@article {pmid32488167, year = {2020}, author = {Rasmussen, MA and Thorsen, J and Dominguez-Bello, MG and Blaser, MJ and Mortensen, MS and Brejnrod, AD and Shah, SA and Hjelmsø, MH and Lehtimäki, J and Trivedi, U and Bisgaard, H and Sørensen, SJ and Stokholm, J}, title = {Ecological succession in the vaginal microbiota during pregnancy and birth.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-0686-3}, pmid = {32488167}, issn = {1751-7370}, abstract = {The mother's vaginal microbiota represents the first microbes to which a child is exposed when delivered vaginally. However, little is known about the composition and development of the vaginal microbiota during pregnancy and birth. Here, we analyzed the vaginal microbiota of 57 women in pregnancy week 24, 36 and at birth after rupture of membranes but before delivery, and further compared the composition with that of the gut and airways of the 1-week-old child. The vaginal community structure had dramatic changes in bacterial diversity and taxonomic distribution, yet carried an individual-specific signature. The relative abundance of most bacterial taxa increased stepwise from week 24 of pregnancy until birth, with a gradual decline of Lactobacillus. Mother-to-child vertical transfer, as suggested by sharing, was modest, with the strongest transfer being for Clostridiales followed by Lactobacillales and Enterobacteriales. In conclusion, late gestation is associated with an increase in maternal vaginal microbiota diversity, and vaginal bacteria at birth only modestly predict the composition of the neonatal microbiota.}, }
@article {pmid32487674, year = {2020}, author = {Brenes, LR and Lohse, MB and Hartooni, N and Johnson, AD}, title = {A Set of Diverse Genes Influence the Frequency of White-Opaque Switching in Candida albicans.}, journal = {G3 (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1534/g3.120.401249}, pmid = {32487674}, issn = {2160-1836}, abstract = {The fungal species Candida albicans is both a member of the human microbiome and a fungal pathogen. C. albicans undergoes several different morphological transitions, including one called white-opaque switching. Here, cells reversibly switch between two states, "white" and "opaque," and each state is heritable through many cell generations. Each cell type has a distinct cellular and colony morphology and they differ in many other properties including mating, nutritional specialization, and interactions with the innate immune system. Previous genetic screens to gain insight into white-opaque switching have focused on certain classes of genes (for example transcriptional regulators or chromatin modifying enzymes). In this paper, we examined 172 deletion mutants covering a broad range of cell functions. We identified 28 deletion mutants with at least a five-fold effect on switching frequencies; these cover a wide variety of functions ranging from membrane sensors to kinases to proteins of unknown function. In agreement with previous reports, we found that components of the pheromone signaling cascade affect white-to-opaque switching; however, our results suggest that the major effect of Cek1 on white-opaque switching occurs through the cell wall damage response pathway. Most of the genes we identified have not been previously implicated in white-opaque switching and serve as entry points to understand new aspects of this morphological transition.}, }
@article {pmid32486497, year = {2020}, author = {Badawy, S and Pajunen, MI and Haiko, J and Baka, ZAM and Abou-Dobara, MI and El-Sayed, AKA and Skurnik, M}, title = {Identification and Functional Analysis of Temperate Siphoviridae Bacteriophages of Acinetobacter baumannii.}, journal = {Viruses}, volume = {12}, number = {6}, pages = {}, doi = {10.3390/v12060604}, pmid = {32486497}, issn = {1999-4915}, support = {288701//Academy of Finland/ ; Decision 2016//Jane ja Aatos Erkon Säätiö/ ; }, abstract = {Acinetobacter baumannii is an opportunistic pathogen that presents a serious clinical challenge due to its increasing resistance to all available antibiotics. Phage therapy has been introduced recently to treat antibiotic-incurable A. baumannii infections. In search for new A. baumannii specific bacteriophages, 20 clinical A. baumannii strains were used in two pools in an attempt to enrich phages from sewage. The enrichment resulted in induction of resident prophage(s) and three temperate bacteriophages, named vB_AbaS_fEg-Aba01, vB_AbaS_fLi-Aba02 and vB_AbaS_fLi-Aba03, all able to infect only one strain (#6597) of the 20 clinical strains, were isolated. Morphological characteristics obtained by transmission electron microscopy together with the genomic information revealed that the phages belong to the family Siphoviridae. The ca. 35 kb genomic sequences of the phages were >99% identical to each other. The linear ds DNA genomes of the phages contained 10 nt cohesive end termini, 52-54 predicted genes, an attP site and one tRNA gene each. A database search revealed an >99% identical prophage in the genome of A.baumannii strain AbPK1 (acc. no. CP024576.1). Over 99% identical prophages were also identified from two of the original 20 clinical strains (#5707 and #5920) and both were shown to be spontaneously inducible, thus very likely being the origins of the isolated phages. The phage vB_AbaS_fEg-Aba01 was also able to lysogenize the susceptible strain #6597 demonstrating that it was fully functional. The phages showed a very narrow host range infecting only two A.baumannii strains. In conclusion, we have isolated and characterized three novel temperate Siphoviridae phages that infect A.baumannii.}, }
@article {pmid32479952, year = {2020}, author = {Singh, A and Nayak, N and Rathi, P and Verma, D and Sharma, R and Chaudhary, A and Agarwal, A and Tripathi, YB and Garg, N}, title = {Microbiome and host crosstalk: A new paradigm to cancer therapy.}, journal = {Seminars in cancer biology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.semcancer.2020.05.014}, pmid = {32479952}, issn = {1096-3650}, abstract = {The commensal microbiome of humans has co-evolved for thousands of years. The microbiome regulates human health and is also linked to several diseases, including cancer. The advances in next-generation sequencing have significantly contributed to our understanding of the microbiome and its association with cancer and cancer therapy. Recent studies have highlighted a close relationship of the microbiome to the pharmacological effect of chemotherapy and immunotherapy. The chemo-drugs usually interfere with the host immune system and reduces the microbiome diversity inside the body, which in turn leads to decreased efficacy of these drugs. The human microbiome, specifically the gut microbiome, increases the potency of chemo-drugs through metabolism, enzymatic degradation, ecological differences, and immunomodulation. Recent research exploits the involvement of microbiome to shape the efficacy and decrease the toxicity of these chemo-drugs. In this review, we have highlighted the recent development in understanding the relationship of the human microbiome with cancer and also emphasize on various roles of the microbiome in the modulation of cancer therapy. Additionally, we also summarize the ongoing research focussed on the improved efficacy of chemotherapy and immunotherapy using the host microbiome.}, }
@article {pmid32475524, year = {2020}, author = {Dahl, WJ and Rivero Mendoza, D and Lambert, JM}, title = {Diet, nutrients and the microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {171}, number = {}, pages = {237-263}, doi = {10.1016/bs.pmbts.2020.04.006}, pmid = {32475524}, issn = {1878-0814}, abstract = {Although there is associative evidence linking fecal microbiome profile to health and disease, many studies have not considered the confounding effects of dietary intake. Consuming food provides fermentable substrate which sustains the microbial ecosystem that resides with most abundance in the colon. Western, Mediterranean and vegetarian dietary patterns have a role in modulating the gut microbiota, as do trending restrictive diets such the paleolithic and ketogenic. Altering the amount or ratio of carbohydrate, protein and fat, particularly at the extremes of intake, impacts the microbiome. Diets high in fermentable carbohydrates support the relative abundance of Bifidobacterium, Prevotella, Ruminococcus, Dorea and Roseburia, among others, capable of degrading polysaccharides, oligosaccharides and sugars. Conversely, very high fat diets increase bile-resistant organisms such as Bilophila and Bacteroides. Food form, whole foods vs. ultra-processed, alters the provision of macronutrient substrate to the colon due to differing digestibility, and thereby may impact the microbiota and its metabolic activity. In addition, phytochemicals in plant-based foods have specific and possibly prebiotic effects on the microbiome. Further, food ingredients such as certain low-calorie sweeteners enhance Bifidobacterium spp. The weight of evidence to date suggests a high level of interindividual variability in the human microbiome vs. clearly defined, dietary-induced profiles. Healthful dietary patterns, emphasizing plant foods high in microbial-available carbohydrate, support favorable microbiome profiles active in saccharolytic fermentation. Future research into diet and microbiome should consider the balance of gut microbial-generated metabolites, an important link between microbiome profile and human health.}, }
@article {pmid32474160, year = {2020}, author = {Prescott, SL}, title = {A Butterfly Flaps its Wings: Extinction of Biological Experience and the Origins of Allergy.}, journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.anai.2020.05.025}, pmid = {32474160}, issn = {1534-4436}, abstract = {OBJECTIVE: The grand global challenges of the Anthropocene are interdependent with ample evidence that reduced early-life 'experience' of biodiversity primes for immune dysregulation and a higher propensity low-grade inflammation, increasing the risk of allergy many other later-onset NCDs -also now implicated in the susceptibility to acute inflammation in COVID-19 infection. The objective of this review is to explore links between biodiversity on all scales and allergic disease as a measure of immune dysregulation.<br><br>DATA SOURCES: Were identified from PubMed and Web of Science using search terms pertaining to biodiversity, nature-relatedness, allergic disease, microbiome, NCDs, COVID-19 and associated terms.<br><br>STUDY SELECTIONS: Studies were selected based on relevance to human health and biodiversity.<br><br>RESULTS: Contact with natural environments enriches the human microbiome, promotes regulated immune responses, and protects from allergy and both acute and chronic inflammatory disorders. These important links to eco-psychological constructs of the 'extinction of experience' which indicates that loss of direct, personal contact with biodiversity-wildlife and the more visible elements of the natural world-might lead to emotional apathy and irresponsible behaviors toward the environment.<br><br>CONCLUSION: The immune system is a useful early barometer of environmental impacts, and via the microbiome, a measure of the way in which our current experiences differ from our ancestral past. While we would benefit from further research, efforts to increase direct, personal contact with biodiversity have clear benefits for multiple aspect of physical and mental health, the skin and gut microbiome, immune function, food choices, sleep, physical activity, and promotes environmental responsibility.}, }
@article {pmid32468338, year = {2020}, author = {Wu, AH and Tseng, C and Vigen, C and Yu, Y and Cozen, W and Garcia, AA and Spicer, D}, title = {Gut microbiome associations with breast cancer risk factors and tumor characteristics: a pilot study.}, journal = {Breast cancer research and treatment}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10549-020-05702-6}, pmid = {32468338}, issn = {1573-7217}, support = {20IB-0105//California Breast Cancer Research Program/ ; }, abstract = {OBJECTIVE: To investigate the association between gut microbiome with breast tumor characteristics (receptor status, stage and grade) and known breast cancer risk factors.<br><br>METHODS: In a pilot cross-sectional study of 37 incident breast cancer patients, fecal samples collected prior to chemotherapy were analyzed by 16S ribosomal RNA (rRNA) gene-based sequencing protocol. Alpha diversity and specific taxa by tumor characteristics and breast cancer risk factors were tested by Wilcoxon rank sum test, and by differential abundance analysis, using a zero-inflated negative binomial regression model with adjustment for total counts, age and race/ethnicity.<br><br>RESULTS: There were no significant alpha diversity or phyla differences by estrogen/progesterone receptor status, tumor grade, stage, parity and body mass index. However, women with human epidermal growth factor receptor 2 positive (HER2+) (n = 12) compared to HER2- (n = 25) breast cancer showed 12-23% lower alpha diversity [number of species (OTU) p = 0.033, Shannon index p = 0.034], lower abundance of Firmicutes (p = 0.005) and higher abundance of Bacteroidetes (p = 0.089). Early menarche (ages ≤ 11) (n = 11) compared with later menarche (ages ≥ 12) (n = 26) was associated with lower OTU (p = 0.036), Chao1 index (p = 0.020) and lower abundance of Firmicutes (p = 0.048). High total body fat (TBF) (> 46%) (n = 12) compared to lower (≤ 46%) TBF was also associated with lower Chao 1 index (p = 0.011). There were other significant taxa abundance differences by HER2 status, menarche age, as well as other tumor and breast cancer risk factors.<br><br>CONCLUSIONS AND RELEVANCE: Further studies are needed to identify characteristics of the human microbiome and the interrelationships between breast cancer hormone receptor status and established breast cancer risk factors.}, }
@article {pmid32456257, year = {2020}, author = {Vernocchi, P and Del Chierico, F and Putignani, L}, title = {Gut Microbiota Metabolism and Interaction with Food Components.}, journal = {International journal of molecular sciences}, volume = {21}, number = {10}, pages = {}, doi = {10.3390/ijms21103688}, pmid = {32456257}, issn = {1422-0067}, abstract = {The human gut contains trillions of microbes that play a central role in host biology, including the provision of key nutrients from the diet. Food is a major source of precursors for metabolite production; in fact, diet modulates the gut microbiota (GM) as the nutrients, derived from dietary intake, reach the GM, affecting both the ecosystem and microbial metabolic profile. GM metabolic ability has an impact on human nutritional status from childhood. However, there is a wide variability of dietary patterns that exist among individuals. The study of interactions with the host via GM metabolic pathways is an interesting field of research in medicine, as microbiota members produce myriads of molecules with many bioactive properties. Indeed, much evidence has demonstrated the importance of metabolites produced by the bacterial metabolism from foods at the gut level that dynamically participate in various biochemical mechanisms of a cell as a reaction to environmental stimuli. Hence, the GM modulate homeostasis at the gut level, and the alteration in their composition can concur in disease onset or progression, including immunological, inflammatory, and metabolic disorders, as well as cancer. Understanding the gut microbe-nutrient interactions will increase our knowledge of how diet affects host health and disease, thus enabling personalized therapeutics and nutrition.}, }
@article {pmid32453194, year = {2020}, author = {Thapa, S and Runge, JK and Venkatachalam, A and Denne, C and Luna, RA and Anon, JB}, title = {The Nasopharyngeal and Gut Microbiota in Children in a Pediatric Otolaryngology Practice.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000002703}, pmid = {32453194}, issn = {1532-0987}, abstract = {BACKGROUND: The human microbiome evolves rapidly in early life with contributions from various factors such as diet, delivery mode, medical history, antibiotics exposure, genetics, immunomodulators and the environment. A high use of antibiotics in pediatric outpatient settings has been well documented, and improvement in antibiotic selection is required to reduce the risks of antibiotic resistance and disruption of the microbiome.<br><br>METHODS: We performed an exploratory study using 16S rRNA gene-based sequencing to characterize the gut and nasopharyngeal microbiome of children (n = 50) age 1-6 years of age in a pediatric otolaryngology practice.<br><br>RESULTS: Relative abundance of Haemophilus and Moraxella were higher in nasopharyngeal swabs, while Prevotella, Bacteroides, Porphyromonas and Faecalibacterium were highly abundant in rectal swabs. The gut microbiome composition in children <2 years old was different compared with children ≥2 years age. Gut bacterial diversity increased with an increase in age of the children. Children taking probiotics had a notable increase in abundance of potentially beneficial gut bacteria such as Bacteroides and Akkermansia. The nasopharyngeal microbiome differed between children who received antibiotics in the 3 months before sample collection compared with those that did not. Haemophilus spp. was highly abundant in children who received antibiotics 3 months before sampling.<br><br>CONCLUSIONS: The pediatric nasopharyngeal and rectal microbiomes differ in bacterial composition and diversity. The increased abundance of Haemophilus spp. in the nasopharyngeal microbiome of children who received antibiotics during the 3 months before sampling suggests a potential impact of antibiotics in colonization with the otopathogen and may be relevant to clinical practice.}, }
@article {pmid32449747, year = {2020}, author = {Sharma, D and Paterson, AD and Xu, W}, title = {TaxoNN: Ensemble of Neural Networks on Stratified Microbiome Data for Disease Prediction.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btaa542}, pmid = {32449747}, issn = {1367-4811}, abstract = {MOTIVATION: Research supports the potential use of microbiome as a predictor of some diseases. Motivated by the findings that microbiome data is complex in nature and there is an inherent correlation due to hierarchical taxonomy of microbial Operational Taxonomic Units (OTUs), we propose a novel machine learning method incorporating a stratified approach to group OTUs into phylum clusters. Convolutional Neural Networks (CNNs) were used to train within each of the clusters individually. Further, through an ensemble learning approach, features obtained from each cluster were then concatenated to improve prediction accuracy. Our two-step approach comprising of stratification prior to combining multiple CNNs, aided in capturing the relationships between OTUs sharing a phylum efficiently, as compared to using a single CNN ignoring OTU correlations.<br><br>RESULTS: We used simulated datasets containing 168 OTUs in 200 cases and 200 controls for model testing. Thirty-two OTUs, potentially associated with risk of disease were randomly selected and interactions between three OTUs were used to introduce non-linearity. We also implemented this novel method in two human microbiome studies: (i) cirrhosis with 118 cases, 114 controls; (ii) type 2 diabetes with 170 cases, 174 controls; to demonstrate the model's effectiveness. Extensive experimentation and comparison against conventional machine learning techniques yielded encouraging results. We obtained mean AUC values of 0.88, 0.92, 0.75, showing a consistent increment (5%, 3%, 7%) in simulations, cirrhosis and type 2 diabetes data respectively, against the next best performing method, Random Forest.<br><br>AVAILABILITY: https://github.com/divya031090/TaxoNN_OTU.}, }
@article {pmid32446759, year = {2020}, author = {Dannenberg, L and Zikeli, D and Benkhoff, M and Ahlbrecht, S and Kelm, M and Levkau, B and Polzin, A}, title = {Targeting the human microbiome and its metabolite TMAO in cardiovascular prevention and therapy.}, journal = {Pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {107584}, doi = {10.1016/j.pharmthera.2020.107584}, pmid = {32446759}, issn = {1879-016X}, abstract = {The human gut microbiota is the most important active part of the intestinal micro-ecosystem. Lifestyle modification, drug intake and nutrition have an impact on the composition of the gut microbiota and its metabolites. This review focuses on the effects of changes in the gut microbiota as well as the important metabolite Trimethylamine-N-oxide (TMAO). Furthermore, relevant therapeutic options to target the human microbiome in patients with cardiovascular disease are presented.}, }
@article {pmid32437658, year = {2020}, author = {Ang, QY and Alexander, M and Newman, JC and Tian, Y and Cai, J and Upadhyay, V and Turnbaugh, JA and Verdin, E and Hall, KD and Leibel, RL and Ravussin, E and Rosenbaum, M and Patterson, AD and Turnbaugh, PJ}, title = {Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2020.04.027}, pmid = {32437658}, issn = {1097-4172}, abstract = {Very low-carbohydrate, high-fat ketogenic diets (KDs) induce a pronounced shift in metabolic fuel utilization that elevates circulating ketone bodies; however, the consequences of these compounds for host-microbiome interactions remain unknown. Here, we show that KDs alter the human and mouse gut microbiota in a manner distinct from high-fat diets (HFDs). Metagenomic and metabolomic analyses of stool samples from an 8-week inpatient study revealed marked shifts in gut microbial community structure and function during the KD. Gradient diet experiments in mice confirmed the unique impact of KDs relative to HFDs with a reproducible depletion of bifidobacteria. In vitro and in vivo experiments showed that ketone bodies selectively inhibited bifidobacterial growth. Finally, mono-colonizations and human microbiome transplantations into germ-free mice revealed that the KD-associated gut microbiota reduces the levels of intestinal pro-inflammatory Th17 cells. Together, these results highlight the importance of trans-kingdom chemical dialogs for mediating the host response to dietary interventions.}, }
@article {pmid32435232, year = {2020}, author = {Ma, ZS}, title = {Assessing and Interpreting the Metagenome Heterogeneity With Power Law.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {648}, doi = {10.3389/fmicb.2020.00648}, pmid = {32435232}, issn = {1664-302X}, abstract = {There are two major sequencing technologies for investigating the microbiome: the amplicon sequencing that generates the OTU (operational taxonomic unit) tables of marker genes (e.g., bacterial 16S-rRNA), and the metagenomic shotgun sequencing that generates metagenomic gene abundance (MGA) tables. The OTU table is the counterpart of species abundance tables in macrobial ecology of plants and animals, and has been the target of numerous ecological and network analyses in recent gold rush for microbiome research and in great efforts for establishing an inclusive theoretical ecology. Nevertheless, MGA analyses have been largely limited to bioinformatics pipelines and ad hoc statistical methods, and systematic approaches to MGAs guided by classic ecological theories are still few. Here, we argue that, the difference between &quot;gene kinds&quot; and &quot;gene species&quot; are nominal, and the metagenome that a microbiota carries is essentially a 'community' of metagenomic genes (MGs). Each row of a MGA table represents a metagenome of a microbiota, and the whole MGA table represents a 'meta-metagenome' (or an assemblage of metagenomes) of N microbiotas (microbiome samples). Consequently, the same ecological/network analyses used in OTU analyses should be equally applicable to MGA tables. Here we choose to analyze the heterogeneity of metagenome by introducing classic Taylor's power law (TPL) and its recent extensions in community ecology. Heterogeneity is a fundamental property of metagenome, particularly in the context of human microbiomes. Recent studies have shown that the heterogeneity of human metagenomes is far more significant than that of human genomes. Therefore, without deep understanding of the human metagenome heterogeneity, personalized medicine of the human microbiome-associated diseases is hardly feasible. The TPL extensions have been successfully applied to measure the heterogeneity of human microbiome based on amplicon-sequencing reads of marker genes (e.g., 16s-rRNA). In this article, we demonstrate the analysis of the metagenomic heterogeneity of human gut microbiome at whole metagenome scale (with type-I power law extension) and metagenomic gene scale (type-III), as well as the heterogeneity of gene clusters, respectively. We further examine the influences of obesity, IBD and diabetes on the heterogeneity, which is of important ramifications for the diagnosis and treatment of human microbiome-associated diseases.}, }
