Differences In Microbiome Research Articles

Shark Microbiome Analysis Demonstrates Unique Microbial Communities in Two Distinct Mediterranean Sea Shark Species.

Our knowledge regarding the role of the microbiome in fish health has been steadily increasing in the last decade, especially for species of commercial interest. Conversely, relatively few studies focus on the microbiomes of wild fish, especially apex predators like sharks, due to lower economic interest and greater difficulty in obtaining samples. Studies investigating microbiome differences between diverse anatomical locations of sharks are limited, and the majority of the available studies are focused on the microbial diversity present on shark teeth, with the aim of preventing infections due to bites of these animals or evaluating the presence of certain pathogens in healthy or diseased specimens. Here, we investigated the skin, mouth, gills, and cloaca microbiomes of five individuals of two phylogenetically distant species of sharks (Prionace glauca and Somniosus rostratus) to obtain a better understanding of the diversity regarding the microbiomes of these animals, how they change throughout different body parts, and how much they are influenced and determined by the ecology and evolutionary relationship between host and microbiome. To confirm the taxonomy of the sharks under study, we barcoded the specimens by sequencing the mtDNA COI from a biopsy of their skin. Microbial diversity based on the 16S rRNA gene reveals that partially overlapping microbiomes inhabit different body parts of each shark species, while the communities are distinct between the two species. Our results suggest that sharks' microbiome species-specific differences are controlled by the ecology of the shark species. This is the first study comparatively analyzing the microbiome diversity of different anatomical locations in two shark species of the Mediterranean Sea.

Small gut intestine microbiota in adolescent girls with obesity

Aim. To characterize the small intestine microbiome in adolescent girls with obesity according to gas chromatography-mass spectrometry of microbial markers (CMSMM). Material and Methods. The research involved 72 adolescents (girls) 12-17 years old, half of the children (group 1) were obese, the other half (group 2) were not obese, as well as did not have any chronic diseases. Microbial markers in blood samples were examined by the CMSMM method. In order to examine correlation between the small intestine microbiota and obesity, a logistic model was formed. ROC analysis was used to determine possible effects of microorganisms on obesity. Results. There were found significant differences in the small intestine microbiome of obese girls, and alike microbiocenosis of children with normal body weight. Obese adolescent girls had higher levels of Nocardia asteroides 504.14[296; 1015] cells/g×10⁵ and Candida spp 241.85[198.09;629.97] cells/g×10⁵. Microorganisms of the opportunistic flora such as Actinobacteria, Firmicutes, Proteobacteria and microscopic fungi, as well as herpesviruses were significantly deficient. Conclusions. Nocardia asteroides and Candida spp. are associated with obesity. The risk of obesity in adolescent girls increases with a growing number of above-mentioned microorganisms.

Ruminal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot Finishing Phase.

The catabolic activity of the ruminal microbial community of cattle enables the conversion of low-quality feedstuffs into meat and milk. The rate at which this conversion occurs is termed feed efficiency, which is of crucial importance given that feed expenses account for up to 70% of the cost of animal production. The present study assessed the relationship between cattle feed efficiency and the composition of their ruminal microbial communities during the feedlot finishing period. Angus steers (n = 65) were fed a feedlot finishing diet for 82 days and their growth performance metrics were evaluated. These included the dry matter intake (DMI), average daily gain (ADG), and residual feed intake (RFI). Steers were rank-ordered based upon their RFI, and the five lowest RFI (most efficient) and five highest RFI (least efficient) steers were selected for evaluations. Ruminal fluid samples were collected on days 0 and 82 of the finishing period. Volatile fatty acids (VFA) were quantified, and microbial DNA was extracted and the 16S rRNA gene was sequenced. The results showed that the ADG was not different (p = 0.82) between efficiency groups during the 82-day feedlot period; however, the efficient steers had lower (p = 0.03) DMI and RFI (p = 0.003). Less-efficient (high RFI) steers developed higher (p = 0.01) ruminal Methanobrevibacter relative abundances (p = 0.01) and tended (p = 0.09) to have more Methanosphaera. In high-efficiency steers (low RFI), the relative abundances of Ruminococcaceae increased (p = 0.04) over the 82-day period. The molar proportions of VFA were not different between the two efficiency groups, but some changes in the concentration of specific VFA were observed over time. The results indicated that the ruminal microbial populations of the less-efficient steers contained a greater relative abundance of methanogens compared to the high-efficiency steers during the feedlot phase, likely resulting in more energetic waste in the form or methane and less dietary energy being harvested by the less-efficient animals.

