Tissue Microbiome Research Articles

Effect of Probiotsid-Phyto and UDP Zn on the intestinal microbiome of Cyprinus carpio

The system analysis of the phytobiotic “Probiocid®-Phyto” and zinc ultradispersed particles (Zn UDP) effect on growth dynamics, chemical composition of muscle tissue and structural microbiome of the common carp gut (Cyprinus carpio) was carried out in this article. The use of modern genetic methods of investigation (polymerase chain reaction with specific 16S prokaryotic primers and with Nextera XT protocol adapters and indices) allowed to determine that the main phylogenetic groups entering the intact group gut microbiome are Proteobacteria (40.49 %), Actinobacteria (28.67 %), Firmicutes (19.01 %) and Bacteroidetes (10.28 %). The most significant effect on the carp microbiome was exerted by Zn UDP, which was expressed by an increase in the specific weight of two types – Proteobacteria 66.64 % and Fusobacteria - 31.18 %, while in the bivalent application group the biodiversity of types was represented as follows: 57.08 % – Proteobacteria, 14.17 % – Firmicutes, 11.86 % – Actinobacteria, 7.85 % – Fusobacteria and 7.43 % – Bacteroidetes. The most significant effect of the preparations on the carp productivity was observed when the compared preparations were fed together; in this case, by the end of the experiment, the increase in carp live weight was 18.45 %. The research allows recommending the combined use of “Probiocid®- Phyto” (2 g/kg feed) and Zn UDP (10 mg/kg feed) as growth activators for common carp (Cyprinus carpio).

Microbiota DNA Translocation Into Mesentery Lymph Nodes Is Associated With Early Development of Pouchitis After IPAA for Ulcerative Colitis.

