Characterization Of Microbiome Research Articles

Characterization of intratumor microbiome in cancer immunotherapy

Characterization of intratumor microbiome in cancer immunotherapy

Features of the microbial landscape of the stomach in children, feeding through the gastrostomy or nasogastric tube

BACKGROUND: In children with dysphagia, an increase in body weight is observed after the placement of a feeding tube, however, subsequently, a regression of body weight is noted, symptoms of an erosive and ulcerative lesion of the gastrointestinal tract appear.
 AIM: To identify the features of the gastric microbiome in children fed through a gastrostomy or a tube.
 MATERIALS AND METHODS: A study of aspirates of gastric contents in 21 patients was carried out using metagenomic sequencing. The participants were divided into 2 groups: group 1 11 children fed through the gastrostomy for less than 1 year; group 2 10 children, fed through the gastrostomy for more than 1 year.
 RESULTS: In group 1, from 8 to 19 phyla were identified, median 12.0. In the second group from 4 to 13, median 7.5, the differences are statistically significant (p 0.05). The samples of both groups were dominated by the phyla Firmicutes, Proteobacteria, Bacteroidota, Actinobacteria, Fusobacteria. The number of representatives of the Bacteroidia and Fusobacteriia classes was significantly reduced in patients with long-term nutrition through the gastrostomy. At the same time, a small number of classes were observed in patients with a gastrostomy in the stomach for about 80 months, as well as in patients with identified gastric pathology. There were about 66 genera for each specimen. At the same time, in children fed through a gastrostomy for less than 1 year, the median is 69.5 OTU. In children fed through a gastrostomy for more than 1 year, even with its regular replacement, the median is significantly less 41 OTU. A significant decrease in microbial biodiversity was revealed with an increase in the standing time of the gastrostomy, the median value of the Shannon index in group 1 was 1.95, in group 2 1.69 (p 0.05).
 CONCLUSIONS: In patients with a long stay of the feeding tube in the stomach, the number of anti-inflammatory symbionts of the genus Prevotella, Parabacteroides is reduced. The contamination of the stomach with Helicobacter pylori was 50%, which further increased the predisposition of the gastric mucosa to inflammation.

Characterization of upper airway microbiome across severity of COVID-19 during hospitalization and treatment.

Longitudinal studies on upper respiratory tract microbiome in coronavirus disease 2019 (COVID-19) without potential confounders such as antimicrobial therapy are limited. The objective of this study is to assess for longitudinal changes in the upper respiratory microbiome, its association with disease severity, and potential confounders in adult hospitalized patients with COVID-19. Serial nasopharyngeal and throat swabs (NPSTSs) were taken for 16S rRNA gene amplicon sequencing from adults hospitalized for COVID-19. Alpha and beta diversity was assessed between different groups. Principal coordinate analysis was used to assess beta diversity between groups. Linear discriminant analysis was used to identify discriminative bacterial taxa in NPSTS taken early during hospitalization on need for intensive care unit (ICU) admission. A total of 314 NPSTS samples from 197 subjects (asymptomatic = 14, mild/moderate = 106, and severe/critical = 51 patients with COVID-19; non-COVID-19 mechanically ventilated ICU patients = 11; and healthy volunteers = 15) were sequenced. Among all covariates, antibiotic treatment had the largest effect on upper airway microbiota. When samples taken after antibiotics were excluded, alpha diversity (Shannon, Simpson, richness, and evenness) was similar across severity of COVID-19, whereas beta diversity (weighted GUniFrac and Bray-Curtis distance) remained different. Thirteen bacterial genera from NPSTS taken within the first week of hospitalization were associated with a need for ICU admission (area under the receiver operating characteristic curve, 0.96; 95% CI, 0.91-0.99). Longitudinal analysis showed that the upper respiratory microbiota alpha and beta diversity was unchanged during hospitalization in the absence of antimicrobial therapy.