@article {pmid32431776, year = {2020}, author = {Sewall, JM and Oliver, A and Denaro, K and Chase, AB and Weihe, C and Lay, M and Martiny, JBH and Whiteson, K}, title = {Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course.}, journal = {Journal of microbiology &amp; biology education}, volume = {21}, number = {1}, pages = {}, doi = {10.1128/jmbe.v21i1.1991}, pmid = {32431776}, issn = {1935-7877}, abstract = {Course-based undergraduate research experiences (CUREs) are an effective way to introduce students to contemporary scientific research. Research experiences have been shown to promote critical thinking, improve understanding and proper use of the scientific method, and help students learn practical skills including writing and oral communication. We aimed to improve scientific training by engaging students enrolled in an upper division elective course in a human microbiome CURE. The &quot;Fiber Force&quot; course is aimed at studying the effect of a wholesome high-fiber diet (40 to 50 g/day for two weeks) on the students' gut microbiomes. Enrolled students participated in a noninvasive diet intervention, designed health surveys, tested hypotheses on the effect of a diet intervention on the gut microbiome, and analyzed their own samples (as anonymized aggregates). The course involved learning laboratory techniques (e.g., DNA extraction, PCR, and 16S sequencing) and the incorporation of computational techniques to analyze microbiome data with QIIME2 and within the R software environment. In addition, the learning objectives focused on effective student performance in writing, data analysis, and oral communication. Enrolled students showed high performance grades on writing, data analysis and oral communication assignments. Pre- and post-course surveys indicate that the students found the experience favorable, increased their interest in science, and heightened awareness of their diet habits. Fiber Force constitutes a validated case of a research experience on microbiology with the capacity to improve research training and promote healthy dietary habits.}, }
@article {pmid32430415, year = {2020}, author = {Gosens, R and Hiemstra, PS and Adcock, IM and Bracke, KR and Dickson, RP and Hansbro, PM and Krauss-Etschmann, S and Smits, HH and Stassen, FRM and Bartel, S}, title = {Host-microbe cross-talk in the lung microenvironment: implications for understanding and treating chronic lung disease.}, journal = {The European respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1183/13993003.02320-2019}, pmid = {32430415}, issn = {1399-3003}, abstract = {Chronic respiratory diseases are highly prevalent worldwide and will continue to rise in the foreseeable future. Despite intensive efforts over the recent decades, the development of novel and effective therapeutic approaches has been slow. There is however new and increasing evidence that communities of microorganisms in our body, the human microbiome, are crucially involved in the development and progression of chronic respiratory diseases. Understanding the detailed mechanisms underlying this cross-talk between host and microbiota is critical for development of microbiome- or host-targeted therapeutics and prevention strategies. Here we review and discuss the most recent knowledge on the continuous reciprocal interaction between the host and microbes in health and respiratory disease. Furthermore, we highlight promising developments in microbiome-based therapies and discuss the need to employ more holistic approaches of restoring both the pulmonary niche and the microbial community.}, }
@article {pmid32429141, year = {2020}, author = {Spruit, CM and Wicklund, A and Wan, X and Skurnik, M and Pajunen, MI}, title = {Discovery of Three Toxic Proteins of Klebsiella Phage fHe-Kpn01.}, journal = {Viruses}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/v12050544}, pmid = {32429141}, issn = {1999-4915}, support = {288701//Academy of Finland/ ; Decision 2016//Jane ja Aatos Erkon Säätiö/ ; }, abstract = {The lytic phage, fHe-Kpn01 was isolated from sewage water using an extended-spectrum beta-lactamase-producing strain of Klebsiella pneumoniae as a host. The genome is 43,329 bp in size and contains direct terminal repeats of 222 bp. The genome contains 56 predicted genes, of which proteomics analysis detected 29 different proteins in purified phage particles. Comparison of fHe-Kpn01 to other phages, both morphologically and genetically, indicated that the phage belongs to the family Podoviridae and genus Drulisvirus. Because fHe-Kpn01 is strictly lytic and does not carry any known resistance or virulence genes, it is suitable for phage therapy. It has, however, a narrow host range since it infected only three of the 72 tested K. pneumoniae strains, two of which were of capsule type KL62. After annotation of the predicted genes based on the similarity to genes of known function and proteomics results on the virion-associated proteins, 22 gene products remained annotated as hypothetical proteins of unknown function (HPUF). These fHe-Kpn01 HPUFs were screened for their toxicity in Escherichia coli. Three of the HPUFs, encoded by the genes g10, g22, and g38, were confirmed to be toxic.}, }
@article {pmid32426004, year = {2020}, author = {Herman, RA}, title = {Increasing allergy: are antibiotics the elephant in the room?.}, journal = {Allergy, asthma, and clinical immunology : official journal of the Canadian Society of Allergy and Clinical Immunology}, volume = {16}, number = {}, pages = {35}, doi = {10.1186/s13223-020-00432-2}, pmid = {32426004}, issn = {1710-1484}, abstract = {Antibiotics cause dramatic changes to the human microbiome. The composition of the microbiome has been associated with changes in the immune system and these changes are beginning to be linked to immune diseases. Thus, antibiotics have been implicated as a significant contributor to the continual rise of allergies and autoimmune disease in developed countries. This recognition will hopefully result in the development of post-antibiotic therapies that restore a healthy microbiome and reduce immune system disorders.}, }
@article {pmid32422014, year = {2019}, author = {Lambring, CB and Siraj, S and Patel, K and Sankpal, UT and Mathew, S and Basha, R}, title = {Impact of the Microbiome on the Immune System.}, journal = {Critical reviews in immunology}, volume = {39}, number = {5}, pages = {313-328}, doi = {10.1615/CritRevImmunol.2019033233}, pmid = {32422014}, issn = {1040-8401}, abstract = {Higher organisms are all born with general immunity as well as with, increasingly, more specific immune systems. All immune mechanisms function with the intent of aiding the body in defense against infection. Internal and external factors alike have varying effects on the immune system, and the immune response is tailored specifically to each one. Accompanying the components of the human innate and adaptive immune systems are the other intermingling systems of the human body. Increasing understanding of the body's immune interactions with other systems has opened new avenues of study, including that of the microbiome. The microbiome has become a highly active area of research over the last 10 to 20 years since the NIH began funding the Human Microbiome Project (HMP), which was established in 2007. Several publications have focused on the characterization, functions, and complex interplay of the microbiome as it relates to the rest of the body. A dysfunction between the microbiome and the host has been linked to various diseases including cancers, metabolic deficiencies, autoimmune disorders, and infectious diseases. Further understanding of the microbiome and its interaction with the host in relation to diseases is needed in order to understand the implications of microbiome dysfunction and the possible use of microbiota in the prevention of disease. In this review, we have summarized information on the immune system, the microbiome, the microbiome's interplay with other systems, and the association of the immune system and the microbiome in diseases such as diabetes and colorectal cancer.}, }
@article {pmid32414567, year = {2020}, author = {Chipollini, J and Wright, JR and Nwanosike, H and Kepler, CY and Batai, K and Lee, BR and Spiess, PE and Stewart, DB and Lamendella, R}, title = {Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study.}, journal = {Urologic oncology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.urolonc.2020.04.014}, pmid = {32414567}, issn = {1873-2496}, abstract = {OBJECTIVES: The human microbiome has been linked to the development of several malignancies, but there is scarcity of data on the microbiome of bladder cancer patients. In this study, we analyzed microbial composition and diversity among patients with and without bladder cancer.<br><br>MATERIAL AND METHODS: Samples were collected from 38 urothelial carcinoma (UC) patients and 10 noncancer controls from August 2018 to May 2019. DNA was extracted and processed for 16 S ribosomal RNA sequencing. Alpha diversity community characteristics including evenness and richness as well as beta diversity metrics were obtained. Linear discriminant analysis effect size was used to identify microbial components whose sequences were more abundant. Pairwise statistics provided quantitative assessment of significant distributions among groups.<br><br>RESULTS: Thirty seven total samples contained high quality sequence data for subsequent analyses and divided into 3 cohorts: control (n = 10), muscle-invasive (n = 15) and superficial UC (n = 12). Control samples had significantly higher species evenness when compared to invasive (P = 0.031) and superficial tumors (P = 0.002). In addition, higher species richness was observed in noncancer versus cancer samples (Faith phylogenetic diversity, P < 0.05). Significantly enriched taxa were found in both control (Bacteroides, Lachnoclostridium, Burkholderiaceae) and cancer samples (Bacteroides and Faecalbacterium).<br><br>CONCLUSION: Significantly decreased microbial community diversity was seen in the urine of patients with bladder cancer when compared to a noncancer group. Distinct taxa were noted suggesting unique microbial communities in the urine of bladder cancer patients.}, }
@article {pmid32411613, year = {2020}, author = {Pinto, D and Calabrese, FM and De Angelis, M and Celano, G and Giuliani, G and Gobbetti, M and Rinaldi, F}, title = {Predictive Metagenomic Profiling, Urine Metabolomics, and Human Marker Gene Expression as an Integrated Approach to Study Alopecia Areata.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {146}, doi = {10.3389/fcimb.2020.00146}, pmid = {32411613}, issn = {2235-2988}, abstract = {Involvement of the microbiome in many different scalp conditions has been investigated over the years. Studies on the role of the scalp microbiome in specific diseases, such as those involving hair growth alterations like non-cicatricial [androgenetic alopecia (AGA), alopecia areata (AA)] and cicatricial alopecia lichen planopilaris, are of major importance. In the present work, we highlighted the differences in microbial populations inhabiting the scalp of AA subjects and a healthy sample cohort by using an integrated approach relying on metagenomic targeted 16S sequencing analysis, urine metabolomics, and human marker gene expression. Significant differences in genera abundances (p < 0.05) were found in the hypodermis and especially the dermis layer. Based on 16S sequencing data, we explored the differences in predicted KEGG pathways and identified some significant differences in predicted pathways related to the AA pathologic condition such as flagellar, assembly, bacterial chemotaxis, mineral absorption, ABC transporters, cellular antigens, glycosaminoglycan degradation, lysosome, sphingolipid metabolism, cell division, protein digestion and absorption, and energy metabolism. All predicted pathways were significantly enhanced in AA samples compared to expression in healthy samples, with the exceptions of mineral absorption, and ABC transporters. We also determined the expression of TNF-α, FAS, KCNA3, NOD-2, and SOD-2 genes and explored the relationships between human gene expression levels and microbiome composition by Pearson's correlation analysis; here, significant correlations both positive (SOD vs. Staphylococcus, Candidatus Aquiluna) and negative (FAS and SOD2 vs. Anaerococcus, Neisseria, and Acinetobacter) were highlighted. Finally, we inspected volatile organic metabolite profiles in urinary samples and detected statistically significant differences (menthol, methanethiol, dihydrodehydro-beta-ionone, 2,5-dimethylfuran, 1,2,3,4, tetrahydro-1,5,7-trimethylnapthalene) when comparing AA and healthy subject groups. This multiple comparison approach highlighted potential traits associated with AA and their relationship with the microbiota inhabiting the scalp, opening up novel therapeutic interventions in such kind of hair growth disorders mainly by means of prebiotics, probiotics, and postbiotics.}, }
@article {pmid32410293, year = {2020}, author = {Qureshi, SS and Kedo, M and Berthrong, ST}, title = {Gender-neutral bathroom surfaces recolonized by microbes more quickly than single gender bathrooms.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/lam.13316}, pmid = {32410293}, issn = {1472-765X}, abstract = {As humans become increasingly urban and spend more time inside the built environment, there will be increased interactions between the humans and shared public surface microbiomes. Recent cultural changes in the United States have led to increases gender-neutral bathrooms. Given that bathroom surfaces are frequently sanitized, we used this increased availability of gender-neutral bathrooms to examine how single or gender-neutral surfaces are recolonized with microbes. Given that male and female microbiomes vary, we hypothesized that rates of recolonization would differ between male, female, and gender-neutral bathroom surfaces. We collected swabs from common hand contacted surfaces in bathrooms and cultured microbes on selective and rich media to determine microbial abundance after cleaning. Recolonization was dominated by gram positive bacteria and was slowest on male, intermediate on female, and fastest on gender-neutral surfaces. These results imply that gender-neutral surfaces approach normal climax microbial communities more quickly than single gender bathrooms.}, }
@article {pmid32408372, year = {2020}, author = {Whitmont, RD}, title = {The Human Microbiome, Conventional Medicine, and Homeopathy.}, journal = {Homeopathy : the journal of the Faculty of Homeopathy}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0040-1709665}, pmid = {32408372}, issn = {1476-4245}, abstract = {Human health is intimately linked to the ecology and diversity of the human microbiome. Together, the human organism and the human microbiome work as a complex super-organism throughout the human life cycle. Microbiome science provides direct evidence and substantiation of the fundamental principles of homeopathy, including holism, psychosomatics, direction of cure, the Law of Similars, individuality and susceptibility, minimum dose, and homeostasis. Whilst many conventional (allopathic) medical treatments irreversibly damage the ecology of the microbiome and trigger chronic immune dysfunction and inflammation, the future sustainability of the entire field of medicine depends on the ability to recognize these inconvenient biological truths and to embrace a safer approach based on this evidence. Fortunately, one of the oldest forms of clinically verifiable, evidence-based, and ecologically sustainable medicine, that does not harm the microbiome, already exists in the form of homeopathy.}, }
@article {pmid32407510, year = {2020}, author = {Ma, ZS}, title = {Heterogeneity-Disease relationship in the human microbiome associated diseases.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiaa093}, pmid = {32407510}, issn = {1574-6941}, abstract = {Space is a critical and also challenging frontier in human microbiome research. It has been found that lack of consideration of scales beyond individual and ignoring of microbe dispersal are two crucial roadblocks in preventing deep understanding of the spatial heterogeneity of human microbiome. Assessing and interpreting the heterogeneity and dispersal in microbiomes explicitly are particularly challenging, but implicit approaches such as Taylor's power law (TPL) can be rather effective. Based on TPL, which achieved a rare status of ecological laws, we introduce a general methodology for characterizing the spatial heterogeneity of microbiome (i.e. characterization of microbial spatial distribution) and further apply it for investigating the heterogeneity-disease relationship (HDR) via analyzing a big dataset of 26 MAD (microbiome-associated disease) studies covering nearly all high-profile MADs including obesity, diabetes and gout. It was found that in majority of the MAD cases, the microbiome was sufficiently resilient to endure the disease disturbances. Specifically, in approximately 10%-16% cases, disease effects were significant-the healthy and diseased cohorts exhibited statistically significant differences in the TPL heterogeneity parameters. We further compared HDR with classic diversity-disease relationship (DDR) and explained their mechanistic differences. Both HDR and DDR cross-verified remarkable resilience of the human microbiomes against MADs.}, }
@article {pmid32406914, year = {2020}, author = {Wang, Y and Bhattacharya, T and Jiang, Y and Qin, X and Wang, Y and Liu, Y and Saykin, AJ and Chen, L}, title = {A novel deep learning method for predictive modeling of microbiome data.}, journal = {Briefings in bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1093/bib/bbaa073}, pmid = {32406914}, issn = {1477-4054}, abstract = {With the development and decreasing cost of next-generation sequencing technologies, the study of the human microbiome has become a rapid expanding research field, which provides an unprecedented opportunity in various clinical applications such as drug response predictions and disease diagnosis. It is thus essential and desirable to build a prediction model for clinical outcomes based on microbiome data that usually consist of taxon abundance and a phylogenetic tree. Importantly, all microbial species are not uniformly distributed in the phylogenetic tree but tend to be clustered at different phylogenetic depths. Therefore, the phylogenetic tree represents a unique correlation structure of microbiome, which can be an important prior to improve the prediction performance. However, prediction methods that consider the phylogenetic tree in an efficient and rigorous way are under-developed. Here, we develop a novel deep learning prediction method MDeep (microbiome-based deep learning method) to predict both continuous and binary outcomes. Conceptually, MDeep designs convolutional layers to mimic taxonomic ranks with multiple convolutional filters on each convolutional layer to capture the phylogenetic correlation among microbial species in a local receptive field and maintain the correlation structure across different convolutional layers via feature mapping. Taken together, the convolutional layers with its built-in convolutional filters capture microbial signals at different taxonomic levels while encouraging local smoothing and preserving local connectivity induced by the phylogenetic tree. We use both simulation studies and real data applications to demonstrate that MDeep outperforms competing methods in both regression and binary classifications. Availability and Implementation: MDeep software is available at https://github.com/lichen-lab/MDeep Contact:chen61@iu.edu.}, }
@article {pmid32400169, year = {2020}, author = {Salehi, B and Dimitrijević, M and Aleksić, A and Neffe-Skocińska, K and Zielińska, D and Kołożyn-Krajewska, D and Sharifi-Rad, J and Stojanović-Radić, Z and Prabu, SM and Rodrigues, CF and Martins, N}, title = {Human microbiome and homeostasis: insights into the key role of prebiotics, probiotics, and symbiotics.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/10408398.2020.1760202}, pmid = {32400169}, issn = {1549-7852}, abstract = {The interest in the study of the gut microbiome has grown exponentially. Indeed, its impact on health and disease has been increasingly reported, and the importance of keeping gut microbiome homeostasis clearly highlighted. However, and despite many advances, there are still some gaps, as well as the real discernment on the contribution of some species falls far short of what is needed. Anyway, it is already more than a solid fact of its importance in maintaining health and preventing disease, as well as in the treatment of some pathologies. In this sense, and given the existence of some ambiguous opinions, the present review aims to discuss the importance of gut microbiome in homeostasis maintenance, and even the role of probiotics, prebiotics, and symbiotics in both health promotion and disease prevention.}, }
@article {pmid32397233, year = {2020}, author = {Satokari, R}, title = {High Intake of Sugar and the Balance between Pro- and Anti-Inflammatory Gut Bacteria.}, journal = {Nutrients}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/nu12051348}, pmid = {32397233}, issn = {2072-6643}, abstract = {The so-called Western diet is rich in saturated fat and sugars and poor in plant-derived fibers, and it is associated with an increased risk of metabolic and cardiovascular diseases, as well as chronic (low grade) inflammation. The detrimental effects of poor diet are in part mediated by gut microbiota, whose composition, functionality and metabolic end products respond to dietary changes. Recent studies have shown that high intake of sugars increase the relative abundance of Proteobacteria in the gut, while simultaneously decreasing the abundance of Bacteroidetes, which can mitigate the effects of endotoxin, as well as reinforce gut barrier function. Thus, a high sugar intake may stagger the balance of microbiota to have increased pro-inflammatory properties and decreased the capacity to regulate epithelial integrity and mucosal immunity. Consequently, high dietary sugar can, through the modulation of microbiota, promote metabolic endotoxemia, systemic (low grade) inflammation and the development of metabolic dysregulation and thereby, high dietary sugar may have many-fold deleterious health effects, in addition to providing excess energy.}, }
@article {pmid32397065, year = {2020}, author = {Bangayan, NJ and Shi, B and Trinh, J and Barnard, E and Kasimatis, G and Curd, E and Li, H}, title = {MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data.}, journal = {Microorganisms}, volume = {8}, number = {5}, pages = {}, doi = {10.3390/microorganisms8050684}, pmid = {32397065}, issn = {2076-2607}, support = {UH2AR057503/NH/NIH HHS/United States ; R01GM099530/NH/NIH HHS/United States ; }, abstract = {The microbiome plays an important role in human physiology. The composition of the human microbiome has been described at the phylum, class, genus, and species levels, however, it is largely unknown at the strain level. The importance of strain-level differences in microbial communities has been increasingly recognized in understanding disease associations. Current methods for identifying strain populations often require deep metagenomic sequencing and a comprehensive set of reference genomes. In this study, we developed a method, metagenomic multi-locus sequence typing (MG-MLST), to determine strain-level composition in a microbial community by combining high-throughput sequencing with multi-locus sequence typing (MLST). We used a commensal bacterium, Propionibacterium acnes, as an example to test the ability of MG-MLST in identifying the strain composition. Using simulated communities, MG-MLST accurately predicted the strain populations in all samples. We further validated the method using MLST gene amplicon libraries and metagenomic shotgun sequencing data of clinical skin samples. MG-MLST yielded consistent results of the strain composition to those obtained from nearly full-length 16S rRNA clone libraries and metagenomic shotgun sequencing analysis. When comparing strain-level differences between acne and healthy skin microbiomes, we demonstrated that strains of RT2/6 were highly associated with healthy skin, consistent with previous findings. In summary, MG-MLST provides a quantitative analysis of the strain populations in the microbiome with diversity and richness. It can be applied to microbiome studies to reveal strain-level differences between groups, which are critical in many microorganism-related diseases.}, }
@article {pmid32393397, year = {2020}, author = {Koh, H and Zhao, N}, title = {A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals.}, journal = {Microbiome}, volume = {8}, number = {1}, pages = {63}, doi = {10.1186/s40168-020-00834-9}, pmid = {32393397}, issn = {2049-2618}, support = {U24OD023382//NIH for the Environmental Influences of Child Health Outcomes (ECHO) Data Analysis Center/ ; 1P30AI094189//Johns Hopkins University Center for AIDS Research/ ; }, abstract = {BACKGROUND: In human microbiome studies, it is crucial to evaluate the association between microbial group (e.g., community or clade) composition and a host phenotype of interest. In response, a number of microbial group association tests have been proposed, which account for the unique features of the microbiome data (e.g., high-dimensionality, compositionality, phylogenetic relationship). These tests generally fall in the class of aggregation tests which amplify the overall group association by combining all the underlying microbial association signals, and, therefore, they are powerful when many microbial species are associated with a given host phenotype (i.e., low sparsity). However, in practice, the microbial association signals can be highly sparse, and this is especially the situation where we have a difficulty to discover the microbial group association.<br><br>METHODS: Here, we introduce a powerful microbial group association test for sparse microbial association signals, namely, microbiome higher criticism analysis (MiHC). MiHC is a data-driven omnibus test taken in a search space spanned by tailoring the higher criticism test to incorporate phylogenetic information and/or modulate sparsity levels and including the Simes test for excessively high sparsity levels. Therefore, MiHC robustly adapts to diverse phylogenetic relevance and sparsity levels.<br><br>RESULTS: Our simulations show that MiHC maintains a high power at different phylogenetic relevance and sparsity levels with correct type I error controls. We also apply MiHC to four real microbiome datasets to test the association between respiratory tract microbiome and smoking status, the association between the infant's gut microbiome and delivery mode, the association between the gut microbiome and type 1 diabetes status, and the association between the gut microbiome and human immunodeficiency virus status.<br><br>CONCLUSIONS: In practice, the true underlying association pattern on the extent of phylogenetic relevance and sparsity is usually unknown. Therefore, MiHC can be a useful analytic tool because of its high adaptivity to diverse phylogenetic relevance and sparsity levels. MiHC can be implemented in the R computing environment using our software package freely available at https://github.com/hk1785/MiHC.}, }
@article {pmid32391057, year = {2020}, author = {Thomas, G and Bain, JM and Budge, S and Brown, AJP and Ames, RM}, title = {Identifying Candida albicans Gene Networks Involved in Pathogenicity.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {375}, doi = {10.3389/fgene.2020.00375}, pmid = {32391057}, issn = {1664-8021}, abstract = {Candida albicans is a normal member of the human microbiome. It is also an opportunistic pathogen, which can cause life-threatening systemic infections in severely immunocompromized individuals. Despite the availability of antifungal drugs, mortality rates of systemic infections are high and new drugs are needed to overcome therapeutic challenges including the emergence of drug resistance. Targeting known disease pathways has been suggested as a promising avenue for the development of new antifungals. However, <30% of C. albicans genes are verified with experimental evidence of a gene product, and the full complement of genes involved in important disease processes is currently unknown. Tools to predict the function of partially or uncharacterized genes and generate testable hypotheses will, therefore, help to identify potential targets for new antifungal development. Here, we employ a network-extracted ontology to leverage publicly available transcriptomics data and identify potential candidate genes involved in disease processes. A subset of these genes has been phenotypically screened using available deletion strains and we present preliminary data that one candidate, PEP8, is involved in hyphal development and immune evasion. This work demonstrates the utility of network-extracted ontologies in predicting gene function to generate testable hypotheses that can be applied to pathogenic systems. This could represent a novel first step to identifying targets for new antifungal therapies.}, }
@article {pmid32391012, year = {2020}, author = {Peroni, DG and Nuzzi, G and Trambusti, I and Di Cicco, ME and Comberiati, P}, title = {Microbiome Composition and Its Impact on the Development of Allergic Diseases.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {700}, doi = {10.3389/fimmu.2020.00700}, pmid = {32391012}, issn = {1664-3224}, abstract = {Allergic diseases, such as food allergy (FA), atopic dermatitis (AD), and asthma, are heterogeneous inflammatory immune-mediated disorders that currently constitute a public health issue in many developed countries worldwide. The significant increase in the prevalence of allergic diseases reported over the last few years has closely paralleled substantial environmental changes both on a macro and micro scale, which have led to reduced microbial exposure in early life and perturbation of the human microbiome composition. Increasing evidence shows that early life interactions between the human microbiome and the immune cells play a pivotal role in the development of the immune system. Therefore, the process of early colonization by a &quot;healthy&quot; microbiome is emerging as a key determinant of life-long health. In stark contrast, the perturbation of such a process, which results in changes in the host-microbiome biodiversity and metabolic activities, has been associated with greater susceptibility to immune-mediated disorders later in life, including allergic diseases. Here, we outline recent findings on the potential contribution of the microbiome in the gastrointestinal tract, skin, and airways to the development of FA, AD, and asthma. Furthermore, we address how the modulation of the microbiome composition in these different body districts could be a potential strategy for the prevention and treatment of allergic diseases.}, }
@article {pmid32390974, year = {2020}, author = {Jiang, T and Chen, W and Cao, L and He, Y and Zhou, H and Mao, H}, title = {Abundance, Functional, and Evolutionary Analysis of Oxalyl-Coenzyme A Decarboxylase in Human Microbiota.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {672}, doi = {10.3389/fmicb.2020.00672}, pmid = {32390974}, issn = {1664-302X}, abstract = {Oxalic acid and its oxalate salts have been linked to kidney stones and other health problems and about 80% kidney stones are made up of calcium oxalate. Oxalyl coenzyme A decarboxylase (OXC) is a key enzyme in the catabolism of oxalate. In this study, we performed bioinformatic and biochemical analysis of OXC. First, we mined the OXC sequences from a public protein database and collected 1396 putative OXC sequences. These sequences were widely spread and mainly distributed in Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, and Betaproteobacteria and classified into seven clusters. The phylogenetic relationship and evolutionary rate of the 7 clusters showed that OXC are highly conserved. Second, the abundance of the different clusters of OXC was explored in 380 human microbiome datasets, which showed that OXCs in Cluster 1 were relatively high in the gut while OXCs in Clusters 2-4 were relatively enriched in the vagina. Third, we measured the activity of one OXC from Mycobacterium mageritense (OXCmm) in Cluster 3, in which there was no experimentally characterized enzymes. Mutation analysis showed that OXCmm shared the same active sites with the OXC from Oxalobacter formigenes. Taken together, this analysis provides a better insight into the distribution and catalysis of OXC and further potential alternative application of OXC active bacteria as probiotics in the management of kidney stone disease.}, }
@article {pmid32384684, year = {2020}, author = {Caparrós-Martín, JA and Flynn, S and Reen, FJ and Woods, DF and Agudelo-Romero, P and Ranganathan, SC and Stick, SM and O'Gara, F}, title = {The Detection of Bile Acids in the Lungs of Paediatric Cystic Fibrosis Patients Is Associated with Altered Inflammatory Patterns.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/diagnostics10050282}, pmid = {32384684}, issn = {2075-4418}, support = {FP7-PEOPLE-2013-ITN, 607786//European Comission/ ; FP7-KBBE-2012-6, CP-TP-312184//European Comission/ ; FP7-KBBE-2012-6, 311975//European Comission/ ; OCEAN 2011-2, 287589//European Comission/ ; Marie Curie 256596//European Comission/ ; EU-634486//European Comission/ ; SSPC-2, 12/RC/2275/SFI_/Science Foundation Ireland/Ireland ; SSP3-Pharm5:13/TIDA/B2625/SFI_/Science Foundation Ireland/Ireland ; 12/TIDA/B2411/SFI_/Science Foundation Ireland/Ireland ; 12/TIDA/B2405/SFI_/Science Foundation Ireland/Ireland ; 14/TIDA/2438/SFI_/Science Foundation Ireland/Ireland ; 15/TIDA/2977/SFI_/Science Foundation Ireland/Ireland ; FIRM/RSF/CoFoRD//The Department of Agriculture and Food/ ; FIRM 08/RDC/629//The Department of Agriculture and Food/ ; FIRM 1/F009/MabS//The Department of Agriculture and Food/ ; FIRM 13/F/516//The Department of Agriculture and Food/ ; HRB-ILP-POR-2019-004/HRBI_/Health Research Board/Ireland ; MRCG-2014-6//Health Research Board/Irish Thoracic Society/ ; Beaufort award C2CRA 2007/082//The Marine Institute/ ; Walsh Fellowship 2013//Teagasc/ ; The Glenn Brown Memorial Grant 2017//The Institute for Respiratory Health/ ; MRCG-2018-16/HRBI_/Health Research Board/Ireland ; Grant CFF 1710//US CF Foundation/ ; }, abstract = {Background: Cystic fibrosis (CF) is a hereditary disorder in which persistent unresolved inflammation and recurrent airway infections play major roles in the initiation and progression of the disease. Little is known about triggering factors modulating the transition to chronic microbial infection and inflammation particularly in young children. Cystic fibrosis respiratory disease starts early in life, with the detection of inflammatory markers and infection evident even before respiratory symptoms arise. Thus, identifying factors that dysregulate immune responsiveness at the earliest stages of the disease will provide novel targets for early therapeutic intervention. Methods: We evaluated the clinical significance of bile acid detection in the bronchoalveolar lavage fluid of clinically stable preschool-aged children diagnosed with CF. Results: We applied an unbiased classification strategy to categorize these specimens based on bile acid profiles. We provide clear associations linking the presence of bile acids in the lungs with alterations in the expression of inflammatory markers. Using multiple regression analysis, we also demonstrate that clustering based on bile acid profiles is a meaningful predictor of the progression of structural lung disease. Conclusions: Altogether, our work has identified a clinically relevant host-derived factor that may participate in shaping early events in the aetiology of CF respiratory disease.}, }