Fungal community analysis of two edible herbs: Citri reticulatae pericarpium and polygalae radix

Citri Reticulatae Pericarpium(CRP) and Polygalae Radix (PR) are traditional Chinese medicinal herbs and dietary supplements, and they are commonly included in most prescriptions. Fungal contamination in CRP and PR has long been a concern for the public. Thus, in this study, the fungal diversity and abundance in CRP and PR were investigated via high-throughput sequencing technology. Analysis was conducted to determine the differences in dominant fungal microbiomes between mouldy and nonmouldy samples, and the correlation between the total number of fungi and fungal diversity in medicinal herbs at different altitudes and latitudes with other research was explored. Results show the fungal contamination of all 12 samples. At the phylum level, Ascomycota prevailed the most in CRP and PR with relative abundances of 56.96%–99.26% and 23.28%–76.06%, respectively. The dominant genera in CRP comprised Xeromyces (2.57%–53.21%), Aspergillus (0.18%–23.04%), Cystofilobasidium (0.032%–28.03) and Xerochrysium (0.31%–34.41%). The dominant genera in PR included Wallemia (0.27%–56.20%), Aspergillus (2.03%–48.06%), Xeromyces (0.20%–48.28%) and Xerochrysium (0.093%–43.95%). Two potential toxigenic fungi were detected: Alternaria alternata and Aspergillus versicolor. In addition, combined with the results of previous studies, the findings reveal the possible relation of diversity and abundance of fungal species to altitude and latitude: As the altitude and latitude decrease, the diversity and abundance of fungal species may increase. In conclusion, for the first time, this study focused on altitude and latitude as indicators and integrated multiple research findings to explore the correlation between the total amount and diversity of fungal species in the two edible herbs. Results reveal the fungal contamination of the surfaces of CRP and PR and provide a theoretical basis for the prevention and control of their fungal contamination.

Interactions between maternal parity and feed additives drive the composition of pig gut microbiomes in the post-weaning period

BackgroundNursery pigs undergo stressors in the post-weaning period that result in production and welfare challenges. These challenges disproportionately impact the offspring of primiparous sows compared to those of multiparous counterparts. Little is known regarding potential interactions between parity and feed additives in the post-weaning period and their effects on nursery pig microbiomes. Therefore, the objective of this study was to investigate the effects of maternal parity on sow and offspring microbiomes and the influence of sow parity on pig fecal microbiome and performance in response to a prebiotic post-weaning. At weaning, piglets were allotted into three treatment groups: a standard nursery diet including pharmacological doses of Zn and Cu (Con), a group fed a commercial prebiotic only (Preb) based on an Aspergillus oryzae fermentation extract, and a group fed the same prebiotic plus Zn and Cu (Preb + ZnCu).ResultsAlthough there were no differences in vaginal microbiome composition between primiparous and multiparous sows, fecal microbiome composition was different (R2 = 0.02, P = 0.03). The fecal microbiomes of primiparous offspring displayed significantly higher bacterial diversity compared to multiparous offspring at d 0 and d 21 postweaning (P < 0.01), with differences in community composition observed at d 21 (R2 = 0.03, P = 0.04). When analyzing the effects of maternal parity within each treatment, only the Preb diet triggered significant microbiome distinctions between primiparous and multiparous offspring (d 21: R2 = 0.13, P = 0.01; d 42: R2 = 0.19, P = 0.001). Compositional differences in pig fecal microbiomes between treatments were observed only at d 21 (R2 = 0.12, P = 0.001). Pigs in the Con group gained significantly more weight throughout the nursery period when compared to those in the Preb + ZnCu group.ConclusionsNursery pig gut microbiome composition was influenced by supplementation with an Aspergillus oryzae fermentation extract, with varying effects on performance when combined with pharmacological levels of Zn and Cu or for offspring of different maternal parity groups. These results indicate that the development of nursery pig gut microbiomes is shaped by maternal parity and potential interactions with the effects of dietary feed additives.

