Microbiome Composition Research Articles

Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV.

Inflammation and innate immune activation are associated with chronic HIV infection, despite effective treatment. Although gut microbiota alterations are linked to systemic inflammation, the relationships between the gut microbiome, inflammation and HIV remain unclear. The UPBEAT-CAD sub-study, examining cardiovascular disease (CVD) risk in HIV, enrolled participants matched on HIV status and traditional CVD risk factors. Subclinical CVD was assessed using coronary computed tomography angiography (CCTA). 34 biomarkers were measured using quantitative immunoassays. Microbiota composition was analysed by 16S rRNA sequencing of stool samples, with taxonomic assignment via the SPINGO pipeline. Differentially abundant species were identified by Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) and correlated to biomarkers, diet and CCTA outcomes using Spearman correlation. Among 81 participants (median age 51 years, 73% male), people with HIV (n=44 , 54%) had a higher prevalence of hypercholesterolaemia (p <0.025) and statin use (p <0.001). A significant separation in gut microbiome β-diversity was observed between people with and without HIV. ANCOM-BC analysis identified 42 differentially abundant species and 10 genera in those with HIV. Enrichment of Bifidobacterium pseudocatenulatum, Megamonas hypermegale and Selenomonas ruminantium and depletion of Fusicatenenibacter correlated with lower plaque burden. Depletion of SCFA-producing Ruminococcus bromii correlated with higher plaque burden and fat intake, while depletion of Bacteroides spp and Alistepes spp correlated with elevated inflammatory biomarkers (D-dimer, CD40-ligand, CRP and IFN-γ). Significant gut microbiota differences in people with HIV were linked to subclinical CVD, diet, and inflammation, suggesting a role for the microbiome in cardiovascular risk in HIV infection.

Exposure to spaceflight enhances the virulence of Purpureocillium lilacinum against Tetranychus cinnabarinus: modulation of the host's enzyme activities and microbiome.

Multiple studies have been conducted to investigate the impact of space conditions on human, plant, and microbial life. This research investigated the virulence of spaceflight mutants of the entomopathogenic fungus Purpureocillium lilacinum (HP7, HP36, HP52) and its original strain (SP535) against Tetranychus cinnabarinus as well as examination of the T. cinnabarinus immune response, including alterations in enzyme profiles and microbiome composition post fungal application. Our observations revealed contrasting, time-specific differences in pathogenicity and tissue infection between the ground-based isolate and spaceflight mutant isolates. Analysis of detoxifying and antioxidant enzymes showed a significant reduction in enzyme activities T. cinnabarinus infected with the most virulent spaceflight mutants at 36h post-fungal infection, compared to ground-based isolates. Additionally, the microbiota was reduced due to a fungal infection, partly due to decreased antioxidant enzyme activities. Our findings indicate that changes in the microbiota of T. cinnabarinus following infection with P. lilacinum (both ground-based and spaceflight mutant isolates) resulted in variations in metabolism and genetic information-related KEGG pathways. This data can help identify potential changes in the host immune system that drive increased virulence after spaceflight mutation.

Lactobacillus rhamnosus GG Combined with Metformin Alleviates Alcohol-Induced Liver Inflammation in Mice by Maintaining the Intestinal Barrier and Regulating Treg/Th1 Cells.

Disturbances of the intestinal barrier enabling bacterial translocation exacerbate alcoholic liver disease (ALD). Lactobacillus rhamnosus GG (LGG) has been shown to exert beneficial effects in gut dysbiosis and chronic liver disease. The current study assessed the combined effects of LGG and metformin, which play roles in anti-inflammatory and immunoregulatory processes, in alcohol-induced liver disease mice. A diet comprising 5% alcohol for 4 weeks was employed to develop an alcohol-induced liver injury model. Mice were orally administered LGG, metformin, or their combination on alternate days. Tight junction (TJ) proteins, gut microbiome composition, inflammatory cytokines, Jun N-terminal kinase (JNK), and p38 signals were assessed. When compared with treatment with LGG or metformin alone, combined LGG and metformin treatment substantially lowered the symptoms of inflammation, steatosis, and elevated liver enzymes caused by alcohol administration. Combination treatment significantly improved intestinal microecology, evidenced by the recovery of intestinal flora, TJ proteins, and intestinal villi. Combination treatment reduced hepatic inflammation by blocking p38 and JNK phosphorylation. The combination of LGG and metformin corrected immune-response dysregulation and improved ALD by enhancing the intestinal microbiome, restoring mucosal barrier integrity, modulating immune function, and decreasing liver injury. These results provide information for the development of intestinal microbiota-based preventive and therapeutic agents against ALD.