@article {pmid32380174, year = {2020}, author = {Price, TK and Lin, H and Gao, X and Thomas-White, KJ and Hilt, EE and Mueller, ER and Wolfe, AJ and Dong, Q and Brubaker, L}, title = {Bladder Bacterial Diversity Differs In Continent and Incontinent Women: A Cross-Sectional Study.}, journal = {American journal of obstetrics and gynecology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajog.2020.04.033}, pmid = {32380174}, issn = {1097-6868}, abstract = {BACKGROUND: Since the discovery of the bladder microbiome (urobiome), interest has grown in learning whether urobiome characteristics have a role in clinical phenotyping and/or provide opportunities for novel therapeutic approaches for women with common forms of urinary incontinence (UI).<br><br>OBJECTIVES: To test our hypothesis that the bladder urobiome differs between continent women and women affected by UI by assessing associations between UI status and the cultured urobiome.<br><br>STUDY DESIGN: With IRB oversight, transurethral catheterized urine specimens were collected from 309 adult women, who were categorized into three groups using response to the validated Pelvic Floor Distress Inventory (PFDI): Continent Controls (N=150) and 2 Urinary Incontinence (UI cohorts) - Stress Urinary Incontinence (SUI) (N=50) and Urgency Urinary Incontinence (UUI) (N=109). Symptom severity was assessed with the Urinary Distress Inventory (UDI) subscale score of the PFDI. Microbes were assessed by the Expanded Quantitative Urine Culture protocol, which detects the most common bladder microbes (bacteria and yeast). Microbes were identified to the species level by MALDI-TOF mass spectrometry. Alpha diversity indices were calculated for culture-positive samples and compared across the three groups. The association between UDI scores versus alpha diversity indices and species abundance were estimated.<br><br>RESULTS: Participants had a mean age of 53 years (range 22-90); most were Caucasian (65%). Women with UI were slightly older (Control=47, SUI=54, UUI=61). By design, UDI symptom scores differed (Control = 8.43 (10.1), SUI = 97.95 (55.36), UUI = 93.71 (49.12), p<0.001). While most participants (216, 70%) had Expanded Quantitative Urine Culture-detected bacteria, the UI cohorts had a higher detection frequency than did the Control cohort (Control=57%, SUI 86%, UUI 81%, p<0.001). The most frequently detected species were as follows: Controls, Lactobacillus iners (12.7%), Streptococcus anginosus (12.7%), L. crispatus (10.7%), and L. gasseri (10%); SUI, S. anginosus (26%), L. iners (18%), Staphylococcus epidermidis (18%), and L. jensenii (16%); UUI, S. anginosus (30.3%), L. gasseri (22%), Aerococcus urinae (18.3%), and Gardnerella vaginalis (17.4%). However, only Actinotignum (formerly Actinobaculum) schaalii, A. urinae, A. sanguinicola, and Corynebacterium lipophile group were found at significantly higher mean abundances in at least one of the UI cohorts when compared to the Control cohort (Wilcoxon p<0.02), and no individual genus differed significantly between the two UI cohorts. Both UI cohorts had increased alpha diversity relative to continent controls with indices of species richness, but not evenness, strongly associated with UI.<br><br>CONCLUSIONS: In adult women, the composition of the culturable bladder urobiome is associated with UI, regardless of common incontinence subtype. Detection of more unique living microbes was associated with worse incontinence severity. Culturable species richness is significantly greater in the UI cohorts than continent controls.}, }
@article {pmid32379704, year = {2020}, author = {Liu, S and Wang, Y and Zhao, L and Sun, X and Feng, Q}, title = {Microbiome succession with increasing age in three oral sites.}, journal = {Aging}, volume = {12}, number = {}, pages = {}, doi = {10.18632/aging.103108}, pmid = {32379704}, issn = {1945-4589}, abstract = {The incidence of oral diseases is remarkably increased with age, and it may be related to oral microbiota. In this study, we systematically investigated the microbiota of gingival crevicular fluid (GCF), tongue back (TB) and saliva (SAL) from various age groups in healthy populations. The microbial diversity results indicated that the α-diversity of bacteria had a tendency to decrease in aging mouth, whereas the β-diversity showed an opposite increasing trend in all three sites. Next, the microbial structure exploration revealed a divergence in bacterial profile in three sites in response to aging, but the intersite differential bacteria demonstrated a uniform bell-shaped variation trend with age. Meanwhile, several age-differentiated genera were shared by GCF, SAL and TB sites, and the bacterial correlation analysis demonstrated a clear shift in the pattern of bacterial correlations with age. Moreover, both the intra- and intersite &quot;core microbiome&quot; showed significantly decreased bacterial diversities with age. Finally, the trending differential bacteria species were used as a biomarker to distinguish the different age groups, and the prediction accuracies in GCF were 0.998, 0.809, 0.668, 0.675 and 0.956. Our results revealed the characteristics of intra- and intersite bacterial succession with age, providing novel insights into senile oral diseases.}, }
@article {pmid32374853, year = {2020}, author = {Bartolomaeus, TUP and Birkner, T and Bartolomaeus, H and Löber, U and Avery, EG and Mähler, A and Weber, D and Kochlik, B and Balogh, A and Wilck, N and Boschmann, M and Müller, DN and Markó, L and Forslund, SK}, title = {Quantifying Technical Confounders in Microbiome Studies.}, journal = {Cardiovascular research}, volume = {}, number = {}, pages = {}, doi = {10.1093/cvr/cvaa128}, pmid = {32374853}, issn = {1755-3245}, abstract = {AIMS: Recent technical developments have allowed the study of the human microbiome to accelerate at an unprecedented pace. Methodological differences may have considerable impact on the results obtained. Thus, we investigated how different storage, isolation and DNA extraction methods can influence the characterization of the intestinal microbiome, compared to the impact of true biological signals such as intraindividual variability, nutrition, health and demographics.<br><br>METHODS AND RESULTS: An observative cohort study in 27 healthy subjects was performed. Participants were instructed to collect stool samples twice spaced by a week, using six different methods (naive and Zymo DNA/RNA Shield on dry ice, OMNIgene GUT, RNALater, 95% ethanol, Zymo DNA/RNA Shield at room temperature). DNA extraction from all samples was performed comparatively using QIAamp Power Fecal and ZymoBIOMICS DNA kits. 16S rRNA sequencing of the gut microbiota as well as qPCRs were performed on the isolated DNA. Metrics included alpha diversity as well as multivariate and univariate comparisons of samples, controlling for covariate patterns computationally. Interindividual differences explained 7.4% of overall microbiome variability, whereas the choice of DNA extraction method explained a further 5.7%. At phylum level, the tested kits differed in their recovery of gram-positive bacteria, which is reflected in a significantly skewed enterotype distribution.<br><br>CONCLUSIONS: DNA extraction methods had the highest impact on observed microbiome variability, and were comparable to interindividual differences, thus may spuriously mimic the microbiome signatures of various health and nutrition factors. Conversely, collection methods had a relatively small influence on microbiome composition. The present study provides necessary insight into the technical variables which can lead to divergent results from seemingly similar study designs. We anticipate that these results will contribute to future efforts towards standardization of microbiome quantification procedures in clinical research.<br><br>TRANSLATIONAL PERSPECTIVES: By applying a framework which is typical for the investigation of the microbiome in cardiovascular disease patients, we assess the role of these confounders under realistic circumstances. Our work allows quality control and design improvement for upcoming translational microbiome studies such as the search for disease biomarkers or efficacy predictors for personalized treatment regimes.}, }
@article {pmid32374655, year = {2020}, author = {Zhu, C and Yuan, C and Wei, FQ and Sun, XY and Zheng, SG}, title = {Intraindividual Variation and Personal Specificity of Salivary Microbiota.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {22034520917155}, doi = {10.1177/0022034520917155}, pmid = {32374655}, issn = {1544-0591}, abstract = {Salivary microbiota is a typical habitat of the human microbiome. This study intended to use salivary microbiota as a model aiming to systematically address the influence of collection methods and temporal dynamics on the human microbiota compared to personal specificity. We carried out a supervised short-term longitudinal study to evaluate the influence of the change of collection methods and sampling time point on salivary microbiota in 10 systemically and orally healthy individuals with certain confounding factors (sex, oral and general health state, medication history, physical exercise, diet, and oral hygiene behavior) controlled before and during the sampling period. The microbial profiles were analyzed by 16S rDNA V3 to V4 hypervariable region amplicon sequencing. The taxonomic structure represented by the dominant species and the weighted UniFrac distance algorithm were used to demonstrate the individual specificity and the intraindividual variation introduced by the change of collection method and sampling time point. The findings suggested individual specificity existed in salivary microbiota from individuals with similar oral and general health status. The intraindividual variation brought by the change of collection method or sampling time point might introduce remarkable perturbation with the personal specificity. Insights into the intraindividual variation and personal specificity of salivary microbiota will enhance our understanding in salivary microbiota-related research. We recommend keeping collection conditions consistent within a study to avoid interference brought by the sampling. The strategy of repeated sampling at multiple time points as representative samples, as well as thorough interpretation of the complex relationships and causality between microbiome composition and disease without the interference of temporal dynamics, is optimal for research exploring the relationship between the salivary microbiome and disease.}, }
@article {pmid32373093, year = {2020}, author = {Woods, DF and Kozak, IM and O'Gara, F}, title = {Microbiome and Functional Analysis of a Traditional Food Process: Isolation of a Novel Species (Vibrio hibernica) With Industrial Potential.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {647}, doi = {10.3389/fmicb.2020.00647}, pmid = {32373093}, issn = {1664-302X}, abstract = {Traditional food preservation processes are vital for the food industry. They not only preserve a high-quality protein and nutrient source but can also provide important value-added organoleptic properties. The Wiltshire process is a traditional food curing method applied to meat, and special recognition is given to the maintenance of a live rich microflora within the curing brine. We have previously analyzed a curing brine from this traditional meat process and characterized a unique microbial core signature. The characteristic microbial community is actively maintained and includes the genera, Marinilactibacillus, Carnobacterium, Leuconostoc, and Vibrio. The bacteria present are vital for Wiltshire curing compliance. However, the exact function of this microflora is largely unknown. A microbiome profiling of three curing brines was conducted and investigated for functional traits by the robust bioinformatic tool, Tax4Fun. The key objective was to uncover putative metabolic functions associated with the live brine and to identify changes over time. The functional bioinformatic analysis revealed metabolic enrichments over time, with many of the pathways identified as being involved in organoleptic development. The core bacteria present in the brine are Lactic Acid Bacteria (LAB), with the exception of the Vibrio genus. LAB are known for their positive contribution to food processing, however, little work has been conducted on the use of Vibrio species for beneficial processes. The Vibrio genome was sequenced by Illumina MiSeq technologies and annotated in RAST. A phylogenetic reconstruction was completed using both the 16S rRNA gene and housekeeping genes, gapA, ftsZ, mreB, topA, gyrB, pyrH, recA, and rpoA. The isolated Vibrio species was defined as a unique novel species, named Vibrio hibernica strain B1.19. Metabolic profiling revealed that the bacterium has a unique substrate scope in comparison to other closely related Vibrio species tested. The possible function and industrial potential of the strain was investigated using carbohydrate metabolizing profiling under food processing relevant conditions. Vibrio hibernica is capable of metabolizing a unique carbohydrate profile at low temperatures. This characteristic provides new application options for use in the industrial food sector, as well as highlighting the key role of this bacterium in the Wiltshire curing process.}, }