Habitat shapes the gut microbiome diversity of Malayan tigers (Panthera tigris jacksoni) as revealed through metabarcoding 16S rRNA profiling.

The gut microbiome refers to the microorganism community living within the digestive tract. The environment plays a crucial role in shaping the gut microbiome composition of animals. The gut microbiome influences the health and behavior of animals, including the critically endangered Malayan tiger(Panthera tigris jacksoni). However, the gut microbiome composition of Malayan tigers, especially those living in their natural habitats, remains poorly understood. To address this knowledge gap, we used next-generation sequencing DNA metabarcoding techniques to analyze the gut microbiome of wild Malayan tigers using fecal samples collected from their natural habitats and in captivity. Our aim was to determine the gut microbiota composition of the Malayan tiger, considering the different types of habitat environments. The results revealed a diverse microbial community within the gut microbiome of Malayan tigers. The prominent phyla that were observed included Firmicutes, Proteobacteria, Actinobacteriota, Fusobacteriota and Bacteroidota. Beta diversity analysis revealed significant differences in gut microbiome composition of Malayan tigers that inhabited oil palm plantations, in villages and protected areas. Diversity analysis also revealed significant difference in the gut microbiome between wild and captive Malayan tigers. However, the distinctions of gut microbiome between wild and captive alpha diversity did not yield significant differences. The differences in microbiome diversity resulted from the interplay of dietary intake and environmental factors. This information will facilitate the establishment of focused conservation approaches and enhance our understanding of the effect of microbiome composition on Malayan tiger health.

Blastocystis: A Mysterious Member of the Gut Microbiome.

Blastocystis is the most common gastrointestinal protist found in humans and animals. Although the clinical significance of Blastocystis remains unclear, the organism is increasingly being viewed as a commensal member of the gut microbiome. However, its impact on the microbiome is still being debated. It is unclear whether Blastocystis promotes a healthy gut and microbiome directly or whether it is more likely to colonize and persist in a healthy gut environment. In healthy people, Blastocystis is frequently associated with increased bacterial diversity and significant differences in the gut microbiome. Based on current knowledge, it is not possible to determine whether differences in the gut microbiome are the cause or result of Blastocystis colonization. Although it is possible that some aspects of this eukaryote's role in the intestinal microbiome remain unknown and that its effects vary, possibly due to subtype and intra-subtype variations and immune modulation, more research is needed to characterize these mechanisms in greater detail. This review covers recent findings on the effects of Blastocystis in the gut microbiome and immune modulation, its impact on the microbiome in autoimmune diseases, whether Blastocystis has a role like bacteria in the gut-brain axis, and its relationship with probiotics.

Metagenomic analysis unravels novel taxonomic differences in the uterine microbiome between healthy mares and mares with endometritis.

The application of high throughput technologies has enabled unravelling of unique differences between healthy mares and mares with endometritis at transcriptomic and proteomic levels. However, differences in the uterine microbiome are yet to be investigated. The present study was aimed at evaluating the differences in uterine microbiome between healthy mares and mares with endometritis. Low-volume lavage (LVL) samples were collected from the uterus of 30 mares classified into healthy (n=15) and endometritis (n=15) based on their reproductive history, intrauterine fluid accumulation, gross appearance of LVL samples, endometrial cytology and bacterial culture. The samples were subjected to 16S rRNA sequencing. Notable differences in the uterine microbiome were observed between healthy mares and mares with endometritis at various taxonomic levels. In healthy mares, the most abundant phylum, class, order and family were Firmicutes, Bacilli, Bacillales and Paenibacillaceae, respectively. In contrast, the most abundant corresponding taxonomic levels in mares with endometritis were Proteobacteria, Gammaproteobacteria, Enterobacterales and Enterobacteriaceae, respectively. At the genus level, Brevibacillus and Paenibacillus were more abundant in healthy mares, whereas Escherichia, Salmonella and Klebsiella were more abundant in mares with endometritis. In healthy mares, Brevibacillus brevis was the most abundant species, followed by Brevibacillus choshinensis and Paenibacillus sp JDR-2. However, in mares with endometritis, Escherichia coli was the most abundant species, followed by Salmonella enterica and Klebsiella pneumoniae. These results confirmed the previously reported presence of a uterine microbiome in healthy mares and helped unravel some alterations that occur in mares with endometritis. The findings can potentially help formulate new approaches to prevent or treat equine endometritis.