The role of bacterial translocation in Crohn's disease has been extensively studied. However, data regarding bacterial translocation into the mesentery in patients with ulcerative colitis were scarce. This study aimed to explore the relationship between bacterial translocation and postoperative outcome by comparing the microbiome profile of different anatomical sites in patients with ulcerative colitis who underwent proctocolectomy and IPAA. A prospective study. This study was conducted at the Jinling Hospital from August 2017 to May 2018. Samples of 27 patients with ulcerative colitis who had IPAA and 15 healthy controls who underwent routine colonoscopy were collected. The microbiome profile of different tissue sites and short- and long-term outcomes after IPAA in patients with ulcerative colitis. Bacterial DNA was detected in mesenteric lymph nodes of 51.9% of patients with ulcerative colitis (14/27) and in mesenteric adipose tissue of 66.7% of patients (18/27). The microbiome in mesenteric lymph nodes and mesenteric adipose tissue resembled the mucosal microbiome to a greater extent than the fecal microbiome. Positive bacterial DNA in mesenteric lymph nodes (8/14 vs 0/13; p = 0.002) was associated with pouchitis within 12 months after IPAA, whereas Bray-Curtis distance in mesenteric lymph nodes was significantly different between patients with pouchitis and without ( p = 0.009). This study was limited by its small sample size and lacked situ experiment to confirm the true bacterial translation. Bacterial translocation was highly prevalent in patients with ulcerative colitis. The translocated bacteria DNA in mesenteric adipose tissue and mesenteric lymph nodes was highly correlated and more likely to originate from mucosal than fecal microbiome. Also, the extent of bacterial translocation and translocation of certain bacteria might be associated with the early development of pouchitis after IPAA. This might represent an unprecedented technique to predict pouchitis using mesenteric lymph node bacterial profiles. See Video Abstract at http://links.lww.com/DCR/C119 . ANTECEDENTES:El papel de la translocación bacteriana en la enfermedad de Crohn se ha estudiado ampliamente en los últimos años. Sin embargo, los datos sobre la translocación bacteriana en el mesenterio en pacientes con colitis ulcerosa fueron escasos.OBJETIVO:El objetivo de este estudio fue explorar la relación entre la translocación bacteriana y el resultado postoperatorio comparando el perfil del microbioma de diferentes sitios anatómicos en pacientes con colitis ulcerosa que se sometieron a proctocolectomía y anastomosis ileoanal con bolsa.DISEÑO:Estudio prospectivo.AJUSTE:Este estudio se realizó en el Hospital Jinling desde agosto de 2017 hasta mayo de 2018.PACIENTES:Se recogieron muestras de 27 pacientes con colitis ulcerosa que tenían anastomosis de bolsa ileoanal y 15 controles sanos que se sometieron a una colonoscopia de rutina.PRINCIPALES MEDIDAS DE RESULTADO:El perfil del microbioma de diferentes sitios de tejido y los resultados a corto y largo plazo después de la anastomosis ileoanal con bolsa en pacientes con colitis ulcerosa.RESULTADOS:Se detectó ADN bacteriano en los ganglios linfáticos mesentéricos del 51,9 % (14/27) de los pacientes con colitis ulcerosa y en el tejido adiposo mesentérico del 66,7 % (18/27) de los pacientes, respectivamente. El microbioma en los ganglios linfáticos mesentéricos y el tejido adiposo mesentérico se parecía más al microbioma de la mucosa que al microbioma fecal. El ADN bacteriano translocado en los ganglios linfáticos mesentéricos y el tejido adiposo mesentérico estaban altamente correlacionados. El ADN bacteriano positivo en los ganglios linfáticos mesentéricos (8/14 frente a 0/13, p = 0,002) se asoció con reservoritis dentro de los 12 meses posteriores a la anastomosis ileoanal con reservorio, mientras que la distancia de Bray-Curtis en los ganglios linfáticos mesentéricos fue significativamente diferente entre reservoritis y no reservorios. -pacientes con reservorio (p = 0,009). Ruminococcus, Bacteroides y Clostridiales se encontraron exclusivamente en los ganglios linfáticos mesentéricos de pacientes con reservoritis.LIMITACIÓN:Este estudio estuvo limitado por el pequeño tamaño de la muestra y la falta de un experimento in situ para confirmar la verdadera traducción bacteriana.CONCLUSIÓN:La translocación bacteriana fue altamente prevalente en pacientes con colitis ulcerosa. El ADN bacteriano translocado en el tejido adiposo mesentérico y los ganglios linfáticos mesentéricos estaba altamente correlacionado y era más probable que se originara en el microbioma de la mucosa que en el fecal. Además, la extensión de la translocación bacteriana y la translocación de ciertas bacterias podría estar asociada con el desarrollo temprano de reservoritis después de la anastomosis del reservorio ileoanal. Esto podría representar una técnica sin precedentes para predecir la reservoritis utilizando perfiles bacterianos de los ganglios linfáticos mesentéricos. Consulte Video Resumen en. http://links.lww.com/DCR/C119(Traducción-Dr. Felipe Bellolio ).

Varieties of Lettuce Forming Distinct Microbial Communities Inhabiting Roots and Rhizospheres with Various Responses to Osmotic Stress

A plant microbiome is an important factor in plant growth, stress resistance, health status, and consumer quality and safety. The rhizosphere microbiome evolves in a negotiation between microbial communities that inhabit soil and plant root tissue. In this study, the rhizosphere and root internal tissue microbiome of six varieties of lettuce were analyzed in normal conditions and under salinity stress. The metabarcoding analysis used 16S rRNA gene and ITS2 region sequencing. The microbiomes of root samples were significantly less diverse with different members of the community compared to those of the rhizosphere. A significant effect of lettuce variety was found on the diversity index for bacteria and fungi. Varieties formed very different communities of bacteria in roots. Pseudomonas, Herbaspirillum, Mycobacterium, potentially pathogenic Enterobacter, and other genera were more prevalent in certain varieties. Salinity stress had a significant negative impact on bacterial diversity and community composition, whereas the diversity of fungi has not changed significantly, and the fungal community has changed less than the bacterial one. Changes were more evident in varieties that were more resistant to salinity stress than in sensitive varieties.

