Tissue Microbiome Research Articles

A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass

ABSTRACT The high background of host RNA poses a major challenge to metatranscriptome analysis of human samples. Hence, metatranscriptomics has been mainly applied to microbe-rich samples, while its application in human tissues with low ratio of microbial to host cells has yet to be explored. Since there is no computational workflow specifically designed for the taxonomic and functional analysis of this type of samples, we propose an effective metatranscriptomics strategy to accurately characterize the microbiome in human tissues with a low ratio of microbial to host content. We experimentally generated synthetic samples with well-characterized bacterial and host cell compositions, and mimicking human samples with high and low microbial loads. These synthetic samples were used for optimizing and establishing the workflow in a controlled setting. Our results show that the integration of the taxonomic analysis of optimized Kraken 2/Bracken with the functional analysis of HUMAnN 3 in samples with low microbial content, enables the accurate identification of a large number of microbial species with a low false-positive rate, while improving the detection of microbial functions. The effectiveness of our metatranscriptomics workflow was demonstrated in synthetic samples, simulated datasets, and most importantly, human gastric tissue specimens, thus providing a proof of concept for its applicability on mucosal tissues of the gastrointestinal tract. The use of an accurate and reliable metatranscriptomics approach for human tissues with low microbial content will expand our understanding of the functional activity of the mucosal microbiome, uncovering critical interactions between the microbiome and the host in health and disease.

Oral Clostridium butyricum on mice endometritis through uterine microbiome and metabolic alternations.

Endometritis occurs frequently in humans and animals, which can negatively affect fertility and cause preterm parturition syndrome. Orally administered Clostridium butyricum, a butyrate-producing gram-positive anaerobe, exhibits anti-inflammatory effects. However, the precise mechanism by which Clostridium butyricum attenuates endometritis remains unclear. This in vivo study evaluated the anti-inflammatory effects of orally administered Clostridium butyricum on uterine tissues. In addition, we conducted uterine microbiome and lipid metabolome analyses to determine the underlying mechanisms. Female Balb/c mice were divided into the following four groups (n = 5-20): (1) mock group, (2) only operation group (mice only underwent operation to exposed uterine horns from the side), (3) control group (mice underwent the same operation with the operation group + perfusion of lipopolysaccharide solution from uterine horns), and (4) Clostridium butyricum administration group (mice underwent the same operation with the control group + oral Clostridium butyricum administration from days 0 to 9). Clostridium butyricum was administered via oral gavage. On day 10, we investigated protein expression, uterine microbiome, and lipid metabolism in uterine tissues. Consequently, orally administered Clostridium butyricum altered the uterine microbiome and induced proliferation of Lactobacillus and Limosilactobacillus species. The effects can contribute to show the anti-inflammatory effect through the interferon-β upregulation in uterine tissues. Additionally, oral Clostridium butyricum administration resulted in the upregulations of some lipid metabolites, such as ω-3 polyunsaturated fatty acid resolvin D5, in uterine tissues, and resolvin D5 showed anti-inflammatory effects. However, the orally administered Clostridium butyricum induced anti-inflammatory effect was attenuated with the deletion of G protein-coupled receptor 120 and 15-lipooxgenase inhibition. In conclusion, Clostridium butyricum in the gut has anti-inflammatory effects on uterine tissues through alterations in the uterine microbiome and lipid metabolism. This study revealed a gut-uterus axis mechanism and provided insights into the treatment and prophylaxis of endometritis.

Abstract A011: Association between Estrogen-Related Genetic and Microbial Factors in Breast Tissue: Implications for Breast Cancer Risk