A quantitative survey of the blueberry (Vaccinium spp.) culturable nectar microbiome: variation between cultivars, locations, and farm management approaches.

Microbes in floral nectar can impact both their host plants and floral visitors, yet little is known about the nectar microbiome of most pollinator-dependent crops. In this study, we examined the abundance and composition of the fungi and bacteria inhabiting Vaccinium spp. nectar, as well as nectar volume and sugar concentrations. We compared wild V. myrsinites with two field-grown V. corymbosum cultivars collected from two organic and two conventional farms. Differences in nectar traits and microbiomes were identified between V. corymbosum cultivars but not Vaccinium species. The microbiome of cultivated plants also varied greatly between farms, whereas management regime had only subtle effects, with higher fungal populations detected under organic management. Nectars were hexose-dominant, and high cell densities were correlated with reduced nectar sugar concentrations. Bacteria were more common than fungi in blueberry nectar, although both were frequently detected and co-occurred more often than would be predicted by chance. "Cosmopolitan" blueberry nectar microbes that were isolated in all plants, including Rosenbergiella sp. and Symmetrospora symmetrica, were identified. This study provides the first systematic report of the blueberry nectar microbiome, which may have important implications for pollinator and crop health.

Urine microbes and predictive metagenomic profiles associate with abnormalities in sperm parameters: implications for male subfertility

To explore the taxonomic and predicted functional relationship between the urine microbiome and alterations of semen analysis (SA) parameters. Cross-sectional study. Academic medical center. Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited and stratified on the basis of alterations, or lack thereof, in SA parameters. Changes in the functional and taxonomic urine microbiome profiles of participants with or without alterations in SA parameters. Seventy-three participants were included in our study. Men with abnormal sperm motility (N = 27) showed a nearly 50-fold higher abundance of Dialister micraerophilus compared with those with normal sperm motility (N = 46). This relationship persisted on canonical correlational analysis (r = 0.439). Men with abnormal sperm concentration (N = 20) showed a lower abundance of Enterococcus faecalis and Staphylococcus aureus, compared with those with normal sperm concentration (N = 53). The urine of participants with impaired sperm motility demonstrated dramatic differences in predictive functional profiles in pathways involved in oxidation-reduction balance and cell longevity. Our findings underscore differences in the urinary microbiome and abnormalities in semen parameters, especially sperm motility. By incorporating predictive functional profiling, we also highlight possible mechanisms that may drive the observed differences in sperm parameters.

(260) Functional and Taxonomic Urine Microbiome Differences in Men with Abnormal Semen Analysis Parameters

Abstract Introduction Male factors contribute to nearly half of all cases of infertility. Next-generation sequencing technologies have allowed for a more nuanced understanding of the widespread influence of the microbiome on health and human disease. Recent evidence has emerged revealing a potential role for the urinary microbiome in impacting male fertility and subfertility, though studies on this topic are sparse. Objective Here, we explore the complex relationship between the urine microbiome and alterations of SA parameters. Methods Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited. Clinical data and urine samples were collected from the patients and SA was performed. Patients were then stratified according to alterations in SA parameters. Urine samples underwent DNA extraction, PCR amplification and 16S rRNA sequencing. Taxonomic microbiome community profiling was performed. Predictive metagenomics was performed using Tax4Fun2 with reference to the KEGG database. Results N = 73 participants were included in the study and were stratified based on alterations, or lack thereof, in SA parameters. Men with abnormal sperm motility (N = 27) showed a higher abundance of urine Dialister micraerophilus (p = 0.0322) compared to those with normal sperm motility (N = 46). This relationship persisted on canonical correlational analysis (r = 0.439, p = 0.0114). Furthermore, when stratifying by sperm motility, nine differentially abundant pathways emerged from predictive metagenomic analysis including pathways critical for basic microbial cell functioning (intermediary metabolism pathways, FoxO signaling, longevity regulating pathways) in addition to pathways synthesizing and breaking down potentially bioactive metabolites (notably long- and short-chain fatty acid metabolism). Men with abnormal sperm concentration (N = 20) showed a lower abundance of urine Enterococcus faecalis (p = 0.0121) and urine Staphylococcus aureus (p = 0.0375), compared to those with normal sperm concentration (N = 53). These findings are outlined in the differential abundance box plots generated from the Analysis of composition of Microbiota with Bias Correction (ANCOM-BC) in Figure 1 and the differential abundance box plots from the predictive functional analysis in Figure 2. Conclusions Our exploratory analysis suggests a role for not just an altered microbial taxonomic profile but also an altered functional profile in men with abnormal SA parameters. These changes in SA parameters may come about through differences in urine microbial metabolite production including short-chain fatty acids or byproducts of intermediary metabolic processes such as those that may contribute to a pro-inflammatory microenvironment. These findings appear to be aligned with the very limited number of studies exploring similar lines of inquiry. These pathways and microbial communities may represent potential therapeutic targets. Further, more mechanistic, investigations are necessary. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: MicrogenDx, Metuchen Pharmaceuticals, Antares Pharma, Boston Scientific, and Endo Pharmaceuticals.

The role of androgen response pathway in association with tumor biology and response to neoadjuvant immune-checkpoint inhibitors (ICI) in muscle-invasive urothelial bladder carcinoma (MIBC).

662 Background: Emerging findings from ICI trials are suggestive of differential outcomes in females compared with males. Sex-specific differences in tumor biology, microbiome, and outcomes in MIBC are well-established. Conversely, limited data are available regarding the role of the androgen response pathway in explaining subtype differences between males and females and, most importantly, response to ICI. Methods: We retrospectively evaluated the biomarker findings of the transurethral resection of the bladder tumors (TURBT) and baseline clinical characteristics of patients (pts) with cT2-4N0M0 MIBC who received neoadjuvant pembrolizumab and radical cystectomy (RC) in the PURE-01 study. Transcriptome-wide expression profiling was performed on 102 TURBT samples. We focused on androgen receptor (AR) gene expression and the hallmark androgen response pathway expression quantifying 117 different genes related to the androgen response pathway as previously reported (PMID: 26771021). Pt and tumor characteristics were compared between subgroups using χ2 tests and two-sided Wilcoxon rank-sum tests. Kaplan-Meier curves and log rank tests evaluated gene expression and signature scores in association with the event-free survival (EFS), calculated from start of pembrolizumab treatment. Signature scores were analyzed as continuous values and were split by median and quartile values. Results: Pts received pembrolizumab and RC from 2017 to 2022. There were 87 (85.3%) males and 15 (14.7%) females. AR gene expression was not significantly different between males and females (p = 0.5), whereas androgen response signature was significantly higher in male (p = 0.03). The AR gene expression and androgen response signature scores were more highly expressed in luminal tumors vs rest of molecular subtypes (p = 0.005 and p &lt; 0.001). Despite AR gene expression was not associated with ypT0N0 response (p = 0.425), hallmark androgen response signature scores were significantly lower in ypT0N0 responders (p = 0.033). Higher hallmark androgen response signature scores were statistically significantly associated with shorter EFS (p = 0.028), whereas AR gene expression was not (p = 0.152). Conclusions: For the first time to our knowledge, we reported the androgen response pathway expression to be a potential biomarker of ICI benefit in MIBC. This signature was also associated with a luminal subtype, linked to inferior responsiveness to ICI. If confirmed at a larger scale these analyses will strengthen the need for sex-specific approaches and potentially new combination therapies in MIBC.

Differences in endometrial and cervical microbiome of uterine fibroids patients – A preliminary study

Differences in endometrial and cervical microbiome of uterine fibroids patients – A preliminary study

Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia

There is growing interest in the role of gut microbiome composition in schizophrenia. However, lifestyle factors are often neglected, and few studies have investigated microbiome composition in treatment-resistant schizophrenia. To explore associations between the gut microbiome and schizophrenia diagnosis, treatment resistance, clozapine response, and treatment-related adverse effects while adjusting for demographic and lifestyle factors. In this case-control study of adults aged 20 to 63 years, stool samples and data on demographic characteristics, lifestyle, and medication use were collected and gut microbiome measures obtained using shotgun metagenomics. Participants with a schizophrenia diagnosis were referred through psychiatric inpatient units and outpatient clinics. Data were collected for 4 distinct groups: control individuals without a psychiatric diagnosis (past or present), individuals with treatment-responsive schizophrenia taking nonclozapine antipsychotic medications, clozapine-responsive individuals with treatment-resistant schizophrenia, and clozapine-nonresponsive individuals with treatment-resistant schizophrenia. Participants were recruited between November 2020 and November 2021. Control individuals were recruited in parallel through posters and online advertisements and matched for age, sex, and body mass index (BMI) to the individuals with schizophrenia. Participants were excluded if taking antibiotics in the past 2 months, if unable to communicate in English or otherwise follow study instructions, were pregnant or planning to become pregnant, or had any concomitant disease or condition making them unsuited to the study per investigator assessment. Data were analyzed from January 2022 to March 2023. Omics relationship matrices, α and β diversity, and relative abundance of microbiome features. Data were collected for 97 individuals (71 [74%] male; mean [SD] age, 40.4 [10.3] years; mean [SD] BMI, 32.8 [7.4], calculated as weight in kilograms divided by height in meters squared). Significant microbiome associations with schizophrenia were observed at multiple taxonomic and functional levels (eg, common species: b2, 30%; SE, 13%; adjusted P = .002) and treatment resistance (eg, common species: b2, 27%; SE, 16%; adjusted P = .03). In contrast, limited evidence was found for microbiome associations with clozapine response, constipation, or metabolic syndrome. Significantly decreased microbial richness was found in individuals with schizophrenia compared to control individuals (t95 = 4.25; P < .001; mean [SD] for control individuals, 151.8 [32.31]; mean [SD] for individuals with schizophrenia, 117.00 [36.2]; 95% CI, 18.6-51.0), which remained significant after a covariate and multiple comparison correction. However, limited evidence was found for differences in β diversity (weighted UniFrac) for schizophrenia diagnosis (permutational multivariate analysis of variance [PERMANOVA]: R2, 0.03; P = .02), treatment resistance (R2, 0.02; P = .18), or clozapine response (R2, 0.04; P = .08). Multiple differentially abundant bacterial species (19) and metabolic pathways (162) were found in individuals with schizophrenia, which were primarily associated with treatment resistance and clozapine exposure. The findings in this study are consistent with the idea that clozapine induces alterations to gut microbiome composition, although the possibility that preexisting microbiome differences contribute to treatment resistance cannot be ruled out. These findings suggest that prior reports of microbiome alterations in individuals with chronic schizophrenia may be due to medication or lifestyle factors and that future studies should incorporate these variables in their design and interpretation.

Differences in the gut microbiome of young adults with schizophrenia spectrum disorder: using machine learning to distinguish cases from controls

While an association between the gut microbiome and schizophrenia spectrum disorders (SSD) has been suggested, the existing evidence is still inconclusive. To this end, we analyzed bacteria and bacterial genes in feces from 52 young adult SSD patients and 52 controls using fecal shotgun metagenomic sequencing. Compared to controls, young SSD patients were found to have significantly lower α-diversity and different β-diversity both regarding bacterial species (i.e., taxonomic diversity) and bacterial genes (i.e., functional diversity). Furthermore, the α-diversity measures ‘Pielou’s evenness’ and ‘Shannon’ were significantly higher for both bacterial species, bacterial genes encoding enzymes and gut brain modules in young SSD patients on antipsychotic treatment (young SSD not on antipsychotics=9 patients, young SSD on antipsychotics=43 patients). We also applied machine learning classifiers to distinguish between young SSD patients and healthy controls based on their gut microbiome. Results showed that taxonomic and functional data classified young SSD individuals with an accuracy of ≥ 70% and with an area under the receiver operating characteristic curve (AUROC) of ≥ 0.75. Differential abundance analysis on the most important features in the classifier models revealed that most of the species with higher abundance in young SSD patients had their natural habitat in the oral cavity. In addition, many of the modules with higher abundance in young SSD patients were amino acid biosynthesis modules. Moreover, the abundances of gut-brain modules of butyrate synthesis and acetate degradation were lower in the SSD patients compared to controls. Collectively, our findings continue to support the presence of gut microbiome alterations in SSD and provide support for the use of machine learning algorithms to distinguish patients from controls based on gut microbiome profiles.

Deciphering Differences in Microbial Community Diversity between Clubroot-Diseased and Healthy Soils.

