ATLANTIC: SEPTEMBER 13 2022PACIFIC: SEPTEMBER 14/15 2022
Investigating and Managing Infectious Diseases in the Microbiome Era
prof Eric Pamer
Eric Pamer received his medical degree from Case Western Reserve University Medical School and completed clinical training in Internal Medicine and Infectious Diseases at UCSD Medical Center. He was a postdoctoral fellow with Charles E. Davis at UCSD, Maggie So at Scripps Research Institute, and Michael Bevan at the University of Washington. He then moved to Yale University and established a laboratory focusing on immune responses to microbial infection. In 2000, he moved his laboratory to Memorial Sloan-Kettering Cancer Center in New York where he was the Chief of Infectious Diseases, Head of the Division of Subspecialty Medicine, and Director of the Center for Microbes, Inflammation and Cancer, which focused on the role of the microbiome in the treatment of cancer. In 2019, Dr. Pamer moved to the University of Chicago to become the Director of the Duchossois Family Institute.
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
Despite extensive efforts to address it, the vastness of uncharacterized ‘dark matter’ microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in long-read and Hi-C technologies, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4,497 medium and high-quality metagenome assembled genomes, 1,708 of which were missing in short-read only analysis and with >28 N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3,413 strains that are unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of all strains were not represented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) not represented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal the significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
Genome Institute of Singapore
Promises for patients with disturbed gut-brain axis signalling: Does the intake of a probiotic mixture improve mental health of healthy subjects?
Gut microbiota modifications, such as by probiotics, have an effect on health and disease via the microbiota-gut-brain axis, amongst others. Several clinical studies have shown that probiotics might affect brain activity and behaviour in healthy subjects and subjects with disturbed gut-brain axis signalling. In this double-blinded, placebo-controlled crossover functional magnetic resonance imaging study, 22 healthy subjects (age 243 years, 6m/16f) underwent a probiotic intervention containing Bifidobacterium longum R0175, Lactobacillus helveticus R0052 and Lactiplantibacillus plantarum R1012 (in total at least 3×109 CFU/day) and a placebo intervention in randomised order for 4 weeks each, separated by a 4-week washout period. The probiotic intervention resulted in significantly altered brain response patterns (brain activity and functional connectivity) towards an acute emotional challenge and an acute mental arithmetic stress task, without effects on subjective stress ratings or cortisol response. Also, alterations in non-evoked resting state functional connectivity were observed upon probiotic intervention. Autonomic nervous system function was not significantly affected, neither at rest nor during stress, by the probiotic intervention compared to the placebo. Also, cognitive performance (assessed by Stroop) was not affected by the probiotic intervention. Apart from effects on brain function, also psychological symptoms, such as depression symptoms and sleep patterns, were slightly affected, even if none of the subjects experienced mental dysfunction at baseline. Other ratings, such as anxiety, perceived health, quality of life and perceived workload were not affected. Similarly, the probiotic intervention did not affect perceived stress nor the cortisol awakening response in non-evoked situations. In terms of signalling molecules, serotonin showed slightly higher baseline-corrected serum concentrations after probiotics compared to placebo, while brain-derived neurotrophic factor concentrations were not affected. Also, markers of intestinal damage or systemic inflammation were not affected. No substantial effects on the gut microbiota composition were observed. The probiotic intervention evoked distinct changes in brain function and subtle changes in psychological symptoms even in a healthy study population. These results give promising hints that patients with a disturbed gut-brain axis function could benefit from probiotic intake.
Nutrition-Gut-Brain Interactions Research Center, School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
The greenhouse phyllosphere microbiome and associations with introduced bumblebees and predatory mites
Greenhouses are highly productive environments in which conditions are regulated to optimize plant growth. The enclosed character of greenhouses usually results in reduced microbial diversity, while it is known that a diverse microbiome is important for plant health. Therefore, we explored the phyllosphere microbiome of tomatoes and strawberries grown in greenhouses. We observed that the microbiome of both crops was low in diversity and abundance, and varied considerably over time and space. Interestingly, the core taxa of tomatoes were Snodgrasella and Gilliamella, genera typically associated with bumblebees. The same amplicon sequence variants (ASVs) were found on reared bumblebees, indicating that bumblebees, present in the sampled greenhouses to pollinate flowers, had introduced and dispersed these bacteria in greenhouses. Overall, we found that 80% of plants contained bumblebee-associated taxa, and on these plants, bumblebee-associated reads accounted up to a quarter of reads on tomatoes and a tenth of reads on strawberries. Furthermore, predatory mites had been introduced for the control of spider mites. Their microbiome was composed of a diverse set of bacteria, which varied between batches ordered at different times. Still, identical ASVs were found on mites and crops and these belonged to the genera Sphingomonas, Staphylococcus, Methylobacterium and Pseudomonas. These new insights should now be further explored and utilized to diversify these ecosystems that are characterized by low diversity and abundancy of microbes.
University of Antwerp, Belgium
A faecal microbiota signature with high specificity for pancreatic cancer
Objective: Following recent evidence suggesting a role for the microbiome in PDAC etiology and progression, we explored the fecal and salivary microbiota as potential diagnostic biomarkers. Design: We applied shotgun metagenomic and 16S rRNA amplicon sequencing to samples from a Spanish case-control study (N=136), including 57 cases, 50 controls, and 29 chronic pancreatitis patients in the discovery phase, and from a German case-control study (N=76), in the validation phase. Results: Fecal metagenomic classifiers performed much better than saliva-based ones and identified PDAC cases with an accuracy of up to 0.84 AUROC based on a set of 27 microbial species, with consistent accuracy across early and late disease stages. Performance further improved to up to 0.94 AUROC when we combined our microbiome-based predictions with serum levels of carbohydrate antigen (CA) 19-9, the only current non-invasive, FDA-approved, low specificity PDAC diagnostic biomarker. Furthermore, a microbiota-based classification model constrained to PDAC-enriched species was highly disease-specific when validated against 25 publicly available metagenomic study populations for various health conditions (N=5,792). Both microbiome-based models had a high prediction accuracy on an external German validation population (N=76). Several fecal PDAC marker species were detectable in pancreatic tumor and non-tumor tissue using 16S rRNA sequencing and fluorescence in situ hybridization. Conclusion: Taken together, our results indicate that non-invasive, robust and specific fecal microbiota-based screening for the early detection of PDAC is feasible.
Link to OA paper: https://gut.bmj.com/content/71/7/1359
Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University and Heidelberg University Hospital, Heidelberg, Germany
Novel high-resolution targeted sequencing of the cervicovaginal microbiome
The cervicovaginal microbiome (CVM) plays a significant role in women’s cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. Results. We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes’ abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. Conclusions. CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions.
Link to OA paper: https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-021-01204-z
Mariano A. Molina
Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands