurry gas emissions was also evaluated. Thirty male Pietrain x (Landrace x Large white) pigs (47.9 ± 4.21 kg) were assigned to three groups: a control group (C), a group fed a diet with 20% partially defatted OC (20PDOC), and a group fed a diet with 20% cyclone OC (20COC) for 21 days. Fecal samples collected before and after providing the experimental diets were analyzed for the V3-V4 region of the 16S rRNA gene. Pigs were weighed, and feed intake was recorded throughout the study. Potential ammonia and methane emissions from slurry were measured. No significant differences in alpha diversity indexes were found. The taxonomic analysis revealed that Firmicutes and Bacteroidota phyla were dominant at the phylum level across all groups. Differential abundance analysis using ALDEx showed significant differences among groups for various bacteria at the phylum, genus, and species levels at the end of the experiment. Pigs from 20PDOC and 20COC groups exhibited increased abundances of health-promoting bacteria, such as Plactomycetota at the phylum level and Allisonella and an unidentified genus from the Eggerthellaceae family at the genus level. These changes influenced short-chain fatty acids' (SCFA) concentration in slurries, leading to greater acetic, butyric, caproic and heptanoic acids in OC-fed groups, especially 20COC pigs. A volatility analysis revealed significant positive correlations (p < 0.05) between Uncultured_Bacteroidales and Unculured_Selenomonadaceae and energy digestibility. Monoglobus and Desulfovibrio showed a positive significant (p < 0.05) correlation with total SCFA, indicating a high impact on gut fermentation. However, growth performance parameters and potential gas emission displayed no significant correlations with a specific bacterial genus. In conclusion, our results suggest that OC inclusion into pig diets could positively modulate and contribute to the gut microbiota's favorable composition and functionality. Also, nutrient digestibility and gut fermentation patterns can be associated with specific microbial populations.

Regulation of gut microbiota and serum neurotransmitters in mice by Streptococcus thermophilus GA8- and Lacticaseibacillus rhamnosus HAO9-fermented milk containing high levels of gamma-aminobutyric acid.

Gamma-aminobutyric acid (GABA) is an important neurotransmitter in the human body, with several negative emotions reported as being associated with GABA dysregulation. This study investigates the safety and modulatory effects of GABA-enriched milk, fermented by Streptococcus thermophilus GA8 and Lacticasebacillus rhamnosus HAO9, on the gut microbiota and neurotransmitter profiles in mice. Through rigorous culturing and fermentation processes, we achieved consistent GABA production in milk, with concentrations reaching 4.6 and 8.5 g L-1 for GA8-fermented and co-fermented milk, respectively, after 48 h. Using SPF male C57BL/6J mice, we administered either mono-culture or combined-culture milk treatments and monitored physiological impacts. The treatments did not affect mouse body weight but induced significant changes in gut microbiota composition. Beta diversity analysis revealed distinct microbial profiles between treatment groups, highlighting fermentation-specific microbial shifts, such as an increase in Verrucomicrobia for the GA8 group and a modulation in Saccharibacteria_genera_incertae_sedis for the GA8 + HAO9 group. Serum neurotransmitter levels were elevated in both treatment groups, with significant increases in l-glutamine, l-tryptophan and, notably, serotonin hydrochloride in the GA8 + HAO9 group. Correlation analysis identified a positive association between specific bacterial genera and neurotransmitter levels, suggesting a probiotic effect on neuroactive substances. These findings suggest that fermented milk has potential as a probiotic supplement for mood improvement and stress relief, highlighting its role in modulating the gut-brain axis. © 2024 Society of Chemical Industry.

Importance of good hosting: reviewing the bi-directionality of the microbiome-gut-brain-axis.