Effects of Methylglyoxal on Intestine and Microbiome Composition in Aged Mice.

Methylglyoxal (MGO), a highly reactive precursor of advanced glycation end products (AGEs), is endogenously produced and prevalent in various ultra-processed foods. MGO has emerged as a significant precursor implicated in the pathogenesis of type 2 diabetes and neurodegenerative diseases. To date, the effects of dietary MGO on the intestine have been limited explored. Thus, this study investigates the impact of prolonged oral administration of MGOs on gut health in aged mice. Aged mice received MGO chronically (100 mg/kg/day) for 4 weeks. Intestinal samples were analyzed using RT-PCR and immunohistochemistry for proinflammatory cytokines, permeability markers, and tight junction proteins. 16S rRNA gene-based microbiome analysis was also performed to characterize microbiome composition and its metabolic potential. MGO treatment induced notable alterations at the intestinal level, characterized by an increased formation of MGO-glycated proteins with a concurrent induction of a pro-inflammatory status and reduced expression and delocalization of zonulin-1 and occludin, tight junction proteins. Changes in intestinal morphology were also observed, including hyperproliferation of Paneth cells and an augmented thickness of the intestinal mucus layer, as indicated by immunohistochemical data from MGO-treated mice. Investigation into the microbiota composition revealed that MGO is effective in selectively modifying its composition and metabolic pathways. A decreased abundance of bacterial genera associated with the production of acetic and butyric acids (i.e. Harryflintia, Intestinimonas and Ruminococcaceae genera) and a substantial increase in Lachnospiraceae and Akkermansia genera were found in MGO-treated mice. These findings highlight how dietary MGO can affect intestinal balance, providing valuable insights into the potential links between glycotoxins, gut microbiota, and overall gut functionality.

The interplay between scion genotype, root microbiome, and Neonectria ditissima apple canker.

Severity of European apple canker caused by Neonectria ditissima can vary between locations and apple genotypes. We investigated how location, cold storage/planting season, and apple scion genotype affect root-associated microbial communities. Additionally, we investigated whether differences in abundance of specific taxa could be associated with canker lesion counts. Seven scion cultivars grafted onto M9 rootstocks were inoculated with N. ditissima in the nursery and then planted in December 2018 or stored at 2°C until planting in April 2019 at three sites in Kent, UK. We assessed canker lesions and collected root samples in June 2021. Quantitative PCR and 16S/ITS amplicon sequencing was used to analyse microbial communities. Site was the primary factor affecting microbiome size, diversity, and composition. Cold storage/planting season had small but significant effects, indicating that differences in the microbiome at planting can persist long-term. Scion genotype had a limited effect on diversity but did influence the abundance of specific root associated taxa. Bacterial α-diversity was associated with canker count in a site-dependent manner. Increased abundances of particular fungal (Rhizophagus irregularis and Epicoccum nigrum) and bacterial (Amycolatopsis and Bradyrhizobium) root associated taxa were associated with fewer cankers.

Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance

Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance

Human embryo implantation: The complex interplay between endometrial receptivity and the microbiome.

The endometrial and vaginal microbiota have co-evolved with the reproductive tract and play a key role in both health and disease. However, the difference between endometrial and vaginal microbiota, as well as their association with reproductive outcomes in women undergoing frozen embryo transfer, remains unclear. 120 women who underwent in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) and whole embryo freezing were enrolled. The vaginal and uterine microbiome were sequenced during the first frozen thawed embryo transfer. Based on whether or not they were pregnant after embryo transfer, women were assigned into two groups, and the microbiome of their reproductive tract was compared. The V3-V4 regions of the 16S rRNA gene were examined in the samples using the Next Generation Sequencing method. In the vagina, the non-pregnant group had higher bacterial species richness and diversity, with significantly lower Lactobacillus levels (91.66 % & 74.50 %) and higher Gardnerella levels (3.92 % & 12.12 %) than pregnant group (P < 0.05). In the uterine cavity, the diversity of uterine microbiome between pregnant group and non-pregnant group showed no significant differences. However, dramatic decrease in Lactobacillus (37.27 % & 33.45 %) and Pseudomonas (9.80 % & 4.08 %) were observed in the non-pregnant group (P < 0.05). There may be a correlation between the composition of female reproductive tract microbiome and the reproductive outcomes of patients with frozen-thawed embryo transfer. Lactobacillus-dominated microbiome in reproductive tract is more likely to be associated with higher clinical and ongoing pregnancy rate.

