Microbiome Analysis Research Articles

Genitourinary syndrome of menopause: Evaluation of symptoms, using a questionnaire, in a research setting, before and after treatment.

Genitourinary syndrome of menopause (GSM) is a common condition, yet there is no defined, objective, and reproducible intervention with which to make a diagnosis. There are many different treatment options available, but without the correct diagnosis, affected women are unable to access the right therapy. This paper reports on the questionnaire arm of the VAN study (VAginal Health - What's Normal?) which aimed to evaluate the performance and acceptability of the methods of assessment of GSM, described below. To determine the value of the Day-to-Day Impact of Vaginal Aging (DIVA) questionnaire: a multidimensional measure of the impact of vaginal symptoms on functioning and well-being in postmenopausal women, in a prospective, observational, feasibility study. 60 women were recruited to the study (20 premenopausal, asymptomatic women (control group) and 40 peri- and postmenopausal, symptomatic women). All women had a baseline assessment, using three different interventions, in addition to the DIVA questionnaire and symptomatic women were offered treatment, followed by a second assessment undertaken at 16weeks, using the same interventions. This paper focusses on the outcomes for the questionnaire and specifically on the paired data sets, before and after treatment. An improvement in the score for all four sections of DIVA (Activities of daily living, Emotions, Sexual Activity, and Feelings about yourself and your body (female embodiment)) was observed, following any treatment. Additional questions were added to DIVA, to assess patient preference in relation to the different diagnostic interventions. These included a speculum examination as part of the clinical assessment, a smear taken from the lateral vaginal wall to assess the vaginal maturation index, both undertaken by a clinician and a self-administered tampon to collect vaginal secretions, to determine the small molecule metabolite profile, using NMR spectroscopy, and to enable analysis of the vaginal microbiome. The medical standard tampon was the preferred intervention, before and after treatment, for women eligible for treatment. The VAN study demonstrates that DIVA, a previously tested questionnaire, is an easily accessible intervention, to assess the impact of urogenital symptoms on quality-of-life indicators in women in the United Kingdom with GSM and that women prefer to use a tampon themselves, rather than have a clinician performed vaginal speculum examination or a vaginal smear.

The Metagenomic Analysis of the Pig Digestive System Microbiome as a Basis for Disease Control on Farming in Tangerang District, Indonesia

The Metagenomic Analysis of the Pig Digestive System Microbiome as a Basis for Disease Control on Farming in Tangerang District, Indonesia

MBCN: A novel reference database for Effcient Metagenomic analysis of human gut microbiome

Metagenomic shotgun sequencing data can identify microbes and their proportions. But metagenomic shotgun data profiling results obtained from multiple projects using different reference databases are difficult to compare and apply meta-analysis. Our work aims to create a novel collection of human gut prokaryotic genomes, named Microbiome Collection Navigator (MBCN). 2379 human gut metagenomic samples are screened, and 16,785 metagenome-assembled genomes (MAGs) are assembled using a standardized pipeline. In addition, MAGs are combined with the representative genomes from public prokaryotic genomes collections to cluster, and pan-genomes for each cluster's genomes are constructed to build Kraken2 and Bracken databases. The databases built by MBCN are more comprehensive and accurate for profiling metagenomic reads comparing with other collections on simulated reads and virtual bio-projects. We profile 1082 human gut metagenomic samples with MBCN database and organize profiles and metadata on the web program. Meanwhile, using MBCN as a reference database, we also develop a unified, standardized, and systematic metagenomic analysis pipeline and platform, named MicrobiotaCN (http://www.microbiota.cn) and common statistical and visualization tools for microbiome research are integrated into the web program. Taken together, MBCN and MicrobiotaCN can be a valuable resource and a powerful tool that allows researchers to perform metagenomic analysis by a unified pipeline efficiently.