Gut microorganisms have been shown to significantly impact on central function and studies that have associated brain disorders with specific bacterial genera have advocated an anomalous gut microbiome as the pathophysiological basis of several psychiatric and neurological conditions. Thus, our knowledge of brain-to-gut-to microbiome communication in this bidirectional axis seems to have been overlooked. This review examines the known mechanisms of the microbiome-to-gut-to-brain axis, highlighting how brain-to-gut-to-microbiome signaling may be key to understanding the cause of disrupted gut microbial communities. We show that brain disorders can alter the function of the brain-to-gut-to-microbiome axis, which will in turn contribute to disease progression, while the microbiome-to gut-to brain direction presents as a more versatile therapeutic axis, since current psychotropic/neurosurgical interventions may have unwanted side effects that further cause disruption to the gut microbiome. A consideration of the brain-to-gut-to-microbiome axis is imperative to better understand how the microbiome-gut-brain axis overall is involved in brain illnesses, and how it may be utilized as a preventive and therapeutic tool.

Causal relationship between gut microbiota and diabetic nephropathy: A bidirectional mendelian randomization study.

In this study, we summarized the key findings and potential implications of association studies investigating the relationship between gut microbiota composition and risks for Diabetic nephropathy (DN). We used Mendelian randomization (MR) analysis to explore the relationship between gut microbiota and DN using two different publicly available DN databases. The results were also summarized using five mainstream MR analysis methods. We controlled for various possible biases in the results. The results showed that specific bacterial genera were associated with increased or decreased risk of DN. These associations can be attributed to a variety of factors, including metabolites produced by certain bacteria. Most of our findings are consistent with the existing research findings, but there are still some differences with the existing results. In addition, we also pointed out that some microbiota that may be associated with DN but remain unnoticed can bring new research directions. Our work made use of MR, a reliable technique for examining causal correlations using genetic data investigating potential processes, carrying out longitudinal studies, looking into intervention options, and using a multi-omics approach may be future research avenues. Further, our findings also point to a few unexplored possible study paths for DN in the future. These initiatives may improve our reconciliation of the internal relationships between the gut microbiota and DN and pave the way for more precise prevention and treatment methods. However, it is also critical to recognize any potential restrictions, such as those caused by sample size, population variety, and analytical techniques.

Effect of metformin and metformin/linagliptin on gut microbiota in patients with prediabetes

Lifestyle modifications, metformin, and linagliptin reduce the incidence of type 2 diabetes (T2D) in people with prediabetes. The gut microbiota (GM) may enhance such interventions' efficacy. We determined the effect of linagliptin/metformin (LM) vs metformin (M) on GM composition and its relationship to insulin sensitivity (IS) and pancreatic β-cell function (Pβf) in patients with prediabetes. A cross-sectional study was conducted at different times: basal, six, and twelve months in 167 Mexican adults with prediabetes. These treatments increased the abundance of GM SCFA-producing bacteria M (Fusicatenibacter and Blautia) and LM (Roseburia, Bifidobacterium, and [Eubacterium] hallii group). We performed a mediation analysis with structural equation models (SEM). In conclusion, M and LM therapies improve insulin sensitivity and Pβf in prediabetics. GM is partially associated with these improvements since the SEM models suggest a weak association between specific bacterial genera and improvements in IS and Pβf.

Heterogeneous changes in gut and tumor microbiota in patients with pancreatic cancer: insights from clinical evidence