The characteristics of gut microbiome in PCOS patients with overweight/obesity individuals

Objective: Polycystic ovary syndrome (PCOS) is one of the most common reproductive and endocrine disorders in women of reproductive age. More than 80% of PCOS patients are overweight/obese. However, the mechanism of PCOS and its combined overweight/obesity remains unclear. Recent studies have found that gut microbiota may be involved in the development of PCOS. This study investigates the characteristics of gut microbiota in overweight/obese PCOS patients.

Eating our way to gut microbiome characterization

A recent study in Nature introduced an innovative ingestible device capable of collecting in situ samplesfrom different regions of the human intestine for multi-omics analysis. This groundbreaking technology enables non-invasive and longitudinal characterization of the gut microbiome and associated metabolites.

A gut bacterial signature in blood and liver tissue characterizes cirrhosis and hepatocellular carcinoma

Background: HCC is the leading cause of cancer in chronic liver disease. A growing body of experimental mouse models supports the notion that gut-resident and liver-resident microbes control hepatic immune responses and, thereby, crucially contribute to liver tumorigenesis. However, a comprehensive characterization of the intestinal microbiome in fueling the transition from chronic liver disease to HCC in humans is currently missing. Methods: Here, we profiled the fecal, blood, and liver tissue microbiome of patients with HCC by 16S rRNA sequencing and compared profiles to nonmalignant cirrhotic and noncirrhotic NAFLD patients. Results: We report a distinct bacterial profile, defined from 16S rRNA gene sequences, with reduced α-and β-diversity in the feces of patients with HCC and cirrhosis compared to NAFLD. Patients with HCC and cirrhosis exhibited an increased proportion of fecal bacterial gene signatures in the blood and liver compared to NAFLD. Differential analysis of the relative abundance of bacterial genera identified an increased abundance of Ruminococcaceae and Bacteroidaceae in blood and liver tissue from both HCC and cirrhosis patients compared to NAFLD. Fecal samples from cirrhosis and HCC patients both showed a reduced abundance for several taxa, including short-chain fatty acid–producing genera, such as Blautia and Agathobacter. Using paired 16S rRNA and transcriptome sequencing, we identified a direct association between gut bacterial genus abundance and host transcriptome response within the liver tissue. Conclusions: Our study indicates perturbations of the intestinal and liver-resident microbiome as a critical determinant of patients with cirrhosis and HCC.

Gut instinct: Sex differences in the gut microbiome are associated with changes in adolescent nociception following maternal separation in rats.

Adolescent chronic pain is a growing public health epidemic. Our understanding of its etiology is limited; however, several factors can increase susceptibility, often developing in response to an acute pain trigger such as a surgical procedure or mild traumatic brain injury (mTBI), or an adverse childhood experience (ACE). Additionally, the prevalence and manifestation of chronic pain is sexually dimorphic, with double the rates in females than males. Despite this, the majority of pre-clinical pain research focuses on males, leaving a gap in mechanistic understanding for females. Given that emerging evidence has linked the gut microbiome and the brain-gut-immune axis to various pain disorders, we aimed to investigate sex-dependent changes in taxonomic and functional gut microbiome features following an ACE and acute injury as chronic pain triggers. Male and female Sprague Dawley rat pups were randomly assigned to either a maternal separation (MS) or no stress paradigm, then further into a sham, mTBI, or surgery condition. Chronically, the von Frey test was used to measure mechanical nociception, and fecal samples were collected for 16S rRNA sequencing. Animals in the surgery group had an increase in pain sensitivity when compared to mTBI and sham groups, and this was complemented by changes to the gut microbiome. In addition, significant sex differences were identified in gut microbiome composition, which were exacerbated in response to MS. Overall, we provide preliminary evidence for sex differences and ACE-induced changes in bacterial composition that, when combined, may be contributing to heterogeneity in pain outcomes.

