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Bibliography on: Human Microbiome

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ESP: PubMed Auto Bibliography 17 Sep 2020 at 01:53 Created: 

Human Microbiome

The human microbiome is the set of all microbes that live on or in humans. Together, a human body and its associated microbiomes constitute a human holobiont. Although a human holobiont is mostly mammal by weight, by cell count it is mostly microbial. The number of microbial genes in the associated microbiomes far outnumber the number of human genes in the human genome. Just as humans (and other multicellular eukaryotes) evolved in the constant presence of gravity, so they also evolved in the constant presence of microbes. Consequently, nearly every aspect of human biology has evolved to deal with, and to take advantage of, the existence of associated microbiota. In some cases, the absence of a "normal microbiome" can cause disease, which can be treated by the transplant of a correct microbiome from a healthy donor. For example, fecal transplants are an effective treatment for chronic diarrhea from over abundant Clostridium difficile bacteria in the gut.

Created with PubMed® Query: "human microbiome" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2020-09-16

Gupta VK, Kim M, Bakshi U, et al (2020)

A predictive index for health status using species-level gut microbiome profiling.

Nature communications, 11(1):4635 pii:10.1038/s41467-020-18476-8.

Providing insight into one's health status from a gut microbiome sample is an important clinical goal in current human microbiome research. Herein, we introduce the Gut Microbiome Health Index (GMHI), a biologically-interpretable mathematical formula for predicting the likelihood of disease independent of the clinical diagnosis. GMHI is formulated upon 50 microbial species associated with healthy gut ecosystems. These species are identified through a multi-study, integrative analysis on 4347 human stool metagenomes from 34 published studies across healthy and 12 different nonhealthy conditions, i.e., disease or abnormal bodyweight. When demonstrated on our population-scale meta-dataset, GMHI is the most robust and consistent predictor of disease presence (or absence) compared to α-diversity indices. Validation on 679 samples from 9 additional studies results in a balanced accuracy of 73.7% in distinguishing healthy from non-healthy groups. Our findings suggest that gut taxonomic signatures can predict health status, and highlight how data sharing efforts can provide broadly applicable discoveries.

RevDate: 2020-09-15
CmpDate: 2020-09-15

Blanchet L, Vitale R, van Vorstenbosch R, et al (2020)

Constructing bi-plots for random forest: Tutorial.

Analytica chimica acta, 1131:146-155.

Current technological developments have allowed for a significant increase and availability of data. Consequently, this has opened enormous opportunities for the machine learning and data science field, translating into the development of new algorithms in a wide range of applications in medical, biomedical, daily-life, and national security areas. Ensemble techniques are among the pillars of the machine learning field, and they can be defined as approaches in which multiple, complex, independent/uncorrelated, predictive models are subsequently combined by either averaging or voting to yield a higher model performance. Random forest (RF), a popular ensemble method, has been successfully applied in various domains due to its ability to build predictive models with high certainty and little necessity of model optimization. RF provides both a predictive model and an estimation of the variable importance. However, the estimation of the variable importance is based on thousands of trees, and therefore, it does not specify which variable is important for which sample group. The present study demonstrates an approach based on the pseudo-sample principle that allows for construction of bi-plots (i.e. spin plots) associated with RF models. The pseudo-sample principle for RF. is explained and demonstrated by using two simulated datasets, and three different types of real data, which include political sciences, food chemistry and the human microbiome data. The pseudo-sample bi-plots, associated with RF and its unsupervised version, allow for a versatile visualization of multivariate models, and the variable importance and the relation among them.

RevDate: 2020-09-12

Golovko G, Kamil K, Albayrak L, et al (2020)

Identification of multidimensional Boolean patterns in microbial communities.

Microbiome, 8(1):131 pii:10.1186/s40168-020-00853-6.

BACKGROUND: Identification of complex multidimensional interaction patterns within microbial communities is the key to understand, modulate, and design beneficial microbiomes. Every community has members that fulfill an essential function affecting multiple other community members through secondary metabolism. Since microbial community members are often simultaneously involved in multiple relations, not all interaction patterns for such microorganisms are expected to exhibit a visually uninterrupted pattern. As a result, such relations cannot be detected using traditional correlation, mutual information, principal coordinate analysis, or covariation-based network inference approaches.

RESULTS: We present a novel pattern-specific method to quantify the strength and estimate the statistical significance of two-dimensional co-presence, co-exclusion, and one-way relation patterns between abundance profiles of two organisms as well as extend this approach to allow search and visualize three-, four-, and higher dimensional patterns. The proposed approach has been tested using 2380 microbiome samples from the Human Microbiome Project resulting in body site-specific networks of statistically significant 2D patterns as well as revealed the presence of 3D patterns in the Human Microbiome Project data.

CONCLUSIONS: The presented study suggested that search for Boolean patterns in the microbial abundance data needs to be pattern specific. The reported presence of multidimensional patterns (which cannot be reduced to a combination of two-dimensional patterns) suggests that multidimensional (multi-organism) relations may play important roles in the organization of microbial communities, and their detection (and appropriate visualization) may lead to a deeper understanding of the organization and dynamics of microbial communities. Video Abstract.

RevDate: 2020-09-11

Mars RAT, Yang Y, Ward T, et al (2020)

Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome.

Cell pii:S0092-8674(20)30998-3 [Epub ahead of print].

The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders. Determining its mechanistic role in disease has been difficult due to apparent disconnects between animal and human studies and lack of an integrated multi-omics view of disease-specific physiological changes. We integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome, and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related variation in microbial composition and function. A subset of identified changes in microbial metabolites correspond to host physiological mechanisms that are relevant to IBS. By integrating multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with translational potential. Our study highlights the importance of longitudinal sampling and integrating complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases. VIDEO ABSTRACT.

RevDate: 2020-09-11

Taddese R, Garza DR, Ruiter LN, et al (2020)

Growth rate alterations of human colorectal cancer cells by 157 gut bacteria.

Gut microbes, 12(1):1-20.

Several bacteria in the human gut microbiome have been associated with colorectal cancer (CRC) by high-throughput screens. In some cases, molecular mechanisms have been elucidated that drive tumorigenesis, including bacterial membrane proteins or secreted molecules that interact with the human cancer cells. For most gut bacteria, however, it remains unknown if they enhance or inhibit cancer cell growth. Here, we screened bacteria-free supernatants (secretomes) and inactivated cells of over 150 cultured bacterial strains for their effects on cell growth. We observed family-level and strain-level effects that often differed between bacterial cells and secretomes, suggesting that different molecular mechanisms are at play. Secretomes of Bacteroidaceae, Enterobacteriaceae, and Erysipelotrichaceae bacteria enhanced cell growth, while most Fusobacteriaceae cells and secretomes inhibited growth, contrasting prior findings. In some bacteria, the presence of specific functional genes was associated with cell growth rates, including the virulence genes TcdA, TcdB in Clostridiales and FadA in Fusobacteriaceae, which both inhibited growth. Bacteroidaceae cells that enhanced growth were enriched for genes of the cobalamin synthesis pathway, while Fusobacteriaceae cells that inhibit growth were enriched for genes of the ethanolamine utilization pathway. Together, our results reveal how different gut bacteria have wide-ranging effects on cell growth, contribute a better understanding of the effects of the gut microbiome on host cells, and provide a valuable resource for identifying candidate target genes for potential microbiome-based diagnostics and treatment strategies.

RevDate: 2020-09-11

Koponen A, Pan G, Kivelä AM, et al (2020)

ORP2, a cholesterol transporter, regulates angiogenic signaling in endothelial cells.

FASEB journal : official publication of the Federation of American Societies for Experimental Biology [Epub ahead of print].

Oxysterol-binding protein-related protein 2 (ORP2), a cholesterol-PI(4,5)P2 countercurrent transporter, was recently identified as a novel regulator of plasma membrane (PM) cholesterol and PI(4,5)P2 content in HeLa cells. Here, we investigate the role of ORP2 in endothelial cell (EC) cholesterol and PI(4,5)P2 distribution, angiogenic signaling, and angiogenesis. We show that ORP2 knock-down modifies the distribution of cholesterol accessible to a D4H probe, between late endosomes and the PM. Depletion of ORP2 from ECs inhibits their angiogenic tube formation capacity, alters the gene expression of angiogenic signaling pathways such as VEGFR2, Akt, mTOR, eNOS, and Notch, and reduces EC migration, proliferation, and cell viability. We show that ORP2 regulates the integrity of VEGFR2 at the PM in a cholesterol-dependent manner, the depletion of ORP2 resulting in proteolytic cleavage by matrix metalloproteinases, and reduced activity of VEGFR2 and its downstream signaling. We demonstrate that ORP2 depletion increases the PM PI(4,5)P2 coincident with altered F-actin morphology, and reduces both VEGFR2 and cholesterol in buoyant raft membranes. Moreover, ORP2 knock-down suppresses the expression of the lipid raft-associated proteins VE-cadherin and caveolin-1. Analysis of the retinal microvasculature in ORP2 knock-out mice generated during this study demonstrates the subtle alterations of morphology characterized by reduced vessel length and increased density of tip cells and perpendicular sprouts. Gene expression changes in the retina suggest disturbance of sterol homeostasis, downregulation of VE-cadherin, and a putative disturbance of Notch signaling. Our data identifies ORP2 as a novel regulator of EC cholesterol and PI(4,5)P2 homeostasis and cholesterol-dependent angiogenic signaling.

RevDate: 2020-09-11

Feng Q, Lan X, Ji X, et al (2020)

Time series analysis of microbiome and metabolome at multiple body sites in steady long-term isolation confinement.

RevDate: 2020-09-10

Sharma A, SH Im (2020)

Special issue on the human microbiome: from symbiosis to therapy.

RevDate: 2020-09-10

Al KF, Daisley BA, Chanyi RM, et al (2020)

Oxalate-Degrading Bacillus subtilis Mitigates Urolithiasis in a Drosophila melanogaster Model.

mSphere, 5(5): pii:5/5/e00498-20.

Kidney stones affect nearly 10% of the population in North America and are associated with high morbidity and recurrence, yet novel prevention strategies are lacking. Recent evidence suggests that the human gut microbiota can influence the development of nephrolithiasis, although clinical trials have been limited and inconclusive in determining the potential for microbially based interventions. Here, we used an established Drosophila melanogaster model of urolithiasis as a high-throughput screening platform for evaluation of the therapeutic potential of oxalate-degrading bacteria in calcium oxalate (CaOx) nephrolithiasis. The results demonstrated that Bacillus subtilis 168 (BS168) is a promising candidate based on its preferential growth in high oxalate concentrations, its ability to stably colonize the D. melanogaster intestinal tract for as long as 5 days, and its prevention of oxalate-induced microbiota dysbiosis. Single-dose BS168 supplementation exerted beneficial effects on D. melanogaster for as long as 14 days, decreasing stone burden in dissected Malpighian tubules and fecal excreta while increasing survival and behavioral markers of health over those of nonsupplemented lithogenic controls. These findings were complemented by in vitro experiments using the established MDCK renal cell line, which demonstrated that BS168 pretreatment prevented increased CaOx crystal adhesion and aggregation. Taking our results together, this study supports the notion that BS168 can functionally reduce CaOx stone burden in vivo through its capacity for oxalate degradation. Given the favorable safety profile of many B. subtilis strains already used as digestive aids and in fermented foods, these findings suggest that BS168 could represent a novel therapeutic adjunct to reduce the incidence of recurrent CaOx nephrolithiasis in high-risk patients.IMPORTANCE Kidney stone disease is a morbid condition that is increasing in prevalence, with few nonsurgical treatment options. The majority of stones are composed of calcium oxalate. Unlike humans, some microbes can break down oxalate, suggesting that microbial therapeutics may provide a novel treatment for kidney stone patients. This study demonstrated that Bacillus subtilis 168 (BS168) decreased stone burden, improved health, and complemented the microbiota in a Drosophila melanogaster urolithiasis model, while not exacerbating calcium oxalate aggregation or adhesion to renal cells in vitro These results identify this bacterium as a candidate for ameliorating stone formation; given that other strains of B. subtilis are components of fermented foods and are used as probiotics for digestive health, strain 168 warrants testing in humans. With the severe burden that recurrent kidney stone disease imposes on patients and the health care system, this microbial therapeutic approach could provide an inexpensive therapeutic adjunct.

RevDate: 2020-09-09

Giangaspero A, Barlaam A, Pane S, et al (2020)

Accidental Nasal Myiasis Caused by Megaselia rufipes (Diptera: Phoridae) in a Child.

Journal of medical entomology pii:5903216 [Epub ahead of print].

A case of a nasal myiasis in a 3-yr-old Italian girl who was referred to Bambino Gesù Hospital in Rome, Italy, is reported. Larvae discharged with the nasal mucus were microscopically identified as Megaselia spp.; DNA barcoding analysis showed that they belonged to the 'scuttle fly' species Megaselia rufipes (Meigen). Based on the patient's history, she became infected when she played outside. This is the first report of myiasis in humans due to M. rufipes (Diptera: Phoridae).

RevDate: 2020-09-09

Federici S, Nobs SP, E Elinav (2020)

Phages and their potential to modulate the microbiome and immunity.

Cellular & molecular immunology pii:10.1038/s41423-020-00532-4 [Epub ahead of print].

Bacteriophages (hence termed phages) are viruses that target bacteria and have long been considered as potential future treatments against antibiotic-resistant bacterial infection. However, the molecular nature of phage interactions with bacteria and the human host has remained elusive for decades, limiting their therapeutic application. While many phages and their functional repertoires remain unknown, the advent of next-generation sequencing has increasingly enabled researchers to decode new lytic and lysogenic mechanisms by which they attack and destroy bacteria. Furthermore, the last decade has witnessed a renewed interest in the utilization of phages as therapeutic vectors and as a means of targeting pathogenic or commensal bacteria or inducing immunomodulation. Importantly, the narrow host range, immense antibacterial repertoire, and ease of manipulating phages may potentially allow for their use as targeted modulators of pathogenic, commensal and pathobiont members of the microbiome, thereby impacting mammalian physiology and immunity along mucosal surfaces in health and in microbiome-associated diseases. In this review, we aim to highlight recent advances in phage biology and how a mechanistic understanding of phage-bacteria-host interactions may facilitate the development of novel phage-based therapeutics. We provide an overview of the challenges of the therapeutic use of phages and how these could be addressed for future use of phages as specific modulators of the human microbiome in a variety of infectious and noncommunicable human diseases.

RevDate: 2020-09-05

Reyes-Gibby CC, Wang J, Zhang L, et al (2020)

Oral microbiome and onset of oral mucositis in patients with squamous cell carcinoma of the head and neck.

Cancer [Epub ahead of print].

BACKGROUND: Oral mucositis (OM) is a debilitating sequela for patients treated for squamous cell carcinoma of the head and neck (HNSCC). This study investigated whether oral microbial features before treatment or during treatment are associated with the time to onset of severe OM in patients with HNSCC.

METHODS: This was a cohort study of newly diagnosed patients with locoregional HNSCC who received chemotherapy with or without radiotherapy from April 2016 to September 2017. OM was based on the National Cancer Institute's Common Terminology Criteria for Adverse Events, version 4.0. The oral microbiome was characterized on the basis of the 16S ribosomal RNA V4 region with the Illumina platform. A mixture cure model was used to generate hazard ratios for the onset of severe OM.

RESULTS: Eighty-six percent of the patients developed OM (n = 57 [33 nonsevere cases and 24 severe cases]) with a median time to onset of OM of 21 days. With adjustments for age, sex, and smoking status, genera abundance was associated with the hazard for the onset of severe OM as follows: 1) at the baseline (n = 66), Cardiobacterium (P = .03) and Granulicatella (P = .04); 2) immediately before the development of OM (n = 57), Prevotella (P = .03), Fusobacterium (P = .03), and Streptococcus (P = .01); and 3) immediately before the development of severe OM (n = 24), Megasphaera (P = .0001) and Cardiobacterium (P = .03). There were no differences in α-diversity between the baseline samples and Human Microbiome Project data.

CONCLUSIONS: Changes in the abundance of genera over the course of treatment were associated with the onset of severe OM. The mechanism and therapeutic implications of these findings need to be investigated in future studies.