BackgroundPancreatic cancer is the foremost contributor to cancer-related deaths globally, and its prevalence continues to rise annually. Nevertheless, the underlying mechanisms behind its development remain unclear and necessitate comprehensive investigation.MethodsIn this study, a total of 29 fresh stool samples were collected from patients diagnosed with pancreatic cancer. The gut microbial data of healthy controls were obtained from the SRA database (SRA data number: SRP150089). Additionally, 28 serum samples and diseased tissues were collected from 14 patients with confirmed pancreatic cancer and 14 patients with chronic pancreatitis. Informed consent was obtained from both groups of patients. Microbial sequencing was performed using 16s rRNA.ResultsThe results showed that compared with healthy controls, the species abundance index of intestinal flora in patients with pancreatic cancer was increased (P < 0.05), and the number of beneficial bacteria at the genus level was reduced (P < 0.05). Compared with patients with chronic pancreatitis, the expression levels of CA242 and CA199 in the serum of patients with pancreatic cancer were increased (P < 0.05). The bacterial richness index of tumor microorganisms in patients with pancreatic cancer increased, while the diversity index decreased(P < 0.05). Furthermore, there was a change in the species composition at the genus level. Additionally, the expression level of CA242 was found to be significantly positively correlated with the relative abundance of Acinetobacter(P < 0.05).ConclusionOver all, the expression levels of serum tumor markers CA242 and CA19-9 in patients with pancreatic cancer are increased, while the beneficial bacteria in the intestine and tumor microenvironment are reduced and pathogenic bacteria are increased. Acinetobacter is a specific bacterial genus highly expressed in pancreatic cancer tissue.

Chaihu Guizhi decoction ameliorates depression symptoms in chronic restraint stress‐induced depressive rats by regulating gut microbiota and short‐chain fatty acids

AbstractChaihu Guizhi decoction (CJY) is a classic formula with antidepressant effects; however, it remains unclear whether the antidepressant mechanism of CJY involves modulation of the gut microbiota and which specific bacterial genera are regulated. The present study investigated the effects of CJY on the gut microbiota in chronic restraint stress (CRS)‐induced depressive rats. The results showed that CJY treatment attenuated depressive‐like behavior, repaired hippocampal neuronal damage, and increased neurotransmitter levels in CRS‐induced depressive rats. CJY reshaped the gut microbiota spectrum by increasing the level of the key bacterial genera that alleviate depression, such as Lactobacillus, while decreasing the level of the key bacterial genera that exacerbate depression, such as Bacteroides, Parabacteroides, and Lachnoclostridium. In addition, CJY restored the gut flora dysbiosis‐derived changes in the production of short‐chain fatty acids, such as acetic acid, propionic acid, and valeric acid. This study lays the foundation for identifying therapeutic targets for CJY and elucidating its underlying mechanisms from the perspective of the microbiota.

In vitro mucin degradation and paracellular permeability by fecal water from Crohn's disease patients.

Aim: This study aimed to examine the impact of fecal water (FW) of active and remissive Crohn's disease (CD) patients on mucin degradation and epithelial barrier function. Methods: FW and bacterial membrane vesicles (MVs) were isolated from fresh fecal samples of six healthy controls (HCs) and 12CD patients. Bacterial composition was determined by 16S rRNA gene amplicon sequencing. Results: In vitro FW-induced mucin degradation was higher in CD samples versusHC (p<0.01), but not associated with specific bacterial genera. FW of three remissive samples decreased transepithelial electrical resistance in Caco-2 cells by 78-87% (p<0.001). MVs did not induce barrier alterations. Conclusion: The higher mucin-degradation capacity of CD-derived FW might suggest contributions of microbial products to CD pathophysiology.

Relationship between Pro-Inflammatory Cytokines and Gut Microbiome in Chronic Coronary Syndrome Patients Undergoing Coronary Angiography: A Cross-Sectional Study

