Impending Mental Health Issues During Coronavirus Disease 2019 – Time for Personalized Nutrition Based on the Gut Microbiota to Tide Over the Crisis?

Coronavirus disease 2019 (COVID-19) is a major pandemic facing the world today caused by SARS-CoV-2 which has implications on our mental health as well. The uncertain future, fear of job loss, lockdown and negative news all around have taken a heavy toll on the mental health of individuals from across the world. Stress and anxiety can affect the COVID-19 patients even more. Recent study suggests COVID-19 infection may lead to post-traumatic stress disorder (PTSD). Certain prebiotics and probiotics have been shown to have anxiolytic effect through gut microbiota modulation. Incidentally, preliminary report also suggests a differential microbial profile in COVID-19 patients as compared to healthy individuals. Gut microbiota’s role in anxiety and depression is well studied. The importance of the “gut-brain” axis has been implicated in overall mental health. It is known that diet, environmental factors and genetics play an important role in shaping gut microbiota. Trials may be initiated to study if personalized diet and supplementation based on individual’s gut microbiome profile may improve the general mental well-being of people prone to anxiety during this pandemic. Also, COVID-19 patients may be provided personalized nutritional therapy based on their gut microbiota profile to see if PTSD and anxiety symptoms can be alleviated.

Endoscopic ultrasound-guided fine-needle biopsy as a tool for studying the intra-tumoral microbiome in pancreatic ductal adenocarcinoma: a pilot study

A new approach by investigating the intra-tumoral microbiome raised great interest because they may influence the host immune response and natural history of the disease. However, previous studies on the intra-tumoral microbiome of pancreatic ductal adenocarcinoma (PDAC) were mostly based on examining the formalin-fixed paraffin-embedded tumor specimens. This study aims to investigate the feasibility of using endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) as a complementary procedure of surgical biopsy to obtain adequate fresh pancreatic cancer tissue for intra-tumoral microbial research. This was a prospective pilot study performed at a single tertiary referral center. We obtained pancreatic cancer tissue by EUS-FNB and surgical biopsy, respectively. We amplified the V3-V4 hyper-variable region of bacterial 16S ribosomal ribonucleic acid (rRNA) genes, constructed a pair-end library, and performed high-throughput sequencing. From August 2020 to November 2020, nine eligible patients with PDAC were enrolled in this study. The intra-tumoral microbiome profile was successfully generated from the PDAC cancer tissue obtained by EUS-FNB as well as by surgical biopsy. There was no significant difference in intra-tumoral alpha-diversity or bacterial taxonomic composition between tissues obtained by EUS-FNB and by surgical biopsy. EUS-FNB can collect sufficient fresh cancer tissue for microbiome analyses without complication. The intra-tumoral microbiome profile in tissues obtained by EUS-FNB had similar alpha-diversity and taxonomic profiles with those obtained by surgical biopsy. It implicated, except for surgical biopsy, EUS-FNB can be another valid and valuable tool for studying intra-tumoral microbiome in patients with resectable and unresectable PDAC.

Poultry gut health – microbiome functions, environmental impacts, microbiome engineering and advancements in characterization technologies

The gastrointestinal tract (GIT) health impacts animal productivity. The poultry microbiome has functions which range from protection against pathogens and nutrients production, to host immune system maturation. Fluctuations in the microbiome have also been linked to prevailing environmental conditions. Healthy poultry birds possess a natural resistance to infection. However, the exploration of environmental impacts and other relevant factors on poultry growth and health have been underplayed. Since good performance and growth rate are central to animal production, the host-microbiome relationship remains integral. Prior to the emergence of metagenomic techniques, conventional methods for poultry microbiome studies were used and were low-throughput and associated with insufficient genomic data and high cost of sequencing. Fortunately, the advent of high-throughput sequencing platforms have circumvented some of these shortfalls and paved the way for increased studies on the poultry gut microbiome diversity and functions. Here, we give an up-to-date review on the impact of varied environments on microbiome profile, as well as microbiome engineering and microbiome technology advancements. It is hoped that this paper will provide invaluable information that could guide and inspire further studies on the lingering pertinent questions about the poultry microbiome.

Endoscopic Ultrasound-Guided Fine-Needle Biopsy As A Valuable Tool for Studying The Intra-Tumoral Microbiome in Pancreatic Ductal Adenocarcinoma

Introduction: A new approach by investigating the intra-tumoral microbiome raised great interest because they may influence the host immune response and natural history of the disease. However, previous studies on the intra-tumoral microbiome of pancreatic ductal adenocarcinoma (PDAC) were mostly based on examining the formalin-fixed paraffin-embedded tumor specimens. This study aims to investigate the feasibility of using endoscopic ultrasound-guided fine-needle biopsy (EUS-FNB) as a complementary procedure of surgical biopsy to obtain adequate fresh pancreatic cancer tissue for intra-tumoral microbial research. Materials and methods: This was a prospective pilot study performed at a single tertiary referral center. We obtained pancreatic cancer tissue by EUS-FNB and surgical biopsy, respectively. We amplified the V3-V4 hyper-variable region of bacterial 16S ribosomal ribonucleic acid (rRNA) genes, constructed a pair-end library, and performed high-throughput sequencing. Results: From August 2020 to November 2020, nine eligible patients with PDAC were enrolled in this study. The intra-tumoral microbiome profile was successfully generated from the PDAC cancer tissue obtained by EUS-FNB as well as by surgical biopsy. There was no significant difference in intra-tumoral alpha-diversity or bacterial taxonomic composition between tissues obtained by EUS-FNB and by surgical biopsy. Conclusion: EUS-FNB can collect sufficient fresh cancer tissue for microbiome analyses without complication. The intra-tumoral microbiome profile in tissues obtained by EUS-FNB had similar alpha-diversity and taxonomic profiles with those obtained by surgical biopsy. It implicated, except for surgical biopsy, EUS-FNB can be another valid and valuable tool for studying intra-tumoral microbiome in patients with resectable and unresectable PDAC.

Metagenomic Investigation Uncovers Presence of Probiotic-Type Microbiome in Kalparasa® (Fresh Unfermented Coconut Inflorescence Sap)

The phloem sap tapped from unopened inflorescence (spadix) of coconut palm using a novel collecting device, “coco-sap chiller,” has been branded Kalparasa® (henceforth as Kalparasa in the text) to distinguish its properties not found in sap harvested by traditional methods. To know its hitherto unidentified microbiome profile, we employed high-throughput sequencing to uncover the bacteriome and mycobiome in fresh and 12-h fermented samples. Fresh Kalparasa had a pH of 7.2, which dropped to 4.5 after 12 h, signifying fermentation of the sap. Diversity analysis indicated fresh Kalparasa having higher bacterial species than the fermented one. Contrary to this, fresh sap had lower fungal/yeast diversity than the fermented sample. Fresh Kalparasa had relatively higher abundance of probiotic-type Leuconostoc genus followed by equal proportions of Gluconobacter, Acetobacter, and Fructobacillus. The 12-h fermented Kalparasa showed a significant increase in Gluconobacter with a sharp decrease in Leuconostoc. Mycobiome data revealed fresh Kalparasa to be preponderant in Saccharomyces and Hanseniaspora genera of yeasts while the fermented sap had higher representation of Hanseniaspora and Cortinarius and lesser Saccharomyces. This suggested that the fermentation of Kalparasa was probably driven by symbiotic culture of bacteria and yeasts (SCOBY), particularly acetic acid bacteria and non-Saccharomyces yeasts. The bacteriome-function predictions highlighted the enrichment of glycerophospholipid, ABC transporters, purine, and pyrimidine metabolisms. Based on our findings, Kalparasa containing large population of Leuconostoc mesenteroides, Fructobacillus fructosus, Saccharomyces cerevisiae, and Hanseniaspora guilliermondii can be promoted as a healthy “unfermented” plant edible food containing live probiotic-type microbiome during its consumption.

The Microbiome Profile In Ulcerative Colitis And Pouchitis

Both ulcerative colitis and pouchitis are associated with an imbalance in the intestinal microbiota, which may be related to the immune response. The objective was to determine the bacterial composition in pouchitis and ulcerative colitis in order to explore the underlying pathogenesis. Microbiome was profiled and evaluated by 16S ribosomal DNA gene sequencing in stool samples of 37 patients with ulcerative colitis, 15 patients with normal ulcerative colitis-pouch, 15 patients with ulcerative colitis-pouchitis and 18 healthy volunteers, PICRUSt and PICRUSt2 were performed to analyze the function of dominant bacteria. In our Chinese cohort, with aggravation of ulcerative colitis, intestinal microorganisms were characterized by a gradual decreased in diversity and numbers of butyrate-producing bacteria and Bacteroides. Besides, in addition to the decrease of probiotics, the bloom of Escherichia-Shigella and Ruminococcus_gnavus was observed in pouchitis which related to multiple infection pathways according to KEEG pathway analysis. Our results showed that pouchitis and ulcerative colitis differ in their intestinal microbial structures and metabolic pathways, but the reasons need to be further explored.

CHARACTERISTICS OF THE MICROBIOME OF THE MAIN BIOTOPES OF THE CASPIAN SEAL

В статье приведены результаты метабаркодирования ДНК микробиома респираторного, урогенитального и желудочно-кишечного трактов каспийского тюленя. Показан профиль микробиома каспийского тюленя и отмечено отсутствие возбудителей бактериальных зоонозов в их бета-сообществе микробиотов. The article presents the results of metabarcoding of the microbiome DNA of the respiratory, urogenital and gastrointestinal tracts of the Caspian seal. The microbiome profile of the Caspian seal is shown, and the absence of pathogens of bacterial zoonoses in their beta microbiota community is noted. Key words: Caspian seal, metagenome, microbiome, sequencing.