RevDate: 2020-09-05

García MG, Pérez-Cárceles MD, Osuna E, et al (2020)

The impact of the human microbiome in forensic sciences: A systematic review.

Applied and environmental microbiology pii:AEM.01451-20 [Epub ahead of print].

Numerous studies relate differences in microbial communities to human health and disease, however little is known about microbial changes that occur post mortem or the possible applications of microbiome analysis in the field of forensic science. The aim of this review was study the microbiome and its applications in forensic sciences, to determine the main lines of investigation that are emerging, as well as its possible contributions in the forensic field. A systematic review of the human microbiome in relation to forensic science was carried out following PRISMA guidelines. This study throws light on the role of microbiome research in the postmortem interval during the process of decomposition; identifying death caused by drowning or sudden death; locating the geographical location of death; establishing a connection between human microbiome and personal items, sexual contact, and the identification of individuals. Actinomycetaceae, Bacteroidaceae, Alcaligenaceae and Bacilli play an important role in determining the postmortem interval. Aeromonas can be used to determine the cause of death, and Corynebacterium or Helicobacter pylori to ascertain personal identity or geographical location. Several studies point to a promising future for microbiome analysis in the different fields of forensic science, opening up an important new area of research.

RevDate: 2020-09-04

Suojanen LU, Ahola AJ, Kupila S, et al (2020)

Effectiveness of a web-based real-life weight management program: Study design, methods, and participants' baseline characteristics.

Contemporary clinical trials communications, 19:100638 pii:100638.

Obesity is an important public health concern with limited effective treatment options. Internet-based technologies offer a cost-effective means to treat obesity. However, most of the online programs have been of short duration, have focused on a limited number of treatment modalities, and have not utilized the potential of coaching as part of the intervention. In this paper, we present the design, methods and participants' baseline characteristics in a real-life internet-based weight management program. Healthy Weight Coaching (HWC) is a 12-month web-based intervention for the management of obesity. The program is based on the Acceptance and Commitment Therapy and includes themes important for weight loss, including diet, physical activity, psychological factors, and sleep. In addition to the automated, interactive program, a personal coach is allocated to each participant. The participants are nationally enrolled through referrals from primary care, occupational health, hospitals, and private health care units. Adult individuals with BMI ≥25 kg/m2 without severe complications are included. On a weekly basis, participants submit their weight logs, training sessions, and lifestyle targets to the internet portal and are scheduled to have online discussions with their coaches 26 times over the course of a year. Questionnaires on lifestyle, diet, physical activity, psychological factors, sleep, and quality of life are completed at baseline, 3, 6, 9, and 12 months, and thereafter yearly until 5 years. Additionally, log data on the use of the service and discussions with the coach are collected. The main outcome is weight change from baseline to 12 months. Recruitment to the HWC is ongoing. Baseline data of the participants recruited between Oct 2016 and Mar 2019 (n = 1189) are provided. This research will bring insight into how internet-based technologies can be implemented in the virtual management of obesity.

Trial registration: The trial is registered at clinicaltrials.cov (Clinical Trials Identifier NCT04019249).

RevDate: 2020-09-04

Katongole P, Sande OJ, Joloba M, et al (2020)

The human microbiome and its link in prostate cancer risk and pathogenesis.

Infectious agents and cancer, 15:53 pii:319.

There is growing evidence of the microbiome's role in human health and disease since the human microbiome project. The microbiome plays a vital role in influencing cancer risk and pathogenesis. Several studies indicate microbial pathogens to account for over 15-20% of all cancers. Furthermore, the interaction of the microbiota, especially the gut microbiota in influencing response to chemotherapy, immunotherapy, and radiotherapy remains an area of active research. Certain microbial species have been linked to the improved clinical outcome when on different cancer therapies. The recent discovery of the urinary microbiome has enabled the study to understand its connection to genitourinary malignancies, especially prostate cancer. Prostate cancer is the second most common cancer in males worldwide. Therefore research into understanding the factors and mechanisms associated with prostate cancer etiology, pathogenesis, and disease progression is of utmost importance. In this review, we explore the current literature concerning the link between the gut and urinary microbiome and prostate cancer risk and pathogenesis.

RevDate: 2020-09-04

Jiang Q, Kainulainen V, Stamatova I, et al (2020)

Mouthwash Effects on LGG-Integrated Experimental Oral Biofilms.

Dentistry journal, 8(3): pii:dj8030096.

In order to investigate the effects of mouthwashes on oral biofilms with probiotics, we compared in biofilms the susceptibility to mouthwashes of probiotic Lactobacillus rhamnosus GG (LGG) and oral pathogens Streptococcus mutans, Streptococcus sanguinis, and Candida albicans. We also evaluated these pathogens' susceptibility to the mouthwashes and their recovery after mouthwash-rinsing in biofilms with/without LGG. First, 1-day-/3-day-old LGG-integrated multi-species biofilms were exposed for 1 min to mouthwashes containing chlorhexidine, essential oils, or amine fluoride/stannous fluoride. Cells were plate-counted and relative survival rates (RSRs) of LGG and pathogens calculated. Second, 1-day-/3-day-old multispecies biofilms with and without LGG were exposed for 1 min to mouthwashes; cells were plate-counted and the pathogens' RSRs were calculated. Third, 1-day-old biofilms were treated for 1 min with mouthwashes. Cells were plate-counted immediately and after 2-day cultivation. Recovery rates of pathogens were calculated and compared between biofilms with/without LGG. Live/Dead® staining served for structural analyses. Our results showed that RSRs of LGG were insignificantly smaller than those of pathogens in both 1-day and 3-day biofilms. No significant differences appeared in pathogens' RSRs and recovery rates after treatment between biofilms with/without LGG. To conclude, biofilm LGG was susceptible to the mouthwashes; but biofilm LGG altered neither the mouthwash effects on oral pathogens nor affected their recovery.

RevDate: 2020-09-03

Odogwu NM, Olayemi OO, AO Omigbodun (2020)

The vaginal microbiome of sub-Saharan African women: revealing important gaps in the era of next-generation sequencing.

PeerJ, 8:e9684 pii:9684.

Accurate characterization of the vaginal microbiome remains a fundamental goal of the Human Microbiome project (HMP). For over a decade, this goal has been made possible deploying high-throughput next generation sequencing technologies (NGS), which indeed has revolutionized medical research and enabled large-scale genomic studies. The 16S rRNA marker-gene survey is the most commonly explored approach for vaginal microbial community studies. With this approach, prior studies have elucidated substantial variations in the vaginal microbiome of women from different ethnicities. This review provides a comprehensive account of studies that have deployed this approach to describe the vaginal microbiota of African women in health and disease. On the basis of published data, the few studies reported from the African population are mainly in non-pregnant post pubertal women and calls for more detailed studies in pregnant and postnatal cohorts. We provide insight on the use of more sophisticated cutting-edge technologies in characterizing the vaginal microbiome. These technologies offer high-resolution detection of vaginal microbiome variations and community functional capabilities, which can shed light into several discrepancies observed in the vaginal microbiota of African women in an African population versus women of African descent in the diaspora.

RevDate: 2020-09-03

Halley A, Leonetti A, Gregori A, et al (2020)

The Role of the Microbiome in Cancer and Therapy Efficacy: Focus on Lung Cancer.

Anticancer research, 40(9):4807-4818.

The microbiome is extremely important for human health; more recently its role in the context of cancer became clear. Microbial effects range from enhancing cancer immunity and cancer therapy efficacy, to promoting cancer progression and inhibiting treatment efficacy. These broad implications led researchers to investigate these specific interactions, as well as how modification of the microbiome can improve cancer survival and treatment efficacy. While these interactions are better established for cancers such as gastric cancer, they are far less understood in others. As non-small cell lung cancer (NSCLC) makes up the majority of lung cancer cases, and is among the top causes of cancer deaths worldwide, understanding the mechanisms by which the microbiome may impact progression and treatment is crucial to improve patient survival and treatment response. A literature review was conducted to reveal the crosslink between human microbiome and lung cancer. This includes immune priming, induction of pro- or anti-tumor response, and the local effects of intra-tumoral microbiota. Overall, this is a complex multifactorial relationship, and there are broad implications as to how this knowledge can improve cancer treatment. Solutions include manipulation of the microbiome using probiotics, bacterial vaccines and antibiotics. Bacteria biomarkers may also be used as a diagnostic tool.

RevDate: 2020-09-02

Ristori MV, Mortera SL, Marzano V, et al (2020)

Proteomics and Metabolomics Approaches towards a Functional Insight onto AUTISM Spectrum Disorders: Phenotype Stratification and Biomarker Discovery.

International journal of molecular sciences, 21(17): pii:ijms21176274.

Autism spectrum disorders (ASDs) are neurodevelopmental disorders characterized by behavioral alterations and currently affect about 1% of children. Significant genetic factors and mechanisms underline the causation of ASD. Indeed, many affected individuals are diagnosed with chromosomal abnormalities, submicroscopic deletions or duplications, single-gene disorders or variants. However, a range of metabolic abnormalities has been highlighted in many patients, by identifying biofluid metabolome and proteome profiles potentially usable as ASD biomarkers. Indeed, next-generation sequencing and other omics platforms, including proteomics and metabolomics, have uncovered early age disease biomarkers which may lead to novel diagnostic tools and treatment targets that may vary from patient to patient depending on the specific genomic and other omics findings. The progressive identification of new proteins and metabolites acting as biomarker candidates, combined with patient genetic and clinical data and environmental factors, including microbiota, would bring us towards advanced clinical decision support systems (CDSSs) assisted by machine learning models for advanced ASD-personalized medicine. Herein, we will discuss novel computational solutions to evaluate new proteome and metabolome ASD biomarker candidates, in terms of their recurrence in the reviewed literature and laboratory medicine feasibility. Moreover, the way to exploit CDSS, performed by artificial intelligence, is presented as an effective tool to integrate omics data to electronic health/medical records (EHR/EMR), hopefully acting as added value in the near future for the clinical management of ASD.

RevDate: 2020-09-02

Neckovic A, A H van Oorschot R, Szkuta B, et al (2020)

Challenges in Human Skin Microbial Profiling for Forensic Science: A Review.

Genes, 11(9): pii:genes11091015.

The human microbiome is comprised of the microbes that live on and within an individual, as well as immediately surrounding them. Microbial profiling may have forensic utility in the identification or association of individuals with criminal activities, using microbial signatures derived from a personal microbiome. This review highlights some important aspects of recent studies, many of which have revealed issues involving the effect of contamination of microbial samples from both technical and environmental sources and their impacts on microbiome research and the potential forensic applications of microbial profiling. It is imperative that these challenges be discussed and evaluated within a forensic context to better understand the future directions and potential applications of microbial profiling for human identification. It is necessary that the limitations identified be resolved prior to the adoption of microbial profiling, or, at a minimum, acknowledged by those applying this new approach.

RevDate: 2020-09-01

Martino C, Shenhav L, Marotz CA, et al (2020)

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics.

Nature biotechnology pii:10.1038/s41587-020-0660-7 [Epub ahead of print].

The translational power of human microbiome studies is limited by high interindividual variation. We describe a dimensionality reduction tool, compositional tensor factorization (CTF), that incorporates information from the same host across multiple samples to reveal patterns driving differences in microbial composition across phenotypes. CTF identifies robust patterns in sparse compositional datasets, allowing for the detection of microbial changes associated with specific phenotypes that are reproducible across datasets.

RevDate: 2020-09-01

Kostopoulos I, Elzinga J, Ottman N, et al (2020)

Akkermansia muciniphila uses human milk oligosaccharides to thrive in the early life conditions in vitro.

Scientific reports, 10(1):14330 pii:10.1038/s41598-020-71113-8.

Akkermansia muciniphila is a well-studied anaerobic bacterium specialized in mucus degradation and associated with human health. Because of the structural resemblance of mucus glycans and free human milk oligosaccharides (HMOs), we studied the ability of A. muciniphila to utilize human milk oligosaccharides. We found that A. muciniphila was able to grow on human milk and degrade HMOs. Analyses of the proteome of A. muciniphila indicated that key-glycan degrading enzymes were expressed when the bacterium was grown on human milk. Our results display the functionality of the key-glycan degrading enzymes (α-L-fucosidases, β-galactosidases, exo-α-sialidases and β-acetylhexosaminidases) to degrade the HMO-structures 2'-FL, LNT, lactose, and LNT2. The hydrolysation of the host-derived glycan structures allows A. muciniphila to promote syntrophy with other beneficial bacteria, contributing in that way to a microbial ecological network in the gut. Thus, the capacity of A. muciniphila to utilize human milk will enable its survival in the early life intestine and colonization of the mucosal layer in early life, warranting later life mucosal and metabolic health.

RevDate: 2020-08-31

Ruokolainen L, Fyhrquist N, Laatikainen T, et al (2020)

Immune-microbiota interaction in Finnish and Russian Karelia young people with high and low allergy prevalence.

Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology [Epub ahead of print].

BACKGROUND: After the Second World War, the populations living in the Karelia area were strictly divided by the border between Finland and Russia. This resulted in the development of starkly different lifestyles, standard of living and exposure to the environment. The remarkable allergy disparity, both in children and adults, calls for immunological explanations.

METHODS: Young people, aged 15-20 years, in the Finnish (n = 69) and Russian (n = 75) Karelia were studied. Sensitisation to common allergens was much more common in the Finnish subjects compared with Russians, e.g. to birch pollen 35% vs 7%. The differences of gene expression (transcriptome) were studied from the blood mononuclear cells (PBMC) in both populations and related to skin and nasal epithelium microbiota. Genome-wide association analysis was used to evaluate the impact of genetic variation between the two populations on the studied phenotype. Findings Pathways of innate immunity were suppressed among Russians compared to Finns, when the function of 261 differentially expressed genes was explored. Differences in the gene expression paralleled the skin and nasal epithelium microbiota disparity, and the network of genes and microbiota was richer and more diverse in the Russian subjects. Moreover, high Acinetobacter abundance in Russians correlated with suppression of innate immune response. The genetic differences between the Finnish and Russian populations did not explain differences in allergy phenotype. Interpretation Young populations living in the Finnish and Russian Karelia host contrasting skin and nasal epithelium microbiota and show marked differences in genome-wide gene expression. The rich gene-microbe network in Russians seems to result in a better-balanced innate immunity and associate with low allergy prevalence.

RevDate: 2020-08-31

Miossec MJ, Valenzuela SL, Pérez-Losada M, et al (2020)

Evaluation of computational methods for human microbiome analysis using simulated data.

PeerJ, 8:e9688 pii:9688.

Background: Our understanding of the composition, function, and health implications of human microbiota has been advanced by high-throughput sequencing and the development of new genomic analyses. However, trade-offs among alternative strategies for the acquisition and analysis of sequence data remain understudied.

Methods: We assessed eight popular taxonomic profiling pipelines; MetaPhlAn2, metaMix, PathoScope 2.0, Sigma, Kraken, ConStrains, Centrifuge and Taxator-tk, against a battery of metagenomic datasets simulated from real data. The metagenomic datasets were modeled on 426 complete or permanent draft genomes stored in the Human Oral Microbiome Database and were designed to simulate various experimental conditions, both in the design of a putative experiment; read length (75-1,000 bp reads), sequence depth (100K-10M), and in metagenomic composition; number of species present (10, 100, 426), species distribution. The sensitivity and specificity of each of the pipelines under various scenarios were measured. We also estimated the relative root mean square error and average relative error to assess the abundance estimates produced by different methods. Additional datasets were generated for five of the pipelines to simulate the presence within a metagenome of an unreferenced species, closely related to other referenced species. Additional datasets were also generated in order to measure computational time on datasets of ever-increasing sequencing depth (up to 6 × 107).