Influence of gut microbiome composition on effect variations of anti-cholesterol treatment among individual mice

This study investigated if the variation in the effect of anti-cholesterol (AC) treatment on individual mice are related to gut microbiome composition. The bile salt hydrolase (BSH) activity of 23 commercial fermented milk products was examined to select a fermented milk product for AC treatment. Mice were fed to different diets for 6 weeks: high-fat (660 % of total calories from fat; D1), high-dietary fibre (20 % cellulose; D2), and low-fat (17.2 % of total calories from fat; D3) diets to change their gut microbiomes. Subsequently, faecal microbiome was transplanted (FMT) into mice treated with high cholesterol diet contained 2 % cholesterol, followed by AC or non-AC (sterile tap water, STW) treatments. Control groups with normal (NC) and high-cholesterol diets (PC) were prepared for both AC and STW treatment. All experimental groups were subjected to serum and liver cholesterol, cholesterol metabolism-related (CMR) gene expression, and intestinal microbiome analyses. D3-FMT mice showed the most significant enhancements in cholesterol ratio and decreased hepatic cholesterol levels with AC treatment. Moreover, upregulation of the Cyp7a1 gene expression was observed in this group. Furthermore, the intestinal microbiome analysis indicated higher abundances of BSH-producing Eubacterium, Bifidobacterium, and Parabacteroides in the D3-FMT + AC group compare to others, potentially contributing to increased bile acid synthesis.

Abstract P168: The Unholy Link: The Herbicide Glyphosate Contributes to Hypertension, Gut Microbiota Dysbiosis, and Sympathetic Overdrive

Introduction: Glyphosate, marketed as Roundup®, is a widely used potent herbicide in the US. Glyphosate inhibits 5-enolpyruvylshikimate-3-phosphate synthase of the shikimate pathway, a non-mammalian signaling pathway present in plants and microbes. Therefore, glyphosate has been deemed safe for humans. However, humans are holobionts with symbiotic gut microbiota susceptible to gut dysbiosis when exposed to glyphosate. Because gut microbiota is an important contributor to hypertension (HTN), we hypothesized that exposure to glyphosate leads to gut dysbiosis and HTN. Methods: Dahl salt-sensitive (S) rats were administered either vehicle or glyphosate (175 mg/kg/day) in drinking water for three weeks ad libitum. In one group of rats (N=4/group), sympathetic nerve activity was assessed using in situ whole nerve recordings and by measuring circulating norepinephrine (NE) levels by ELISA. In separate rats (N=6–8/group), blood pressure (BP) was measured once a week for three weeks by radiotelemetry, and circulating NE was determined by ELISA. At the endpoint, fecal microbiome analyses were performed using the Illumina and Oxford Nanopore platforms. Results: Exposure to glyphosate for just one week was sufficient to significantly increase systolic (173 mmHg vs 160 mmHg, p<0.0001) and mean arterial pressure (MAP) (148 mmHg vs 141 mmHg, p<0.0002), but not diastolic BP of S rats. Through week three, BP continued to rise in glyphosate-treated rats with greater differences in the systolic (195 mmHg vs 176 mmHg, p<0.0001), diastolic (142 mmHg vs 135 mmHg, p<0.0001), and MAP (168 mmHg vs 155 mmHg, p<0.0001). This was accompanied by increased sympathetic nerve activity and serum NE as early as one week of exposure to glyphosate (5.85 ng/mL vs 4.77 ng/mL, p<0.001), which continued at week three of glyphosate exposure (13.31 ng/mL vs 6.16 ng/mL, p<0.001), indicative of adrenergic overdrive. 16S data showed that glyphosate altered the composition of commensal gut microbiota, reducing bacterial α-diversity (Shannon entropy; p<0.05) and β-diversity (Bray-Curtis; p<0.02). Whole metagenomic analysis revealed a higher abundance of several bacterial species, including Candidatus spp., Erysipelaclostridium ramosum , and Clostridium sporogenes in the glyphosate-treated rats. Conclusions: Glyphosate exposure elevated BP, increased sympathetic nerve activity, and altered gut microbiota composition. This is the first proof-of-concept study to demonstrate that glyphosate contributes to HTN.