Characteristic metabolic and microbial profiles in acute ischemic stroke patients with phlegm-heat pattern

To explore the characteristics of plasma metabolites, feces gut microbiota and the crosstalk between gut microbiota and host metabolism in patients with acute ischemic stroke and phlegm-heat pattern (AIS-PHP). The metabolic and microbiome profiles of 20 AIS-PHP patients and 20 healthy controls (HCs) were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics and 16s rDNA sequencing, respectively. The covariation between LC-MS/MS-based metabolite data and 16s rDNA sequence data was presented. Distinct alterations in the plasma metabolic phenotype of AIS-PHP patients were found, in which 16 metabolites differed significantly between the AIS-PHP patients and the HCs. These metabolites represented 17 different metabolic pathways, including amino acid metabolism, lipid metabolism, and nucleotide metabolism. Additionally, significant alterations of gut microbiota composition and taxon were revealed at the phylum level between the AIS-PHP patients and the HCs. In AIS-PHP, Bacteroidetes, Firmicutes, and Proteobacteria dominated. Moreover, some microbes that differed between the 2 groups manifested a sole association with certain metabolites, such as the connection between Bacteroides and inosine and between Lachnospiraceae_unclassified and hypoxanthine. The present study preliminarily investigated the metabolomic and gut microbiome characteristics of AIS-PHP patient indicators. The link between metabolic and microbial dysbiosis in AIS-PHP sheds new light on the function of gut microbiota and associated metabolomics in the pathogenesis of the disease.

Ultra-Endurance triathlon competition shifts fecal metabolome independent of changes to microbiome composition.

Understanding changes to gut microbiota composition and metabolic output in response to acute exercise may be necessary for understanding the mechanisms mediating the long-term health and performance benefits of exercise. Our primary objective was to characterize acute changes in the fecal microbiome and metabolome following participation in an ultra-endurance (3.9 km swim, 180.2 km bike, 42.2 km run) triathlon. An exploratory aim was to determine associations between athlete-specific factors [race performance (i.e., completion time) and lifetime years of endurance training] with pre-race gut microbiota and metabolite profiles. Stool samples from 12 triathletes (9 males/3 females; 43 ± 14 yr, 23 ± 2 kg/m2) were collected ≤48 h before and the first bowel movement following race completion. Intra- and inter-individual diversity of bacterial species and individual bacterial taxa were unaltered following race completion (P > 0.05). However, significant reductions (P < 0.05) in free and secondary bile acids [deoxycholic acid (DCA), 12-keto-lithocholic acid (12-ketoLCA)] and short-chain fatty acids (butyric and pivalic acids), and significant increases (P < 0.05) in long-chain fatty acids (oleic and palmitoleic acids) were observed. Exploratory analyses revealed several associations between pre-race bacterial taxa and fecal metabolites with race performance and lifetime history of endurance training (P < 0.05). These findings suggest that 1) acute ultra-endurance exercise shifts microbial metabolism independent of changes to community composition and 2) athlete performance level and training history relate to resting-state gut microbial ecology.NEW & NOTEWORTHY This is the first study to characterize acute changes in gut microbial ecology and metabolism following an ultra-endurance triathlon. We demonstrate changes in gut microbial community function, but not structure, as well as several associations between gut microbiome and fecal metabolome characteristics with race completion time and lifetime history of endurance training. These data add to a small but growing body of literature seeking to characterize the acute and chronic effects of exercise on the gut microbial ecosystem.