Grocery intervention and DNA-based assessment to improve diet quality in pediatric obesity: a pilot randomized controlled study.

We assessed the impact of a food-provisioning intervention on diet quality in children with obesity. Participants (n = 33, aged 6-11 years) were randomly assigned to either usual care (intensive health behavior and lifestyle treatment) or intervention (usual care + food provisioning; high-fiber, low-dairy diet) for 4 weeks. The primary outcome was a change in child diet quality at Week 4. Secondary outcomes were changes in weight, food insecurity, gut microbiome composition (16S ribosomal RNA), and dietary intake, measured via an objective DNA-based biomarker (i.e., FoodSeq). Genomic dietary data were analyzed against a larger pediatric adolescent obesity cohort (n = 195, aged 10-18 years) from similar households. Intervention demonstrated changes across all assessed diet components and was more effective than usual care in increasing whole grain (β = 0.20, 95% CI: 0.05 to 0.34; p = 0.013) and fiber (β = 2.52, 95% CI: 1.28 to 3.76; p < 0.001) and decreasing dairy (β = -1.31, 95% CI: -2.02 to -0.60; p = 0.001). FoodSeq results, highly concordant with grocery orders (adjusted R2 = 0.65; p < 0.001), indicated a dietary shift toward low-energy-density plant taxa in the intervention relative to a prior survey of diet in a related cohort (β = 8.64, 95% CI: 5.18 to 12.14; p < 0.001). No significant changes were observed in microbiome, weight, or food insecurity. Our study supports the potential of dietitian-guided food provisioning for improving diet quality in children with obesity and demonstrates an objective genomic approach for evaluating dietary shifts.

Gut Microbiome Modulation in Allergy Treatment: The Role of Fecal Microbiota Transplantation.

The prevalence of allergic diseases has been rising, paralleling lifestyle changes and environmental exposures that have altered human microbiome composition. This review article examines the intricate relationship between the gut microbiome and allergic diseases, emphasizing the potential of fecal microbiota transplantation as a promising novel treatment approach. It explains how reduced microbial exposure in modern societies contributes to immune dysregulation and the increasing incidence of allergies. The discussion also addresses immune homeostasis and its modulation by the gut microbiome, highlighting the shift from eubiosis to dysbiosis in allergic conditions. Furthermore, this article reviews existing studies and emerging research on the role of fecal microbiota transplantation in restoring microbial balance, providing insights into its mechanisms, efficacy, and safety.

Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands

Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.

Biochemical strategy-based hybrid hydrogel dressing-mediated in situ synthesis of selenoproteins for DFU immunity-microbiota homeostasis regulation.

Chronic consequences of diabetes that are most commonly encountered are diabetic foot ulcers (DFUs), driven by microbiota-immune system dyshomeostasis, eventually leading to delayed wound healing. Available therapies, such as systemic or topical administration of anti-inflammatory or antimicrobial agents, are limited due to antibiotic resistance and immune dysfunction. Herein, a hybrid hydrogel dressing is developed as the artificial bioadhesive barrier at wound sites to maintain microbial and immunological homeostasis locally and have potent anti-inflammatory effects. Specifically, Zero-valent selenium nanoparticles are synthesized and encapsulated into the alginate-polyacrylamide interpenetrating hydrogel networks, during which trehalose is adopted to modify the network defects. Besides, as an anti-adhesion agent, trehalose has shown the ability to prevent immune degradation by reducing bacteria binding to HUVECs. The obtained hybrid hydrogel dressing serves as a physical barrier against microbiome invasion, further regulates the composition of the wound microbiome to restore microbial immune homeostasis at the wound site, and cooperatively relieves DFU-associated symptoms. Meanwhile, the hydrogel dressing can synthesize selenoproteins in situ based on biochemical strategies and significantly reduce the secretion of proinflammatory cytokines. The proposed biochemical strategy based on the hybrid hydrogel dressings can efficiently restore microbiota-immune homeostasis in the wounds, presenting a promising approach for DFU therapy in clinics.