The Maleth program: Malta's first space mission discoveries on the microbiome of diabetic foot ulcers

The purpose of the Maleth Program, also known as Project Maleth, is Malta's first space program to evaluate human skin tissue microbiome changes in type 2 diabetes mellitus (T2DM) patients afflicted with diabetic foot ulcers (DFU). This was carried out in both ground-based models and spaceflight. The first mission (Maleth I) under this program was carried out to uncover the effects of spaceflight, microgravity and radiation on human skin tissue microbiome samples from six T2DM patients recruited into the study. Each patient human skin tissue sample was split in three, with one section processed immediately for genomic profiling by 16S typing and the rest were processed for longer term ground-control and spaceflight experiments. Ground-control and spaceflight human skin tissue samples were also processed for genomic profiling upon mission re-entry and completion. Maleth I's overall objective was achieved, as human skin tissue samples with their microbiomes travelled to space and back yielding positive results by both standard microbiology techniques and genetic typing using 16S rRNA amplicon sequencing. Preliminary findings of this mission are discussed in light of its innovative approach at DFU microbiome research, and the clinical implications that may emerge from this and other future similar studies.

Microbiome insights into pediatric familial adenomatous polyposis

BackgroundIndividuals with familial adenomatous polyposis (FAP) harbor numerous polyps with inevitable early progression to colon cancer. Complex microbiotic-tumor microenvironment perturbations suggest a dysbiotic relationship between polyp and microbiome. In this study, we performed comprehensive analyses of stool and tissue microbiome of pediatric FAP subjects and compared with unaffected cohabiting relatives through 16S V4 region amplicon sequencing and machine learning platforms.ResultsWithin our FAP and control patient population, Firmicutes and Bacteroidetes were the predominant phyla in the tissue and stool samples, while Proteobacteria dominated the polyp/non-polyp mucosa. A decline in Faecalibacterium in polyps contrasted with a decline in Bacteroides in the FAP stool. The alpha- and beta-diversity indices differed significantly within the polyp/non-polyp groups, with a concurrent shift towards lower diversity in polyps. In a limited 3-year longitudinal study, the relative abundance of Proteobacteria and Fusobacteria was higher in polyps compared to non-polyp and stool specimens over time. Through machine learning, we discovered that Archaeon_enrichment_culture_clone_A13, Micrococcus_luteus, and Eubacterium_hallii in stool and PL-11B10, S1-80, and Blastocatellaceae in tissues were significantly different between patients with and without polyps.ConclusionsDetection of certain bacterial concentrations within stool or biopsied polyps could serve as adjuncts to current screening modalities to help identify higher-risk patients.

A multi-omics machine learning framework in predicting the recurrence and metastasis of patients with pancreatic adenocarcinoma.

Local recurrence and distant metastasis are the main causes of death in patients with pancreatic adenocarcinoma (PDAC). Microbial content in PDAC metastasis is still not well-characterized. Here, the tissue microbiome was comprehensively compared between metastatic and non-metastatic PDAC patients. We found that the pancreatic tissue microbiome of metastatic patients was significantly different from that of non-metastatic patients. Further, 10 potential bacterial biomarkers (Kurthia, Gulbenkiania, Acetobacterium and Planctomyces etc.) were identified by differential analysis. Meanwhile, significant differences in expression patterns across multiple omics (lncRNA, miRNA, and mRNA) of PDAC patients were found. The highest accuracy was achieved when these 10 bacterial biomarkers were used as features to predict recurrence or metastasis in PDAC patients, with an AUC of 0.815. Finally, the recurrence and metastasis in PDAC patients were associated with reduced survival and this association was potentially driven by the 10 biomarkers we identified. Our studies highlight the association between the tissue microbiome and recurrence or metastasis of pancreatic adenocarcioma patients, as well as the survival of patients.

Impact of Sublethal Concentrations of Nitrite on Goldfish (Carassius auratus) Microbiomes.

Elevated concentrations of nitrite are toxic to fish and can cause a myriad of well documented issues. However, the effects of sublethal concentrations of nitrite on fish health, and specifically, fish tissue microbiomes have not been studied. To test the effects of nitrite exposure, goldfish were exposed to sublethal concentrations of nitrite, 0.0mM, 0.1mM, and 1.0mM, for 2months. The bacteria in the nose, skin, gills, and water were then extracted and sequenced to identify changes to the microbial composition. The water microbiome was not significantly changed by the added nitrite; however, each of the tissue microbiomes was changed by at least one of the treatments. The skin and gill microbiomes were significantly different between the control and 1.0mM treatment and the nose microbiome showed significant changes between the control and both the 0.1mM and 1.0mM treatments. Thus, sublethal concentrations of nitrite in the environment caused a shift in the fish tissue microbiomes independently of the water microbiome. These changes could lead to an increased chance of infection, disrupt organ systems, and raise the mortality rate of fish. In systems with high nitrite concentrations, like intensive aquaculture setups or polluted areas, the effects of nitrite on the microbiomes could negatively affect fish populations.

Gut microbiota distinct between colorectal cancers with deficient and proficient mismatch repair: A study of 230 CRC patients.

Colorectal cancers (CRCs) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) exhibit heterogeneous tumor characteristics, distinct responses to immunotherapy, and different survival outcomes. However, it is unclear whether gut microbiota is distinct between CRCs with different MMR status. In this study, we used immunohistochemistry for four major MMR proteins to determine the MMR status in 230 CRC patients. The gut microbiota was profiled in cancerous and adjacent normal tissues by using bacterial 16S rRNA sequencing. The differences in microbiota diversity, composition and related metabolic pathways between patients with dMMR and pMMR CRCs were explored. Linear discriminant analysis effect size (LEfSe) analysis was further applied to validate the significant taxonomic differences at the genus level. In our study cohort, dMMR status was identified in 29 of 230 (12.61%) tumors. The richness (alpha-diversity) of gut microbiome in dMMR tumor tissue was higher compared with pMMR tumor tissues. The microbial community composition (beta-diversity) between the two groups was significantly different. The dMMR group was enriched considerably for some microbiota, including Fusobacteria, Firmicutes, Verrucomicrobia, and Actinobacteria at the phylum level and Fusobacterium, Akkermansia, Bifidobacterium, Faecalibacterium, Streptococcus, and Prevotella bacteria at the genus level. However, the pMMR group was dominated by Proteobacteria at the phylum level and Serratia, Cupriavidus and Sphingobium at the genus level. Moreover, a wide variety of microbiota associated functional pathways were observed with different MMR status. KEGG pathway analysis indicated a higher abundance of the biosynthesis and metabolic pathways of glycan and nucleotide, cell growth and death pathways, genetic replication and repair pathways in dMMR samples compared with the pMMR group. These findings demonstrate that CRC patients with different MMR status have distinct gut bacterial community richness, compositions and related metabolic pathways, suggesting basis that may explain the effectiveness of immunotherapy in dMMR tumors.

Dynamic gill and mucus microbiomes during a gill disease episode in farmed Atlantic salmon

Amoebic gill disease (AGD) and complex gill disease (CGD) are recurrent gill disorders in Atlantic salmon, resulting in significant aquaculture losses. The role of gill microbiomes in gill disease development is unclear. We undertook a longitudinal study to characterise the gill tissue and gill mucus microbiomes of farmed Atlantic salmon before, and during, a gill disease episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from microbiomes of gill samples taken from 105 individual salmon on a farm, over a summer season. The AGD aetiological agent, Neoparamoeba perurans, was PCR-quantified targeting 18S rRNA genes. Similar analyses were carried out on mucus samples. Mucus scrapings were suitable, non-lethal substitutes for characterisation of the gill prokaryotic community in this study. Gill tissue and gill mucus microbiomes changed during the campaign, correlating with N. perurans concentrations. Time explained 35% of the gill tissue and gill mucus microbiome variance, while N. perurans concentrations explained 5%. Genera including Dyadobacter, Shewanella and Pedobacter were maximally abundant in gill and mucus samples at the timepoint prior to the the detection of gill disorder signs, at T3. Shewanella was significantly more abundant before than during the gill disease episode, and we suggest this genus could be considered in future studies addressing relationships between gill disease and the gill microbiome.