Features of the rumen microbiome in reindeer with necrobacteriosis

Reindeer are a unique animal species that have adapted to the harsh Arctic conditions. Adaptive features of the structure of the gastrointestinal tract of reindeer allows you to eat actively digest and assimilate lichens, foliage, shrubs, snowy greens. Along with beneficial microflora, pathogenic and conditionally pathogenic microorganisms live in the reindeer rumen. The purpose of our research is to study and compare the features of the rumen microbiome in healthy and sick reindeer with necrobacteriosis. The subject of the study was samples of cicatricial contents taken from 38 reindeer (Rangifer tarandus) of the Nenets breed of different age groups. Microbiome studies were performed by NGS sequencing on the MiSeq next generation sequencing platform (Illumina, USA) using primers for the V3-V4 region of 16S rRNA.Based on the studies, it was possible to establish that the microbiome of the reindeer rumen in summer and winter is characterized by certain differences. During the summer grazing period, the presence of a greater number of pathogenic bacteria such as Fusobacterium sp., Parvimonas sp. and Porphyromonas endodontalis, while in the spectrum of pathogenic microorganisms, bacteria of the genus Fusobacterium, which are considered the main infectious agent in necrobacteriosis, were most often isolated. In the same period, the presence of bacteria of the genus Sharpea, belonging to the phylum Erysipelotrichaceae, which ferment sugars with the formation of lactic acid and can cause the development of lactic acidosis, was established in deer rumen samples. In calves, during the disease, the number of chytridiomycete fungi, which are involved in the fermentation of polysaccharides, decreases.

Maternal Magnolol Supplementation during Pregnancy and Lactation Promotes Antioxidant Capacity, Improves Gut Health, and Alters Gut Microbiota and Metabolites of Weanling Piglets.

Maternal nutrition exerts a profound effect on the postnatal performance of offspring, especially during the weaning period. The multifunctional bioactive component magnolol (MAG) has shown promise as a dietary supplement. This study aimed to explore the effects of maternal MAG supplementation on the antioxidant capacity, gut health, gut microbiome, and metabolome composition of weanling piglets. Fifty pregnant sows were randomly divided into two equally sized groups, the control group and the group supplemented with 100 g/t MAG during the gestation and lactation periods, and 7 days postweaning, the pups were euthanized. The microbiome and metabolome features of weanling piglet colons were compared. Our results revealed that maternal MAG supplementation modified the serum redox status of weanling piglets by decreasing malondialdehyde concentration and increasing superoxide dismutase activity and total antioxidant capacity. Moreover, the decreased indicators of diarrhea were accompanied by improved gut barrier function, in which serum diamine oxidase concentration was decreased, and expressions of zona occludens-1, claudin-1, and intestinal alkaline phosphatase were increased in the colon of weanling piglets from sows supplemented with MAG. Further analysis of the gut microbiota indicated that maternal MAG supplementation significantly increased the relative abundance of beneficial bacteria in the colon of weanling piglets, including Faecalibacterium prausnitzii and Oscillospira. Metabolome analysis identified 540 differential metabolites in the colon of piglets from MAG-fed dams, of which glycerophospholipid classes were highly correlated with progeny gut health and key beneficial bacteria. Our findings indicated that maternal MAG supplementation can improve the oxidative status and gut health of weanling piglets, possibly due to alterations in the gut microbiota and metabolites.

The microbiota of long-living and cancer-free blind mole rat $\textit{(Nannospalax xanthodon)}$ from the edge of its distribution in Northern Anatolia

The mammalian gut is colonized by microorganisms that affect development, immune system, energy metabolism, and reproduction. The majority of studies focused on laboratory or domestic animals in artificial setups, leaving the research focused on wild species underrepresented. The Anatolian Blind Molerat (hereafter ABMR), $\textit{Nannospalax xanthodon}$, is a subterranean rodent that receives much attention due to its unique traits, such as tolerance to extreme hypoxic stress, resistance to cancer, and longer lifespan compared to similarly sized rodents. In this study, we characterize the gut microbiota of ABMR from its northernmost geographic distribution using 16S rRNA metabarcoding and compare our results with the microbiome characteristics of a few other ABMR populations studied previously, as well as other rodent species. The 16S rRNA barcode dataset revealed that approximately 90% of the ABMR gut microbiota comprises Firmicutes and Bacteriodota bacterial phyla, typical of most mammals. In addition, the ABMR gut microbiota has a high abundance of performance- and longevity-linked bacterial families. Overall, our results generally align well with the previous studies on blind molerats and emphasize the importance of studying the microbiome of natural populations.