Clubroot (Plasmodiophora brassicae) is an important soilborne disease that causes severe damage to cruciferous crops in China. This study aims to compare the differences in chemical properties and microbiomes between healthy and clubroot-diseased soils. To reveal the difference, we measured soil chemical properties and microbial communities by sequencing 18S and 16S rRNA amplicons. The available potassium in the diseased soils was higher than in the healthy soils. The fungal diversity in the healthy soils was significantly higher than in the diseased soils. Ascomycota and Proteobacteria were the most dominant fungal phylum and bacteria phylum in all soil samples, respectively. Plant-beneficial microorganisms, such as Chaetomium and Sphingomonas, were more abundant in the healthy soils than in the diseased soils. Co-occurrence network analysis found that the healthy soil networks were more complex and stable than the diseased soils. The link number, network density, and clustering coefficient of the healthy soil networks were higher than those of the diseased soil networks. Our results indicate that the microbial community diversity and network structure of the clubroot-diseased soils were different from those of the healthy soils. This study is of great significance in exploring the biological control strategies of clubroot disease.

P1222 Gut microbiome differences regarding lifestyle and the history of COVID-19 infection in ulcerative colitis patients

Abstract Background The microbiome contributes to the pathogenesis of ulcerative colitis (UC) but the contribution of different lifestyle and environmental factors to the compositional variability of the gut microbiota is unclear. Also, it is known that microbiota plays an important role in infectious diseases like coronavirus disease 2019 (COVID-19). Methods In 6-month time (June 2021 to December 2021) 49 UC outpatients from Riga East Clinical University Hospital were included in a Cross-sectional study. All patients were divided into groups according to COVID-19 status (COVID-19posvs COVID-19neg) within 6 months. The effect of the lifestyle (smoking cigarettes, alcohol intake, sports activities, and high psychological stress level) and COVID-19 to the gut microbiota in patients with UC was investigated. For taxonomical classifying of the gut microbiome metagenome data, MetaPhlAn v.2.6.0 tool was used. In further analysis gut microbiome (mostly bacteria phyla) and related data was analysed with SPSS 20.0. Results Out of 49 patients, 31(63%) were male and 18(37%) were female, the mean age was Md=38 [IQR:34-51]. Fourteen patients (28.6%) have been COVID-19 pos and 35(71.4%) COVID-19 neg. There were no statistically significant differences between COVID-19 pos and COVID-19 neg patients and their microbiota, nor between COVID-19 pos symptomatic 12(24.5%) and asymptomatic 37(75.5%) patients and their gut microbiome. Out of 49, 24(49%) were doing sports, of those 18(51.4%) were COVD-19neg vs. 6 (42.9%) COVID-19pos, p=0.82. Evaluating differences in the gut microbiome regarding physical activities there was no statistical significance. Of 49 patients, 30(61.2%) have smoked before, while 19(38.8%) haven’t smoked. Medium smoking time was 8 years Md=8 [IQR:4.50-20.0]. Analysing gut microbiome in smokers/non-smokers, and the length of smoking, there were found no statistically significant differences. Thirty-five (71.4%) were using alcohol, and 14(28.6%) were not. Those who were using alcohol had statistically significantly more Firmicutes in their gut microbiome Md= 64.8[IQR:53.7-70.4] than no users Md=48[IQR:37.5-66.3], p=0.041. Regarding high stress levels, those who had less stress 18(36.7%), had more Actinobacteria in their gut microbiome Md=11.7[IQR:6.92-14.8] vs stressful patients 31(63.3%) Md=6.03[IQR:2.23-13.8], p=0.03. Conclusion There were no changes in gut microbiome in COVID-19 positive and COVID-19 negative patients, nor in smokers and no smokers. Alcohol users had more bacteria Firmicutes in their gut microbiome. There were no differences in gut microbiome in UC patients doing or lacking sports. UC patients with less stress had more Actinobacteria in their gut microbiome.

Homogeneity Gut microbiome Characteristics in Autoimmune Epithelitis: Primary Biliary Cholangitis and Primary Sjögren’s Syndrome.