Adipose Tissue, Bile Acids, and Gut Microbiome Species Associated With Gallstones After Bariatric Surgery

Several risk factors are associated with gallstone disease after bariatric surgery, but the underlying pathophysiological mechanisms of gallstone formation are unclear. We hypothesize that gallstone formation after bariatric surgery is induced by different pathways compared with gallstone formation in the general population, since postoperative formation occurs rapidly in patients who did not develop gallstones in preceding years. To identify both pathophysiological and potentially protective mechanisms against postoperative gallstone formation, we compared the preoperative fasting metabolome, fecal microbiome, and liver and adipose tissue transcriptome obtained before or during bariatric surgery of obese patients with and without postoperative gallstones. In total, 88 patients were selected from the BARIA longitudinal cohort study. Within this group, 32 patients had postoperative gallstones within 2 years. Gut microbiota metagenomic analyses showed group differences in abundance of 41 bacterial species, particularly abundance of Lactobacillaceae and Enterobacteriaceae in patients without gallstones. Subcutaneous adipose tissue transcriptomic analyses revealed four genes that were suppressed in gallstone patients compared with patients without gallstones. These baseline gene expression and gut microbiota composition differences might relate to protective mechanisms against gallstone formation after bariatric surgery. Moreover, baseline fasting blood samples of patients with postoperative gallstones showed increased levels of several bile acids. Overall, we revealed different genes and bacteria associated with gallstones than those previously reported in the general population, supporting the hypothesis that gallstone formation after bariatric surgery follows a different trajectory. Further research is necessary to confirm the involvement of the bile acids, adipose tissue activity, and microbial species observed here.

358P Analysis of microbiome signatures in plasma for early CRC detection

Colorectal cancer (CRC) represents the 3rd leading cause of cancer-related deaths in the United States. Patients diagnosed with distant stage of the disease represent 22% of all CRC cases and have 15% 5-years survival rates, in contrast to 91% 5-years survival rate of patients with localized disease at diagnosis, indicating how CRC early detection represents an urgent clinical need. Tissue microbiome has been identified as a promising biomarker for the early identification of several cancer types, including CRC.

The Microbiome-Immune Axis Therapeutic Effects in Cancer Treatments.

During the last decades, research and therapeutic methods in cancer treatment have been evolving. As the results, nowadays, cancer patients are receiving several types of treatments, ranging from chemotherapy and radiation therapy to surgery and immunotherapy. In fact, most cancer patients take a combination of current anti-cancer therapies to improve the efficacy of treatment. However, current strategies still cause some side effects to patients, such as pain and depression. Therefore, there is the need to discover better ways to eradicate cancer whilst minimizing side effects. Recently, immunotherapy, particularly immune checkpoint blockade, is rising as an effective anti-cancer treatment. Unlike chemotherapy or radiation therapy, immunotherapy has few side effects and a higher tumor cell removal efficacy depend on cellular immunological mechanisms. Moreover, recent studies suggest that tissue immune responses are regulated by their microbiome composition. Each tissue has their specific microenvironment, which makes their microbiome composition different, particularly in the context of different types of cancer, such as breast, colorectal, kidney, lung, and skin. Herein, we review the current understanding of the relationship of immune responses and tissue microbiome in cancer in both animal and human studies. Moreover, we discuss the cancermicrobiome-immune axis in the context of cancer development and treatment. Finally, we speculate on strategies to control tissue microbiome alterations that may synergistically affect the immune system and impact cancer treatment outcomes.

Bladder Tissue Microbiome Composition in Patients of Bladder Cancer or Benign Prostatic Hyperplasia and Related Human Beta Defensin Levels.