Characterization of periprosthetic environment microbiome in patients after total joint arthroplasty and its potential correlation with inflammation

AimsPeriprosthetic joint infection (PJI) is one of the most serious complications after total joint arthroplasty (TJA) but the characterization of the periprosthetic environment microbiome after TJA remains unknown. Here, we performed a prospective study based on metagenomic next-generation sequencing to explore the periprosthetic microbiota in patients with suspected PJI.MethodsWe recruited 28 patients with culture-positive PJI, 14 patients with culture-negative PJI, and 35 patients without PJI, which was followed by joint aspiration, untargeted metagenomic next-generation sequencing (mNGS), and bioinformatics analysis. Our results showed that the periprosthetic environment microbiome was significantly different between the PJI group and the non-PJI group. Then, we built a “typing system” for the periprosthetic microbiota based on the RandomForest Model. After that, the ‘typing system’ was verified externally.ResultsWe found the periprosthetic microbiota can be classified into four types generally: “Staphylococcus type,” “Pseudomonas type,” “Escherichia type,” and “Cutibacterium type.” Importantly, these four types of microbiotas had different clinical signatures, and the patients with the former two microbiota types showed obvious inflammatory responses compared to the latter ones. Based on the 2014 Musculoskeletal Infection Society (MSIS) criteria, clinical PJI was more likely to be confirmed when the former two types were encountered. In addition, the Staphylococcus spp. with compositional changes were correlated with C-reactive protein levels, the erythrocyte sedimentation rate, and the synovial fluid white blood cell count and granulocyte percentage.ConclusionsOur study shed light on the characterization of the periprosthetic environment microbiome in patients after TJA. Based on the RandomForest model, we established a basic “typing system” for the microbiota in the periprosthetic environment. This work can provide a reference for future studies about the characterization of periprosthetic microbiota in periprosthetic joint infection patients.

Features of the intestinal microbiome in patients with gluten-sensitive diseases who are on a gluten-free diet

Background. Intestinal dysbiosis is associated with violating both quantitative and qualitative intestinal microbiome (IM) composition. It accompanies different gastrointestinal disorders, including non-celiac gluten sensitivity (NCGS) and celiac disease (CD). A gluten-free diet is the only existing treatment for CD and NCGS. One of the questions of interest is the characteristics of the IM of patients with gluten-related diseases and its relationship with diet therapy. Materials and methods. The study included 25 adults, 14 (56 %) with CD and 11 (44 %) with NCGS; all were on agliadin diet. We determined the faecal content of the Bacteroidetes, Firmicutes, and Actinobacteria and the rest bacterial DNA (“other” indicator) using the real-time polymerase chain reaction. Results. The Bacteroidetes content was 28.4 (Q1-Q3 9.195–37.83) % in CD and 24.98 (Q1-Q3 9.615–30.597) % in NCGS patients, p = 0.565. Firmicutes content was 53.47 (Q1-Q3 49.98–56.798) % in CD patients and 53.0 (Q1-Q3 48.12–68.53) % in NCGS, p = 0.763. The Actinobacteria content was 4.8 (Q1-Q3 3.82–6.84) % in CD patients and 5.37 (Q1-Q3 4.09–7.77) % in NCGS, p = 0.572. There was a moderate positive correlation with the diet duration (p = 0.397, p = 0.03). The Firmicutes/Bacteroidetes ratio was 1.996 (Q1-Q3 1.35–6.85) in CD patients and 2.0 (Q1-Q3 1.65–7.58) in NCGS patients, p = 0.681. The content of “other” types of IM was 15.39 (Q1-Q3 7.44–22.33) % in CD patients and 13.78 (Q1-Q3 10.65–15.58) % in NCGS patients, p = 0.936. Conclusions. We found similar intestinal microbiome features in patients with celiac disease and non-celiac gluten sensitivity. The detected intestinal microbiome changes are most likely to be a consequence of dietary features in such patients, namely the side effect of maintaining an agliadin diet.