Abstract Breast cancer (BC) is the most prevalent cancer globally for women, contributing to 11.7% of all cancers in 2020. As a heterogeneous disease, BC is influenced by factors such as sex, age, and hormones. Although a number of genetic variants are linked to BC, roughly 90-95% of BC cases have an unknown hereditary link. Estrogen is critically related to BC, and genes within the estrogen pathway have been heavily studied. However, whether variations in the breast tissue microbiome are associated with genetic variation in estrogen receptor genes is currently unknown. We hypothesized that the genetic variation in and the expression of estrogen-related genes are associated with variations in local breast tissue microbes. To test our hypothesis, we conducted 30X whole genome sequencing on 60 breast tissue samples (healthy (n=15), pre-diagnostic (n=15), tumors (n=15), and adjacent normal (n=15)) donated by women to the Susan G. Komen and Indiana University Simon Cancer Center Tissue Banks. These same samples were previously analyzed for microbiome composition and function (mSystems, 2022).Following sequence pre-processing, variant calling, and alternate allele frequency calculation by the UC Davis Bioinformatics Core, we selected high and moderate variants with a quality score≥55 for further analysis. We ran generalized linear models to select variants with differences in frequency among tissue types (H, PD, AN, T, p≤0.2). Alternate allele frequencies and genotypes of the genes (BCL2L10, FOSL2-AS2, RAF1, and MAPK10) that passed this filter were then associated with bacterial ASVs deemed differentially abundant relative to the H tissue type (mSystems, 2022) using MaAsLin2. We also analyzed beta diversity (PC2) among the 60 tissues and conducted associations with variant frequencies and genotypes. We identified an association between the mut/mut genotype of MAPK10 and the genus Streptococcus (ASV415 q≤0.001, p≤0.001 and ASV7 q≤0.001, p≤0.001) and mut/mut genotype of BCL2L10 was also associated with the genus Proteus (mut/mut q=0.073, p≤0.001). Further, frequency of RAF1 was negatively associated with the genus Oceanobacillus (ASV916 q=0.806, p=0.010 and ASV10 q=0.806, p=0.011). For beta diversity, we observed the frequency of RAF1 (q=0.204, p=0.031) positively associated with PC2, while FOSL2-AS1 (q=0.204, p=0.059) and MAPK10 (q=0.204, p=0.055) frequency to be negatively associated with PC2.In conclusion, we highlight the identification of various associations between certain estrogen pathway genes with breast bacteria, suggesting that there is a relationship between breast tissue microbiome and the host genome. Next steps for this work involve analysis of transcription of MAPK10, RAF1, and BCL210 via qPCR to determine if the microbiome is associated with transcriptional alterations in these genes. This knowledge may be implemented as a predictive tool in assessing risk of BC development by using microbes as biomarkers for variation in host estrogen genetics and/or BC. Citation Format: Rachel Jiang, Ariana McCaw, Lindsey Marian, Leah T Stiemsma. Association between Estrogen-Related Genetic and Microbial Factors in Breast Tissue: Implications for Breast Cancer Risk [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A011.

Meteorin-like Protein and Zonulin in Polycystic Ovary Syndrome: Exploring Associations with Obesity, Metabolic Parameters, and Inflammation.

Polycystic ovary syndrome (PCOS) is a prevalent hormonal and metabolic disorder, wherein the adipose tissue and gut microbiome have been demonstrated to contribute to its pathogenesis. This study aims to assess the concentrations of the adipokine, meteorin-like protein (Metrnl) and the protein, zonulin, related to intestine permeability, in individuals with PCOS with a particular emphasis on their relationship with obesity, clinical manifestations, hormonal profiles, and metabolic parameters. A cohort comprising 58 women with PCOS, classified according to the Rotterdam criteria, was enrolled. The study also considered age, body mass index (BMI), and ethnicity-matched controls (n = 30). Comprehensive anthropometric and clinical evaluations, hormonal assays, and biochemical analyses were conducted during the follicular phase. Subsequent subgroup analyses were executed within the PCOS cohort based on waist-to-height ratio (WHtR), insulin resistance (IR), and free androgen index (FAI). Serum concentrations of Metrnl and zonulin were quantified via the enzyme-linked immunosorbent assay (ELISA) technique. The Metrnl and zonulin levels exhibited no significant disparity between PCOS patients and controls. Nevertheless, within the entire participant cohort and the PCOS group exclusively, overweight/obese participants demonstrated higher Metrnl concentrations relative to their normal-weight counterparts (p < 0.001, p = 0.001, respectively). Furthermore, higher Metrnl concentrations were identified in subgroups characterized by high WHtR and IR in comparison to those with low WHtR (p = 0.001) and without IR (p = 0.001), respectively. A correlation emerged between Metrnl levels and various anthropometric and metabolic parameters, as well as sex-hormone-binding globulin (SHBG) and interleukin-18 (IL-18) within the PCOS group. Multiple linear regression analysis identified HOMA-IR as the sole independent predictor of Metrnl levels. While Metrnl and zonulin levels do not serve as diagnostic indicators of PCOS, elevated Metrnl concentrations exhibited robust associations with proinflammatory and metabolic irregularities within the PCOS population.

Species diversity and network diversity in the human lung cancer tissue microbiomes.

This study explores the relationship between microbial diversity and disease status in human lung cancer tissue microbiomes, using a sample size of 1212. Analysis divided the data into primary tumour (PT) and normal tissue (NT) categories. Differences in microbial diversity between PT and NT were significant in 57% of comparisons, although dataset dependence was a factor in the diversity levels. Shared species analysis (SSA) indicated no significant differences between PT and NT in over 90% of comparisons. Network diversity assessments revealed significant differences between NT and PT regarding species relative abundances and network link abundances for q=0-3. Additionally, significant variations were found between NT and lung squamous cell carcinoma (LUSC) at q=0. in network link probabilities, illustrating the diversity in species interactions. Our findings suggest a stable overall microbiome diversity and composition in lung cancer patients' lung tissues despite patients with diagnosed lung tumours, indicating modified microbial interactions within the tumour. These results highlight an association between altered microbiome interaction patterns and lung tumours, offering new insights into the ecological dynamics of lung cancer microbiomes.

A gauge of coral physiology: re-examining temporal changes in Endozoicomonas abundance correlated with natural coral bleaching.

Bacteria contribute to many physiological functions of coral holobionts, including responses to bleaching. The bacterial genus, Endozoicomonas, dominates the microbial flora of many coral species and its abundance appears to be correlated with coral bleaching. However, evidences for decoupling of bleaching and Endozoicomonas abundance changes have also been reported. In 2020, a severe bleaching event was recorded at reefs in Taiwan, providing a unique opportunity to re-examine bleaching-Endozoicomonas association using multiple stony corals in natural environments. In this study, we monitored tissue color and microbiome changes in three coral species (Montipora sp., Porites sp., and Stylophora pistillata) in Kenting National Park, following the bleaching event. All tagged Montipora sp. and Porites sp. recovered from bleaching within 1 year, while high mortality occurred in S. pistillata. Microbiome analysis found no correlation of Endozoicomonas relative abundance and bleaching severity during the sampling period, but found a stronger correlation when the month in which bleaching occurred was excluded. Moreover, Endozoicomonas abundance increased during recovery months in Montipora sp. and Porites sp., whereas in S. pistillata it was nearly depleted. These results suggest that Endozoicomonas abundance may represent a gauge of coral health and reflect recovery of some corals from stress. Interestingly, even though different Endozoicomonas strains predominated in the three corals, these Endozoicomonas strains were also shared among coral taxa. Meanwhile, several Endozoicomonas strains showed secondary emergence during coral recovery, suggesting possible symbiont switching in Endozoicomonas. These findings indicate that it may be possible to introduce Endozoicomonas to non-native coral hosts as a coral probiotic.

Seasonal dynamics and environmental drivers of tissue and mucus microbiomes in the staghorn coral Acropora pulchra.

Rainfall-induced coastal runoff represents an important environmental impact in near-shore coral reefs that may affect coral-associated bacterial microbiomes. Shifts in microbiome community composition and function can stress corals and ultimately cause mortality and reef declines. Impacts of environmental stress may be site specific and differ between coral microbiome compartments (e.g., tissue versus mucus). Coastal runoff and associated water pollution represent a major stressor for near-shore reef-ecosystems in Guam, Micronesia. Acropora pulchra colonies growing on the West Hagåtña reef flat in Guam were sampled over a period of 8 months spanning the 2021 wet and dry seasons. To examine bacterial microbiome diversity and composition, samples of A. pulchra tissue and mucus were collected during late April, early July, late September, and at the end of December. Samples were collected from populations in two different habitat zones, near the reef crest (farshore) and close to shore (nearshore). Seawater samples were collected during the same time period to evaluate microbiome dynamics of the waters surrounding coral colonies. Tissue, mucus, and seawater microbiomes were characterized using 16S DNA metabarcoding in conjunction with Illumina sequencing. In addition, water samples were collected to determine fecal indicator bacteria (FIB) concentrations as an indicator of water pollution. Water temperatures were recorded using data loggers and precipitation data obtained from a nearby rain gauge. The correlation structure of environmental parameters (temperature and rainfall), FIB concentrations, and A. pulchra microbiome diversity was evaluated using a structural equation model. Beta diversity analyses were used to investigate spatio-temporal trends of microbiome composition. Acropora pulchra microbiome diversity differed between tissues and mucus, with mucus microbiome diversity being similar to the surrounding seawater. Rainfall and associated fluctuations of FIB concentrations were correlated with changes in tissue and mucus microbiomes, indicating their role as drivers of A. pulchra microbiome diversity. A. pulchra tissue microbiome composition remained relatively stable throughout dry and wet seasons; tissues were dominated by Endozoicomonadaceae, coral endosymbionts and putative indicators of coral health. In nearshore A. pulchra tissue microbiomes, Simkaniaceae, putative obligate coral endosymbionts, were more abundant than in A. pulchra colonies growing near the reef crest (farshore). A. pulchra mucus microbiomes were more diverse during the wet season than the dry season, a distinction that was also associated with drastic shifts in microbiome composition. This study highlights the seasonal dynamics of coral microbiomes and demonstrates that microbiome diversity and composition may differ between coral tissues and the surface mucus layer.

Influence of diabetes on microbiome in prostate tissues of patients with prostate cancer.

Although microbiota in prostatic tissues of patients with prostate cancer have been studied, results of different studies have been inconsistent. Different ethnicity of study subjects, different study designs, and potential contaminations during sample collection and experiments might have influenced microbiome results of prostatic tissues. In this study, we analyzed microbiota and their potential functions in benign and malignant tissues of prostate cancer considering possible contaminants and host variables. A total of 118 tissue samples (59 benign tissues and 59 malignant tissues) obtained by robot-assisted laparoscopic radical prostatectomy were analyzed and 64 negative controls (from sampling to sequencing processes) were included to reduce potential contaminants. Alteration of the microbiome in prostate tissues was detected only in patients with diabetes. Furthermore, the influence of diabetes on microbiome was significant in malignant tissues. The microbiome in malignant tissues of patients with diabetes was influenced by pathologic stages. The relative abundance of Cutibacterium was reduced in the high pathologic group compared to that in the intermediate group. This reduction was related to microbial pathways increased in the high pathologic group. Results of this study indicate that diabetes can influence the progression of prostate cancer with microbiome alteration in prostate tissues. Although further studies are necessary to confirm findings of this study, this study can help us understand tissue microbiome in prostate cancer and improve clinical therapy strategies.

Colorectal cancer-specific microbiome in peripheral circulation and cancer tissues.

Accumulating evidence has supported that gut microbiota and metabolite profiles play indispensable roles in the pathogenesis of colorectal cancer (CRC), which ranks as the third most common cancer and the second leading cause of cancer-related deaths worldwide. However, alterations in tumoral or circulating microbiomes in CRC remain incompletely understood. It has been well-documented that tissue or serum microbiomes with low microbial biomass could be screened by use of 2bRAD sequencing for microbiome (2bRAD-M) at the species resolution. In order to validate the microbial biomarkers distinguishing CRC and the variations in microorganisms present in serum and tumors, we performed 2bRAD-M to characterize the microbiomes in serum and cancer tissues of CRC patients with and without lymph node or liver metastasis. The composition of dominated microbiota in serum was different from that of tissue samples, while the microbial community composition of tumors was similar to that of the tumor-adjacent tissues. The analysis of α-diversity and β-diversity has revealed notable variations in serum microbiota diversities in CRC patients, particularly those with liver metastasis. Multiple CRC-specific microbial species, such as Moraxella A cinereus, Flavobacterium sp001800905, and Acinetobacter albensis, were identified in serum. Complicated functions and KEGG pathways were also confirmed in CRC according to the metastasis status. This study has found significant alterations in the microbial compositions and diversities in CRC and CRC-specific microbial species in both circulation and cancer tissues, which may serve as promising biomarkers for the screening, diagnosis and prognosis prediction of CRC. In particular, CRC-specific bacterial taxa are promising markers, holding transformative potentials in establishing personalized screening and risk stratification, refining much earlier non-invasive diagnostic approaches, and enhancing diagnostic sensitivity.

Duodenal and pancreatic tissue microbiome profiles of PPI users and non-users

Factors that influence the pancreas microbiome are not well understood. Regular proton pump inhibitor (PPI) use induces significant alterations in the gut microbiome, including an increase in the abundance of Streptococcus, and may be associated with pancreatic cancer risk. The aim of this study was to examine whether PPI use is associated with pancreatic and duodenal tissue microbiomes. We compared 16S rRNA microbiome profiles of normal pancreatic and duodenal tissue from 103 patients undergoing pancreatic surgery for non-malignant indications, including 34 patients on PPIs, accounting for factors including age, smoking, body mass index and the presence of main pancreatic duct dilation. Histologically normal tissue from the pancreatic head had higher alpha diversity and enrichment of Firmicutes by phylum-level analysis and Streptococcus species compared to normal pancreas body/tail tissues (16.8 % vs 8.8 %, P = .02, and 5.9 % vs 1.4 %, P = .03, respectively). Measures of beta diversity differed significantly between the pancreas and the duodenum, but in subjects with main pancreatic duct dilation, beta diversity of pancreatic head tissue was more similar to normal duodenal tissue than those without pancreatic duct dilation. Duodenal tissue of PPI users had significant enrichment of Firmicute phyla (34.7 % vs. 14.1 %, P = .01) and Streptococcus genera (19.5 % vs. 5.2 %, P = .01) compared to non-users; these differences were not evident in pancreas tissues. By multivariate analysis, PPI use was associated with alpha diversity in the duodenum, but not in the pancreas. However, some differences in pancreas tissue beta diversity were observed between PPI users and non-users. In summary, we find differences in the microbiome profiles of the pancreas head versus the pancreatic body/tail and we find PPI use is associated with alterations in duodenal and pancreatic tissue microbiome profiles.

Exploring HPV as an Etiologic Factor for Breast Cancer

Abstract Introduction/Objective Breast ducts communicate with skin, which can expose one to infectious agents. Recent studies demonstrate differences between breast microbiome in normal tissues versus tumor, suggesting a potential role in carcinogenesis. Human Papilloma Virus (HPV) is the etiologic factor in numerous cancers, and studies suggest it may play a role in breast carcinoma. A recent case report identified an analogue to HPV-related multiphenotypic sinonasal carcinoma in the breast. This sinonasal tumor, closely associated with HPV type 33, consists of adenoid cystic-like morphology, basaloid and/or squamous cytology and multi-lineage differentiation (ductal and myoepithelial). Our aim was to determine if HPV is a driver of breast carcinomas with the outlined phenotype by testing with immunohistochemistry (IHC) for p16 and in-situ hybridization (ISH) for High Risk HPV (HR-HPV) E6/E7 mRNA. Methods/Case Report Breast cases from 2010- June 2022 were searched with the terms “adenoid cystic,” “myoepithelial differentiation,” or “basaloid.” Cases of adenoid cystic carcinoma with a diagnostic fusion were excluded. Those with basaloid and/or squamous morphologic features containing ductal and myoepithelial differentiation proven by IHC were included. Nine identified cases were submitted for p16 IHC and HR-HPV ISH. Results (if a Case Study enter NA) Patients ranged in age from 50 to 85. No cases resulted with positive HR-HPV, however all cases displayed staining for p16. All cases with benign breast tissue (6/9) exhibited some p16 positivity within luminal and myoepithelial cells. Conclusion HR-HPV ISH is a sensitive test; however, no cases were positive. Most tumors and benign breast expressed p16 in some form. p16 in basal-like breast cancer has been described, but only 3/7 cases with biomarkers were triple negative. Accordingly, p16 is not a reliable screening tool if detection of HPV becomes clinically relevant in the future. In this series, the phenotypic features assessed do not appear to be consistent harbingers of HPV infection. More studies are needed to assess the breast microbiome and oncogenic organisms to identify potential new therapeutic targets.

Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing.

This study explored alterations in the respiratory microbiome and transcriptome after Mycobacterium tuberculosis infection in tuberculosis (TB) patients. Metagenomic next-generation sequencing (mNGS) was adopted to reveal the microbiome in lung tissues from 110 TB and 25 nontuberculous (NonTB) patients. Transcriptome sequencing was performed in TB tissues (n = 3), tissues adjacent to TB (ParaTB, n = 3), and NonTB tissues (n = 3) to analyze differentially expressed genes (DEGs) and functional pathways. The microbial β diversity (p = 0.01325) in TB patients differed from that in the NonTB group, with 17 microbial species distinctively distributed. Eighty-three co-up-regulated DEGs were identified in the TB versus NonTB and the TB versus ParaTB comparison groups, and six were associated with immune response to Mtb. These DEGs were significantly enriched in the signaling pathways such as immune response, NF-κB, and B cell receptor. Data in the lung tissue microbiome and transcriptome in TB patients offer a sufficient understanding of the pathogenesis of TB.

Bacterial microbiome and host inflammatory gene expression in foreskin tissue

The penile epithelial microbiome remains underexplored. We sequenced human RNA and a segment of the bacterial 16S rRNA gene from the foreskin tissue of 144 adolescents from South Africa and Uganda collected during penile circumcision after receipt of 1–2 doses of placebo, emtricitabine + tenofovir disoproxil fumarate, or emtricitabine + tenofovir alafenamide to investigate the microbiome of foreskin tissue and its potential changes with antiretroviral use. We identified a large number of anaerobic species, including Corynebacterium acnes, which was detected more frequently in participants from South Africa than Uganda. Bacterial populations did not differ by treatment received, and no differentially abundant taxa were identified between placebo versus active drug recipients. The relative abundance of specific bacterial taxa was negatively correlated with expression of genes downstream of the innate immune response to bacteria and regulation of inflammation. Our results show no difference in the tissue microbiome of the foreskin with short-course antiretroviral use but that bacterial taxa were largely inversely correlated with inflammatory gene expression, consistent with commensal colonization.

Tumor microbiome analysis provides prognostic value for patients with stage III colorectal cancer.

Although patients with colorectal cancer (CRC) can receive optimal treatment, the risk of recurrence remains. This study aimed to evaluate whether the tumor microbiome can be a predictor of recurrence in patients with stage III CRC. Using 16S rRNA gene sequencing, we analyzed the microbiomes of tumor and adjacent tissues acquired during surgery in 65 patients with stage III CRC and evaluated the correlation of the tissue microbiome with CRC recurrence. Additionally, the tumor tissue microbiome data of 71 patients with stage III CRC from another center were used as a validation set. The microbial diversity and abundance significantly differed between tumor and adjacent tissues. In particular, Streptococcus and Gemella were more abundant in tumor tissue samples than in adjacent tissue samples. The microbial diversity and abundance in tumor and adjacent tissues did not differ according to the presence of recurrence, except for one genus in the validation set. Logistic regression analysis revealed that a recurrence prediction model including tumor tissue microbiome data had a better prediction performance than clinical factors (area under the curve [AUC] 0.846 vs. 0.679, p = 0.009), regardless of sex (male patients: AUC 0.943 vs. 0.818, p = 0.043; female patients: AUC 0.885 vs. 0.590, p = 0.017). When this prediction model was applied to the validation set, it had a higher AUC value than clinical factors in female patients. Our results suggest that the tumor microbiome of patients with CRC be a potential predictor of postoperative disease recurrence.

Potential Role of the Intratumoral Microbiota in Prognosis of Head and Neck Cancer.

The tumor microbiome, a relatively new research field, affects tumor progression through several mechanisms. The Cancer Microbiome Atlas (TCMA) database was recently published. In the present study, we used TCMA and The Cancer Genome Atlas and examined microbiome profiling in head and neck squamous cell carcinoma (HNSCC), the role of the intratumoral microbiota in the prognosis of HNSCC patients, and differentially expressed genes in tumor cells in relation to specific bacterial infections. We investigated 18 microbes at the genus level that differed between solid normal tissue (n = 22) and primary tumors (n = 154). The tissue microbiome profiles of Actinomyces, Fusobacterium, and Rothia at the genus level differed between the solid normal tissue and primary tumors of HNSCC patients. When the prognosis of groups with rates over and under the median for each microbe at the genus level was examined, rates for Leptotrichia which were over the median correlated with significantly higher overall survival rates. We then extracted 35 differentially expressed genes between the over- and under-the-median-for-Leptotrichia groups based on the criteria of >1.5 fold and p < 0.05 in the Mann-Whitney U-test. A pathway analysis showed that these Leptotrichia-related genes were associated with the pathways of Alzheimer disease, neurodegeneration-multiple diseases, prion disease, MAPK signaling, and PI3K-Akt signaling, while protein-protein interaction analysis revealed that these genes formed a dense network. In conclusion, probiotics and specific antimicrobial therapy targeting Leptotrichia may have an impact on the prognosis of HNSCC.

SAT636 Obesity And Aging Interactions Modify The Breast Tissue Microbiome Influencing Cancer Risk

Abstract Disclosure: N.M. Iyengar: None. A. Chiba: None. M. Howard-McNatt: None. A. Thomas: None. D.R. Soto-Pantoja: None. K.L. Cook: None. Obesity is one of the few modifiable risk factors for postmenopausal breast cancer. While obesity influences on the gut microbiome are established, the effect of diet and adiposity on tissue resident microbiome populations are underexplored. Studies have shown that breast tissue has a distinct microbiome, which is shifted in the presence of tumors or diet. However, whether obesity and menopause modify the breast microbiome is unknown. Using a cohort of non-cancerous breast tissue samples (n=80) taken at surgery from women that underwent mastectomy for breast cancer, we now demonstrate that obesity and aging interact to shift the breast microbiome. DNA isolated from breast tissue collected at surgery was used to perform V3-V4 amplicon 16S bacterial sequencing. Breast tissue from postmenopausal women with obesity (mean BMI 34.7 ±3.7) displayed a significantly higher α-diversity than breast tissue from postmenopausal lean women (mean BMI 21.9 ±1.7). Postmenopausal women with obesity also displayed a significantly different β-diversity than all other groups (Bray-Curtis; PERMANOVA p&amp;lt;0.02). At the species level, breast tissue from postmenopausal women with obesity had a significantly elevated Akkermansia mucinphila proportional abundance (5.6%) when compared with all other groups (0.05-0.3% proportional abundance), demonstrating obesity and menopause interact to modify the breast tissue microbiome. Akkermansia muciniphila is a mucin-degrading bacteria. Breast tumors display aberrant mucin glycosylation and abundance, which previously were shown to promote carcinogenesis. Staining ER+ breast tumors for mucin-1 from patients with or without obesity indicates patient BMI positively correlates with tumor mucin-1 abundance, suggesting obesity regulation of mucin and/or mucin-degrading bacteria may promote breast tumorigenesis. To determine physiological relevance of breast Akkermansia muciniphila abundance, Western diet-fed MMTV-PyMT mice were intra-nipple injected with saline or Akkermanisa muciniphila bacteria into the mammary gland (MG) at 5, 7, and 9 weeks of age and palpated weekly for tumor formation. Elevated MG Akkermansia presence was associated with increased mammary tumorigenesis and multiplicity. Tumor mucin-1 was decreased with A. muciniphila administration. Flow cytometry analysis of single cell suspensions of breast tumors indicate A. muciniphila modified infiltrating immune populations. Overall, these results suggest obesity and aging may interact to enrich breast mucin-degrading bacteria abundance as a risk factor for postmenopausal breast cancer. Presentation: Saturday, June 17, 2023

Exploration and macroscopic characterization of microbiomes (fungi and bacteria) on anthracnose-Infected chili plants in lowlands fields of Deli Serdang North Sumatra

Anthracnose is one of the main obstacles in chili cultivation. This disease reduces chili production by 40% to 100% during the rainy season. Most techniques used to control anthracnose is using synthetic fungicides that potentially cause resistance and environmental pollution. Disease management by the microbiome of plants with antagonistic properties is an alternative biological control. The aim of the study was to explore the diversity of the microbiome (fungi and bacteria) in various tissues (rhizosphere, endosphere and phylosphere) of large red chili plants infected with anthracnose macroscopically. The object of this research was the leaves, stems, and roots of 5 months old of chili plants affected by anthracnose from two different locations of planting areas. The exploration of the microbiome of anthracnose- infected chili plants in a lowland area in Sumatera Utara in 3 DAI discovered 13 fungi and 12 bacteria, whilst 10 fungi and 11 bacteria in the second location by tissue cropping technique. Besides that, by grinding technique, resulted in 14 fungi isolates dan 13 bacteria in the first location and 16 fungi isolates and 14 bacteria in the second location. At 7 DAI, there found 130 bacteria in the first location and 146 bacteria in location 2 by grinding technique. By tissue cropping technique, there were 124 bacteria in the first location and 102 bacteria in the second location. Morphologically, fungi were identified as Fusariumsp, Aspergillus sp, Penicillum sp, Trichoderma sp, Humicola sp, Colleotetrichum sp, Idriella sp, Alternaria sp, Rhizopus sp and Curvularia sp while the bacteria obtained 9 different isolates based on the morphology of colony.