Microbiomics and metabolomics insights into the microbial regulation on the formation of flavor components in the traditional fermentation process of Chinese Hongqu aged vinegar

This study aimed to investigate microbial succession and metabolic dynamics during the traditional fermentation of Hongqu aged vinegar, and explore the core functional microbes closely related to the formation of flavor components. Microbiome analysis demonstrated that Lactobacillus, Acetobacter, Bacillus, Enterobacter, Lactococcus, Leuconostoc and Weissella were the predominant bacterial genera, while Aspergillus piperis, Aspergillus oryzae, Monascus purpureus, Candida athensensis, C. xylopsoci, Penicillium ochrosalmoneum and Simplicillium aogashimaense were the predominant fungal species. Correlation analysis revealed that Acetobacter was positively correlated with the production of tetramethylpyrazine, acetoin and acetic acid, Lactococcus showed positive correlation with the production of 2-nonanone, 2-heptanone, ethyl caprylate, ethyl caprate, 1-hexanol, 1-octanol and 1-octen-3-ol, C. xylopsoci and C. rugosa were positively associated with the production of diethyl malonate, 2,3-butanediyl diacetate, acetoin, benzaldehyde and tetramethylpyrazine. Correspondingly, non-volatile metabolites were also detected through ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry. A variety of amino acids and functional dipeptides were identified during the traditional brewing of Hongqu aged vinegar. Correlation analysis revealed that Lactobacillus was significantly associated with DL-lactate, indolelactic acid, D-(+)-3-phenyllactic acid, pimelic acid, pregabalin and 3-aminobutanoic acid. This study is useful for understanding flavor formation mechanism and developing effective strategies for the suitable strains selection to improve the flavor quality of Hongqu aged vinegar.

Impacts of industrial food wastes on nutritional value of mealworm (Tenebrio molitor) and its gut microbiota community shift

The extensive investigation into the capacity of mealworms to digest diverse food by-products, as well as plastic wastes, has been a focal point in recent years. The transition from traditional diet sources like brans to food wastes has the potential to impact the physiological properties of mealworms. This study explored the utilization of various industrial food wastes such as okara, barley spent grain (BSG), sesame oil meal (SOM), and spent coffee grounds (SCG) as feed alternatives, and reports on their survival rate, biomass variations, and nutritional composition. In additional, the shift in their gut microbiota was also assessed. Among the range of industrial food wastes, mealworms exhibited the most robust growth performance when nourished with BSG. This particular group showed a survival rate of 98.33 % and a biomass increase of 23.06 %. In contrast, mealworms fed with SCG demonstrated the lowest survival rate and experienced a significant reduction in biomass. Although the groups fed with okara and SCG displayed moderate growth performance, both exhibited protein levels comparable to those observed in the oatmeal-fed group (used as the positive control). Notably, the inclusion of BSG in the mealworm diet exhibited the potential to enrich their omega-3 fatty acid content, suggesting potential benefits for applications as animal feed or even human consumption. Furthermore, an analysis of the gut microbiome was conducted to investigate the associations between specific diets and the composition of mealworm gut microbiota. In summary, food wastes such as BSG may be repurposed as feed substrates for mealworms before converting them into an alternative source of protein.

Unde venis? Bacterial resistance from environmental reservoirs to lettuce: tracking microbiome and resistome over a growth period.

Fresh produce is suggested to contribute highly to shaping the gut resistome. We investigated the impact of pig manure and irrigation water quality on microbiome and resistome of field-grown lettuce over an entire growth period. Lettuce was grown under four regimes, combining soil amendment with manure (with/without) with sprinkler irrigation using river water with an upstream wastewater input, disinfected by UV (with/without). Lettuce leaves, soil, and water samples were collected weekly and analysed by bacterial cultivation, 16S rRNA gene amplicon sequencing, and shotgun metagenomics from total community DNA. Cultivation yielded only few clinically relevant antibiotic-resistant bacteria (ARB), but numbers of ARB on lettuce increased over time, while no treatment-dependent changes were observed. Microbiome analysis confirmed a temporal trend. Antibiotic resistance genes (ARGs) unique to lettuce and water included multidrug and β-lactam ARGs, whereas lettuce and soil uniquely shared mainly glycopeptide and tetracycline ARGs. Surface water carried clinically relevant ARB (e.g. ESBL-producing Escherichia coli or Serratia fonticola) without affecting the overall lettuce resistome significantly. Resistance markers including biocide and metal resistance were increased in lettuce grown with manure, especially young lettuce (increased soil contact). Overall, while all investigated environments had their share as sources of the lettuce resistome, manure was the main source especially on young plants. We therefore suggest minimizing soil-vegetable contact to minimize resistance markers on fresh produce.

Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease

BackgroundThis study aims to identify distinct microbial and functional biomarkers characteristic of body-first or brain-first subtypes of Parkinson's disease (PD). This could illuminate the unique pathogenic mechanisms within these subtypes. MethodsIn this cross-sectional study, we classified 36 well-characterized PD patients into body-first, brain-first, or undetermined subtypes based on the presence of premotor REM sleep behavior disorder (RBD) and cardiac meta-iodobenzylguanidine (MIBG) uptake. We then conducted an in-depth shotgun metagenomic analysis of the gut microbiome for each subtype and compared the results with those from age- and sex-matched healthy controls. ResultsSignificant differences were found in the gut microbiome of body-first PD patients (n = 15) compared to both brain-first PD patients (n = 9) and healthy controls. The gut microbiome in body-first PD showed a distinct profile, characterized by an increased presence of Escherichia coli and Akkermansia muciniphila, and a decreased abundance of short-chain fatty acid-producing commensal bacteria. These shifts were accompanied by a higher abundance of microbial genes associated with curli protein biosynthesis and a lower abundance of genes involved in putrescine and spermidine biosynthesis. Furthermore, the combined use of premotor RBD and MIBG criteria was more strongly correlated with these microbiome differences than the use of each criterion independently. ConclusionsOur findings highlight the significant role of dysbiotic and pathogenic gut microbial alterations in body-first PD, supporting the body-first versus brain-first hypothesis. These insights not only reinforce the gut microbiome's potential as a therapeutic target in PD but also suggest the possibility of developing subtype-specific treatment strategies.

Influence of cadmium and zinc contamination on the sediment microbiome of estuarine and coastal ecosystems in the Southwest Coast of India.

Metals and their nanoparticles can induce toxicities that influence the survival of both microorganisms and macroorganisms. The current study reports on the impact of heavy metal pollution on the microbiome of estuarine and coastal sediments, where the settling and final remineralization of organic matter occur. Sediment samples collected from the Cochin estuary along the southwest coast of India and its adjacent coast showed high concentrations of cadmium (Cd) and zinc (Zn). The contamination factor (CF), calculated by comparing the concentration of metals in each station with that of shale value for Cd and Zn, ranged from 5.2 to 8.7 and 1.5 to 2.0 respectively, in the estuarine and coastal stations. Microbiome analysis revealed that bacteria were common across all stations but varied in relative abundance. Proteobacteria, Chloroflexi, Actinobacteria, Desulfobacteria, and Acidobacteria were the major bacterial phylum found in all stations. More than 70% of the bacteria were tolerant to 1mM concentration of Cd. The findings of our study suggest that metal pollution can influence the microbiome of sediments in the estuaries and coasts. Bacteria with metal tolerance may dominate in polluted areas, but their participation in remineralization may be impaired, as evident in our previous reports. This impairment could ultimately influence the dynamics of the food web and the biogeochemical cycling of nutrients, necessitating further research.

Widely Targeted Lipidomics and Microbiomics Perspectives Reveal the Mechanism of Auricularia auricula Polysaccharide's Effect of Regulating Glucolipid Metabolism in High-Fat-Diet Mice.