P-317 Associations between endometrial microbiome composition and cellular senescence

Abstract Study question Is there an association between the percentage of senescent cells and microbiome composition in human endometrium? Summary answer We found that cellular senescence is negatively associated with the relative abundance of certain bacterial taxa. What is known already Recent studies indicated that endometrial microbiome characteristics and certain levels of cellular senescence are essential for the establishment of normal endometrial receptivity and successful embryo implantation. The secretion of senescence-associated secretory phenotype (SASP) components is responsible for immune cell activation and might cause endometrial dysbiosis. On the other hand, some studies suggest that the presence of specific metabolic groups of bacteria and their metabolites could influence cellular stress response that might suppress the development of senescent cells. However, the direct relationship between the quantity of senescent cells and microbiome content in the endometrium has never been studied. Study design, size, duration This was a prospective observational cohort study performed between April 2021 and January 2023. Endometrial biopsies were collected from 30 women aged between 34 and 45 during the mid-luteal phase (LH + 7) in a natural cycle. Each biopsy was divided for genetic and immunohistochemical analyses. The exclusion criteria were history of recent inflammatory disease, chronic endometritis, recent antibiotic treatment, endocrinological disorders, autoimmune diseases, oncological diseases, moderate or severe endometriosis, adenomyosis, uterine hyperplasia, and endometrial polyps. Participants/materials, setting, methods We used immunohistochemical biomarker p16ink4a (MAD-000690QD–7, Master Diagnostica) to identify senescent cells. The percentages of positively stained cells in the endometrial stroma and in the luminal epithelium were calculated by HALO image analysis software (version 2.3, IndicaLabs). Endometrial microbiota composition was analyzed after DNA isolation from the endometrial samples using 16S rRNA (v4-v5 region) gene sequencing. Statistical analysis was performed by Spearman’s correlation test using SPSS v.21 (IBM Corp., Armonk, NY, USA). Main results and the role of chance A total of 271 distinct bacterial species and 668 genera were identified across the studied 30 endometrial samples. The percentage of p16+ senescent endometrial stromal cells ranged from 0 to 1.7%, with a mean value of 0.37%, while the percentage of p16+ luminal epithelial cells ranged between 2.5% and 74.0%, with a mean value of 21.5% Spearman analysis revealed significant negative correlation between the percentage of p16+ stromal cells and the relative abundance of Porphyromonas sp. (R = −0.41, p = 0.03) and Sphingobacterium sp. (R = −0.37, p = 0.05). The percentage of p16+ luminal senescent cells correlated negatively with the abundance of Micrococcus luteus (R = −0.44, p = 0.02), Moraxella osloensis (R = −0.37, p = 0.05), Rubellimicrobium sp. (R = −0.46, p = 0.02), Stenotrophomonas sp. (R = − 0.45, p = 0.03), Chryseobacterium sp. (R = −0.41, p = 0.04), Carnobacterium sp. (R = −0.40, p = 0.04), Deinococcus sp. (R = −0.38, p = 0.05), and Enhydrobacter sp. (R = − 0.37, p = 0.05). Limitations, reasons for caution The study was limited in sample size. The assessment includes only endometrial samples from the mid-luteal phase of the cycle. Wider implications of the findings We found that the level of senescence is negatively associated with the relative abundance of certain bacteria taxa in human endometrium, including some related to impaired reproductive function and early embryonic development arrest. These findings suggest a possible specific interaction between senescent cells and microbiome that might influence endometrial receptivity. Trial registration number The current research was funded by National Science Fund, Ministry of Education, Bulgaria, Contract № KP-06-N53/14/16.11.2021

In situ Nanopore sequencing reveals metabolic characteristics of the Qilian glacier meltwater microbiome.