Balance between the microbiome associated with bladder mucosa and human beta defensin (HBD) levels in urine is a dynamic, sensitive and host-specific relationship. HBD1—possessing both antitumor and antibacterial activity—is produced constitutively, while the inducible production of antibacterial HBD2 and HBD3 is affected by bacteria. Elevated levels of HBD2 were shown to cause treatment failure in anticancer immunotherapy. Our aim was to assess the relationship between microbiome composition characteristic of tumor tissue, defensin expression and HBD levels measured in urine. Tissue samples for analyses were removed during transurethral resection from 55 bladder carcinoma and 12 prostatic hyperplasia patients. Microbiome analyses were carried out with 16S rRNS sequencing. Levels of HBD mRNA expression were measured with qPCR from the same samples, and urinary amounts of HBD1, 2 and 3 were detected with ELISA in these patients, in addition to 34 healthy volunteers. Mann–Whitney U test, Wilcoxon rank sum test (alpha diversity) and PERMANOVA analysis (beta diversity) were performed. Defensin-levels expressed in the tumor did not clearly determine the amount of defensin measurable in the urine. The antibacterial and antitumor defensin (HBD1) showed decreased levels in cancer patients, while others (HBD2 and 3) were considerably increased. Abundance of Staphylococcus, Corynebacterium and Oxyphotobacteria genera was significantly higher, the abundance of Faecalibacterium and Bacteroides genera were significantly lower in tumor samples compared to non-tumor samples. Bacteroides, Parabacteroides and Faecalibacterium abundance gradually decreased with the combined increase in HBD2 and HBD3. Higher Corynebacterium and Staphylococcus abundances were measured together with higher HBD2 and HBD3 urinary levels. Among other factors, defensins and microorganisms also affect the development, progression and treatment options for bladder cancer. To enhance the success of immunotherapies and to develop adjuvant antitumor therapies, it is important to gain insight into the interactions between defensins and the tumor-associated microbiome.

The Common and Unique Pattern of Microbiome Profiles among Saliva, Tissue, and Stool Samples in Patients with Crohn's Disease.

This study aimed to elucidate common and unique microbiome patterns in saliva, intestinal tissue biopsy, and stool samples from patients with Crohn’s disease (CD). Saliva, tissue, and stool samples from patients with CD were prospectively collected. Quantitative and phylogenetic analyses of 16s rRNA sequencing data were performed with bioinformatical pipelines. A total of 30 patients were enrolled in this study. The composition of major microbial taxa was similar between tissue and stool samples. A total of 11 of the 20 most abundant microbiota were found in both samples. The microbial community in saliva was significantly distinct from that in tissue and stool. The major species of microbiota and their composition also differed significantly from those of tissue and stool samples. However, Streptococcus and Prevotella are common genera in saliva, tissue, and stool microbiome. The abundance of Streptococcus, Pantoea, and Actinomyces from the saliva sample group were significantly different, varying with the location of the inflammation. Saliva has a distinct microbial community compared with tissues and stools in patients with CD. Prevotella and Streptococcus, which are commonly observed in saliva, stool, and tissue, can be considered a potential biomarker related to the diagnosis or prognosis of CD.

Differential Microbial Signature Associated With Benign Prostatic Hyperplasia and Prostate Cancer.

Apart from other risk factors, chronic inflammation is also associated with the onset of Prostate Cancer (PCa), wherein pathogen infection and tissue microbiome dysbiosis are known to play a major role in both inflammatory response and cancer development. However, except for a few studies, the link between microbes and PCa remained poorly understood. To explore the potential microbiome signature associated with PCa in Indian patients, we investigated differential compositions of commensal bacteria among patients with benign prostatic hyperplasia (BPH) and PCa using 16S rRNA amplicon sequencing followed by qPCR analyses using two distinct primer sets. Using two independent cohorts, we show that Prevotella copri, Cupriavidus campinensis, and Propionibacterium acnes represent the three most abundant bacteria in diseased prostate lesions. LEfSe analyses identified that while Cupriavidus taiwanensis and Methylobacterium organophilum are distinctly elevated in PCa samples, Kocuria palustris and Cellvibrio mixtus are significantly enriched in BPH samples. Furthermore, we identify that a number of human tumor viruses, including Epstein-Barr virus (EBV) and hepatitis B virus (HBV), along with two high-risk human papillomaviruses - HPV-16 and HPV-18, are significantly associated with the PCa development and strongly correlated with PCa bacterial signature. The study may thus offer to develop a framework for exploiting this microbial signature for early diagnosis and prognosis of PCa development.