Recent insights of obesity-induced gut and adipose tissue dysbiosis in type 2 diabetes.

An imbalance in microbial homeostasis, referred to as dysbiosis, is critically associated with the progression of obesity-induced metabolic disorders including type 2 diabetes (T2D). Alteration in gut microbial diversity and the abundance of pathogenic bacteria disrupt metabolic homeostasis and potentiate chronic inflammation, due to intestinal leakage or release of a diverse range of microbial metabolites. The obesity-associated shifts in gut microbial diversity worsen the triglyceride and cholesterol level that regulates adipogenesis, lipolysis, and fatty acid oxidation. Moreover, an intricate interaction of the gut-brain axis coupled with the altered microbiome profile and microbiome-derived metabolites disrupt bidirectional communication for instigating insulin resistance. Furthermore, a distinct microbial community within visceral adipose tissue is associated with its dysfunction in obese T2D individuals. The specific bacterial signature was found in the mesenteric adipose tissue of T2D patients. Recently, it has been shown that in Crohn's disease, the gut-derived bacterium Clostridium innocuum translocated to the mesenteric adipose tissue and modulates its function by inducing M2 macrophage polarization, increasing adipogenesis, and promoting microbial surveillance. Considering these facts, modulation of microbiota in the gut and adipose tissue could serve as one of the contemporary approaches to manage T2D by using prebiotics, probiotics, or faecal microbial transplantation. Altogether, this review consolidates the current knowledge on gut and adipose tissue dysbiosis and its role in the development and progression of obesity-induced T2D. It emphasizes the significance of the gut microbiota and its metabolites as well as the alteration of adipose tissue microbiome profile for promoting adipose tissue dysfunction, and identifying novel therapeutic strategies, providing valuable insights and directions for future research and potential clinical interventions.

Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses

The dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, Oʻahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.

A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types.

Background. Local recurrence and distant metastasis are the main causes of death in patients with cancer. Only considering species abundance changes when identifying markers of recurrence and metastasis in patients hinders finding solutions.Hypothesis. Consideration of microbial abundance changes and microbial interactions facilitates the identification of microbial markers of tumour recurrence and metastasis.Aim. This study aims to simultaneously consider microbial abundance changes and microbial interactions to identify microbial markers of recurrence and metastasis in multiple cancer types.Method. One thousand one hundred and six non-RM (patients without recurrence and metastasis within 3 years after initial surgery) tissue samples and 912 RM (patients with recurrence or metastasis within 3 years after initial surgery) tissue samples representing 11 cancer types were collected from The Cancer Genome Atlas (TCGA).Results. Tumour tissue bacterial composition differed significantly among 11 cancers. Among them, the tissue microbiome of four cancers, head and neck squamous cell carcinoma (HNSC), lung squamous cell carcinoma (LUSC), stomach adenocarcinoma (STAD) and uterine corpus endometrial carcinoma (UCEC), showed relatively good performance in predicting recurrence and metastasis in patients, with areas under the receiver operating characteristic curve (AUCs) of 0.78, 0.74, 0.91 and 0.93, respectively. Considering both species abundance changes and microbial interactions for the four cancers, a combination of nine genera (Niastella, Schlesneria, Thioalkalivibrio, Phaeobacter, Sphaerotilus, Thiomonas, Lawsonia, Actinobacillus and Spiroplasma) performed best in predicting patient survival.Conclusion. Taken together, our results imply that comprehensive consideration of microbial abundance changes and microbial interactions is helpful for mining bacterial markers that carry prognostic information.