Nanopore metagenomic sequencing enables rapid annotating microbiological ecosystems, and the previous glacier-related sequencing applications (e.g., targeted ice sheets, ice lake, and cryoconite holes) inspire us to explore high-altitude glacier meltwater at Qilian Mountain, China (3000 to 4000 m above sea level, MASL). Our findings suggest that (1) despite only several hundred meters apart, the microbial communities and functionalities are quite different among vertical alpine distributions; (2) the high-altitude Qilian meltwater microbiome serve several main metabolic functions, including sulfur oxidation, selenite decomposing, photosynthesis, energy production, enzymic, and UV tolerant activities. Meanwhile, our Nanopore metagenomic results indicate that the microbial classifications and functionalities (e.g., chaperones, cold-shock, specific tRNA species, oxidative stress, and resistance to toxic compounds) of Qilian meltwater are highly consistent with the other glacial microbiome, emphasizing that only certain microbial species can survive in the cold environment and the molecular adaptions and lifestyles remain stable all over the world. Besides, we have shown Nanopore metagenomic sequencing can provide reliable prokaryotic classifications within or among studies, which therefore can encourage more applications in the field given faster turnaround time. However, we recommend accumulating at least 400 ng nucleic acids (after extraction) and maximizing Nanopore library preparation efficiency before on-site sequencing to obtain better resolutions.

Comparison of the gut microbiome composition between men with erectile dysfunction and a matched cohort: a pilot study.

To-date there have been minimal studies to investigate an association between the gut microbiome and erectile dysfunction. There have been many inflammatory diseases linked to gut microbiome dysbiosis; such as cardiovascular disease and metabolic syndrome. These same inflammatory diseases have been heavily linked to erectile dysfunction. Given the correlations between both conditions and cardiovascular disease and the metabolic syndrome, we believe that it is worthwhile to investigate a link between the two. To investigate the potential association between the gut microbiome and erectile dysfunction. Stool samples were collected from 28 participants with erectile dysfunction and 32 age-matched controls. Metatranscriptome sequencing was used to analyze the samples. No significant differences were found in the gut microbiome characteristics, including Kyoto Encyclopedia of Genes and Genomes richness (p=0.117), Kyoto Encyclopedia of Genes and Genomes diversity (p=0.323), species richness (p=0.364), and species diversity (p=0.300), between the erectile dysfunction and control groups. The association of gut microbiome dysbiosis and pro-inflammatory conditions has been well studied and further literature continues to add to this evidence. Our main limitation for this study was our small-sample size due to recruitment issues. We believe that a study with a larger population size may find an association between the gut microbiome and erectile dysfunction. The results of this study do not support a significant association between the gut microbiome and erectile dysfunction. Further research is needed to fully understand the relationship between these two conditions.

185-OR: Machine-Learning Approach Reveals Microbiome, Metabolome, Lipidome, and Their Interaction in Type 1 Diabetes Mellitus

Background: An increasing amount of research shows that the gut microbiota and metabolites play a role in type 1 diabetes mellitus (T1D). We aimed to use machine learning to explore gut microbiota, serum metabolites, and lipids signatures in T1D individuals. Methods: We evaluated 137 individuals in a cross-sectional cohort that included 38 T1D patients, 38 healthy controls, and 61 T1D patients for validation. After clinical examination and biospecimen collection, we characterized the gut microbiome profile with 16S rRNA gene amplicon sequencing and analyzed serum metabolites and lipids with liquid chromatography-mass spectrometry. All molecular data were analyzed using a combination of univariate, multivariate, and machine-learning approaches (Logistic Regression, Support Vector Machine, Gaussian Naive Bayes, and Random Forest). Results: Machine-learning approaches using microbiota composition did not accurately predict T1D status (model accuracy=0.7555), while the accuracy of model using metabolite composition was 0.9333. Based on bacterial species-level composition, Ruminococcus torques, Anaerostipes, Veillonella, Erysipelotrichaceae UCG-003, Blautia, and Coprococcus were coincident microbes which all increased in T1D. Increased 3-hydroxybutyric acid and 9-oxo-ode (AUC=0.70 and 0.67) were meaningful coincident metabolites in T1D. PC(36:4e)(rep) was the most significant lipid (coefficient index=3.11e-9, increased in T1D). We confirmed the biological relevance of the microbiome, metabolome, and lipidome features in the validation group. Ruminococcus torques was positively associated with 3-hydroxybutyric acid (p&amp;lt;0.01). Conclusions: By using machine-learning algorithms and multi-omics, we demonstrated that T1D patients are associated with altered microbiota, metabolites, and lipidomic signatures or functions. Machine-learning approaches have potential clinical applications in T1D diagnostics and treatment. Disclosure H.Tan: None. J.Yan: None. S.Luo: None. J.Weng: None. X.Zheng: None. Y.Shi: None. T.Yue: None. D.Zheng: None. C.Wang: None. Z.Liu: None. D.Yang: None. Y.Ding: None. W.Xu: None. Funding National Natural Science Foundation of China (82100822); Anhui Provincial Natural Science Foundation (2008085MH248, 2008085MH278); Guangdong Basic and Applied Basic Research Foundation (2019A1515010979); National Key R&amp;D Program (2017YFC1309600)