The role of Auricularia auricula polysaccharide (AP) in the regulation of glycolipid metabolism was investigated using a high-fat-diet-induced hyperlipidemic mouse model. In a further step, its potential mechanism of action was investigated using microbiome analysis and widely targeted lipidomics. Compared to high-fat mice, dietary AP supplementation reduced body weight by 13.44%, liver index by 21.30%, epididymal fat index by 50.68%, fasting blood glucose (FBG) by 14.27%, serum total cholesterol (TC) by 20.30%, serum total triglycerides (TGs) by 23.81%, liver non-esterified fatty acid (NEFA) by 20.83%, liver TGs by 20.00%, and liver malondialdehyde (MDA) by 21.05%, and increased liver glutathione oxidase (GSH-PX) activity by 52.24%, total fecal bile acid (TBA) by 46.21%, and fecal TG by 27.16%, which significantly regulated glucose and lipid metabolism. Microbiome analysis showed that AP significantly downregulated the abundance of the Desulfobacterota phylum, as well as the genii Desulfovibrio, Bilophila, and Oscillbacter in the cecum of hyperlipidemic mice, which are positively correlated with high lipid indexes, while it upregulated the abundance of the families Eubacterium_coprostanoligenes_group and Ruminococcaceae, as well as the genii Eubacterum_xylanophilum_group, Lachnospiraceae_NK4A136_group, Eubacterium_siraeum_group, and Parasutterella, which were negatively correlated with high lipid indexes. In addition, AP promoted the formation of SCFAs by 119.38%. Widely targeted lipidomics analysis showed that AP intervention regulated 44 biomarkers in metabolic pathways such as sphingolipid metabolism and the AGE-RAGE signaling pathway in the hyperlipidemic mice (of which 15 metabolites such as unsaturated fatty acids, phosphatidylserine, and phosphatidylethanolamine were upregulated, and 29 metabolites such as phosphatidylcholine, ceramide, carnitine, and phosphatidylinositol were downregulated), thereby correcting glucose and lipid metabolism disorders.

Lactobacillus plantarum NCHBL-004 modulates high-fat diet–induced weight gain and enhances GLP-1 production for blood glucose regulation

ObjectivesThis study investigated the therapeutic potential of Lactobacillus plantarum NCHBL-004 (NCHBL-004) in the treatment of obesity and associated metabolic disorders. MethodsMice were fed either a normal diet (ND) or a high-fat diet (HFD) with oral administration of NCHBL-004. After euthanasia, blood, liver and adipose tissue were collected. Furthermore, the microbiome and short-chain fatty acids (SCFAs) were analyzed from feces. ResultsOral administration of live NCHBL-004 to mice fed a HFD resulted in notable reductions in weight gain, improvements in glucose metabolism, and maintenance of balanced lipid levels. A comparative analysis with other Lactobacillus strains highlighted the superior efficacy of NCHBL-004. Moreover, heat-killed NCHBL-004 demonstrated beneficial effects similar to those of live NCHBL-004. Additionally, administration of live NCHBL-004 induced glucagon-like peptide 1 (GLP-1) production and increased the levels of short-chain fatty acids (SCFAs), including acetate and propionate, in feces, positively influencing liver lipid metabolism and mitigating inflammation. Consistent with this, analysis of the gut microbiome following NCHBL-004 administration showed increases in SCFA-producing microbes with increased proportions of Lactobacillus spp. and a significant increase in the proportion of microbes capable of promoting GLP-1 secretion. ConclusionsThese findings underscore the potential of both live and inactivated NCHBL-004 as potential therapeutic approaches to managing obesity and metabolic disorders, suggesting avenues for further investigation and clinical applications.

The gut microbiome and serum metabolome are altered and interrelated in patients with intracranial atherosclerotic stenosis

ObjectivesTo evaluate the relationship among the gut microbiome, serum metabolites and the Intracranial atherosclerosis stenosis. Materials and methodsIntegrated analysis of 16S rDNA sequencing of fecal samples and untargeted serum metabolomics was applied to identify alterations in the gut microbiome and serum metabolome in 29 Intracranial atherosclerosis stenosis patients and 29 healthy control individuals. ResultsCompared to healthy control individuals, the abundances of forty-five genera and one hundred seventy-seven metabolites were significantly altered in Intracranial atherosclerosis stenosis patients. At the species level, the Intracranial atherosclerosis stenosis group exhibited higher abundances of Bacteroidetes and lower abundances of Megaphaera and Muribacoccaceae. Microbial functional prediction analysis revealed enhanced activity of bacterial chemotaxis and oxidative phosphorylation within the Intracranial atherosclerosis stenosis group. In terms of metabolomic findings, the levels of dulcitol were significantly increased in the Intracranial atherosclerosis stenosis group. The levels of specific metabolites within the phosphatidylcholine and lysophosphatidylcholine families, such as PC (14:0e/24:4) and LPC 20:5, were increased, while the levels of certain other specific metabolites were decreased. Dysregulation of certain pathways, such as unsaturated fatty acid metabolism, arginine and proline metabolism may be involved in the development of Intracranial atherosclerosis stenosis. Correlation analysis of the gut microbiome and metabolites revealed a positive correlation between Bacteroides and multiple metabolites, such as Acar 12:3 and PC (8:0/22:6). ConclusionsOur analysis revealed that Bacteroides is a key bacterial genus in gut dysbiosis and may be related to the development of Intracranial atherosclerosis stenosis.