Background : Accumulating studies had revealed that dysbiosis of the gut microbiome was involved in the occurrence and development of Primary biliary cholangitis (PBC) and Primary Sjögren’s syndrome (pSS). Aims : To examine the similarities and differences in gut microbiome as well as the relationship with pathogenesis in PBC and pSS. Methods : High throughput sequencing was conducted to analyze the 16S rDNA V3-V4 region of fecal microbial samples from 109 subjects including PBC (n=38), pSS (n=41) and healthy controls (HC, n=30) from the Affiliated Hospital of Qingdao University. The composition, diversity and markers of gut microbiome were compared between PBC, pSS and HC. Inter-group comparisons were conducted using analysis

DOP30 Cross-ethnic microbiome analyses identify shared and specific signals for Northern Indian IBD patients

Abstract Background Clinical manifestation of the inflammatory bowel disease (IBD) shows considerable variation across the world. We hypothesized these differences may be influenced by geographical differences in gut microbiome. To test this, we investigated the correlation between gut microbiota and the disease phenotypes of IBD in a cohort form the Northern part of India. Methods Stool samples and clinical metadata were collected from 226 IBD patients (198 ulcerative colitis and 28 Crohn’s disease) and 66 controls from a population cohort from the Northern India. We used metagenomic shotgun sequencing to determine diversity, composition and function of the gut microbiota of the participants. Microbiome was then associated to IBD and its subtypes and clinical metadata (e.g. medication use, drug response, and disease activity). We replicated our results in 436 IBD patients and 903 population controls from the Netherlands analyzed using an identical workflow and used machine learning to assess how well do the Indian IBD signals generalize to Dutch IBD. Results We identified reduction in microbiome diversity and changes in beta diversity in Indian IBD patients (FDR &amp;lt; 0.05, replicated in Dutch population) and identified that 319 taxa and 71 biochemical pathways are altered in Indian patients (FDR &amp;lt; 0.05). Of note, 39% of these signals were replicated in the Dutch cohort (at FDR &amp;lt; 0.05 level). We identified strong dysbiosis shared across Indian and Dutch IBD patients, characterized by expansion of opportunistic pathogens (e.g. Genera Clostridium, Streptococcus and Lactobacilli) and oral bacteria (e.g. Streptococcus oralis and Bifidobacterium dentium) as well as reduction in butyrate producers such as Faecalibacterium prausnitzii, Roseburia hominis and Blautia massiliensis. In addition, we found novel pathobionts specific to the Indian cohort (including oral bacteria from Genus Scardovia and Oribacterium; Actinomyces dentalis and Klebsiella pneumoniae). Machine-learning models trained on the Indian cohort were highly predictive in the Indian test set (Sensitivity 0.84, Specificity 0.95) and generalized to Dutch cohort (Sensitivity 0.77, Specificity 0.69). In addition to IBD-associated dysbiosis, we identified links between medication use and gut microbiota independent of the disease activity: use of Tofacitinib (used by 26 UC patients) was linked to decrease in Lactobacilliales and increase in Clostridia, while Prednisolone and Azathioprine associated to reduction in Roseburia and increase in Streptococcus and Granulicatella. Conclusion The IBD patients from Northern India show gut dysbiosis similar to European patients, but also show enrichment in India-specific pathobionts. The microbiome-based diagnostic models generalize across these populations.

A longitudinal field study of commercial honey bees shows that non-native probiotics do not rescue antibiotic treatment, and are generally not beneficial

Probiotics are widely used in agriculture including commercial beekeeping, but there is little evidence supporting their effectiveness. Antibiotic treatments can greatly distort the gut microbiome, reducing its protective abilities and facilitating the growth of antibiotic resistant pathogens. Commercial beekeepers regularly apply antibiotics to combat bacterial infections, often followed by an application of non-native probiotics advertised to ease the impact of antibiotic-induced gut dysbiosis. We tested whether probiotics affect the gut microbiome or disease prevalence, or rescue the negative effects of antibiotic induced gut dysbiosis. We found no difference in the gut microbiome or disease markers by probiotic application or antibiotic recovery associated with probiotic treatment. A colony-level application of the antibiotics oxytetracycline and tylosin produced an immediate decrease in gut microbiome size, and over the longer-term, very different and persistent dysbiotic effects on the composition and membership of the hindgut microbiome. Our results demonstrate the lack of probiotic effect or antibiotic rescue, detail the duration and character of dysbiotic states resulting from different antibiotics, and highlight the importance of the gut microbiome for honeybee health.