Background: Chronic coronary syndrome (CCS) patients have a high mortality rate globally. Atherosclerosis, a cause of CCS, is influenced by inflammation. Pro-inflammatory cytokines such as tumor necrosis factor-alpha (TNF-α), interleukin-1 (IL-1), and interleukin-6 (IL-6) have a key role in the process of atherosclerosis. Moreover, gut microbiota dysbiosis can lead to leaky gut syndrome, subsequently triggering abnormal immune responses and contributing to diseases, including atherosclerosis and coronary artery disease (CAD). Objective: To study the relationship between pro-inflammatory cytokines and gut microbiome in CCS patients undergoing coronary angiography. Material and Methods: Participants were divided into two groups by using statistical matching techniques with age and gender, as CCS patients and healthy participants. Each patient’s blood was collected on the day of the appointment. All patients’ feces were collected one day before an appointment. The present research was a cross-sectional study. Results: Fifty-three patients, including 28 CCS patients and 25 healthy participants were enrolled. CCS patients had a higher level of TNF-α compared to healthy participants with statistical significance at 79.31 pg/mL. Phascolarctobacterium, Sutterella, and Prevotella could distinguish CCS patients from healthy participants based on receiver operating characteristic (ROC) analysis. Proteus and Phascolarctobacterium were positively correlated with TNF-α. Conclusion: There is a potential relationship between gut microbiome composition and inflammatory biomarkers in CCS patients. Pro-inflammatory cytokines and specific bacterial genera may be related to indicate significant CAD in CCS patients undergoing coronary angiography. Keywords: Cardiovascular disease; Interleukin-1; Interleukin-6; Tumor necrosis factor-alpha; Pro-inflammatory cytokines; Gut microbiome; Chronic coronary syndrome

Impact of semen microbiota on the composition of seminal plasma.

Several studies have found associations between specific bacterial genera and semen parameters. Bacteria are known to influence the composition of their niche and, consequently, could affect the composition of the seminal plasma. This study integrated microbiota profiling and metabolomics to explore the influence of seminal bacteria on semen metabolite composition in infertile couples, revealing associations between specific bacterial genera and metabolite profiles. Amino acids and acylcarnitines were the predominant metabolite groups identified in seminal plasma. Different microbiota profiles did not result in globally diverse metabolite compositions in seminal plasma. Nevertheless, levels of specific metabolites increased in the presence of a dysbiotic microbiota. Urocanate was significantly increased in abnormal semen samples (adjusted P-value < 0.001) and enriched in samples dominated by Prevotella spp. (P-value < 0.05), which was previously linked to a negative impact on semen. Therefore, varying microbiota profiles can influence the abundance of certain metabolites, potentially having an immunomodulatory effect, as seen with urocanate.IMPORTANCEMale infertility is often considered idiopathic since the specific cause of infertility often remains unidentified. Recently, variations in the seminal microbiota composition have been associated with normal and abnormal semen parameters and may, therefore, influence male infertility. Bacteria are known to alter the metabolite composition of their ecological niches, and thus, seminal bacteria might affect the composition of the seminal fluid, crucial in the fertilization process. Our research indicates that distinct seminal microbiota profiles are not associated with widespread changes in the metabolite composition of the seminal fluid. Instead, the presence of particular metabolites with immunomodulatory functions, such as urocanate, could shed light on the interplay between seminal microbiota and variations in semen parameters.

Causal relationship between gut microbiota and kidney diseases: a two-sample Mendelian randomization study.

The interplay between gut microbiome genera and inflammatory kidney-related diseases, such as nephrotic syndrome, glomerulonephritis, tubulo-interstitial nephritis, and chronic kidney disease, has been observed. However, the causal relationships between specific bacterial genera and these renal diseases have not been fully elucidated. To investigate the potential causal links between different genera of the gut microbiome and the susceptibility to various renal conditions utilizing two-sample Mendelian randomization (MR) analyses. Genome-wide association study (GWAS) summary statistics of gut microbiota and inflammatory kidney-related diseases were obtained from published GWASs. Two-sample MR analyses were conducted using methods including inverse-variance weighted (IVW), MR Egger, and others to identify potential causal links between gut microbial genera and renal conditions. Sensitivity analyses, including Cochran's Q test and the MR-PRESSO global test, were performed to validate the robustness of the results and detect horizontal pleiotropy. In addition, a reverse MR analysis was conducted to assess reverse causation possibilities. By synthesizing insights from both primary and sensitivity analyses, this study unveiled critical associations of 12 bacterial genera with nephrotic syndrome, 7 bacterial genera with membranous nephropathy, 3 bacterial genera with glomerulonephritis, 4 bacterial genera with acute tubulo-interstitial nephritis, 6 bacterial genera with chronic tubulo-interstitial nephritis, and 7 bacterial genera with chronic kidney disease. Various genera were pinpointed as having either positive or negative causal relationships with these renal conditions, as evidenced by specific ranges of IVW-OR values (all P< 0.05). The congruence of the sensitivity analyses bolstered the primary findings, displaying no marked heterogeneity or horizontal pleiotropy. Notably, the reverse MR analysis with nephritis as the exposure did not reveal any causal relationships, thereby strengthening the resilience and validity of the primary associations. This study explored the causal associations between several gut microbial genera and the risk of several inflammatory kidney-related diseases, uncovering several associations between specific gut microbial genera and nephrotic syndrome, membranous nephropathy, glomerulonephritis, tubulo-interstitial nephritis, and chronic kidney disease. These findings enhance our understanding of the complex interplay between the gut microbiome and kidney diseases, and they will be beneficial for early diagnosis and subsequent treatment.