Comparison of the lower genital tract microbiome composition in patients with benign gynecological disease

Comparison of the lower genital tract microbiome composition in patients with benign gynecological disease

Staphylococcus aureus carriage is associated with microbiome composition in the nares and oropharynx, not the hand, of monozygotic twins

Staphylococcus aureus carriage is associated with microbiome composition in the nares and oropharynx, not the hand, of monozygotic twins

Characteristics of tongue coating microbiota in diabetic and non-diabetic kidney patients receiving hemodialysis

BackgroundTongue-coating microbiota, especially known as the tongue microbiome, holds significant value as both a prospective clinical diagnostic biomarker and therapeutic target, which plays a crucial role in the oral microecological health. However, there is limited understanding of the composition and function of tongue coating microbiota in chronic kidney disease patients undergoing hemodialysis.MethodsThirty-one non-diabetic hemodialysis patients (nonDM_HD), 29 diabetic hemodialysis patients (DM_HD) and 33 healthy controls (HC) were enrolled. Swabs from tongue coating were collected. The 16S rDNA (V3-V4 region) was sequenced to scrutinize the tongue-coating bacterial microbiome difference.ResultsBoth nonDM_HD and DM_HD showed distinct bacterial communities of oral microbiota compared to HC. The abundance of Streptococcus, Lactobacillus, Ruminococcaceae G1, Ligilactobacillus and Abiotrophia showed a significant increase (p < 0.05) in DM_HD and nonDM_HD compared to HC, while Haemophilus, Lachnoanaerobaculum, Peptostreptococcaceae G1, Peptostreptococcus showed a significant decrease (p < 0.05) respectively. Veillonella, Lactobacillus, Limosilactobacillus etc. may serve as potential biomarkers for DM_HD. While Streptococcus, Ruminococcaceae G1, Actinobacillus, Abiotrophia can be considered alternative biomarkers for nonDM_HD. Moreover, the enriched Haemophilus, Actinomyces, Lachnoanaerobaculum were prominent features of the tongue coating microbiota in HC, which could be used as the potential therapeutic targets of chronic kidney disease. Network analysis revealed a less complex interaction relationship among the tongue coating bacterial microbiota of nonDM_HD and DM_HD. Furthermore, correlations were identified between the microbiome composition and clinical parameters of the individuals.ConclusionIn conclusion, deciphering the tongue coating microbiota of kidney patients undergoing hemodialysis will helpful in assessing the role of oral microbiota in pathobiology and development of kidney disease, which is expected to become a potential biomarkers and adjuvant therapeutic target.

Enhancing the Immunogenicity of Nivolumab plus Ipilimumab with Live Bacterial Supplementation in Metastatic Renal Cell Carcinoma.

Dysbiosis may hinder effective tumor immunity and reduce the efficacy of therapies such as immune checkpoint blockade (ICB) in renal cell carcinoma (RCC). CBM588, a product containing live Clostridium butyricum, has shown promise in enhancing ICB effectiveness in metastatic RCC in terms of response rates and progression-free survival. Further research to confirm these findings should take factors such as diet and microbiome composition into account and include predictive biomarkers for patient selection.

Alcohol Consumption and Autoimmune Diseases.