Analysis of microbiome in gastrointestinal stromal tumors: Looking for different players in tumorigenesis and novel therapeutic options.

Preclinical forms of gastrointestinal stromal tumor (GIST), small asymptomatic lesions, called microGIST, are detected in approximately 30% of the general population. Gastrointestinal stromal tumor driver mutation can be already detected in microGISTs, even if they do not progress into malignant cancer; these mutations are necessary, but insufficient events to foster tumor progression. Here we profiled the tissue microbiota of 60 gastrointestinal specimens in three different patient cohorts—micro, low‐risk, and high‐risk or metastatic GIST—exploring the compositional structure, predicted function, and microbial networks, with the aim of providing a complete overview of microbial ecology in GIST and its preclinical form. Comparing microGISTs and GISTs, both weighted and unweighted UniFrac and Bray–Curtis dissimilarities showed significant community‐level separation between them and a pronounced difference in Proteobacteria, Firmicutes, and Bacteroidota was observed. Through the LEfSe tool, potential microbial biomarkers associated with a specific type of lesion were identified. In particular, GIST samples were significantly enriched in the phylum Proteobacteria compared to microGISTs. Several pathways involved in sugar metabolism were also highlighted in GISTs; this was expected as cancer usually displays high aerobic glycolysis in place of oxidative phosphorylation and rise of glucose flux to promote anabolic request. Our results highlight that specific differences do exist in the tissue microbiome community between GIST and benign lesions and that microbiome restructuration can drive the carcinogenesis process.

SO-26 Identification and quantification of the microbiome in colorectal cancer metastases

Recent research has identified the existence of living bacteria in the tumor microenvironment, as well as cancer-specific bacteria in blood of patients. Early evidence suggested a role of the gut and tissue microbiome in the development of colorectal cancer (CRC). However, the part of this intra-tumor microbiome in promoting or aiding metastasis to distant organs remains unexplored. Interestingly, similar bacterial strains from CRC primary tumors have been identified in patient-matched liver metastases. Few mechanistic hypotheses have been proposed of how bacterial translocation to distant sites occurs, or whether the tumor-resident microbiome can influence the spreading or the behavior of metastases and their local immune response. We aimed to characterize the intra-tumor bacterial signature of metastatic colorectal cancer (mCRC) through a large-scale study with different cohorts from several biobanks in Belgium. We collected 378 frozen samples from 99 patients composed by 104 primary colorectal tumors (PT) and 99 patient-matched liver metastases (LMT), both associated with normal adjacent tissue (NAT) as control (n = 83 and 58, respectively). We added primary liver tumors (hepatocellular carcinoma (HCC, n=28) and cholangiocarcinoma (CGC, n=6)) from 27 patients as comparative cohort for LMT. The V4 region of the bacterial 16S rRNA gene was sequenced. The computational DADA2 pipeline was used to process the sequencing data and determine the abundance of amplicon sequence variants (ASV). We strictly applied sterile conditions from sample collection to sequencing, with negative and positive controls along the process to minimize contamination and misinterpretation of the results. Potential contaminants were removed bioinformatically by applying a series of stringent filters. Bacterial sequences were identified in all tissue types. Based on preliminary results, the principal component analysis based on bacterial composition of the samples revealed significant sample grouping (PERMANOVA, p-value = 1e-04) per tissue type (PT, LMT and HCC-CGC). The read number and bacterial composition of associated NAT were similar to their associated tumor tissue. PT, as expected by their colonic origin, presented higher bacterial biomass than LMT, yet the patient-specific microbiome composition in LMT was partially overlapping with PT, consisting with previously reported prevalent taxa. The number of shared ASVs between PT and LMT was significantly higher within than between patients (linear regression model with p-value = 4,22e-10), suggesting an individual bacterial transfer. This transfer appeared to be a probabilistic event, as it correlated with taxa abundance, and this transfer was more likely for the most abundant bacteria in the PT. Our preliminary results suggest the presence of a low bacterial biomass in LMT with characteristics closer to PT compared to primary tumors of the liver, suggesting a “per-tumor type” rather than “per-organ” bacterial signature and abundance. A within-patient bacterial transfer from PT to LMT seems to be observed for the most abundant taxa. These preliminary results are currently in a validation process. If our results are confirmed, this multicentric large-scale study would allow us to characterize and classify tumor tissue bacterial signature in mCRC to compare it with genomic and immune tumor features.