P–399 Temporal dynamics of an IVF/ICSI success prediction test based on the vaginal microbiome

Study question What is the influence of time on the vaginal microbiome-based prediction of IVF/ICSI success? Summary answer Time influences the vaginal microbiome-based prediction of IVF/ICSI success. What is known already The association between the microbiome of the lower female reproductive tract and subfertility is discussed extensively suggesting its importance for fertility and fertility treatment. Using a modified next generation sequencing technique, an assay of the vaginal microbiome that predicts the pregnancy chances before starting the IVF/ICSI procedure has been developed and validated (1) displaying profiles associated with a low, medium and high chance of implantation. The vaginal microbiome is already known to change over time (2). However, it remains unclear to what extent spontaneous improvement from a low score can occur and over what time period. Study design, size, duration To investigate the spontaneous reversal capacity and associated time period of a low score microbiome profile in IVF-ICSI patients, an observational prospective cohort study of 77 women was performed using the ReceptIVFity assay. Women with medium or high profiles were encouraged to proceed with their ART treatment, whereas women with a low profile were suggested to delay the treatment for 1 month until a subsequent swab was taken with a maximum of 4 repeats. Participants/materials, setting, methods The study was carried out in a University based single center setting. Ethical approval was obtained (6259R MPG§23b). Patients between 24 and 41 years of age were included when eligible for their first, second or third IVF or IVF-ICSI attempt. Exclusion criteria were: antibiotic treatment in the 3 months prior to the test, women who have started with hormone treatment in the last 2 months in the context of ovarian stimulation, or downregulation of endometriosis. Main results and the role of chance Of the 77 patients included, 53 had a high or medium profile and proceeded with their treatment. 24 had a low profile and were supposed to delay the treatment in favor of a subsequent test. The low profile patients were followed up as indicated in the study description. Unfortunately, 11 of the 24 low score patients dropped out of the study. This relatively high number can only in parts be explained by unswayable medical reasons as no fertilization or embryo arrest but a comparable number of patients dropped out most likely due to Corona restrictions or Corona-related anxiety reasons. In the low score group, 1 month after the initial test, 12 patients repeated the swab; 4 remained low (33,33%), whereas 8 shifted to the medium or high (66,67%) groups. After 2 months, 4 patients had another test; 1 remained low (25%), 3 shifted to medium and high (75%). Therewith, in two months’ time 91,7% shifted from low to a better (medium/high) profile. So far, only 1 patient of the initial lows remained low for 5 months. The 12 shifters had a clinical pregnancy rate of 40% after the first embryo transfer after changing the microbiome profile from low to medium/high. Limitations, reasons for caution The results described were generated from a smaller group than intended initially due to a relative high dropout rate for no medical reasons. Wider implications of the findings: Patients suffering from infertility have a clinical benefit from performing a ReceptIVFity test before ART treatment and to delay treatment, when the result is low, since the spontaneous conversion time to a better profile, and therewith a higher pregnancy chance, occurred within 2 month in almost all patients. Trial registration number 2018124928

New Approaches to Profile the Microbiome for Treatment of Neurodegenerative Disease

Progressive neurodegenerative diseases represent some of the largest growing treatment challenges for public health in modern society. These diseases mainly progress due to aging and are driven by microglial surveillance and activation in response to changes occurring in the aging brain. The lack of efficacious treatment options for Alzheimer’s disease (AD), as the focus of this review, and other neurodegenerative disorders has encouraged new approaches to address neuroinflammation for potential treatments. Here we will focus on the increasing evidence that dysbiosis of the gut microbiome is characterized by inflammation that may carry over to the central nervous system and into the brain. Neuroinflammation is the common thread associated with neurodegenerative diseases, but it is yet unknown at what point and how innate immune function turns pathogenic for an individual. This review will address extensive efforts to identify constituents of the gut microbiome and their neuroactive metabolites as a peripheral path to treatment. This approach is still in its infancy in substantive clinical trials and requires thorough human studies to elucidate the metabolic microbiome profile to design appropriate treatment strategies for early stages of neurodegenerative disease. We view that in order to address neurodegenerative mechanisms of the gut, microbiome and metabolite profiles must be determined to pre-screen AD subjects prior to the design of specific, chronic titrations of gut microbiota with low-dose antibiotics. This represents an exciting treatment strategy designed to balance inflammatory microglial involvement in disease progression with an individual’s manifestation of AD as influenced by a coercive inflammatory gut.