Results: Testing of eight pipelines against 144 simulated metagenomic datasets initially produced 1,104 discrete results. Pipelines using a marker gene strategy; MetaPhlAn2 and ConStrains, were overall less sensitive, than other pipelines; with the notable exception of Taxator-tk. This difference in sensitivity was largely made up in terms of runtime, significantly lower than more sensitive pipelines that rely on whole-genome alignments such as PathoScope2.0. However, pipelines that used strategies to speed-up alignment between genomic references and metagenomic reads, such as kmerization, were able to combine both high sensitivity and low run time, as is the case with Kraken and Centrifuge. Absent species genomes in the database mostly led to assignment of reads to the most closely related species available in all pipelines. Our results therefore suggest that taxonomic profilers that use kmerization have largely superseded those that use gene markers, coupling low run times with high sensitivity and specificity. Taxonomic profilers using more time-consuming read reassignment, such as PathoScope 2.0, provided the most sensitive profiles under common metagenomic sequencing scenarios. All the results described and discussed in this paper can be visualized using the dedicated R Shiny application ( All of our datasets, pipelines and results are made available through the GitHub repository for future benchmarking.

RevDate: 2020-08-30

Fidel PL, Moyes D, Samaranayake L, et al (2020)

Interplay between oral immunity in HIV and the microbiome.

Oral diseases, 26 Suppl 1:59-68.

This Basic Science Workshop addressed the oral microbiome. At the 7th World Workshop on Oral Health & Disease in HIV/AIDS in India in 2014, some aspects of the human microbiome were discussed, and research questions formulated. Since that time, there have been major advances in technology, which have stimulated a number of publications on many aspects of the human microbiome, including the oral cavity. This workshop aimed to summarize current understanding of the "normal" microbiome of the oral cavity compared to that during HIV infection, and how oral immune factors and other clinical variables alter or control the oral microbiome. An important question is whether successful treatment with anti-retroviral therapy, which leads to a significant drop in viral loads and immune reconstitution, is associated with any change or recovery of the oral microbiome. Additionally, the workshop addressed the issue of which parameters are most appropriate/correct to evaluate the oral microbiome and how clinically relevant are shifts/changes in the oral microbiome. The workshop evaluated current knowledge in five research areas related to five basic questions and identified further topics where further research is required.

RevDate: 2020-08-27

Bilen M (2020)

Strategies and advancements in human microbiome description and the importance of culturomics.

Microbial pathogenesis pii:S0882-4010(20)30826-3 [Epub ahead of print].

The human microbiota gained a big interest among the scientific community with numerous studies being performed to better understand its role in health and diseases. Even with all the success achieved in studying the bacterial populations at the different body sites and its interaction among each other and with the host, some links remain missing and might have therapeutic benefits. In this review, we summarize the main means used for bacterial identification, human microbiota description and the role of culturomics in leading the way towards the development of new bacterio-therapeutic approaches.

RevDate: 2020-08-27

Lahtinen P, Jalanka J, Hartikainen A, et al (2020)

Letter: faecal microbiota transplantation for irritable bowel syndrome-room for improvement. Authors' reply.

Alimentary pharmacology & therapeutics, 52(5):925-926.

RevDate: 2020-08-27

Griffiths JC, De Vries J, McBurney MI, et al (2020)

Measuring health promotion: translating science into policy.

European journal of nutrition pii:10.1007/s00394-020-02359-1 [Epub ahead of print].

Commonly, it is the end of life when our health is deteriorating, that many will make drastic lifestyle changes to improve their quality of life. However, it is increasingly recognized that bringing good health-promoting behaviors into practice as early in life as possible has the most significant impact across the maximal healthspan. The WHO has brought clarity to health promotion over the last fifteen years, always centering on language relating to a process of enabling people to increase control over, and to improve, their physical, mental and social health. A good healthspan is not just freedom from morbidity and mortality, it is that joie de vivre ("joy of living") that should accompany every day of our lifespan. Therefore, health promotion includes not only the health sector, but also needs individual commitment to achieve that target of a healthspan aligned with the lifespan. This paper explores health promotion and health literacy, and how to design appropriate nutritional studies to characterize contributors to a positive health outcome, the role the human microbiome plays in promoting health and addressing and alleviating morbidity and diseases, and finally how to characterize phenotypic flexibility and a physiologic resilience that we must maintain as our structural and functional systems are bombarded with the insults and perturbations of life.

RevDate: 2020-08-27

Khazaei T, Williams RL, Bogatyrev SR, et al (2020)

Metabolic multistability and hysteresis in a model aerobe-anaerobe microbiome community.

Science advances, 6(33):eaba0353 pii:aba0353.

Major changes in the microbiome are associated with health and disease. Some microbiome states persist despite seemingly unfavorable conditions, such as the proliferation of aerobe-anaerobe communities in oxygen-exposed environments in wound infections or small intestinal bacterial overgrowth. Mechanisms underlying transitions into and persistence of these states remain unclear. Using two microbial taxa relevant to the human microbiome, we combine genome-scale mathematical modeling, bioreactor experiments, transcriptomics, and dynamical systems theory to show that multistability and hysteresis (MSH) is a mechanism describing the shift from an aerobe-dominated state to a resilient, paradoxically persistent aerobe-anaerobe state. We examine the impact of changing oxygen and nutrient regimes and identify changes in metabolism and gene expression that lead to MSH and associated multi-stable states. In such systems, conceptual causation-correlation connections break and MSH must be used for analysis. Using MSH to analyze microbiome dynamics will improve our conceptual understanding of stability of microbiome states and transitions between states.

RevDate: 2020-08-27

Wagner Mackenzie B, West AG, Waite DW, et al (2020)

A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis.

Frontiers in cellular and infection microbiology, 10:398.

Human microbiome studies remain focused on bacteria, as they comprise the dominant component of the microbiota. Recent advances in sequencing technology and optimization of amplicon sequencing protocols have allowed the description of other members of the microbiome, including eukaryotes (fungi) and, most recently, archaea. There are no known human-associated archaeal pathogens. Their diversity and contribution to health and chronic respiratory diseases, such as chronic rhinosinusitis (CRS), are unknown. Patients with CRS suffer from long-term sinus infections, and while the microbiota is hypothesized to play a role in its pathogenesis, the exact mechanism is poorly understood. In this cross-sectional study, we applied a recently optimized protocol to describe the prevalence, diversity and abundance of archaea in swab samples from the middle meatus of 60 individuals with and without CRS. A nested PCR approach was used to amplify the archaeal 16S rRNA gene for sequencing, and bacterial and archaeal load (also based on 16S rRNA genes) were estimated using Droplet Digital™ PCR (ddPCR). A total of 16 archaeal amplicon sequence variants (ASVs) from the phyla Euryarchaeota and Thaumarchaeota were identified. Archaeal ASVs were detected in 7/60 individuals, independent of disease state, whereas bacterial ASVs were detected in 60/60. Bacteria were also significantly more abundant than archaea. The ddPCR method was more sensitive than amplicon sequencing at detecting archaeal DNA in samples. Phylogenetic trees were constructed to visualize the evolutionary relationships between archaeal ASVs, isolates and clones. ASVs were placed into phylogenetic clades containing an apparent paucity of human-associated reference sequences, revealing how little studied the human archaeome is. This is the largest study to date to examine the human respiratory-associated archaeome, and provides the first insights into the prevalence, diversity and abundance of archaea in the human sinuses.

RevDate: 2020-08-26

Bushin LB, Covington BC, Rued BE, et al (2020)

Discovery and Biosynthesis of Streptosactin, a Sactipeptide with an Alternative Topology Encoded by Commensal Bacteria in the Human Microbiome.

Journal of the American Chemical Society [Epub ahead of print].

Mammalian microbiomes encode thousands of biosynthetic gene clusters (BGCs) and represent a new frontier in natural product research. We recently found an abundance of quorum sensing-regulated BGCs in mammalian microbiome streptococci that code for ribosomally synthesized and post-translationally modified peptides (RiPPs) and contain one or more radical S-adenosylmethionine (RaS) enzymes, a versatile superfamily known for catalyzing some of the most unusual reactions in biology. In the current work, we target a wide-spread group of streptococcal RiPP BGCs and elucidate both the reaction carried out by its encoded RaS enzyme and identify its peptide natural product, which we name streptosactin. Streptosactin is the first sactipeptide identified from Streptococcus spp.; it contains two sequential four amino acid sactionine macrocycles, an unusual topology for this compound family. Bioactivity assays reveal potent but narrow-spectrum activity against the producing strain and its closest relatives that carry the same BGC, suggesting streptosactin may be a long-suspected fratricidal agent of Streptococcus thermophilus. Our results highlight mammalian streptococci as a rich source of unusual enzymatic chemistries and bioactive natural products.

RevDate: 2020-08-27

Li WZ, Stirling K, Yang JJ, et al (2020)

Gut microbiota and diabetes: From correlation to causality and mechanism.

World journal of diabetes, 11(7):293-308.

In this review, we summarize the recent microbiome studies related to diabetes disease and discuss the key findings that show the early emerging potential causal roles for diabetes. On a global scale, diabetes causes a significant negative impact to the health status of human populations. This review covers type 1 diabetes and type 2 diabetes. We examine promising studies which lead to a better understanding of the potential mechanism of microbiota in diabetes diseases. It appears that the human oral and gut microbiota are deeply interdigitated with diabetes. It is that simple. Recent studies of the human microbiome are capturing the attention of scientists and healthcare practitioners worldwide by focusing on the interplay of gut microbiome and diabetes. These studies focus on the role and the potential impact of intestinal microflora in diabetes. We paint a clear picture of how strongly microbes are linked and associated, both positively and negatively, with the fundamental and essential parts of diabetes in humans. The microflora seems to have an endless capacity to impact and transform diabetes. We conclude that there is clear and growing evidence of a close relationship between the microbiota and diabetes and this is worthy of future investments and research efforts.

RevDate: 2020-08-26

Jalanka J, Cheng J, Hiippala K, et al (2020)

Colonic Mucosal Microbiota and Association of Bacterial Taxa with the Expression of Host Antimicrobial Peptides in Pediatric Ulcerative Colitis.

International journal of molecular sciences, 21(17): pii:ijms21176044.

Inflammatory bowel diseases (IBD), ulcerative colitis (UC) and Crohn's disease (CD), are chronic debilitating disorders of unknown etiology. Over 200 genetic risk loci are associated with IBD, highlighting a key role for immunological and epithelial barrier functions. Environmental factors account for the growing incidence of IBD, and microbiota are considered as an important contributor. Microbiota dysbiosis can lead to a loss of tolerogenic immune effects and initiate or exacerbate inflammation. We aimed to study colonic mucosal microbiota and the expression of selected host genes in pediatric UC. We used high-throughput 16S rDNA sequencing to profile microbiota in colonic biopsies of pediatric UC patients (n = 26) and non-IBD controls (n = 27). The expression of 13 genes, including five for antimicrobial peptides, in parallel biopsies was assessed with qRT-PCR. The composition of microbiota between UC and non-IBD differed significantly (PCoA, p = 0.001). UC children had a decrease in Bacteroidetes and an increase in several family-level taxa including Peptostreptococcaceae and Enterobacteriaceae, which correlated negatively with the expression of antimicrobial peptides REG3G and DEFB1, respectively. Enterobacteriaceae correlated positively with the expression siderophore binding protein LCN2 and Betaproteobacteria negatively with DEFB4A expression. The results indicate that reciprocal interaction of epithelial microbiota and defense mechanisms play a role in UC.

RevDate: 2020-08-25

Nurgaziyev M, Sergazy S, Chulenbayeva L, et al (2020)


Georgian medical news.

Antibiotic resistance and its impact on human microbiome remains a global public health concern. Studies have shown that treatment with antibiotics leads to dramatic changes in composition and function of gut microbiome. This review focuses on the association between antibiotics use and its impact on gut microbiome of adults and children, gut microbiota metabolic interactions and presents the current understanding of the link between human gut microbiome and immune system.

RevDate: 2020-08-24

Dong M, Li L, Chen M, et al (2020)

Predictive analysis methods for human microbiome data with application to Parkinson's disease.

PloS one, 15(8):e0237779 pii:PONE-D-19-32701.

Microbiome data consists of operational taxonomic unit (OTU) counts characterized by zero-inflation, over-dispersion, and grouping structure among samples. Currently, statistical testing methods are commonly performed to identify OTUs that are associated with a phenotype. The limitations of statistical testing methods include that the validity of p-values/q-values depend sensitively on the correctness of models and that the statistical significance does not necessarily imply predictivity. Predictive analysis using methods such as LASSO is an alternative approach for identifying associated OTUs and for measuring the predictability of the phenotype variable with OTUs and other covariate variables. We investigate three strategies of performing predictive analysis: (1) LASSO: fitting a LASSO multinomial logistic regression model to all OTU counts with specific transformation; (2) screening+GLM: screening OTUs with q-values returned by fitting a GLMM to each OTU, then fitting a GLM model using a subset of selected OTUs; (3) screening+LASSO: fitting a LASSO to a subset of OTUs selected with GLMM. We have conducted empirical studies using three simulation datasets generated using Dirichlet-multinomial models and a real gut microbiome data related to Parkinson's disease to investigate the performance of the three strategies for predictive analysis. Our simulation studies show that the predictive performance of LASSO with appropriate variable transformation works remarkably well on zero-inflated data. Our results of real data analysis show that Parkinson's disease can be predicted based on selected OTUs after the binary transformation, age, and sex with high accuracy (Error Rate = 0.199, AUC = 0.872, AUPRC = 0.912). These results provide strong evidences of the relationship between Parkinson's disease and the gut microbiome.

RevDate: 2020-08-24

Kurian SM, Gordon S, Barrick B, et al (2020)

Feasibility and Comparison Study of Fecal Sample Collection Methods in Healthy Volunteers and Solid Organ Transplant Recipients Using 16S rRNA and Metagenomics Approaches.

Biopreservation and biobanking [Epub ahead of print].

The human microbiome encompasses a variety of microorganisms that change dynamically and are in close contact with the body. The microbiome influences health and homeostasis, as well as the immune system, and any significant change in this equilibrium (dysbiosis) triggers both acute and chronic health conditions. Microbiome research has surged, in part, due to advanced sequencing technologies enabling rapid, accurate, and cost-effective identification of the microbiome. A major prerequisite for stool sample collection to study the gut microbiome in longitudinal prospective studies requires standardized protocols that can be easily replicated. However, there are still significant bottlenecks to stool specimen collection that contribute to low patient retention rates in microbiome studies. These barriers are further exacerbated in solid organ transplant recipients where diarrhea is estimated to occur in up to half the patient population. We sought to test two relatively easy sample collection methods (fecal swab and wipes) and compare them to the more cumbersome "gold" standard collection method (scoop) using two different sequencing technologies (16S ribosomal RNA sequencing and shotgun metagenomics). Our comparison of the collection methods shows that both the swabs and the wipes are comparable to the scoop method in terms of bacterial abundance and diversity. The swabs, however, were closer in representation to the scoop and were easier to collect and process compared to the wipes. Potential contamination of the swab and the wipe samples by abundant skin commensals was low in our analysis. Comparison of the two sequencing technologies showed that they were complementary, and that 16S sequencing provided enough coverage to detect and differentiate between bacterial species identified in the collected samples. Our pilot study demonstrates that alternative collection methods for stool sampling are a viable option in clinical applications, such as organ transplant studies. The use of these methods may result in better patient retention recruitment rates in serial microbiome studies.

RevDate: 2020-08-22

Nava Lara RA, Beltrán JA, Brizuela CA, et al (2020)

Relevant Features of Polypharmacologic Human-Target Antimicrobials Discovered by Machine-Learning Techniques.

Pharmaceuticals (Basel, Switzerland), 13(9): pii:ph13090204.

Polypharmacologic human-targeted antimicrobials (polyHAM) are potentially useful in the treatment of complex human diseases where the microbiome is important (e.g., diabetes, hypertension). We previously reported a machine-learning approach to identify polyHAM from FDA-approved human targeted drugs using a heterologous approach (training with peptides and non-peptide compounds). Here we discover that polyHAM are more likely to be found among antimicrobials displaying a broad-spectrum antibiotic activity and that topological, but not chemical features, are most informative to classify this activity. A heterologous machine-learning approach was trained with broad-spectrum antimicrobials and tested with human metabolites; these metabolites were labeled as antimicrobials or non-antimicrobials based on a naïve text-mining approach. Human metabolites are not commonly recognized as antimicrobials yet circulate in the human body where microbes are found and our heterologous model was able to classify those with antimicrobial activity. These results provide the basis to develop applications aimed to design human diets that purposely alter metabolic compounds proportions as a way to control human microbiome.

RevDate: 2020-08-21

Sharma AK (2020)

Special Issue: Mining human microbiome bringing newer paradigms to anticancer therapeutics.

RevDate: 2020-08-21

Cafiero C, Re A, Pisconti S, et al (2020)

Dysbiosis in intestinal microbiome linked to fecal blood determined by direct hybridization.

3 Biotech, 10(8):358.

The important physiological and pathophysiological roles of intestinal human microbiome (HMB) in human health have been emerging, owing to the access to molecular biology techniques. Herein we evaluated, for the first time, the intestinal HMB through direct hybridization approach using n-counter flex DX technology which bypasses the amplification procedure currently applied by other technologies to study the human microbiome. To this purpose, a clinical study was carried out on fecal samples, recruiting both healthy volunteers (N-FOB) and subjects positive for occult blood (P-FOB). A relevant custom panel of 79 16S rRNA target gene was engineered and 32 of them displayed a variation between the two clusters of subjects. Our findings revealed that bacteria belonging to Proteobacteria have higher distribution in P-FOB describing dysbiosis. Similarly, Bacteroidetes and Firmicutes phylum display high distribution in P-FOB. Of interest, the presence of Clostridium difficile that belongs to Firmicutes phylum displayed about 70% of low presence in N-FOB compared to P-FOB subjects. Only one bacterium belonging to the Actinobacteria phylum, the Bifidobacterium bifidum, was present.

RevDate: 2020-08-20

Britton GJ, Contijoch EJ, Spindler MP, et al (2020)

Defined microbiota transplant restores Th17/RORγt+ regulatory T cell balance in mice colonized with inflammatory bowel disease microbiotas.

Proceedings of the National Academy of Sciences of the United States of America pii:1922189117 [Epub ahead of print].

The building evidence for the contribution of microbiota to human disease has spurred an effort to develop therapies that target the gut microbiota. This is particularly evident in inflammatory bowel diseases (IBDs), where clinical trials of fecal microbiota transplantation have shown some efficacy. To aid the development of novel microbiota-targeted therapies and to better understand the biology underpinning such treatments, we have used gnotobiotic mice to model microbiota manipulations in the context of microbiotas from humans with inflammatory bowel disease. Mice colonized with IBD donor-derived microbiotas exhibit a stereotypical set of phenotypes, characterized by abundant mucosal Th17 cells, a deficit in the tolerogenic RORγt+ regulatory T (Treg) cell subset, and susceptibility to disease in colitis models. Transplanting healthy donor-derived microbiotas into mice colonized with human IBD microbiotas led to induction of RORγt+ Treg cells, which was associated with an increase in the density of the microbiotas following transplant. Microbiota transplant reduced gut Th17 cells in mice colonized with a microbiota from a donor with Crohn's disease. By culturing strains from this microbiota and screening them in vivo, we identified a specific strain that potently induces Th17 cells. Microbiota transplants reduced the relative abundance of this strain in the gut microbiota, which was correlated with a reduction in Th17 cells and protection from colitis.

RevDate: 2020-08-21

Lamont EI, Hendrickson EL, McLean JS, et al (2020)

Complete Genome Sequence of Strain BB001, a Novel Epibiont Bacterium from the Candidate Phylum Saccharibacteria (TM7).

Microbiology resource announcements, 9(34): pii:9/34/e00810-20.

Strain BB001 is cultivated from the human oral cavity on its basibiont bacterial host Actinomyces sp. It is an ultrasmall bacterium with a reduced genome that grows obligately on its bacterial host. BB001 is the first member of human microbiome taxon 957.

RevDate: 2020-08-20

Yan R, Murphy M, Genoni A, et al (2020)

Does Fibre-fix provided to people with irritable bowel syndrome who are consuming a low FODMAP diet improve their gut health, gut microbiome, sleep and mental health? A double-blinded, randomised controlled trial.

BMJ open gastroenterology, 7(1):.

INTRODUCTION: A diet low in fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAP) is an effective way to reduce gut symptoms in people with irritable bowel syndrome (IBS). This diet reduces the intake of fermentable fibres, leading to changes of the gut microbiota and insufficient fermentation in the large bowel, resulting in reduced production of short-chain fatty acids (SCFAs), such as butyrate, which has unfavourable implications for gut health, sleep and mental health. This study will examine the effect of Fibre-fix, a supplement containing a mix of dietary fibres, on the human gut microbiome composition, fermentative capacity, sleep, quality of life (QOL) and mental health of people with IBS who consume a low FODMAP diet (LFD).

METHODS AND ANALYSIS: A randomised, double-blind, placebo-controlled, study design is proposed to examine whether Fibre-fix added to an existing LFD may help modulate gastrointestinal function, improve markers of sleep, mental health and promote QOL in patients with IBS. Participants will provide stool and blood samples, daily bowel symptoms diaries and 3-day diet records. Additionally, they will complete validated questionnaires relating to FODMAP intake, sleep, mental health and QOL before and after a 3-week intervention. Gut health will be assessed via faecal microbiome composition, faecal pH and SCFA levels. Alteration of sleep will be recorded using an actigraphy device worn by all participants over the whole study. Multivariate analysis will be used to examine the gut microbiome and repeated measures Analysis of variance (ANOVA) will be used for dependent variables from questionnaires related to bowel symptoms, stool type, sleep, mental health and QOL to assess the differences between intervention and control groups after adjustment for confounding variables.

ETHICS AND DISSEMINATION: Ethics approval was obtained from the Human Research Ethics Committee of Edith Cowan University (2019-00619-YAN). Results will be disseminated in peer-review journal publications, and conference presentations. Participants will be provided with a summary of findings once the study is completed. If Fibre-fix is shown to result in favourable changes in gut microbial composition, SCFA production, sleep and mental well-being without exacerbating symptoms, this will provide additional dietary management options for those with IBS following an LFD.


RevDate: 2020-08-20

Vidanaarachchi R, Shaw M, Tang SL, et al (2020)

IMPARO: inferring microbial interactions through parameter optimisation.

BMC molecular and cell biology, 21(Suppl 1):34 pii:10.1186/s12860-020-00269-y.

BACKGROUND: Microbial Interaction Networks (MINs) provide important information for understanding bacterial communities. MINs can be inferred by examining microbial abundance profiles. Abundance profiles are often interpreted with the Lotka Volterra model in research. However existing research fails to consider a biologically meaningful underlying mathematical model for MINs or to address the possibility of multiple solutions.

RESULTS: In this paper we present IMPARO, a method for inferring microbial interactions through parameter optimisation. We use biologically meaningful models for both the abundance profile, as well as the MIN. We show how multiple MINs could be inferred with similar reconstructed abundance profile accuracy, and argue that a unique solution is not always satisfactory. Using our method, we successfully inferred clear interactions in the gut microbiome which have been previously observed in in-vitro experiments.

CONCLUSIONS: IMPARO was used to successfully infer microbial interactions in human microbiome samples as well as in a varied set of simulated data. The work also highlights the importance of considering multiple solutions for MINs.

RevDate: 2020-08-18

Kari OK, Tavakoli S, Parkkila P, et al (2020)

Light-Activated Liposomes Coated with Hyaluronic Acid as a Potential Drug Delivery System.

Pharmaceutics, 12(8): pii:pharmaceutics12080763.

Light-activated liposomes permit site and time-specific drug delivery to ocular and systemic targets. We combined a light activation technology based on indocyanine green with a hyaluronic acid (HA) coating by synthesizing HA-lipid conjugates. HA is an endogenous vitreal polysaccharide and a potential targeting moiety to cluster of differentiation 44 (CD44)-expressing cells. Light-activated drug release from 100 nm HA-coated liposomes was functional in buffer, plasma, and vitreous samples. The HA-coating improved stability in plasma compared to polyethylene glycol (PEG)-coated liposomes. Liposomal protein coronas on HA- and PEG-coated liposomes after dynamic exposure to undiluted human plasma and porcine vitreous samples were hydrophilic and negatively charged, thicker in plasma (~5 nm hard, ~10 nm soft coronas) than in vitreous (~2 nm hard, ~3 nm soft coronas) samples. Their compositions were dependent on liposome formulation and surface charge in plasma but not in vitreous samples. Compared to the PEG coating, the HA-coated liposomes bound more proteins in vitreous samples and enriched proteins related to collagen interactions, possibly explaining their slightly reduced vitreal mobility. The properties of the most abundant proteins did not correlate with liposome size or charge, but included proteins with surfactant and immune system functions in plasma and vitreous samples. The HA-coated light-activated liposomes are a functional and promising alternative for intravenous and ocular drug delivery.

RevDate: 2020-08-18

Sun Y, Kong L, Wu G, et al (2020)

DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome.

Biomolecules, 10(8): pii:biom10081175.

The DNA phosphorothioate (PT) modification existing in many prokaryotes, including bacterial pathogens and commensals, confers multiple characteristics, including restricting gene transfer, influencing the global transcriptional response, and reducing fitness during exposure to chemical mediators of inflammation. While PT-containing bacteria have been investigated in a variety of environments, they have not been studied in the human microbiome. Here, we investigated the distribution of PT-harboring strains and verified their existence in the human microbiome. We found over 2000 PT gene-containing strains distributed in different body sites, especially in the gastrointestinal tract. PT-modifying genes are preferentially distributed within several genera, including Pseudomonas, Clostridioides, and Escherichia, with phylogenic diversities. We also assessed the PT modification patterns and found six new PT-linked dinucleotides (CpsG, CpsT, ApsG, TpsG, GpsC, ApsT) in human fecal DNA. To further investigate the PT in the human gut microbiome, we analyzed the abundance of PT-modifying genes and quantified the PT-linked dinucleotides in the fecal DNA. These results confirmed that human microbiome is a rich reservoir for PT-containing microbes and contains a wide variety of PT modification patterns.

RevDate: 2020-08-17

Lichota A, Gwozdzinski K, EM Szewczyk (2020)

Microbial Modulation of Coagulation Disorders in Venous Thromboembolism.

Journal of inflammation research, 13:387-400 pii:258839.

Venous thromboembolism (VTE), including deep vein thrombosis (DVT) and pulmonary embolism (PE), is the third leading cause of cardiovascular death in the world. Important risk factors of thrombosis include bed restraint, surgery, major trauma, long journeys, inflammation, pregnancy, and oral contraceptives, previous venous thromboembolism, cancer, and bacterial infections. Sepsis increases the risk of blood clot formation 2-20 times. In this review, we discussed various mechanisms related to the role of bacteria in venous thrombosis also taking into consideration the role of the human microbiome. Many known bacteria, such as Helicobacter pylori, Chlamydia pneumoniae, Mycoplasma pneumoniae, Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, and Escherichia coli, causing infections may increase the risk of thrombotic complications through platelet activation or may lead to an inflammatory reaction involving the fibrinolytic system. Additionally, the bacteria participate in the production of factors causing or increasing the risk of cardiovascular diseases. An example can be trimethylamine N-oxide (TMAO) but also uremic toxins (indoxyl sulfate), short-chain fatty acids (SCFA) phytoestrogens, and bile acids. Finally, we presented the involvement of many bacteria in the development of venous thromboembolism and other cardiovascular diseases.

RevDate: 2020-08-15

Bayar E, Bennett PR, Chan D, et al (2020)

The pregnancy microbiome and preterm birth.

Seminars in immunopathology pii:10.1007/s00281-020-00817-w [Epub ahead of print].

Preterm birth is a global health concern and continues to contribute to substantial neonatal morbidity and mortality despite advances in obstetric and neonatal care. The underlying aetiology is multi-factorial and remains incompletely understood. In this review, the complex interplay between the vaginal microbiome in pregnancy and its association with preterm birth is discussed in depth. Advances in the study of bacteriology and an improved understanding of the human microbiome have seen an improved awareness of the vaginal microbiota in both health and in disease.

RevDate: 2020-08-14

Farahani L, Tharakan T, Yap T, et al (2020)

The semen microbiome and its impact on sperm function and male fertility: A systematic review and meta-analysis.

Andrology [Epub ahead of print].

BACKGROUND: Male factor is attributable in up to 50% of cases of infertility. In-vitro studies demonstrate that bacteria can negatively impact sperm function. The use of next-generation sequencing (NGS) techniques have provided a better understanding of the human microbiome, and dysbiosis has been reported to impact health. Evidence regarding the impact of the semen microbiome on sperm function and fertility remains conflicting.

MATERIALS AND METHODS: A systematic search was conducted in accordance with the Preferred Reporting Items for Reviews and Meta-analysis (PRISMA) statement. The databases MEDLINE, OVID and PubMed were searched to identify English language studies related to the identification of bacteria in the semen of infertile and fertile men, between 1992-2019. 55 observational studies were included, with 51299 subjects. We included studies identifying bacteria using NGS, culture or polymerase chain reaction (PCR).

RESULTS: The semen microbiome (SM) was rich and diverse in both fertile and infertile men. Three NGS studies reported clustering of the seminal microbiome with a predominant species. Lactobacillus and Prevotella were dominant in respective clusters. Lactobacillus was associated with improvements in semen parameters. Prevotella appeared to exert a negative effect on sperm quality. Bacteriospermia negatively impacted sperm concentration and progressive motility (PM), and DNA fragmentation index (DFI) (MD 3.518,95%CI 0.907 to 6.129, p=0.008). There was an increased prevalence of Ureaplasma urealyticum(UU) in infertile men(OR 2.25, 95% CI 1.47-3.46). UU negatively impacted concentration and morphology. There was no difference in the prevalence of chlamydia trachomatis (CT) between fertile and infertile men and no significant impact on semen parameters. Enterococcus faecalis (EF) negatively impacted total motility and Mycoplasma hominis (MH) negatively impacted concentration, PM and morphology.

RevDate: 2020-08-14

Moran GP, N Al-Hebshi (2020)

Editorial: The Human Microbiome and Cancer.

Frontiers in microbiology, 11:1514.

RevDate: 2020-08-14

Yan Y, Nguyen LH, Franzosa EA, et al (2020)

Strain-level epidemiology of microbial communities and the human microbiome.

Genome medicine, 12(1):71 pii:10.1186/s13073-020-00765-y.

The biological importance and varied metabolic capabilities of specific microbial strains have long been established in the scientific community. Strains have, in the past, been largely defined and characterized based on microbial isolates. However, the emergence of new technologies and techniques has enabled assessments of their ecology and phenotypes within microbial communities and the human microbiome. While it is now more obvious how pathogenic strain variants are detrimental to human health, the consequences of subtle genetic variation in the microbiome have only recently been exposed. Here, we review the operational definitions of strains (e.g., genetic and structural variants) as they can now be identified from microbial communities using different high-throughput, often culture-independent techniques. We summarize the distribution and diversity of strains across the human body and their emerging links to health maintenance, disease risk and progression, and biochemical responses to perturbations, such as diet or drugs. We list methods for identifying, quantifying, and tracking strains, utilizing high-throughput sequencing along with other molecular and "culturomics" technologies. Finally, we discuss implications of population studies in bridging experimental gaps and leading to a better understanding of the health effects of strains in the human microbiome.

RevDate: 2020-08-13

Wang L, Chen F, Yang L, et al (2020)

[Role of nasal microbiome in chronic sinusitis].

Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology, head, and neck surgery, 34(5):474-477.

Chronic sinusitis is a common disease in otolaryngology head and neck surgery, but the pathogenesis is unknown. For a long time, we have used fungi, bacterial biofilms, superantigens, and low host immunity as the cause of chronic sinusitis. With the rapid development of molecular biology technology, especially the advancement of DNA sequencing technology, people's research on human microbiome is deeper. We gradually realize the role of bacterial community in chronic sinusitis. This review will describe the role of bacteria in chronic sinusitis from three aspects: the composition of nasal bacterial community, the relationship between bacterial community and inflammatory phenotype, and the role between bacteria-host interaction.

RevDate: 2020-08-13

McCracken BA, NM Garcia (2020)

Phylum Synergistetes in the oral cavity: A possible contributor to periodontal disease.

Anaerobe pii:S1075-9964(20)30106-2 [Epub ahead of print].

Microbial contributions to periodontal disease have been under renewed scrutiny with the advent of newer technologies to identify their presence and gene expression at the molecular level. Members of the phylum Synergistetes are some of the more recent bacteria to be associated with periodontal disease. Bacteria classified in this phylum can be found in a wide variety of habitats including both inside and outside of a mammalian host. Members of this phylum have been identified as part of the human microbiome. Indeed, many of the identified phylotypes have yet to be cultivated. Here we consider contributions of three named and formally described species to the oral microbial community and to pathogenesis of periodontal disease.

RevDate: 2020-08-13

Kim YY, Joh JS, JY Lee (2020)

Importance of microbial extracellular vesicle in the pathogenesis of asthma and chronic obstructive pulmonary disease and its diagnostic potential.

Asia Pacific allergy, 10(3):e25.

There are rising evidences of the human microbiome as a potentially influential player that is actively engaged in shaping the pathogenetic processes and other unresolved issues both in asthma and other chronic respiratory diseases, particularly of the airways. The biological components such as microbiome in inhaled air can induce immune dysfunction and inflammation, leading to inflammatory pulmonary disorders such as asthma and chronic obstructive pulmonary disease (COPD). Microbe-derived extracellular vesicles (EVs) with biologically active information or functions can reprogram their respective target cells and EV may have a role for the development of asthma and COPD. To evaluate the role of microbe-derived EV in the pathogenesis of asthma and COPD and its role in diagnosis, the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement method was used for the study. An electronic search was performed using PubMed, PubMed Central, and Embase up to 2020. EVs serve as an intercellular transporter of miRNAs for cell-to-cell communication in the lungs. Bacteria-derived EVs have distinctive characteristics in the lungs of patients with asthma and COPD compared to healthy controls. Furthermore, bacterial EV IgG antibody titers in serum were significantly higher in patients with asthma and COPD than in healthy controls, suggesting that antibacterial EV antibodies titers can be used as a diagnostic tool for lung disease. Taken together, microbial EVs and miRNAs have important roles in the pathogenesis of asthma and COPD and they can provide novel diagnostic biomarkers for asthma and COPD.

RevDate: 2020-08-13

Jiang X, Liu S, Zhang Y, et al (2020)

Free-Flow Isoelectric Focusing for comprehensive separation and analysis of human salivary microbiome for lung cancer.

Analytical chemistry [Epub ahead of print].

Human microbiome contains billions of microorganisms that play important roles in biological system and different diseases. Due to its complexity, conventional culture-independent technology may underestimate the value of low abundant bacteria, which calls for highly efficient method for its enrichment and comprehensive analysis. In this study, we developed a recycling free-flow isoelectric focusing (RFFIEF) method based electrophoresis method to separate salivary microbiome. First, we used E. coli (DH5α) as a model for RFFIEF method development, which was focused in a narrow pH range (0.38 pH unit). The recovery rate was 80.81% with 5.85% relative standard deviation (n=5). The optimized method was then adopted to separate the human salivary microbiome into 32 fractions, followed by 16S rRNA gene sequencing and metaproteomics analysis. After RFFIEF fractionation, we identified 508 bacterial genera, which increased by 225% on average (n=3) when compared to the results of before-fractionation. We further compared the compositional change of microbiome in the saliva of lung cancer group (n=22) and control group (n=21) through RFFIEF. Quantitative results demonstrated six bacterial genera were upregulated dramatically in lung cancer group, while two genera were downregulated. Through qPCR verification in an independent sample set (n = 48), we confirmed that genus Granulicatella was significantly upregulated in lung cancer group, whereas Pseudomonas was remarkably downregulated (p<0.001). RFFIEF is an efficient and reproducible technology to fractionate the microbiome for its comprehensive analysis, which can be further applied to the in-depth study of the complex microbiomes and contribute to the discovery of disease associated bacteria.

RevDate: 2020-08-12

Chen L, Collij V, Jaeger M, et al (2020)

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity.

Nature communications, 11(1):4018 pii:10.1038/s41467-020-17840-y.

The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease.

RevDate: 2020-08-11

Crimarco A, Springfield S, Petlura C, et al (2020)

A randomized crossover trial on the effect of plant-based compared with animal-based meat on trimethylamine-N-oxide and cardiovascular disease risk factors in generally healthy adults: Study With Appetizing Plantfood-Meat Eating Alternative Trial (SWAP-MEAT).

The American journal of clinical nutrition pii:5890315 [Epub ahead of print].

BACKGROUND: Despite the rising popularity of plant-based alternative meats, there is limited evidence of the health effects of these products.

OBJECTIVES: We aimed to compare the effect of consuming plant-based alternative meat (Plant) as opposed to animal meat (Animal) on health factors. The primary outcome was fasting serum trimethylamine-N-oxide (TMAO). Secondary outcomes included fasting insulin-like growth factor 1, lipids, glucose, insulin, blood pressure, and weight.

METHODS: SWAP-MEAT (The Study With Appetizing Plantfood-Meat Eating Alternatives Trial) was a single-site, randomized crossover trial with no washout period. Participants received Plant and Animal products, dietary counseling, lab assessments, microbiome assessments (16S), and anthropometric measurements. Participants were instructed to consume ≥2 servings/d of Plant compared with Animal for 8 wk each, while keeping all other foods and beverages as similar as possible between the 2 phases.

RESULTS: The 36 participants who provided complete data for both crossover phases included 67% women, were 69% Caucasian, had a mean ± SD age 50 ± 14 y, and BMI 28 ± 5 kg/m2. Mean ± SD servings per day were not different by intervention sequence: 2.5 ± 0.6 compared with 2.6 ± 0.7 for Plant and Animal, respectively (P = 0.76). Mean ± SEM TMAO concentrations were significantly lower overall for Plant (2.7 ± 0.3) than for Animal (4.7 ± 0.9) (P = 0.012), but a significant order effect was observed (P = 0.023). TMAO concentrations were significantly lower for Plant among the n = 18 who received Plant second (2.9 ± 0.4 compared with 6.4 ± 1.5, Plant compared with Animal, P = 0.007), but not for the n = 18 who received Plant first (2.5 ± 0.4 compared with 3.0 ± 0.6, Plant compared with Animal, P = 0.23). Exploratory analyses of the microbiome failed to reveal possible responder compared with nonresponder factors. Mean ± SEM LDL-cholesterol concentrations (109.9 ± 4.5 compared with 120.7 ± 4.5 mg/dL, P = 0.002) and weight (78.7 ± 3.0 compared with 79.6 ± 3.0 kg, P < 0.001) were lower during the Plant phase.

CONCLUSIONS: Among generally healthy adults, contrasting Plant with Animal intake, while keeping all other dietary components similar, the Plant products improved several cardiovascular disease risk factors, including TMAO; there were no adverse effects on risk factors from the Plant products.This trial was registered at as NCT03718988.

RevDate: 2020-08-11

Cairns J, Jokela R, Becks L, et al (2020)

Repeatable ecological dynamics govern the response of experimental communities to antibiotic pulse perturbation.

Nature ecology & evolution pii:10.1038/s41559-020-1272-9 [Epub ahead of print].

In an era of pervasive anthropogenic ecological disturbances, there is a pressing need to understand the factors that constitute community response and resilience. A detailed understanding of disturbance response needs to go beyond associations and incorporate features of disturbances, species traits, rapid evolution and dispersal. Multispecies microbial communities that experience antibiotic perturbation represent a key system with important medical dimensions. However, previous microbiome studies on this theme have relied on high-throughput sequencing data from uncultured species without the ability to explicitly account for the role of species traits and immigration. Here, we serially passage a 34-species defined bacterial community through different levels of pulse antibiotic disturbance, manipulating the presence or absence of species immigration. To understand the ecological community response measured using amplicon sequencing, we combine initial trait data measured for each species separately and metagenome sequencing data revealing adaptive mutations during the experiment. We found that the ecological community response was highly repeatable within the experimental treatments, which could be attributed in part to key species traits (antibiotic susceptibility and growth rate). Increasing antibiotic levels were also coupled with an increasing probability of species extinction, making species immigration critical for community resilience. Moreover, we detected signals of antibiotic-resistance evolution occurring within species at the same time scale, leaving evolutionary changes in communities despite recovery at the species compositional level. Together, these observations reveal a disturbance response that presents as classic species sorting, but is nevertheless accompanied by rapid within-species evolution.

RevDate: 2020-08-11

Sherrill-Mix S, Connors K, Aldrovandi GM, et al (2020)

A summary of the fifth annual Virology Education HIV Microbiome workshop.

AIDS research and human retroviruses [Epub ahead of print].

This year marked the fifth meeting of the International Workshop on Microbiome in HIV held at the NIH1-4. In the past year, appreciation for the interplay between the human microbiome and HIV infection has continued to grow. New studies presented here help clarify the role of the microbiome on chronic inflammation and vaccine design and reveal the interaction between the effects of genetics, environment, sexual practice and HIV infection on the microbiome. Further, reports on the development and clinical trials of microbiome-based therapeutic approaches investigate the potential of microbiome alterations to decrease the probability of acquisition/transmission or ameliorate sequellae of HIV. Essential to all studies is the continued development and standardization of best methods for data analysis and consistency across studies and approaches. The keynote address by Dr. Jacques Ravel focused on his work to improve the analysis and resolution of microbiome data.

RevDate: 2020-08-10

Méhes G, Roy A, Strakosas X, et al (2020)

Organic Microbial Electrochemical Transistor Monitoring Extracellular Electron Transfer.

Advanced science (Weinheim, Baden-Wurttemberg, Germany), 7(15):2000641 pii:ADVS1868.

Extracellular electron transfer (EET) denotes the process of microbial respiration with electron transfer to extracellular acceptors and has been exploited in a range of microbial electrochemical systems (MESs). To further understand EET and to optimize the performance of MESs, a better understanding of the dynamics at the microscale is needed. However, the real-time monitoring of EET at high spatiotemporal resolution would require sophisticated signal amplification. To amplify local EET signals, a miniaturized bioelectronic device, the so-called organic microbial electrochemical transistor (OMECT), is developed, which includes Shewanella oneidensis MR-1 integrated onto organic electrochemical transistors comprising poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) combined with poly(vinyl alcohol) (PVA). Bacteria are attached to the gate of the transistor by a chronoamperometric method and the successful attachment is confirmed by fluorescence microscopy. Monitoring EET with the OMECT configuration is achieved due to the inherent amplification of the transistor, revealing fast time-responses to lactate. The limits of detection when using microfabricated gates as charge collectors are also investigated. The work is a first step toward understanding and monitoring EET in highly confined spaces via microfabricated organic electronic devices, and it can be of importance to study exoelectrogens in microenvironments, such as those of the human microbiome.

RevDate: 2020-08-10

Chomicki G, Werner GDA, West SA, et al (2020)

Compartmentalization drives the evolution of symbiotic cooperation.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 375(1808):20190602.

Across the tree of life, hosts have evolved mechanisms to control and mediate interactions with symbiotic partners. We suggest that the evolution of physical structures that allow hosts to spatially separate symbionts, termed compartmentalization, is a common mechanism used by hosts. Such compartmentalization allows hosts to: (i) isolate symbionts and control their reproduction; (ii) reward cooperative symbionts and punish or stop interactions with non-cooperative symbionts; and (iii) reduce direct conflict among different symbionts strains in a single host. Compartmentalization has allowed hosts to increase the benefits that they obtain from symbiotic partners across a diversity of interactions, including legumes and rhizobia, plants and fungi, squid and Vibrio, insects and nutrient provisioning bacteria, plants and insects, and the human microbiome. In cases where compartmentalization has not evolved, we ask why not. We argue that when partners interact in a competitive hierarchy, or when hosts engage in partnerships which are less costly, compartmentalization is less likely to evolve. We conclude that compartmentalization is key to understanding the evolution of symbiotic cooperation. This article is part of the theme issue 'The role of the microbiome in host evolution'.

RevDate: 2020-08-10

Eggers S, Gennings C, Malecki KMC, et al (2020)

Exposure to environmental chemical mixtures is associated with nasal colonization by Staphylococcus aureus: NHANES 2001-2004.

Environmental research, 190:109994 pii:S0013-9351(20)30891-4 [Epub ahead of print].

BACKGROUND: Understanding the health effects of exposure to chemical mixtures is critically important given the broad range of concurrent exposures throughout the life-course. While investigations of environmental chemicals and components of the human microbiome are becoming more common, few have examined associations with chemical mixtures. This study assesses the association between exposure to mixtures of 66 different environmental chemicals and nasal colonization of Staphylococcus aureus (SA) and methicillin resistant SA (MRSA).

METHODS: Data came from the National Health and Nutrition Examination Survey (NHANES) 2001-2004. The analytical sample consists of 10,312 participants, age 6 years and older, subdivided into 8 groups with different chemical exposure mixtures. Within each of 6 chemical classes (metals, phthalates, polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs), polyfluorochemicals (PFCs), and phenols), weighted quantile sum (WQS) regression was used to analyze the joint association of the component compounds and nasal SA colonization. WQS was also used to assess the joint association of 3 chemical mixtures (metals, metal and PAHs, and metal and triclosan) and nasal MRSA colonization. All regression models were adjusted for confounders.

RESULTS: The analytical sample was between ages 6-85, slightly more female, and predominantly non-smokers. Prevalence of SA carriage was 29.2%, and MRSA colonization prevalence was 1.2%. Within each chemical class, odds of SA colonization increased statistically significantly with exposure to mixtures of metals (OR = 1.11, 95% CI = 1.02-1.20), phthalates (OR = 1.09, 95% CI = 1.04-1.14), and phenols (OR = 1.08, 95% CI = 1.01-1.15). Exposure to a mixture of metals combined with PAHs was also associated with increased odds of MRSA carriage (OR = 1.38, 95% CI = 1.02-1.86).

CONCLUSION: Results indicate an association between multiple environmental chemical mixtures and SA colonization, including MRSA. These findings support the need for further analysis of associations between chemical mixtures and SA colonization, as well as other components of the human microbiome.

RevDate: 2020-08-09

Tan Y, Shen J, Si T, et al (2020)

Engineered Live Biotherapeutics: Progress and Challenges.

Biotechnology journal [Epub ahead of print].

The human microbiome plays an important role in human health, from metabolism to immunity. In the last few decades, advances in synthetic biology have enabled scientists to design and engineer live microorganisms for therapeutic purposes. In this review, we outline major strategies for manipulating the microbiome, which include three emerging areas with promising therapeutic applications: engineered commensal bacteria, synthetic microbial consortia and targeted modulation by phages. Furthermore, we highlight the applications of engineered live biotherapeutics in treating a variety of human diseases, including pathogenic infections, metabolic disorders, inflammatory bowel disease and colorectal cancer. Finally, we provide an overview of the challenges and opportunities in the future development of engineered live biotherapeutics. This article is protected by copyright. All rights reserved.

RevDate: 2020-08-08

Tan GSE, Tay HL, Tan SH, et al (2020)

Gut Microbiota Modulation: Implications for Infection Control and Antimicrobial Stewardship.

Advances in therapy pii:10.1007/s12325-020-01458-z [Epub ahead of print].

The human microbiome comprises a complex ecosystem of microbial communities that exist within the human body, the largest and most diverse of which are found within the human intestine. It has been increasingly implicated in human health and diseases, demonstrably playing a critical role in influencing host immune response, protection against pathogen overgrowth, biosynthesis, and metabolism. As our understanding of the links between the gut microbiota with host immunity and infectious diseases deepens, there is a greater need to incorporate methods of modulating it as a means of therapy or infection prevention in daily clinical practice. Traditional antimicrobial stewardship principles have been evaluated to assess their impact on the gut microbiota diversity and the consequent repercussions, taking into consideration antibiotic pharmacokinetic and pharmacodynamic properties. Novel strategies of selective digestive decontamination and fecal microbiota transplantation to regulate the gut microbiota have also been tested in different conditions with variable results. This review seeks to provide an overview of the available literature on the modulation of the gut microbiota and its implications for infection control and antimicrobial stewardship. With increased understanding, gut microbiota profiling through metataxonomic analysis may provide further insight into modulating microbial communities in the context of infection prevention and control.

RevDate: 2020-08-07

Kantonen J, Mahzabin S, Mäyränpää MI, et al (2020)

Neuropathologic features of four autopsied COVID-19 patients.

Published descriptions of the neuropathological features of COVID-19 patients have been controversial, ranging from only modest or no pathology to severe hypoxic and hemorrhagic phenotypes, thrombotic complications, acute disseminated encephalomyelitis-like changes, and encephalitis and meningitis. Here we describe the neuropathological findings of four COVID-19-positive patients autopsied at the Helsinki University Hospital during the spring of 2020. While three of the patients (age range 63-90) exhibited merely mild to moderate hypoxia-associated changes, one 38-year-old subject with obesity, diabetes (type 2), Parkinson's disease, and a very severe clinical course was found to have severe ischemic injury, abundant microhemorrhages and enlarged perivascular spaces most pronounced in the white matter and deep gray matter. The pattern of ischemic changes suggested a defect in microcirculation. In addition, a few small perivascular white matter lesions, with macrophages engulfing myelin, were found. No signs of encephalitis or meningitis were detected in any of the patients. When conducting RT-PCR and immunohistochemical analyses of brain tissue we could not demonstrate in any of the patients marked injury or presence of SARS-CoV2 in the olfactory epithelium, olfactory bulbs, or brain areas responsible for respiratory control. In conclusion, our small autopsy series demonstrates various hypoxia-associated neuropathological features in COVID-19 patients, but no evidence of neurotropism or meningitis/encephalitis.

RevDate: 2020-08-07

Jouhten H, Ronkainen A, Aakko J, et al (2020)

Cultivation and Genomics Prove Long-Term Colonization of Donor's Bifidobacteria in Recurrent Clostridioides difficile Patients Treated With Fecal Microbiota Transplantation.

Frontiers in microbiology, 11:1663.

Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridioides difficile infection (rCDI) and it's also considered for treating other indications. Metagenomic studies have indicated that commensal donor bacteria may colonize FMT recipients, but cultivation has not been employed to verify strain-level colonization. We combined molecular profiling of Bifidobacterium populations with cultivation, molecular typing, and whole genome sequencing (WGS) to isolate and identify strains that were transferred from donors to recipients. Several Bifidobacterium strains from two donors were recovered from 13 recipients during the 1-year follow-up period after FMT. The strain identities were confirmed by WGS and comparative genomics. Our results show that specific donor-derived bifidobacteria can colonize rCDI patients for at least 1 year, and thus FMT may have long-term consequences for the recipient's microbiota and health. Conceptually, we demonstrate that FMT trials combined with microbial profiling can be used as a platform for discovering and isolating commensal strains with proven colonization capacity for potential therapeutic use.

RevDate: 2020-08-06

Sierra MA, Li Q, Pushalkar S, et al (2020)

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community.

Genes, 11(8): pii:genes11080878.

There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.

RevDate: 2020-08-06

Afzal M, Mazhar SF, Sana S, et al (2020)

Neurological and cognitive significance of probiotics: a holy grail deciding individual personality.

Future microbiology [Epub ahead of print].

The role of the human microbiome in the brain and behavioral development is an area of increasing attention. Recent investigations have found that diverse mechanisms and signals including the immune, endocrine and neural associations are responsible for the communication between gut microbiota and the brain. The studies have suggested that alteration of intestinal microbiota using probiotic formulations may offer a significant role in the maturation and organization of the brain and can shape the brain and behavior as well as mood and cognition in human subjects. The understanding of the possible impact of gut microflora on neurological function is a promising phenomenon that can surely transform the neurosciences and may decipher the novel etiologies for neurodegenerative and psychiatric disorders.

RevDate: 2020-08-05

Achufusi TGO, Sharma A, Zamora EA, et al (2020)

Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods.

Cureus, 12(6):e8860.

Small intestinal bacterial overgrowth (SIBO) is a commonly diagnosed gastrointestinal disorder affecting millions of individuals throughout the United States. It refers to a condition in which there is an excess and imbalance of small intestinal bacteria. Despite its prevalence, it remains underdiagnosed due to the invasive nature of diagnostic testing. Symptoms observed in SIBO, including abdominal distension, bloating, diarrhea, and gas formation, are nonspecific and can overlap with other gastrointestinal disorders. Frequently cited predisposing factors include gastric acid suppression, dysmotility, gastric bypass, and opioids. The diagnostic gold standard remains small bowel aspirate and culture. However, due to its invasive nature, it remains an unpopular method among patients and clinicians alike. Glucose and lactulose breath testing have become the go-to diagnostic method in clinical practice due to its noninvasive nature and low cost. Treatment is guided towards the eradication of bacteria in the small bowel and usually consists of a prolonged course of oral antibiotics. Due to recent advances in our understanding of the human microbiome, we are surely poised for a transformation in our approach to diagnosing and treating this condition.

RevDate: 2020-08-05

García-Velasco JA, Budding D, Campe H, et al (2020)

The reproductive microbiome - clinical practice recommendations for fertility specialists.

Reproductive biomedicine online pii:S1472-6483(20)30339-4 [Epub ahead of print].

The interest in and understanding of the human microbiome has grown remarkably over recent years. Advances in molecular techniques have allowed researchers to identify and study the microbiota and also use this information to develop therapeutic solutions for a spectrum of conditions. Alongside the growing interest in the microbiome, societal changes have resulted in many couples looking to start families later in life, therefore increasing the demand for assisted reproductive technologies. Combining these trends, it makes sense that clinicians are eager to understand and exploit the microbiome of their patients, i.e. the reproductive microbiome, in order to help them achieve their goal of becoming parents. This paper aims to provide an overview of the current and future research into the reproductive microbiome in relation to fertility and also share clinical practice recommendations for physicians who are new to this field or unsure about how they can utilise what is known to help their patients.

RevDate: 2020-08-03

Wagner J, Kancherla J, Braccia D, et al (2020)

Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz.

F1000Research, 9:601.

The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual's health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. We describe integrative statistical and visual analyses of two datasets from iHMP using Metaviz along with the metagenomeSeq R/Bioconductor package for statistical analysis of differential abundance analysis. These use cases demonstrate the utility of a combined approach to access and analyze data from this resource.

RevDate: 2020-07-31

Guan X, Ma F, Sun X, et al (2020)

Gut Microbiota Profiling in Patients With HER2-Negative Metastatic Breast Cancer Receiving Metronomic Chemotherapy of Capecitabine Compared to Those Under Conventional Dosage.

Frontiers in oncology, 10:902.

Purpose: Low-dose metronomic chemotherapy can achieve disease control with reduced toxicity compared to conventional chemotherapy in maximum tolerated dose. Characterizing the gut microbiota of cancer patients under different dosage regimens may describe a new role of gut microbiota associated with drug efficacy. Therefore, we evaluated the composition and the function of gut microbiome associated with metronomic capecitabine compared to conventional dosage. Methods: The fecal samples of HER2-negative metastatic breast cancer patients treated with capecitabine as maintenance chemotherapy were collected and analyzed by 16S ribosome RNA gene sequencing. Results: A total of 15 patients treated with metronomic capecitabine were compared to 16 patients under a conventional dose. The unweighted-unifrac index of the metronomic group was statistically significantly lower than that of the routine group (P = 0.025). Besides that, the Bray-Curtis distance-based redundancy analysis illustrated that the microbial genera between the two groups can be separated partly. Nine Kyoto Encyclopedia of Genes and Genomes (KEGG) modules were enriched in the metronomic group, while no KEGG modules were significantly enriched in the routine group. Moreover, univariate and multivariate analyses suggested that the median progression-free survival (PFS) was significantly shorter in patients with the gut microbial composition of Slackia (9.2 vs. 32.7 months, P = 0.004), while the patients with Blautia obeum had a significantly prolonged PFS than those without (32.7 vs. 12.9 months, P = 0.013). Conclusions: The proof-of-principle study suggested that the gut microbiota of patients receiving metronomic chemotherapy was different in terms of diversity, composition, and function from those under conventional chemotherapy, and the presence of specific bacterial species may act as microbial markers associated with drug resistance monitoring and prognostic evaluation.

RevDate: 2020-07-30

Fontana F, Lindstedt H, Correia A, et al (2020)

Influence of Cell Membrane Wrapping on the Cell-Porous Silicon Nanoparticle Interactions.

Advanced healthcare materials [Epub ahead of print].

Biohybrid nanosystems represent the cutting-edge research in biofunctionalization of micro- and nano-systems. Their physicochemical properties bring along advantages in the circulation time, camouflaging from the phagocytes, and novel antigens. This is partially a result of the qualitative differences in the protein corona, and the preferential targeting and uptake in homologous cells. However, the effect of the cell membrane on the cellular endocytosis mechanisms and time has not been fully evaluated yet. Here, the effect is assessed by quantitative flow cytometry analysis on the endocytosis of hydrophilic, negatively charged porous silicon nanoparticles and on their membrane-coated counterparts, in the presence of chemical inhibitors of different uptake pathways. Principal component analysis is used to analyze all the data and extrapolate patterns to highlight the cell-specific differences in the endocytosis mechanisms. Furthermore, the differences in the composition of static protein corona between naked and coated particles are investigated together with how these differences affect the interaction with human macrophages. Overall, the presence of the cell membrane only influences the speed and the entity of nanoparticles association with the cells, while there is no direct effect on the endocytosis pathways, composition of protein corona, or any reduction in macrophage-mediated uptake.

RevDate: 2020-07-30

Huybrechts I, Zouiouich S, Loobuyck A, et al (2020)

The human microbiome in relation to cancer risk: a systematic review of epidemiological studies.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology pii:1055-9965.EPI-20-0288 [Epub ahead of print].

The microbiome has been hypothesized to play a role in cancer development. Due to the diversity of published data, an overview of available epidemiological evidence linking the microbiome with cancer is now needed. We conducted a systematic review using a tailored search strategy in Medline and EMBASE databases to identify and summarize the current epidemiologic literature on the relationship between the microbiome and different cancer outcomes published until December 2019. One hundred and twenty-four eligible articles were identified. The large diversity of parameters used to describe microbial composition made it impossible to harmonize the different studies in a way that would allow meta-analysis, therefore only a qualitative description of results could be performed. Fifty studies reported differences in the gut microbiome between colorectal cancer patients and various control groups. The most consistent findings were for Fusobacterium, Porphyromonas and Peptostreptococcus being significantly enriched in fecal and mucosal samples from colorectal cancer patients. For the oral microbiome, significantly increased and decreased abundance was reported for Fusobacterium and Streptococcus, respectively, in oral cancer patients compared to controls. Overall, although there was a large amount of evidence for some of these alterations, most require validation in high quality, preferably prospective, epidemiological studies.

RevDate: 2020-07-29

Druart C, Plovier H, Van Hul M, et al (2020)

Toxicological safety evaluation of pasteurized Akkermansia muciniphila.

Journal of applied toxicology : JAT [Epub ahead of print].

Gut microorganisms are vital for many aspects of human health, and the commensal bacterium Akkermansia muciniphila has repeatedly been identified as a key component of intestinal microbiota. Reductions in A. muciniphila abundance are associated with increased prevalence of metabolic disorders such as obesity and type 2 diabetes. It was recently discovered that administration of A. muciniphila has beneficial effects and that these are not diminished, but rather enhanced after pasteurization. Pasteurized A. muciniphila is proposed for use as a food ingredient, and was therefore subjected to a nonclinical safety assessment, comprising genotoxicity assays (bacterial reverse mutation and in vitro mammalian cell micronucleus tests) and a 90-day toxicity study. For the latter, Han Wistar rats were administered with the vehicle or pasteurized A. muciniphila at doses of 75, 375 or 1500 mg/kg body weight/day (equivalent to 4.8 × 109 , 2.4 × 1010 , or 9.6 × 1010 A. muciniphila cells/kg body weight/day) by oral gavage for 90 consecutive days. The study assessed potential effects on clinical observations (including detailed arena observations and a modified Irwin test), body weight, food and water consumption, clinical pathology, organ weights, and macroscopic and microscopic pathology. The results of both in vitro genotoxicity studies were negative. No test item-related adverse effects were observed in the 90-day study; therefore, 1500 mg/kg body weight/day (the highest dose tested, equivalent to 9.6 × 1010 A. muciniphila cells/kg body weight/day) was established as the no-observed-adverse-effect-level. These results support that pasteurized A. muciniphila is safe for use as a food ingredient.

RevDate: 2020-07-29

Rojas MI, Cavalcanti GS, McNair K, et al (2020)

A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes.

mSystems, 5(4): pii:5/4/e00648-20.

Many commensal bacteria antagonize each other or their host by producing syringe-like secretion systems called contractile injection systems (CIS). Members of the Bacteroidales family have been shown to produce only one type of CIS-a contact-dependent type 6 secretion system that mediates bacterium-bacterium interactions. Here, we show that a second distinct cluster of genes from Bacteroidales bacteria from the human microbiome may encode yet-uncharacterized injection systems that we term Bacteroidales injection systems (BIS). We found that BIS genes are present in the gut microbiomes of 99% of individuals from the United States and Europe and that BIS genes are more prevalent in the gut microbiomes of healthy individuals than in those individuals suffering from inflammatory bowel disease. Gene clusters similar to that of the BIS mediate interactions between bacteria and diverse eukaryotes, like amoeba, insects, and tubeworms. Our findings highlight the ubiquity of the BIS gene cluster in the human gut and emphasize the relevance of the gut microbiome to the human host. These results warrant investigations into the structure and function of the BIS and how they might mediate interactions between Bacteroidales bacteria and the human host or microbiome.IMPORTANCE To engage with host cells, diverse pathogenic bacteria produce syringe-like structures called contractile injection systems (CIS). CIS are evolutionarily related to the contractile tails of bacteriophages and are specialized to puncture membranes, often delivering effectors to target cells. Although CIS are key for pathogens to cause disease, paradoxically, similar injection systems have been identified within healthy human microbiome bacteria. Here, we show that gene clusters encoding a predicted CIS, which we term Bacteroidales injection systems (BIS), are present in the microbiomes of nearly all adult humans tested from Western countries. BIS genes are enriched within human gut microbiomes and are expressed both in vitro and in vivo Further, a greater abundance of BIS genes is present within healthy gut microbiomes than in those humans with with inflammatory bowel disease (IBD). Our discovery provides a potentially distinct means by which our microbiome interacts with the human host or its microbiome.

RevDate: 2020-07-29

Nazik H, Sass G, Déziel E, et al (2020)

Aspergillus Is Inhibited by Pseudomonas aeruginosa Volatiles.

Journal of fungi (Basel, Switzerland), 6(3): pii:jof6030118.

BACKGROUND: Pseudomonas aeruginosa (Pa) and Aspergillus fumigatus (Af) compete with each other for nutrients and survival in natural environments, and have been extensively studied because of their intermicrobial interactions in the human microbiome. These are the principal microbes infecting immunocompromised patients and persons with cystic fibrosis, particularly the airways. These intermicrobial studies have largely been conducted in liquid medium or on agar, and thus focus on soluble or diffusible microbial products. Several key inhibitory molecules were defined in such studies.

METHODS: in the present report, we examine several methodologies which can be conveniently used to study the interaction of microbial volatiles, including capture methods and kinetics.

RESULTS: Pa volatiles inhibit Af, and the inhibitory mechanism appears to be the incorporation of the inhibitory molecules into the substrate nourishing the Af, rather than directly onto Af structures. We define by mass spectroscopy some specific volatile Pa products that can inhibit Af. Some of these molecules are selected for interest by the study of gene deletion mutants, producing a few Pa strains that were impaired in inhibition. We presumed the volatiles of these latter strains could be excluded from the search for inhibitors.

CONCLUSION: the Pa inhibition of Af via a gaseous phase could be critical components in their competition, particularly in airways, where more direct contact may not be extensive.

RevDate: 2020-07-29

Pearson AL, Pechal J, Lin Z, et al (2020)

Associations detected between measures of neighborhood environmental conditions and human microbiome diversity.

The Science of the total environment, 745:141029 pii:S0048-9697(20)34558-7 [Epub ahead of print].