Comparison of host DNA depletion methods in gastric tissue microbiome analysis based on high-throughput sequencing

在组织共生微生物组的研究中，由于组织样本中微生物细胞比例远低于宿主细胞，导致高通量测序数据中属于微生物的序列比例很低，不足以准确反应菌群多样性和结构组成。本文比较了HostZERO™ Microbial DNA Kit(ZYM)和NEBNext mircobiome DNA enrichment kit(NEB)两款商用DNA提取试剂盒、16S rRNA基因V3-V4高变区测序文库构建过程中的巢式PCR(NES)和扩增产物切胶回收(GEL)四种方法。与未经去除宿主DNA的方法相比，四种方法都使胃组织样本测序结果中细菌序列占比显著增加。NES和ZYM明显改变了纯菌菌株混合样本和胃组织样本菌群的组成；NEB未对菌株混合样本菌群组成造成明显影响，但对胃组织样本菌群结构影响大；只有GEL方法对样本菌群结构影响较小。综上所述，GEL方法能够去除大部分宿主序列又对菌群组成影响最小，这为研究组织微生物组时减少测序数据中宿主序列的方法选择提供了参考。

Body Microbiota and Its Relationship With Benign and Malignant Breast Tumors: A Systematic Review.

Breast cancer is the most frequent type of cancer as well as one of the main causes of cancer-related mortality in women. Human microbial dysbiosis, which has been related to a range of malignancies, is one of the variables that may impact the chance of developing breast disorders. In this review, we aimed to investigate the relationship between breast cancer and benign breast tumors with dysbiosis of the microbiome at different body sites. We performed a systematic review of MEDLINE, Scopus, Ovid, and Cochrane Library to identify original articles published until July 2020 that reported studies of breast disease and microbiota. Twenty-four original articles were included in the study, which looked at the features and changes in breast, gut, urine, lymph node, and sputum microbial diversity in patients with benign and malignant breast tumors. In breast cancer, the breast tissue microbiome demonstrated changes in terms of bacterial load and diversity; in benign breast tumors, the microbiome was more similar to a malignant tumor than to normal breast tissue. Triple-negative (TNBC) and triple-positive (TPBC) types of breast cancer have a distinct microbial pattern. Moreover, in breast cancer, gut microbiota displayed changes in the compositional abundance of some bacterial families and microbial metabolites synthesis. Our review concludes that breast carcinogenesis seems to be associated with microbial dysbiosis. This information can be further explored in larger-scale studies to guide new prophylactic, diagnostic, and therapeutic measures for breast cancer.

The Microbiome in Pancreatic Cancer-Implications for Diagnosis and Precision Bacteriophage Therapy for This Low Survival Disease.

While the mortality rates for many cancers have decreased due to improved detection and treatments, that of pancreatic cancer remains stubbornly high. The microbiome is an important factor in the progression of many cancers. Greater understanding of the microbiome in pancreatic cancer patients, as well as its manipulation, may assist in diagnosis and treatment of this disease. In this report we reviewed studies that compared microbiome changes in pancreatic cancer patients and non-cancer patients. We then identified which bacterial genera were most increased in relative abundance across the oral, pancreatic, duodenal, and faecal tissue microbiomes. In light of these findings, we discuss the potential for utilising these bacteria as diagnostic biomarkers, as well as their potential control using precision targeting with bacteriophages, in instances where a causal oncogenic link is made.