Gut microbiome and plasma lipidome analysis reveals a specific impact of Clostridioides difficile infection on intestinal bacterial communities and sterol metabolism.

There is increasing evidence about the influence the changes in microbiota and its metabolism has on numerous diseases and infections such as Clostridioides difficile infection (CDI). The knowledge of these changes at local and systemic levels can help us manage this infection to avoid recurrences and apply the best therapies, such as fecal microbiota transfer (FMT). This study shows a better restoration of the gut in FMT-treated patients than in antibiotic-treated patients, resembling healthy controls and showing increased levels of cholesterol-reducing bacteria. Furthermore, it evidences the CDI impact on plasma lipidome. We observed in CDI patients a global depletion in circulating lipids, particularly cholesteryl esters, and a specific decrease in linoleic acid-containing lipids, an essential fatty acid. Our observations could impact CDI management because the lipid content was only partially recovered after treatment, suggesting that continued nutritional support, aiming to restore healthy lipid levels, could be essential for a full recovery.

Mechanisms of levan in ameliorating hyperuricemia: Insight into levan on serum metabolites, gut microbiota, and function in hyperuricemia rats

This study aims to investigate the effects of levan on the progression of hyperuricemia (HUA) rats and elucidate its underlying mechanisms. After levan intervention, both low and high-dose groups exhibited a significant decrease in serum uric acid (UA) levels, reaching 71.0 % and 77.5 %, respectively, compared to the model group. Furthermore, levan could alleviate renal pathological damage caused by glomerular cell vacuolation, inflammatory infiltration and collagen deposition. The results of enzyme activity assay and real-time fluorescence quantitative PCR showed that levan decreased UA production by inhibiting adenosine deaminase (ADA) activity and gene expression in liver; it upregulated ATP-binding cassette subfamily G member 2 protein (ABCG2) and organic anion transporter 1 (OAT1) transporter gene expression in the kidney, promoting UA excretion. Gut microbiome analysis indicated that levan regulated gut flora dysbiosis induced by HUA, resulting in up-regulated the abundance of beneficial bacteria (Muribaculaceae, Faecalibaculum, Bifidobacterium, and Lactobacillus) and decreased conditioned pathogenic bacteria (Escherichia_Shigella and Proteus). Non-targeted metabolomics showed changes in various serum metabolites associated with glycerophospholipid metabolism, lipid metabolism, and inflammation following oral administration of levan. Therefore, levan may be a promising functional dietary supplement for regulating the gut flora and remodeling of metabolic disorders in individuals with HUA.

Enhanced salt tolerance in Glycyrrhiza uralensis Fisch. via Bacillus subtilis inoculation alters microbial community.