Exploring the gut microbiome and immunological landscape in kidney cancer: a Mendelian randomization analysis.

Kidney cancer (KC) is a significant health burden globally, with over 400,000 new cases estimated in 2020. The prognosis of KC is influenced by various factors, including tumor spread, pathological characteristics, and molecular genetic changes. Recent studies have emphasized the involvement of gut microbiota and the immune system's contribution in the onset of KC. This extensive research endeavor sought to investigate the potential associations between diverse immune cell phenotypes, specific gut microbiota species, and their impact on the risk of developing KC, alongside the examination of circulating inflammatory proteins. Adhering to the STROBE-MR guidelines, our investigation involved a two-stage Mendelian randomization (2SMR) analysis grounded on three fundamental assumptions: relevance, independence, and exclusion restriction. The exposure data utilized in this study originated from genome-wide association studies (GWAS) specifically designed to explore immune traits, inflammatory proteins, and gut microbiota compositions. Our analysis identified 25 immune phenotypes, 4 circulating inflammatory proteins, and 12 gut microbiota features that exhibited significant causal associations with KC (P < 0.05). 10 immune phenotypes were protective against KC, while 15 were risk factors. Among the inflammatory proteins, CCL28 and IL-2 were protective, whereas FGF-23 and β-NGF were risk factors. Gut microbiota features associated with reduced KC risk included biosynthetic pathways involving amino acids and specific bacterial genera, whereas others, like Butyrivibrio crossotus and Odoribacter splanchnicus, were risk factors. Immune, inflammatory, and gut microbiota factors impact KC development. Identified factors hint at biomarkers and therapeutic targets. It is very important to understand the relationship between these factors and KC.

Impact of complementary feeding on infant gut microbiome, metabolites and early development.

Introducing complementary foods is critical for promoting infant health and development. During the weaning period, the dietary patterns provide essential nutrients and facilitate the development of a diverse gut microbiome, which plays significant roles in the regulation of immune, metabolic, and neurological functions. This study enrolled 200 families to assess the impact of complementary feeding on infant growth and health outcomes. Data included detailed records of feeding practices, infant growth measurements, health assessments, and fecal samples and breast milk collected between weeks 12 and 32 postpartum. The gut microbiome was analyzed using 16S rRNA sequencing, while metabolites such as human milk oligosaccharides (HMOs), monosaccharides, and short-chain fatty acids (SCFAs) were measured using chromatography-mass spectrometry. Results revealed a high prevalence of breastfeeding, with complementary food introduced at around 16 weeks. Significant alterations in the infant gut microbiome were observed, particularly in the genera Lactobacillus, Akkermansia, and Staphylococcus. Additionally, the levels of HMOs, monosaccharides, and SCFAs were found to be influenced by the introduction of complementary foods. Significant correlations emerged between complementary feeding practices, gut microbiome diversity, specific bacterial genera (e.g., Streptococcus, Lactobacillus, Bifidobacterium, and Clostridioides), and key metabolites (such as lacto-N-tetraose, lacto-N-neotetraose, mannose, and butyric acid). This study offers valuable insights into the complex interactions between complementary feeding, gut microbiome development, and metabolite profiles during early infant growth. Future research with larger cohorts and targeted dietary interventions is recommended to further elucidate the underlying mechanisms.