While emerging research suggests urban green space revegetation increases soil microbiota diversity and native plant species affect skin microbiome diversity, there is still a paucity of knowledge on relationships between neighborhood environmental conditions and the human microbiome. This study leveraged data on human microbiome samples (nose, mouth, rectum) taken at autopsy at the Wayne County Medical Examiner's Office (2014-2015). We evaluated relationships between the microbiome and five measures of environmental conditions (NDVI standard deviation, NDVI mean, percent trees, percent grassland and soil type) near the home of 126 decedents. For the rectum microbiome, NDVI sd had negative, significant associations with diversity (ASVs β = -0.20, p = 0.045; Faith PD β = -0.22, p = 0.026). In contrast, while insignificant, there were consistent, positive associations between diversity and NDVI sd for the mouth microbiome (ASVs β = 0.09, p = 0.337, Faith PD β = 0.14, p = 0.149, Shannon diversity β = 0.14, p = 0.159, Heip's evenness β = 0.11, p = 0.259) and a significant association for the nose microbiome (eigenvalues 3 β = 0.18, p = 0.057). We found consistent, significant, negative associations between percent grassland and diversity of the nose microbiome (ASVs β = -0.25, p = 0.008, Faith PD β = -0.25, p = 0.009, Shannon diversity β = -0.17, p = 0.062). For the mouth microbiome, we found a small effect of percent trees on diversity (eigenvalues 1 β = -0.08, p = 0.053). Clay loam soil was negatively (eigenvalues 2 β = -0.47, p = 0.053) and positively associated (eigenvalues 3 β = 0.65, p = 0.008) with rectum microbiome diversity, compared to loam soil. There was no potential indicator taxon among NDVI quartiles. These findings may be relevant for urban planning and management of urban outdoor spaces in ways that may support healthy human microbiomes. Still, future research is needed to link variation in NDVI, vegetation, plant and/or soil microbe diversity and to confirm or negate our findings that environmental conditions may have contrasting influence on the microbiome of the rectum versus the nose and mouth and that grasslands affect the nose microbiome.

RevDate: 2020-07-27

Chadha J, Nandi D, Atri Y, et al (2020)

Significance of Human Microbiome in Breast Cancer: Tale of an invisible and an invincible.

Seminars in cancer biology pii:S1044-579X(20)30167-X [Epub ahead of print].

The human microbiome is a mysterious treasure of the body playing endless important roles in the well-being of the host metabolism, digestion, and immunity. On the other hand, it actively participates in the development of a variety of pathological conditions including cancer. With the Human Microbiome Project initiative, metagenomics, and next-generation sequencing technologies in place, the last decade has witnessed immense explorations and investigations on the enigmatic association of breast cancer with the human microbiome. However, the connection between the human microbiome and breast cancer remains to be explored in greater detail. In fact, there are several emerging questions such as whether the host microbiota contributes to disease initiation, or is it a consequence of the disease is an irrevocably important question that demands a valid answer. Since the microbiome is an extremely complex community, gaps still remain on how this vital microbial organ plays a role in orchestrating breast cancer development. Nevertheless, undeniable evidence from studies has pinpointed the presence of specific microbial elements of the breast and gut to play a role in governing breast cancer. It is still unclear if an alteration in microbiome/dysbiosis leads to breast cancer or is it vice versa. Though specific microbial signatures have been detected to be associated with various breast cancer subtypes, the structure and composition of a core "healthy" microbiome is yet to be established. Probiotics seem to be a promising antidote for targeted prevention and treatment of breast cancer. Interestingly, these microbial communities can serve as potential biomarkers for prognosis, diagnosis, and treatment of breast cancer, thereby leading to the rise of a completely new era of personalized medicine. This review is a humble attempt to summarize the research findings on the human microbiome and its relation to breast cancer.

RevDate: 2020-07-27

Spacova I, Dodiya HB, Happel AU, et al (2020)

Future of Probiotics and Prebiotics and the Implications for Early Career Researchers.

Frontiers in microbiology, 11:1400.

The opportunities in the fields of probiotics and prebiotics to a great degree stem from what we can learn about how they influence the microbiota and interact with the host. We discuss recent insights, cutting-edge technologies and controversial results from the perspective of early career researchers innovating in these areas. This perspective emerged from the 2019 meeting of the International Scientific Association for Probiotics and Prebiotics - Student and Fellows Association (ISAPP-SFA). Probiotic and prebiotic research is being driven by genetic characterization and modification of strains, state-of-the-art in vitro, in vivo, and in silico techniques designed to uncover the effects of probiotics and prebiotics on their targets, and metabolomic tools to identify key molecules that mediate benefits on the host. These research tools offer unprecedented insights into the functionality of probiotics and prebiotics in the host ecosystem. Young scientists need to acquire these diverse toolsets, or form inter-connected teams to perform comprehensive experiments and systematic analysis of data. This will be critical to identify microbial structure and co-dependencies at body sites and determine how administered probiotic strains and prebiotic substances influence the host. This and other strategies proposed in this review will pave the way for translating the health benefits observed during research into real-life outcomes. Probiotic strains and prebiotic products can contribute greatly to the amelioration of global issues threatening society. The intent of this article is to provide an early career researcher's perspective on where the biggest opportunities lie to advance science and impact human health.

RevDate: 2020-07-27

Garvey M (2020)

Bacteriophages and the One Health Approach to Combat Multidrug Resistance: Is This the Way?.

Antibiotics (Basel, Switzerland), 9(7): pii:antibiotics9070414.

Antimicrobial resistance necessitates action to reduce and eliminate infectious disease, ensure animal and human health, and combat emerging diseases. Species such as Acinetobacter baumanniii, vancomycin resistant Enterococcus, methicillin resistance Staphylococcus aureus, and Pseudomonas aeruginosa, as well as other WHO priority pathogens, are becoming extremely difficult to treat. In 2017, the EU adopted the "One Health" approach to combat antibiotic resistance in animal and human medicine and to prevent the transmission of zoonotic disease. As the current therapeutic agents become increasingly inadequate, there is a dire need to establish novel methods of treatment under this One Health Framework. Bacteriophages (phages), viruses infecting bacterial species, demonstrate clear antimicrobial activity against an array of resistant species, with high levels of specificity and potency. Bacteriophages play key roles in bacterial evolution and are essential components of all ecosystems, including the human microbiome. Factors such are their specificity, potency, biocompatibility, and bactericidal activity make them desirable options as therapeutics. Issues remain, however, relating to their large-scale production, formulation, stability, and bacterial resistance, limiting their implementation globally. Phages used in therapy must be virulent, purified, and well characterized before administration. Clinical studies are warranted to assess the in vivo pharmacokinetics and pharmacodynamic characteristics of phages to fully establish their therapeutic potential.

RevDate: 2020-07-21

Buongermino Pereira M, Österlund T, Eriksson KM, et al (2020)

A comprehensive survey of integron-associated genes present in metagenomes.

BMC genomics, 21(1):495 pii:10.1186/s12864-020-06830-5.

BACKGROUND: Integrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.

RESULTS: Here, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.

CONCLUSIONS: Our results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.

RevDate: 2020-07-20

Descheemaeker L, S de Buyl (2020)

Stochastic logistic models reproduce experimental time series of microbial communities.

eLife, 9: pii:55650 [Epub ahead of print].

We analyze properties of experimental microbial time series, from plankton and the human microbiome, and investigate whether stochastic generalized Lotka-Volterra models could reproduce those properties. We show that this is the case when the noise term is large and a linear function of the species abundance, while the strength of the self-interactions varies over multiple orders of magnitude. We stress the fact that all the observed stochastic properties can be obtained from a logistic model, i.e. without interactions, even the niche character of the experimental time series. Linear noise is associated with growth rate stochasticity, which is related to changes in the environment. This suggests that fluctuations in the sparsely sampled experimental time series may be caused by extrinsic sources.

RevDate: 2020-07-20

Joseph TA, Pasarkar AP, I Pe'er (2020)

Efficient and Accurate Inference of Mixed Microbial Population Trajectories from Longitudinal Count Data.

Cell systems, 10(6):463-469.e6.

The recently completed second phase of the Human Microbiome Project has highlighted the relationship between dynamic changes in the microbiome and disease, motivating new microbiome study designs based on longitudinal sampling. Yet, analysis of such data is hindered by presence of technical noise, high dimensionality, and data sparsity. Here, we introduce LUMINATE (longitudinal microbiome inference and zero detection), a fast and accurate method for inferring relative abundances from noisy read count data. We demonstrate that LUMINATE is orders of magnitude faster than current approaches, with better or similar accuracy. We further show that LUMINATE can accurately distinguish biological zeros, when a taxon is absent from the community, from technical zeros, when a taxon is below the detection threshold. We conclude by demonstrating the utility of LUMINATE on a real dataset, showing that LUMINATE smooths trajectories observed from noisy data. LUMINATE is freely available from

RevDate: 2020-07-18

Daisley BA, Chmiel JA, Pitek AP, et al (2020)

Missing Microbes in Bees: How Systematic Depletion of Key Symbionts Erodes Immunity.

Trends in microbiology pii:S0966-842X(20)30185-2 [Epub ahead of print].

Pesticide exposure, infectious disease, and nutritional stress contribute to honey bee mortality and a high rate of colony loss. This realization has fueled a decades-long investigation into the single and combined effects of each stressor and their overall bearing on insect physiology. However, one element largely missing from this research effort has been the evaluation of underlying microbial communities in resisting environmental stressors and their influence on host immunity and disease tolerance. In humans, multigenerational bombardment by antibiotics is linked with many contemporary diseases. Here, we draw a parallel conclusion for the case in honey bees and suggest that chronic exposure to antimicrobial xenobiotics can systematically deplete honey bees of their microbes and hamper cross-generational preservation of host-adapted symbionts that are crucial to health.

RevDate: 2020-07-17

Le S, Toussi A, Maverakis N, et al (2020)

The cutaneous and intestinal microbiome in psoriatic disease.

Clinical immunology (Orlando, Fla.) pii:S1521-6616(20)30433-2 [Epub ahead of print].

Psoriasis (PsO) and psoriatic arthritis (PsA) are chronic immune-mediated inflammatory diseases of multifactorial etiology. In addition to genetic and environmental factors, evidence supports involvement of a dysregulated human microbiome in the pathogenesis of psoriatic disease. In particular, alterations in the composition of the microbiome, termed dysbiosis, can result in downstream proinflammatory effects in the gut, skin, and joints. Both the cutaneous and intestinal microbial populations are implicated in the pathogenesis of psoriatic disease, although exact mechanisms are unclear. Herein, we review the relationship between the human microbiome and psoriatic disease. Further insight into the functions of the microbiome may allow for greater understanding of inflammatory disease processes and identification of additional therapeutic targets.

RevDate: 2020-07-17

Gao W, Baumgartel KL, SA Alexander (2020)

The Gut Microbiome as a Component of the Gut-Brain Axis in Cognitive Health.

Biological research for nursing [Epub ahead of print].

INTRODUCTION: The human microbiome, the microorganisms living in and on the body, plays a vital role in brain physiology and pathophysiology. The gut microbiome (GMB) has been identified as a link in the gut-brain axis moderating cognitive development and health.

OBJECTIVES: The objectives of this scoping review are to discuss mechanisms of the microbiome-gut-brain axis in cognition, review the existing literature on the GMB and cognition, and discuss implications for nursing research.

METHODS: We searched Pubmed using the terms "gut microbiome," "brain," and "cognition" and the terms "gut brain axis," "microbiome," and "cognition"; removed duplicates, studies not published in English, and unrelated publications; and added additional articles identified through references. We retained the 85 most relevant publications for this review.

RESULTS: Common themes in the current literature include GMB components; interactions on cognitive development; effects of GMB-gut-brain interactions on cognition, mild cognitive impairment and Alzheimer's disease; effects of GMB interactions with physiologic stress on cognition in critical care; and GMB modification for improved cognition. Review of the literature on each of these topics reveals multiple theoretical mechanisms of action for GMB-gut-brain interaction that modify cognitive development and function across the lifespan.

DISCUSSION: GMB components and dysbiosis have been implicated in many cognitive states, and specific microbiota constituents contribute to cognitive development, stability, and impairment. The study of these interactions is relevant to nursing research as it addresses the holistic human experience and microbiome constituents are modifiable, facilitating translation into the clinical setting.

RevDate: 2020-07-17

Dupont HL, Jiang ZD, Dupont AW, et al (2020)


Transactions of the American Clinical and Climatological Association, 131:178-197.

The Human Microbiome Initiative of NIH, begun in 2007, has opened the door to the power of the intestinal microbiome in health and disease. The 100 trillion gut microbes influence body function through three pathways: (1) via the neural route where 500 million neurons of the enteric nervous system (the body's second brain) connect to the brain and spinal cord, (2) via the immune route where the gut-immune capacity prevents infection and elicits immune response to vaccines, and (3) by the hormonal route wherein biologically active chemicals are released from enteroendocrine cells to control mood and body functions. Through research, the identification of diseases and disorders associated with abnormal microbiome ("dysbiosis") has increased in number with potential for reversibility. Our team has developed an orally administered fecal microbiota transplantation product that is effective in reversing dysbiosis in recurrent Clostridioides difficile (C. difficile) and is being used to reverse abnormal microbiomes in chronic dysbiotic disorders.

RevDate: 2020-07-16

Giannoni E, Baud D, Agri VD, et al (2020)

Probiotics and COVID-19.

The lancet. Gastroenterology & hepatology, 5(8):720-721.

RevDate: 2020-07-17

Hadrich D (2020)

New EU projects delivering human microbiome applications.

Future science OA, 6(6):FSO474.

Over recent years, the number of studies and projects showing correlations between the human microbiome and diseases has increased enormously. The potential of the human microbiome for healthcare is big. However, many confounders have been discovered and the relevant disease mechanisms and the causalities of these diseases still require more efforts and better understanding. The EU called for project proposals exploiting the application potential of human microbiome research and finally decided to fund the three top excellent new H2020 projects ONCOBIOME, MICROB-PREDICT and GEMMA. They get a total EU funding of €44 M and started in January 2019 with the aim to deliver high impact through validated clinical tools that are helpful for end-users.

RevDate: 2020-07-15

Matenchuk BA, Mandhane PJ, AL Kozyrskyj (2020)

Sleep, circadian rhythm, and gut microbiota.

Sleep medicine reviews, 53:101340 pii:S1087-0792(20)30083-6 [Epub ahead of print].

From asthma and heart disease to diabetes and obesity, the human microbiome plays a role in the pathogenesis of each chronic health condition plaguing today's society. Recent work has shown that the gut microbiota and its metabolites exhibit diurnal rhythmicity which predominantly respond to the feeding/fasting cycle. Persistent jet lag, an obesogenic diet, and clock gene deficiency can dampen the oscillatory nature of gut bacterial composition, which can subsequently be rescued by time restricted feeding. Contrastingly, gut microbial metabolites influence central and hepatic clock gene expression and sleep duration in the host and regulate body composition through circadian transcription factors. Both sleep fragmentation and short sleep duration are associated with gut dysbiosis which may be due to activation of the HPA-axis. Metabolic disturbances associated with sleep loss may in fact be mediated through the overgrowth of specific gut bacteria. Reciprocally, the end products of bacterial species which grow in response to sleep loss are able to induce fatigue. Furthermore, probiotic supplementation has been found to improve subjective sleep quality. Sleep quality and duration may be an important target for supporting healthy gut microbiota composition, but the cyclic nature of this relationship should not be overlooked.

RevDate: 2020-07-15

Zhao C, Wei Z, Yang J, et al (2020)

Characterization of the Vaginal Microbiome in Women with Infertility and Its Potential Correlation with Hormone Stimulation during In Vitro Fertilization Surgery.

mSystems, 5(4): pii:5/4/e00450-20.