The widespread prevalence of saline environments poses a significant global environmental challenge. Salt stress, induced by saline soils, disrupts soil microecology and affects the plant-microbe-soil cycling process. Utilizing microbial fungicides stands as a primary strategy to mitigate salt stress-induced damage to plants and soils. This study investigated the influence of Bacillus subtilis (Bs) inoculation on the microbial community, assembly processes, and functional changes in bacteria and fungi in Glycyrrhiza uralensis Fisch. (licorice) seedlings under varying salt stress levels, primarily employing microbiomics techniques. Soil enzyme activities displayed a declining trend with increasing salt stress, which was mitigated by Bs inoculation. Microbiome analysis revealed a significant increase in bacterial and fungal operational taxonomic units, particularly in Ascomycetes and Nitrogen-fixing Bacteria, thereby enhancing soil denitrification. The abundance of Proteobacteria, Actinobacteriota, Bacteroidota, and Firmicutes in bacteria, as well as Ascomycota in fungi, increased with higher salt stress levels, a process facilitated by Bs inoculation. However, functional predictions indicated a reduction in the relative abundance of Dung Saprotrophs with Bs inoculation. Salt stress disrupted soil assembly processes, showcasing a continuous decline in diffusion limitation with increased salt concentration, where Bs inoculation reached a peak under moderate stress. In summary, this research elucidates the communication mechanism of Bs in enhancing salt tolerance in licorice from a microbiome perspective, contributing to a comprehensive understanding of abiotic and biotic factors.IMPORTANCELicorice is a herb that grows in deserts or saline soils. Enhancing the salt tolerance of licorice is necessary to maintain the quality of cultivated licorice and to ensure the supply of medicinal herbs. In the past, we have demonstrated the effectiveness of inoculation with Bacillus subtilis (Bs) to enhance the salt tolerance of licorice and revealed the key metabolic pathways for the development of salt tolerance through multi-omics. In this study, we used the microbiomics approach to reveal the plant-microbe-soil interactions at the level of inoculation of Bs affecting the dynamics of soil microbial communities from bacterial and fungal perspectives, thus bridging the interactions between biotic and abiotic factors.

Combining the Vaginal Microbiome and Serum Metabolome to Screen for Potential Biomarkers of Early Pregnancy in Cows.

Early pregnancy diagnostic techniques are of significant importance in livestock farming, particularly in dairy farming. This study aimed to screen artificially inseminated cows for potential biomarkers at day 21 of pregnancy using microbiota-metabolomics analysis. The microbiome analysis revealed significant changes (p < 0.05) in the composition and abundance of the vaginal microbiota in cows after pregnancy. Notably, there was an increase in the abundance of [Eubacterium]_hallii_group (p < 0.05) associated with the production of short-chain fatty acids in the pregnant group compared with the non-pregnant group. Furthermore, significant alterations were observed in the serum metabolome, with notable changes in the concentrations of prolyl-hydroxyproline (Pro-Hyp) (p < 0.01) and bonactin (p < 0.01). The majority of differential metabolites clustered within the pathways of amino acid metabolism and lipid metabolism, with lipid metabolism exhibiting a higher proportion and playing a pivotal role in early pregnancy. An enzyme-linked immunosorbent assay was employed to quantify three key metabolites of the arachidonic acid pathway. The results demonstrated significant decreases in serum concentrations of leukotriene B4 (LTB4) (p < 0.05) and prostaglandin F2α (PGF2α) (p < 0.01) and no significant changes in arachidonic acid (AA) (NS) concentrations after 21 days of gestation in cows. Spearman's correlation analysis was utilized to investigate the interrelationship between the vaginal microbiota and serum metabolites. In conclusion, the present study demonstrated that biomaterials such as bonactin, Pro-hyp, LTB4, PGF2α in serum metabolites and [Eubacterium]_hallii_group in the vaginal flora of cows could be utilized as potential biomarkers for 21 days of gestation in cows.

Effect of Waiting Period on Initial Adverse Vaginal Microbiome Composition in IVF-ICSI Patients.

Background/Objectives: In this observational prospective cohort study, conducted at the Fertility Centre of the University Hospital, Duesseldorf Germany, the spontaneous reversal capacity and the effect of waiting time on an adverse vaginal microbiome profile in subfertile patients were investigated. Methods: Vaginal swabs of 76 patients were obtained before starting a fertility treatment using a commercially available test to perform a microbiome analysis. Patients with a favorable microbiome profile ("medium" or "high profile") according to the manufacturer's algorithm proceeded with the fertility treatment. Patients with an unfavorable microbiome profile ("low profile") postponed their fertility treatment and were sampled up to four times in each successive cycle or until a shift to a more favorable profile was detected. Results: Initially, 54/76 subjects had a high or medium profile and 23/76 had a low profile. Within 3 months, 75% of patients with an initial low profile shifted to a more favorable profile (7/23 dropouts). The presence of Lactobacillus crispatus in the initial sample was associated with a higher likelihood of a spontaneous shift to a more favorable profile. Conclusions: The vaginal microbiome is subject to strong fluctuations. Even an unfavorable microbiome profile can develop into a favorable microbiome profile within a few months without treatment.