The essential role of intestinal microbiota in cytomegalovirus reactivation.

Human cytomegalovirus (HCMV) is a member of Herpesviridae. It has been reported that HCMV is reactivated in the breast milk of HCMV-seropositive lactating women. As we have reported various aspects of the roles of indigenous microbiota, its role in the murine CMV (MCMV) reactivation was examined in this study. MCMV was latently infected in the salivary gland, mammary tissues, and colon in the pregnant mice. When the salivary gland, mammary tissues, and colon were removed 5 days after delivery, MCMV reactivation of latent infection in each organ was confirmed by the detection of MCMV IE1 mRNA using reverse transcription-quantitative PCR. MCMV reactivation was observed in 100% of the mice during pregnancy. Next, for the elimination of intestinal microbiota, the pregnant mice were treated with low-dose or high-dose non-absorbable antibiotics. Although the numbers of aerobe/anaerobe in cecal content in low-dose antibiotic-treated mice were comparable to those in untreated controls, high-dose antibiotic treatment decreased the number of aerobe/anaerobe microbes from ca.9.0 Log10 to ca.3.0 Log10 (cfu/g). However, it could not be confirmed in 16S rRNA analysis that specific bacterial phylum or genus was eliminated by this high-dose treatment. Interestingly, MCMV reactivation was also observed in 100% of low-dose antibiotic-treated mice, whereas, in high-dose antibiotic-treated mice, MCMV reactivation was not observed in the salivary gland or colon. MCMV IE1 mRNA was detected only in 33% of the mammary tissues of those high-dose-treated mice. These results suggest that the indigenous microbiota played a crucial role in the reactivation of latent infection. IMPORTANCE Human cytomegalovirus (HCMV) infection via breast milk is a serious problem for very preterm infants such as developing a sepsis-like syndrome, cholestasis, or bronchopulmonary dysplasia, among others. It has been reported that HCMV is reactivated in the breast milk of HCMV-seropositive lactating women. In this study, the roles of indigenous microbiota in the murine CMV (MCMV) reactivation were examined using a mouse model. In MCMV latently infected mice, MCMV reactivation was observed in 100% of the mice during pregnancy. For the elimination of intestinal microbiota, MCMV-latent mice were treated with non-absorbable antibiotics. After delivery, MCMV reactivation was not observed in antibiotic-treated mice. This result suggested that the indigenous microbiota played a crucial role in the reactivation of latent infection.

Gut microbiome in men with chronic prostatitis/chronic pelvic pain syndrome: profiling and its predictive significance.

To investigate the difference in gut microbiome composition between patients with chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) and healthy controls, and to assess the potential of gut microbiota as predictive markers for CP/CPPS risk. The present study included 41 CP/CPPS patients and 43 healthy controls in China. Fecal specimen data were obtained and analysed using 16S rRNA gene sequencing. Alpha and beta-diversity indices, relative microbiome abundances, cluster analysis, and linear discriminant analysis effect size (LEfSe) were employed. Microbial biomarkers were selected for the development of a diagnostic classification model, and the functional prediction was conducted using PICRUSt2. Alpha-diversity measures revealed no statistically significant difference in bacterial community structure between CP/CPPS patients and controls. However, significant differences were observed in the relative abundances of several bacterial genera. Beta-diversity analysis revealed a distinct separation between the two groups. Significant inter-group differences were noted at various taxonomic levels, with specific bacterial genera being significantly different in abundance. The LEfSe analysis indicated that three bacterial species were highly representative and seven bacterial species were low in CP/CPPS patients as compared to the control group. A diagnostic model for CP/CPPS based on microbial biomarkers exhibited good performance. PICRUSt2 functional profiling indicated significant differences in the development and regeneration pathway. Significant differences in the gut microbiome composition were found between groups. The study provided a novel diagnostic model for CP/CPPS based on microbiota, presenting promising potential for future therapeutic targets and non-invasive diagnostic biomarkers for CP/CPPS patients.