Perturbation of vaginal microbiome of reproductive-age women influences all the phases of a woman's reproductive life. Although studies have shown that dynamic changes in vaginal microbiome can affect pregnancy, its role in secondary infertility (i.e., inability to become pregnant or to carry a pregnancy successfully after previous success in delivering a child) and in vitrofertilization (IVF) remains to be unraveled. To determine the vaginal microbiome in women undergoing in vitrofertilization and embryo transfer (IVF-ET) and investigate its potential correlations with hormone stimulation, we recruited 30 patients with secondary infertility and receiving IVF and 92 matched healthy women and analyzed their vaginal microbiome composition using 16S rRNA gene sequencing. Our results show that women suffering from infertility (infertile women) exhibit a significant decrease in microbiome diversity and richness compared with healthy women during the nonovulation period (follicular phase) (P < 0.01), whereas vaginal microbiome of healthy women reveals dramatic fluctuations during ovulation (P < 0.05). Interestingly, infertility patients show no change of the vaginal microbiome under conditions of gonadotropin-releasing hormone (GnRH) agonist and recombinant human chorionic gonadotropin (r-hCG) induction (P > 0.05). Moreover, our results indicate that infertile women show characteristic variations in vaginal microbiome, such as increased abundance of Atopobium, Aerococcus, and Bifidobacterium and decreased abundance of Lactobacillus and LeuconostocIMPORTANCE The microbiome had been hypothesized to be involved in the physiology and pathophysiology of assisted reproduction before the first success in IVF, while the data supporting or refuting this hypothesis were less than conclusive. Thanks to sequencing data from the 16S rRNA subunit, we characterized the microbiome in the reproductive tract of infertile women, and we found that changes in the vaginal microbiome are related to female infertility. We also found that the characteristic microbiome bacteria are mainly members of several genera and that the vaginal microbiome of infertile women is not sensitive to hormonal changes during IVF. In conclusion, our report provides data that can be used for discovering the role of the vaginal microbiome in patients suffering from secondary infertility.

RevDate: 2020-07-14

Arnolds KL, Martin CG, CA Lozupone (2020)

Blood type and the microbiome- untangling a complex relationship with lessons from pathogens.

Current opinion in microbiology, 56:59-66 pii:S1369-5274(20)30080-1 [Epub ahead of print].

The complex communities of microbes that constitute the human microbiome are influenced by host and environmental factors. Here, we address how a fundamental aspect of human biology, blood type, contributes to shaping this microscopic ecosystem. Although this question remains largely unexplored, we glean insights from decades of work describing relationships between pathogens and blood type. The bacterial strategies, molecular mechanisms, and host responses that shaped those relationships may parallel those that characterize how blood type and commensals interact. Understanding these nuanced interactions will expand our capacity to analyze and manipulate the human microbiome.

RevDate: 2020-07-14

Koslovsky MD, M Vannucci (2020)

MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package.

BMC bioinformatics, 21(1):301 pii:10.1186/s12859-020-03640-0.

BACKGROUND: Understanding the relation between the human microbiome and modulating factors, such as diet, may help researchers design intervention strategies that promote and maintain healthy microbial communities. Numerous analytical tools are available to help identify these relations, oftentimes via automated variable selection methods. However, available tools frequently ignore evolutionary relations among microbial taxa, potential relations between modulating factors, as well as model selection uncertainty.

RESULTS: We present MicroBVS, an R package for Dirichlet-tree multinomial models with Bayesian variable selection, for the identification of covariates associated with microbial taxa abundance data. The underlying Bayesian model accommodates phylogenetic structure in the abundance data and various parameterizations of covariates' prior probabilities of inclusion.

CONCLUSION: While developed to study the human microbiome, our software can be employed in various research applications, where the aim is to generate insights into the relations between a set of covariates and compositional data with or without a known tree-like structure.

RevDate: 2020-07-14

Huh JW, TY Roh (2020)

Opportunistic detection of Fusobacterium nucleatum as a marker for the early gut microbial dysbiosis.

BMC microbiology, 20(1):208 pii:10.1186/s12866-020-01887-4.

BACKGROUND: The essential roles of gut microbiome have been emphasized in modulating human health and disease. Fusobacterium nucleatum (F. nucleatum), an obligate Gram-negative microorganism residing in oral cavity, gastrointestinal tract and elsewhere, has been recently considered as a potential oncobacterium associated with human cancers. However, the consequence of its enrichment was not extensively explored in terms of microbial homeostasis and stability at the early stage of disease development.

RESULT: Our analysis on longitudinal metagenomic data generated by the Integrative Human Microbiome Project (iHMP) showed that F. nucleatum was frequently found in inflammatory bowel diseases (IBD) subjects with reduced microbial diversity. Using non-parametric logarithmic linear discriminant analysis (LDA) effect size (LEfSe) algorithm, 12 IBD- and 14 non-IBD-specific bacterial species were identified in the fecal metagenome and the IBD-specific ones were over-represented in the F. nucleatum-experienced subjects during long-term surveillance. In addition, F. nucleatum experience severely abrogated intra-personal stability of microbiome in IBD patients and induced highly variable gut microbiome between subjects. From the longitudinal comparison between microbial distributions prior and posterior to F. nucleatum detection, 41 species could be proposed as indicative "classifiers" for dysbiotic gut state. By multiple logistic regression models established on these classifiers, the high probability of experiencing F. nucleatum was significantly correlated with decreased alpha-diversity and increased number of biomarker species for IBD and colorectal cancer (CRC). Finally, microbial clustering confirmed that biomarker species for IBD and non-IBD conditions as well as CRC signature markers were well distinguishable and could be utilized for explaining gut symbiosis and dysbiosis.

CONCLUSION: F. nucleatum opportunistically appeared under early dysbiotic condition in gut, and discriminative classifier species associated with F. nucleatum were successfully applied to predict microbial alterations in both IBD and non-IBD conditions. Our prediction model and microbial classifier biomarkers for estimating gut dysbiosis should provide a novel aspect of microbial homeostasis/dynamics and useful information on non-invasive biomarker screening.

RevDate: 2020-07-13

Sutherland VL, McQueen CA, Mendrick D, et al (2020)

The Gut Microbiome and Xenobiotics: Identifying Knowledge Gaps.

Toxicological sciences : an official journal of the Society of Toxicology, 176(1):1-10.

There is an increasing awareness that the gut microbiome plays a critical role in human health and disease, but mechanistic insights are often lacking. In June 2018, the Health and Environmental Sciences Institute (HESI) held a workshop, "The Gut Microbiome: Markers of Human Health, Drug Efficacy and Xenobiotic Toxicity" ( to identify data gaps in determining how gut microbiome alterations may affect human health. Speakers and stakeholders from academia, government, and industry addressed multiple topics including the current science on the gut microbiome, endogenous and exogenous metabolites, biomarkers, and model systems. The workshop presentations and breakout group discussions formed the basis for identifying data gaps and research needs. Two critical issues that emerged were defining the microbial composition and function related to health and developing standards for models, methods and analysis in order to increase the ability to compare and replicate studies. A series of key recommendations were formulated to focus efforts to further understand host-microbiome interactions and the consequences of exposure to xenobiotics as well as identifying biomarkers of microbiome-associated disease and toxicity.

RevDate: 2020-07-13

Lahtinen P, Jalanka J, Hartikainen A, et al (2020)

Letter: faecal microbiota transplantation for irritable bowel syndrome. Authors' reply.

Alimentary pharmacology & therapeutics, 52(3):557-558.

RevDate: 2020-07-12

Cavaleiro Rufo J, Paciência IR, Hoffimann E, et al (2020)

The neighbourhood natural environment is associated with asthma in children: a birth cohort study.

Allergy [Epub ahead of print].

BACKGROUND: A lower exposure to the natural environment has been hypothesized to adversely affect the human microbiome and its immunomodulatory capacity. However,the underlying effects of this hypothesis are stillnot understood. We aimed to evaluate the effect of early-life exposure to greenness and species richness on the development of allergic diseases and asthma in children.

METHODS: A longitudinal study was conducted comprising 1050 children from a population-based birth cohort recruited in Portugal. Residential normalized difference vegetation index (NDVI) and species richness index (SRI) were assessed at baseline to estimate their association with allergic diseases and asthma at the ages of 4 and 7.

RESULTS: Significant predisposingassociations were observed between the exposure to species richness at baseline and the onset of asthma and wheezing at the age of 7. Children living in neighbourhoods surrounded by high levels of SRI were at a significantly higher risk developing allergic sensitization(OR [95%CI]= 2.00 [1.04 : 3.86] at age 4; 2.35 [1.20 : 4.63] at age 7). Living surrounded by greener environments was significantly associated with a lower prevalence of asthma and rhinitis at the age of 7(0.41 [0.18 : 0.97] and 0.37 [0.15 : 0.93], respectively).

CONCLUSIONS: Living in close proximity to a greener environment at birth has a protective effect on the development of allergic diseases and asthma at the age of 7. Conversely, living in neighbourhoods with a high number of fauna species appears to be associated with a higher risk for allergy, asthma and wheezing.

RevDate: 2020-07-10

Wiley CA (2020)

Emergent Viral Infections of the CNS.

Journal of neuropathology and experimental neurology pii:5869577 [Epub ahead of print].

Biological evolution of the microbiome continually drives the emergence of human viral pathogens, a subset of which attack the nervous system. The sheer number of pathogens that have appeared, along with their abundance in the environment, demand our attention. For the most part, our innate and adaptive immune systems have successfully protected us from infection; however, in the past 5 decades, through pathogen mutation and ecosystem disruption, a dozen viruses emerged to cause significant neurologic disease. Most of these pathogens have come from sylvatic reservoirs having made the energetically difficult, and fortuitously rare, jump into humans. But the human microbiome is also replete with agents already adapted to the host that need only minor mutations to create neurotropic/toxic agents. While each host/virus symbiosis is unique, this review examines virologic and immunologic principles that govern the pathogenesis of different viral CNS infections that were described in the past 50 years (Influenza, West Nile Virus, Zika, Rift Valley Fever Virus, Hendra/Nipah, Enterovirus-A71/-D68, Human parechovirus, HIV, and SARS-CoV). Knowledge of these pathogens provides us the opportunity to respond and mitigate infection while at the same time prepare for inevitable arrival of unknown agents.

RevDate: 2020-07-08

Filik K, Szermer-Olearnik B, Wernecki M, et al (2020)

The Podovirus ϕ80-18 Targets the Pathogenic American Biotype 1B Strains of Yersinia enterocolitica.

Frontiers in microbiology, 11:1356.

We report here the complete genome sequence and characterization of Yersinia bacteriophage vB_YenP_ϕ80-18. ϕ80-18 was isolated in 1991 using a Y. enterocolitica serotype O:8 strain 8081 as a host from a sewage sample in Turku, Finland, and based on its morphological and genomic features is classified as a podovirus. The genome is 42 kb in size and has 325 bp direct terminal repeats characteristic for podoviruses. The genome contains 57 predicted genes, all encoded in the forward strand, of which 29 showed no similarity to any known genes. Phage particle proteome analysis identified altogether 24 phage particle-associated proteins (PPAPs) including those identified as structural proteins such as major capsid, scaffolding and tail component proteins. In addition, also the DNA helicase, DNA ligase, DNA polymerase, 5'-exonuclease, and the lytic glycosylase proteins were identified as PPAPs, suggesting that they might be injected together with the phage genome into the host cell to facilitate the take-over of the host metabolism. The phage-encoded RNA-polymerase and DNA-primase were not among the PPAPs. Promoter search predicted the presence of four phage and eleven host RNA polymerase -specific promoters in the genome, suggesting that early transcription of the phage is host RNA-polymerase dependent and that the phage RNA polymerase takes over later. The phage tolerates pH values between 2 and 12, and is stable at 50°C but is inactivated at 60°C. It grows slowly with a 50 min latent period and has apparently a low burst size. Electron microscopy revealed that the phage has a head diameter of about 60 nm, and a short tail of 20 nm. Whole-genome phylogenetic analysis confirmed that ϕ80-18 belongs to the Autographivirinae subfamily of the Podoviridae family, that it is 93.2% identical to Yersinia phage fHe-Yen3-01. Host range analysis showed that ϕ80-18 can infect in addition to Y. enterocolitica serotype O:8 strains also strains of serotypes O:4, O:4,32, O:20 and O:21, the latter ones representing similar to Y. enterocolitica serotype O:8, the American pathogenic biotype 1B strains. In conclusion, the phage ϕ80-18 is a promising candidate for the biocontrol of the American biotype 1B Y. enterocolitica.

RevDate: 2020-07-08

Puccetti M, Xiroudaki S, Ricci M, et al (2020)

Postbiotic-Enabled Targeting of the Host-Microbiota-Pathogen Interface: Hints of Antibiotic Decline?.

Pharmaceutics, 12(7): pii:pharmaceutics12070624.

Mismanagement of bacterial infection therapies has undermined the reliability and efficacy of antibiotic treatments, producing a profound crisis of the antibiotic drug market. It is by now clear that tackling deadly infections demands novel strategies not only based on the mere toxicity of anti-infective compounds. Host-directed therapies have been the first example as novel treatments with alternate success. Nevertheless, recent advances in the human microbiome research have provided evidence that compounds produced by the microbial metabolism, namely postbiotics, can have significant impact on human health. Such compounds target the host-microbe-pathogen interface rescuing biotic and immune unbalances as well as inflammation, thus providing novel therapeutic opportunities. This work discusses critically, through literature review and personal contributions, these novel nonantibiotic treatment strategies for infectious disease management and resistance prevention, which could represent a paradigm change rocking the foundation of current antibiotic therapy tenets.


ESP Quick Facts

ESP Origins

In the early 1990's, Robert Robbins was a faculty member at Johns Hopkins, where he directed the informatics core of GDB — the human gene-mapping database of the international human genome project. To share papers with colleagues around the world, he set up a small paper-sharing section on his personal web page. This small project evolved into The Electronic Scholarly Publishing Project.

ESP Support

In 1995, Robbins became the VP/IT of the Fred Hutchinson Cancer Research Center in Seattle, WA. Soon after arriving in Seattle, Robbins secured funding, through the ELSI component of the US Human Genome Project, to create the original ESP.ORG web site, with the formal goal of providing free, world-wide access to the literature of classical genetics.

ESP Rationale

Although the methods of molecular biology can seem almost magical to the uninitiated, the original techniques of classical genetics are readily appreciated by one and all: cross individuals that differ in some inherited trait, collect all of the progeny, score their attributes, and propose mechanisms to explain the patterns of inheritance observed.

ESP Goal

In reading the early works of classical genetics, one is drawn, almost inexorably, into ever more complex models, until molecular explanations begin to seem both necessary and natural. At that point, the tools for understanding genome research are at hand. Assisting readers reach this point was the original goal of The Electronic Scholarly Publishing Project.

ESP Usage

Usage of the site grew rapidly and has remained high. Faculty began to use the site for their assigned readings. Other on-line publishers, ranging from The New York Times to Nature referenced ESP materials in their own publications. Nobel laureates (e.g., Joshua Lederberg) regularly used the site and even wrote to suggest changes and improvements.

ESP Content

When the site began, no journals were making their early content available in digital format. As a result, ESP was obliged to digitize classic literature before it could be made available. For many important papers — such as Mendel's original paper or the first genetic map — ESP had to produce entirely new typeset versions of the works, if they were to be available in a high-quality format.

ESP Help

Early support from the DOE component of the Human Genome Project was critically important for getting the ESP project on a firm foundation. Since that funding ended (nearly 20 years ago), the project has been operated as a purely volunteer effort. Anyone wishing to assist in these efforts should send an email to Robbins.

ESP Plans

With the development of methods for adding typeset side notes to PDF files, the ESP project now plans to add annotated versions of some classical papers to its holdings. We also plan to add new reference and pedagogical material. We have already started providing regularly updated, comprehensive bibliographies to the ESP.ORG site.

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

The ESP began as an effort to share a handful of key papers from the early days of classical genetics. Now the collection has grown to include hundreds of papers, in full-text format.

Digital Books

Along with papers on classical genetics, ESP offers a collection of full-text digital books, including many works by Darwin (and even a collection of poetry — Chicago Poems by Carl Sandburg).


ESP now offers a much improved and expanded collection of timelines, designed to give the user choice over subject matter and dates.


Biographical information about many key scientists.

Selected Bibliographies

Bibliographies on several topics of potential interest to the ESP community are now being automatically maintained and generated on the ESP site.

ESP Picks from Around the Web (updated 07 JUL 2018 )