Protective effects of Nogo-B deficiency in NAFLD mice and its multiomics analysis of gut microbiology and metabolism

BackgroundNonalcoholic fatty liver disease (NAFLD) is a prevalent chronic liver ailment that can lead to serious conditions such as cirrhosis and hepatocellular carcinoma. Hepatic Nogo-B regulates glucose and lipid metabolism, and its inhibition has been shown to be protective against metabolic syndrome. Increasing evidence suggests that imbalances in the gut microbiota (GM) and lipid metabolism disorders are significant contributors to NAFLD progression. Nevertheless, it is not yet known whether Nogo-B can affect NAFLD by influencing the gut microbiota and metabolites. Hence, the aim of the present study was to characterize this process and explore its possible underlying mechanisms.MethodsA NAFLD model was constructed by administering a high-fat diet (HFD) to Nogo-B−/− and WT mice from the same litter, and body weight was measured weekly in each group. The glucose tolerance test (GTT) and insulin tolerance test (ITT) were performed to assess blood glucose levels. At the end of the 12-week period, samples of serum, liver, and intestinal contents were collected and used for serum biochemical marker and inflammatory factor detection; pathology evaluation; and gut microbiome and metabolomics analysis. Spearman’s correlation analysis was performed to determine possible correlations between differential gut microbiota and differential serum metabolites between groups.ResultsNogo-B deficiency attenuated the effects of the HFD, including weight gain, liver weight gain, impaired glucose tolerance, hepatic steatosis, elevated serum lipid biochemicals levels, and liver function. Nogo-B deficiency suppressed M1 polarization and promoted M2 polarization, thus inhibiting inflammatory responses. Furthermore, Nogo-B−/−-HFD-fed mice presented increased gut microbiota richness and diversity, decreased Firmicutes/Bacteroidota (F/B) ratios, and altered serum metabolites compared with those of WT-HFD-fed mice. During analysis, several differential gut microbiota, including Lachnoclostridium, Harryflintia, Odoribacter, UCG-009, and unclassified_f_Butyricoccaceae, were screened between groups. These microbiota were found to be positively correlated with upregulated purine metabolism and bile acid metabolites in Nogo-B deficiency, while they were negatively correlated with downregulated corticosterone and tricarboxylic acid cyclic metabolites in Nogo-B deficiency.ConclusionNogo-B deficiency delayed NAFLD progression, as demonstrated by reduced hepatocellular lipid accumulation, attenuated inflammation and liver injury, and ameliorated gut microbiota dysbiosis and metabolic disorders. Importantly, Odoribacter was strongly positively correlated with ALB and taurodeoxycholic acid, suggesting that it played a considerable role in the influence of Nogo-B on the progression of NAFLD, a specific feature of NAFLD in Nogo-B−/− mice. The regulation of bile acid metabolism by the gut microbiota may be a potential target for Nogo-B deficiency to ameliorate NAFLD.

Research Note: Integrative analysis of transcriptome and gut microbiome reveals foie gras capacity difference between cage and floor rearing systems

To explore the differences in foie gras performance between geese raised in cages and on the ground, we conducted an integrative analysis of liver transcriptome and gut microbial metagenomes. The results showed extremely significant differences in the liver weight (P < 0.01) and liver lipid accumulation of FRS and CRS groups. The levels of triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) of CRS were significantly higher than those of FRS (P < 0.05). Transcriptome analysis showed that 3,917 upregulated and 1,395 downregulated genes were identified, and lipid metabolism pathway and fatty acid metabolism were significantly enriched. Analysis of cecum microbiota revealed that several inflammation-related bacteria (including Gallibacterium, Escherichia-Shigella, Desulfovibrio, Alistipes, and Fournierella) were enriched in CRS, while beneficial bacteria (including Lactobacillus, Limosilactobacillus, and Ligilactobacillus) were significantly enriched in FRS. In conclusion, CRS was better than FRS in foie gras production, which was more conducive to lipid deposition in the goose liver.