Alcohol is the second-most misused substance after tobacco. It has been identified as a causal factor in more than 200 diseases and 5.3% of all deaths and is associated with significant behavioral, social, and economic difficulties. As alcohol consumption may modulate the immune system's regulatory mechanisms to avoid attacking the body's tissues, it has been proven to play a dichotomic role in autoimmune diseases (ADs) based on the quantity of consumption. In this review, we report updated evidence on the role of alcohol in ADs, with a focus on alcohol addiction and the human biological immune system and the relationship between them, with alcohol as a risk or protective factor. Then, in this narrative review, we report the main evidence on the most studied ADs where alcohol represents a key modulator, including autoimmune thyroiditis, multiple sclerosis, rheumatoid arthritis, systemic lupus erythematosus, diabetes, allergic rhinitis, and primary biliary cholangitis. Alcohol at low-moderate dosages seems mostly to have a protective role in these diseases, while at higher dosages, the collateral risks surpass possible benefits. The specific mechanisms by which low-to-moderate alcohol intake relieves AD symptoms are not yet fully understood; however, emerging studies suggest that alcohol may have a systemic immunomodulatory effect, potentially altering the balance of anti-inflammatory innate and adaptive immune cells, as well as cytokines (via the NF-κB or NLRP3 pathways). It might influence the composition of the gut microbiome (increasing amounts of beneficial gut microbes) and the production of their fatty acid metabolites, such as short-chain fatty acids (SCFAs) and polyunsaturated fatty acids (PUFAs), as well as elevated concentrations of acetate, high-density lipoprotein (HDL), and nitric oxide (NO). Unfortunately, a definite acceptable daily intake (ADI) of ethanol is complicated to establish because of the many mechanisms associated with alcohol consumption such that despite the interesting content of these findings, there is a limit to their applicability and risks should be weighed in cases of alcoholic drinking recommendations. The aim of future studies should be to modulate those beneficial pathways involved in the alcohol-protective role of ADs with various strategies to avoid the risks associated with alcohol intake.

Multi-cohort analysis identifying core ocular surface microbiome and bacterial alterations in eye diseases.

Inconsistency exists among reported studies on the composition of human ocular surface microbiome (OSM). The roles of OSM in ocular diseases remain uncertain. In this study, we aimed to determine the composition of OSM and to evaluate its potential roles and functions from multiple cohorts. Raw 16 s sequencing data were obtainable from publicly available repositories, sourced from 17 published studies. Employing a standardized method, we processed the data and conducted a cross-cohort analysis. Through bioinformatics pipelines QIIME2 and PICRUSt2, we processed a total of 1875 ocular surface samples. Core microbiome analyses, genera comparisons, and MetaCyc pathway analyses were performed within each cohort independently. The results were then combined to identify shared patterns across different datasets. The core OSM comprised seven genera: Corynebacterium, Staphylococcus, Acinetobacter, Streptococcus, Pseudomonas, Cutibacterium and Bacillus. Corynebacterium and Staphylococcus are the most abundant genera on ocular surface. Most ocular diseases showed OSM alterations and eight genera demonstrated a non-specific, shared response among two or more ocular diseases. Moreover, changes in various metabolic pathways were predicted following OSM alteration, indicating potential roles of OSM in biological processes. We refined the core OSM candidates combining multiple cohorts. The common pattern shared by different cohorts is worth further investigation. Changes in metabolic pathways based on bioinformatic analysis indicated a role of OSM on ocular diseases. Our results help extend the knowledge and encourage further investigations on the associations between OSM and ocular diseases.

Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet

The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts’ adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.

A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.

Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome. Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively. Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera. These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.

Changes in microbiome composition during ontogeny and dispersal of the coral boring sponge Thoosa mismalolli

Dispersal is an important life history trait that plays a key role in the demography and evolution of species. We employed a combined approach of DNA sequencing and transmission electron microscopy to examine the changes in the microbiome during the ontogeny and dispersal of the coral-excavating sponge Thoosa mismalolli. The results show that sponge can acquired their associated bacteria via both vertical (VT) and horizontal transmission (HT). Adult sponges, brooding larvae, and early free-swimming sponge larvae harbor a similar high-diversity microbial assemblage, dominated by Proteobacteria and Chloroflexi, which change throughout the larval dispersal phase. Larvae collected offshore showed a reorganization of their microbiome with a significant reduction of the dominance of inherited bacteria (Proteobacteria and Chloroflexi), and an enrichment of environmentally derived bacteria taxa (Bacteroidetes, Tenericutes, and Firmicutes). TEM confirmed a substantial change in cell structure and microbial composition, attributed to symbionts’ massive phagocytosis. This research provides information on microbiome dynamics through the sponge ontogeny and sheds on their possible role in the dispersal capacity of their larvae.