Municipal separate storm sewer system (MS4) dry weather flows and potential flow sources as assessed by conventional and advanced bacterial analyses

Municipal separate storm sewer systems (MS4s) function in urbanized areas to convey flows during both wet weather (i.e., stormwater) and dry weather (i.e., urban runoff as well as subsurface sources of flow) to receiving waters. While urban stormwater is known to contain microbial and chemical pollutants, MS4 dry weather flows, or non-stormwater discharges (NSWDs), are much less studied, although they are also known to contain pollutants, especially when these flows include raw sewage. In addition, some natural NSWDs (e.g., from groundwater infiltrating MS4 pipes) are critical for aquatic habitat protection. Thus, it is important to distinguish NSWD sources to prevent non-natural flows while retaining natural waters (i.e., groundwater). Here, MS4 dry weather flows were assessed by analyzing water samples from MS4 outfalls across multiple watersheds and water provider service areas in south Orange County, CA; potential NSWD sources including sewage, recycled water, potable water, and groundwater were sampled and analyzed for their likely contributions to overall NSWDs. Geochemical and microbiological water quality indicators, as well as bacterial communities, differed across NSWDs, yet water quality within most locations did not vary significantly diurnally or by sampling date. Meanwhile, NSWD source waters had distinctly different bacterial taxa abundances and specific bacterial genera. Shared geochemical and microbial characteristics of certain sources and outfall flows suggested the contributions of sources to outfall flows. The average proportions by sources contributing to MS4 outfalls were further estimated by SourceTracker and FEAST, respectively. The results of this study highlight the use of multiple tools when assessing chemical and microbiological water quality to predict sources of NSWDs contributing to urban MS4 flows during dry weather. This information can be used to support management actions to reduce unnatural and high risk sources of dry weather drainage while preserving natural sources important to environmental health in downstream receiving waters.

The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIME® Model.

From the estimated 2.2 to 3.8 million fungal species existing on Earth, only a minor fraction actively colonizes the human gastrointestinal tract. In fact, these fungi only represent 0.1% of the gastrointestinal biosphere. Despite their low abundance, fungi play dual roles in human health-both beneficial and detrimental. Fungal infections are often associated with bacterial dysbiosis following antibiotic use, yet our understanding of gut fungi-bacteria interactions remains limited. Here, we used the SHIME® gut model to explore the colonization of human fecal-derived fungi across gastrointestinal compartments. We accounted for the high inter-individual microbial diversity by using fecal samples from healthy adults, healthy babies, and Crohn's disease patients. Using quantitative Polymerase Chain Reaction and targeted next-generation sequencing, we demonstrated that SHIME®-colonized mycobiomes change upon loss of transient colonizers. In addition, SHIME® reactors from Crohn's disease patients contained comparable bacterial levels as healthy adults but higher fungal concentrations, indicating unpredictable correlations between fungal levels and total bacterial counts. Our findings rather link higher bacterial α-diversity to limited fungal growth, tied to colonization resistance. Hence, while healthy individuals had fewer fungi engrafting the colonic reactors, low α-diversity in impaired (Crohn's disease patients) or immature (babies) microbiota was associated with greater fungal abundance. To validate, antibiotic-treated healthy colonic microbiomes demonstrated increased fungal colonization susceptibility, and bacterial taxa that were negatively correlated with fungal expansion were identified. In summary, fungal colonization varied individually and transiently, and bacterial resistance to fungal overgrowth was more related with specific bacterial genera than total bacterial load. This study sheds light on fungal-bacterial dynamics in the human gut.