Distinct taxonomic and functional profiles of high Arctic and alpine permafrost-affected soil microbiomes

BackgroundGlobal warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze–thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses of the microbiomes in permafrost-affected soils have been widely documented, studies about how the microbial genetic potential, especially pathways involved in C and N cycling, changes between active-layer soils and permafrost soils are rare. Here, we used shotgun metagenomics to analyze the microbial and functional diversity and the metabolic potential of permafrost-affected soil collected from an alpine site (Val Lavirun, Engadin area, Switzerland) and a High Arctic site (Station Nord, Villum Research Station, Greenland). The main goal was to discover the key genes abundant in the active-layer and permafrost soils, with the purpose to highlight the potential role of the functional genes found.ResultsWe observed differences between the alpine and High Arctic sites in alpha- and beta-diversity, and in EggNOG, CAZy, and NCyc datasets. In the High Arctic site, the metagenome in permafrost soil had an overrepresentation (relative to that in active-layer soil) of genes involved in lipid transport by fatty acid desaturate and ABC transporters, i.e. genes that are useful in preventing microorganisms from freezing by increasing membrane fluidity, and genes involved in cell defense mechanisms. The majority of CAZy and NCyc genes were overrepresented in permafrost soils relative to active-layer soils in both localities, with genes involved in the degradation of carbon substrates and in the degradation of N compounds indicating high microbial activity in permafrost in response to climate warming.ConclusionsOur study on the functional characteristics of permafrost microbiomes underlines the remarkably high functional gene diversity of the High Arctic and temperate mountain permafrost, including a broad range of C- and N-cycling genes, and multiple survival and energetic metabolisms. Their metabolic versatility in using organic materials from ancient soils undergoing microbial degradation determine organic matter decomposition and greenhouse gas emissions upon permafrost thawing. Attention to their functional genes is therefore essential to predict potential soil-climate feedbacks to the future warmer climate.

CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis

This study aimed to identify shared specific genes associated with rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) through bioinformatic analysis and to examine the role of the gut microbiome in RA. The data were extracted from the 3 RA and 1 IBD gene expression datasets and 1 RA gut microbiome metagenomic dataset. Weighted correlation network analysis (WGCNA) and machine learnings was performed to identify candidate genes associated with RA and IBD. Differential analysis and two different machine learning algorithms were used to investigate RA’s gut microbiome characteristics. Subsequently, the shared specific genes related to the gut microbiome in RA were identified, and an interaction network was constructed utilizing the gutMGene, STITCH, and STRING databases. We identified 15 candidates shared genes through a joint analysis of the WGCNA for RA and IBD. The candidate gene CXCL10 was identified as the shared hub gene by the interaction network analysis of the corresponding WGCNA module gene to each disease, and CXCL10 was further identified as the shared specific gene by two machine learning algorithms. Additionally, we identified 3 RA-associated characteristic intestinal flora (Prevotella, Ruminococcus, and Ruminococcus bromii) and built a network of interactions between the microbiomes, genes, and pathways. Finally, it was discovered that the gene CXCL10 shared between IBD and RA was associated with the three gut microbiomes mentioned above. This study demonstrates the relationship between RA and IBD and provides a reference for research into the role of the gut microbiome in RA.