@article {pmid32372951, year = {2020}, author = {Abdelsalam, NA and Ramadan, AT and ElRakaiby, MT and Aziz, RK}, title = {Toxicomicrobiomics: The Human Microbiome vs. Pharmaceutical, Dietary, and Environmental Xenobiotics.}, journal = {Frontiers in pharmacology}, volume = {11}, number = {}, pages = {390}, doi = {10.3389/fphar.2020.00390}, pmid = {32372951}, issn = {1663-9812}, abstract = {The harmful impact of xenobiotics on the environment and human health is being more widely recognized; yet, inter- and intraindividual genetic variations among humans modulate the extent of harm, mostly through modulating the outcome of xenobiotic metabolism and detoxification. As the Human Genome Project revealed that host genetic, epigenetic, and regulatory variations could not sufficiently explain the complexity of interindividual variability in xenobiotics metabolism, its sequel, the Human Microbiome Project, is investigating how this variability may be influenced by human-associated microbial communities. Xenobiotic-microbiome relationships are mutual and dynamic. Not only does the human microbiome have a direct metabolizing potential on xenobiotics, but it can also influence the expression of the host metabolizing genes and the activity of host enzymes. On the other hand, xenobiotics may alter the microbiome composition, leading to a state of dysbiosis, which is linked to multiple diseases and adverse health outcomes, including increased toxicity of some xenobiotics. Toxicomicrobiomics studies these mutual influences between the ever-changing microbiome cloud and xenobiotics of various origins, with emphasis on their fate and toxicity, as well the various classes of microbial xenobiotic-modifying enzymes. This review article discusses classic and recent findings in toxicomicrobiomics, with examples of interactions between gut, skin, urogenital, and oral microbiomes with pharmaceutical, food-derived, and environmental xenobiotics. The current state and future prospects of toxicomicrobiomic research are discussed, and the tools and strategies for performing such studies are thoroughly and critically compared.}, }
@article {pmid32369899, year = {2020}, author = {Lee-Sarwar, KA and Lasky-Su, J and Kelly, RS and Litonjua, AA and Weiss, ST}, title = {Metabolome-Microbiome Crosstalk and Human Disease.}, journal = {Metabolites}, volume = {10}, number = {5}, pages = {}, doi = {10.3390/metabo10050181}, pmid = {32369899}, issn = {2218-1989}, support = {K08 HL148178/NH/NIH HHS/United States ; K01 HL146980/NH/NIH HHS/United States ; R01HL123915/NH/NIH HHS/United States ; R01HL141826/NH/NIH HHS/United States ; UH3OD023268/NH/NIH HHS/United States ; }, abstract = {In this review, we discuss the growing literature demonstrating robust and pervasive associations between the microbiome and metabolome. We focus on the gut microbiome, which harbors the taxonomically most diverse and the largest collection of microorganisms in the human body. Methods for integrative analysis of these &quot;omics&quot; are under active investigation and we discuss the advances and challenges in the combined use of metabolomics and microbiome data. Findings from large consortia, including the Human Microbiome Project and Metagenomics of the Human Intestinal Tract (MetaHIT) and others demonstrate the impact of microbiome-metabolome interactions on human health. Mechanisms whereby the microbes residing in the human body interact with metabolites to impact disease risk are beginning to be elucidated, and discoveries in this area will likely be harnessed to develop preventive and treatment strategies for complex diseases.}, }
@article {pmid32366680, year = {2020}, author = {Zhou, X and Johnson, JS and Spakowicz, D and Zhou, W and Zhou, Y and Sodergren, E and Snyder, M and Weinstock, GM}, title = {Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 with Clostridia and Insulin Sensitivity in Humans.}, journal = {Diabetes}, volume = {}, number = {}, pages = {}, doi = {10.2337/db19-0592}, pmid = {32366680}, issn = {1939-327X}, abstract = {Recent studies using mouse models suggest that interaction between the gut microbiome and IL-17/IL-22 producing cells plays a role in the development of metabolic diseases. We investigated this relationship in humans using data from the prediabetes study of the Integrated Human Microbiome Project (iHMP). Specifically, we addressed the hypothesis that early in the onset of metabolic diseases there is a decline in serum levels of IL-17/IL-22, with concomitant changes in the gut microbiome. Clustering iHMP study participants on the basis of longitudinal IL-17/IL-22 profiles identified discrete groups. Individuals distinguished by low levels of IL-17/IL-22 were linked to established markers of metabolic disease, including insulin sensitivity. These individuals also displayed gut microbiome dysbiosis, characterized by decreased diversity, and IL-17/IL-22-related declines in the phylum Firmicutes, class Clostridia, and order Clostridiales. This ancillary analysis of the iHMP data therefore supports a link between the gut microbiome, IL-17/IL-22 and the onset of metabolic diseases. This raises the possibility for novel, microbiome-related therapeutic targets that may effectively alleviate metabolic diseases in humans as they do in animal models.}, }
@article {pmid32360945, year = {2020}, author = {Piggott, DA and Tuddenham, S}, title = {The Gut Microbiome and Frailty.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.trsl.2020.03.012}, pmid = {32360945}, issn = {1878-1810}, abstract = {The human microbiome is constituted by an extensive network of organisms that lie at the host/environment interface and transduce signals that play vital roles in human health and disease across the lifespan. Frailty is a critical aging-related syndrome marked by diminished physiologic reserve and heightened vulnerability to stress, predictive of major adverse clinical outcomes including death. While recent studies suggest the microbiome may impact key pathways critical to frailty pathophysiology, direct evaluation of the microbiome-frailty relationship remains limited. In this article, we review the complex interplay of biological, behavioral and environmental factors that may influence shifts in gut microbiome composition and function in aging populations and the putative implications of such shifts for progression to frailty. We discuss HIV infection as a key prototype for elucidating the complex pathways via which the microbiome may precipitate frailty. Finally, we review considerations for future research efforts.}, }
@article {pmid32351023, year = {2020}, author = {Ndika, J and Ilves, M and Kooter, IM and Gröllers-Mulderij, M and Duistermaat, E and Tromp, PC and Kuper, F and Kinaret, P and Greco, D and Karisola, P and Alenius, H}, title = {Mechanistic Similarities between 3D Human Bronchial Epithelium and Mice Lung, Exposed to Copper Oxide Nanoparticles, Support Non-Animal Methods for Hazard Assessment.}, journal = {Small (Weinheim an der Bergstrasse, Germany)}, volume = {}, number = {}, pages = {e2000527}, doi = {10.1002/smll.202000527}, pmid = {32351023}, issn = {1613-6829}, support = {309329//Seventh Framework Programme/ ; 297885//Academy of Finland/ ; 307768//Academy of Finland/ ; }, abstract = {The diversity and increasing prevalence of products derived from engineered nanomaterials (ENM), warrants implementation of non-animal approaches to health hazard assessment for ethical and practical reasons. Although non-animal approaches are becoming increasingly popular, there are almost no studies of side-by-side comparisons with traditional in vivo assays. Here, transcriptomics is used to investigate mechanistic similarities between healthy/asthmatic models of 3D air-liquid interface (ALI) cultures of donor-derived human bronchial epithelia cells, and mouse lung tissue, following exposure to copper oxide ENM. Only 19% of mouse lung genes with human orthologues are not expressed in the human 3D ALI model. Despite differences in taxonomy and cellular complexity between the systems, a core subset of matching genes cluster mouse and human samples strictly based on ENM dose (exposure severity). Overlapping gene orthologue pairs are highly enriched for innate immune functions, suggesting an important and maybe underestimated role of epithelial cells. In conclusion, 3D ALI models based on epithelial cells, are primed to bridge the gap between traditional 2D in vitro assays and animal models of airway exposure, and transcriptomics appears to be a unifying dose metric that links in vivo and in vitro test systems.}, }
@article {pmid32350240, year = {2020}, author = {Xiao, J and Fiscella, KA and Gill, SR}, title = {Oral microbiome: possible harbinger for children's health.}, journal = {International journal of oral science}, volume = {12}, number = {1}, pages = {12}, doi = {10.1038/s41368-020-0082-x}, pmid = {32350240}, issn = {2049-3169}, support = {K23 DE027412/DE/NIDCR NIH HHS/United States ; }, abstract = {The human microbiome functions as an intricate and coordinated microbial network, residing throughout the mucosal surfaces of the skin, oral cavity, gastrointestinal tract, respiratory tract, and reproductive system. The oral microbiome encompasses a highly diverse microbiota, consisting of over 700 microorganisms, including bacteria, fungi, and viruses. As our understanding of the relationship between the oral microbiome and human health has evolved, we have identified a diverse array of oral and systemic diseases associated with this microbial community, including but not limited to caries, periodontal diseases, oral cancer, colorectal cancer, pancreatic cancer, and inflammatory bowel syndrome. The potential predictive relationship between the oral microbiota and these human diseases suggests that the oral cavity is an ideal site for disease diagnosis and development of rapid point-of-care tests. The oral cavity is easily accessible with a non-invasive collection of biological samples. We can envision a future where early life salivary diagnostic tools will be used to predict and prevent future disease via analyzing and shaping the infant's oral microbiome. In this review, we present evidence for the establishment of the oral microbiome during early childhood, the capability of using childhood oral microbiome to predict future oral and systemic diseases, and the limitations of the current evidence.}, }
@article {pmid32343000, year = {2020}, author = {Lahtinen, P and Jalanka, J and Hartikainen, A and Mattila, E and Hillilä, M and Punkkinen, J and Koskenpato, J and Anttila, VJ and Tillonen, J and Satokari, R and Arkkila, P}, title = {Randomised clinical trial: faecal microbiota transplantation versus autologous placebo administered via colonoscopy in irritable bowel syndrome.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/apt.15740}, pmid = {32343000}, issn = {1365-2036}, support = {0313471-7//Finnish Academy/ ; 200230042//The Competitive State Research Financing/ ; //Sigrid Juselius Foundation/ ; }, abstract = {BACKGROUND: Irritable bowel syndrome (IBS) has been associated with microbial dysbiosis.<br><br>AIM: To investigate the efficacy of faecal microbiota transplantation (FMT) in the treatment of IBS.<br><br>METHODS: Forty-nine IBS patients were randomised to receive autologous or allogenic FMT via colonoscopy. The primary endpoint was a sustained, minimum of 50-point, reduction in the IBS Symptom Severity Score. The secondary outcomes were levels of anxiety and depression, changes in quality of life, gut microbiota and faecal water content as assessed with validated questionnaires, intestinal microbiota composition and stool dry weight.<br><br>RESULTS: The primary endpoint was not achieved in either group. However, there was a transient reduction in the mean IBS Symptom Severity Score in the FMT group at 12 weeks after treatment as compared to baseline (P = 0.01). The groups did not differ in the number of patients achieving clinical response at 12 weeks. In the FMT-treated patients, microbial composition had changed to resemble that of the donor and the stool water content decreased significantly compared to baseline. The depression score decreased in patients with a reduction in IBS symptoms after FMT, but not in those placebo-treated patients who experienced a reduction in IBS symptoms.<br><br>CONCLUSIONS: FMT provided only a transient relief of symptoms, although it induced a sustained alteration in the microbiota of IBS patients. Therefore, FMT delivered by a single infusion via colonoscopy cannot be recommended as a treatment for IBS in clinical practice. ClinicalTrials.Org, Trial registration number: NCT03561519.}, }
@article {pmid32340923, year = {2020}, author = {Gotschlich, EC and Colbert, RA and Gill, T}, title = {Methods in microbiome research: Past, present, and future.}, journal = {Best practice &amp; research. Clinical rheumatology}, volume = {}, number = {}, pages = {101498}, doi = {10.1016/j.berh.2020.101498}, pmid = {32340923}, issn = {1532-1770}, abstract = {The human microbiome is impressively immense and participates in many aspects of our health and wellness, particularly involving the development and maintenance of a healthy immune system. Not only do our microbes teach the immune system to fight infection, they also teach immune tolerance and help maintain homeostasis. From this knowledge, we have learned that the loss of tolerance to microbiota in both innate and adaptive processes plays an important role in immune-mediated and autoimmune disease. In this chapter, we will be discussing about methods used to study the microbiome, both old and new methods, fundamental concepts that have taken hold within the field, and how these principles relate to rheumatology, including thoughts on how microbiome research may be focused in the next decade.}, }
@article {pmid32337052, year = {2018}, author = {Shaw, LP and Sugden, NC}, title = {Portable sequencing, genomic data, and scale in global emerging infectious disease surveillance.}, journal = {Geo : geography and environment}, volume = {5}, number = {2}, pages = {e00066}, doi = {10.1002/geo2.66}, pmid = {32337052}, issn = {2054-4049}, abstract = {Emerging infectious diseases (EIDs) occur when pathogens unpredictably spread into new contexts. EID surveillance systems seek to rapidly identify EID outbreaks to contain spread and improve public health outcomes. Sequencing data has historically not been integrated into real-time responses, but portable DNA sequencing technology has prompted optimism among epidemiologists. Specifically, attention has focused on the goal of a &quot;sequencing singularity&quot;: the integration of portable sequencers in a worldwide event-based surveillance network with other digital data (Gardy &amp; Loman, Nature Reviews Genetics, 19, 2018, p. 9). The sequencing singularity vision is a powerful socio-technical imaginary, shaping the discourse around the future of portable sequencing. Ethical and practical issues are bound by the vision in two ways: they are framed only as obstacles, and they are formulated only at the scales made visible by its implicit geography. This geography privileges two extremes of scale - the genomic and the global - and leaves intermediate scales comparatively unmapped. We explore how widespread portable sequencing could challenge this geography. Portable sequencers put the ability to produce genomic data in the hands of the individual. The explicit assertion of rights over data may therefore become a matter disputed more at an interpersonal scale than an international one. Portable sequencers also promise ubiquitous, indiscriminate sequencing of the total metagenomic content of samples, raising the question of what (or who) is under surveillance and inviting consideration of the human microbiome and more-than-human geographies. We call into question a conception of a globally integrated stream of sequencing data as composed mostly of &quot;noise,&quot; within which signals of pathogen &quot;emergence&quot; are &quot;hidden,&quot; considering it instead from the perspective of recent work into more-than-human geographies. Our work highlights a practical need for researchers to consider both the alternative possibilities they foreclose as well as the exciting opportunities they move towards when they deploy their visions of the future.}, }
@article {pmid32334114, year = {2020}, author = {Zhou, J and Sun, T and Kang, W and Tang, D and QiangFeng, }, title = {Pathogenic and antimicrobial resistance genes in Streptococcus oralis strains revealed by comparative genome analysis.}, journal = {Genomics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ygeno.2020.04.014}, pmid = {32334114}, issn = {1089-8646}, abstract = {Streptococcus oralis is an early colonizer bacterium in dental plaques and is considered a potential pathogen of infective endocarditis (IE) disease. In this study, we built a complete genome map of Streptococcus oralis strain SOT, Streptococcus oralis strain SOD and Streptococcus infantis strain SO and performed comparative genomic analysis among these three strains. The results showed that there are five genomic islands (GIs) in strain SOT and one CRISPR in strain SOD. Each genome harbors various pathogenic genes related to diseases and drug resistance, while the antibiotic resistance genes in strains SOT and SOD were quite similar but different from those in strain SO. In addition, we identified 17 main virulence factors and capsule-related genes in three strains. These results suggest the pathogenic potential of Streptococcus strains, which lay a foundation for the prevention and treatment of a Streptococcus oralis infection.}, }
@article {pmid32332073, year = {2020}, author = {Manasson, J and Blank, RB and Scher, JU}, title = {The microbiome in rheumatology: Where are we and where should we go?.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/annrheumdis-2019-216631}, pmid = {32332073}, issn = {1468-2060}, abstract = {From birth, humans coexist and coevolve with trillions of micro-organisms inhabiting most body surfaces and cavities, referred to as the human microbiome. Advances in sequencing technologies and computational methods have propelled the exploration of the microbiome's contribution to human health and disease, spearheaded by massive efforts such as the Human Microbiome Project and the Europe-based MetaHit Consortium. Yet, despite the accumulated body of literature and a growing awareness among patients, microbiome research in rheumatology has not had a key impact on clinical practice. Herein, we describe some of the landmark microbiome studies in autoimmunity and rheumatology, the challenges and opportunities of microbiome research and how to navigate them, advances in related fields that have overcome these pitfalls, and future directions of harnessing the microbiome for diagnostic and therapeutic purposes.}, }
@article {pmid32329665, year = {2020}, author = {Jia, B and Park, D and Hahn, Y and Jeon, CO}, title = {Metagenomic analysis of the human microbiome reveals the association between the abundance of gut bile salt hydrolases and host health.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/19490976.2020.1748261}, pmid = {32329665}, issn = {1949-0984}, abstract = {Bile acid metabolism by the gut microbiome exerts both beneficial and harmful effects on host health. Microbial bile salt hydrolases (BSHs), which initiate bile acid metabolism, exhibit both positive and negative effects on host physiology. In this study, 5,790 BSH homologs were collected and classified into seven clusters based on a sequence similarity network. Next, the abundance and distribution of BSH in 380 metagenomes from healthy participants were analyzed. It was observed that different clusters occupied diverse ecological niches in the human microbiome and that the clusters with signal peptides were relatively abundant in the gut. Then, the association between BSH clusters and 12 human diseases was analyzed by comparing the abundances of BSH genes in patients (n = 1,605) and healthy controls (n = 1,540). The analysis identified a significant association between BSH gene abundance and 10 human diseases, including gastrointestinal diseases, obesity, type 2 diabetes, liver diseases, cardiovascular diseases, and neurological diseases. The associations were further validated by separate cohorts with inflammatory bowel diseases and colorectal cancer. These large-scale studies of enzyme sequences combined with metagenomic data provide a reproducible assessment of the association between gut BSHs and human diseases. This information can contribute to future diagnostic and therapeutic applications of BSH-active bacteria for improving human health.}, }
@article {pmid32327694, year = {2020}, author = {Yang, H and Zhang, J and Xue, Z and Zhao, C and Lei, L and Wen, Y and Dong, Y and Yang, J and Zhang, L}, title = {Potential Pathogenic Bacteria in Seminal Microbiota of Patients with Different Types of Dysspermatism.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {6876}, doi = {10.1038/s41598-020-63787-x}, pmid = {32327694}, issn = {2045-2322}, abstract = {Human microbiota play an important role in the health of their human hosts. Recent studies have demonstrated that microbiota exist in seminal plasma. The current study aims to elucidate whether seminal microbiota exist in patients with different types of dysspermatism and whether bacterial biomarkers can be identified for them. A total of 159 study participants were recruited, including 22 patients with oligoasthenospermia, 58 patients with asthenospermia, 8 patients with azoospermia, 13 patients with oligospermia, and 58 matched healthy controls. Seminal microbiota composition was analyzed using 16S rRNA gene-based sequencing. The results showed that the composition of seminal microbiota of patients with dysspermatism differed from those of healthy controls. Comparison of the microbiota composition in semen samples from patients with different types of dysspermatism showed that microbiota in patients with asthenospermia and oligoasthenospermia were distinct from healthy controls in beta diversity (P < 0.05). Characteristic biomarkers, including Ureaplasma, Bacteroides, Anaerococcus, Finegoldia, Lactobacillus and Acinetobacter lwoffii, were identified based on LEfSe analysis. Inferred functional analysis based on seminal microbiome data further indicated the presence of potential pathogenic biomarkers in patients with asthenospermia and oligoasthenospermia. These results provided profiles of seminal microbiota exhibited in different types of dysspermatism, thus providing new insights into their pathogenesis.}, }
@article {pmid32326394, year = {2020}, author = {Garcia-Mazcorro, JF and Minamoto, Y and Kawas, JR and Suchodolski, JS and de Vos, WM}, title = {Akkermansia and Microbial Degradation of Mucus in Cats and Dogs: Implications to the Growing Worldwide Epidemic of Pet Obesity.}, journal = {Veterinary sciences}, volume = {7}, number = {2}, pages = {}, doi = {10.3390/vetsci7020044}, pmid = {32326394}, issn = {2306-7381}, abstract = {Akkermansia muciniphila is a mucin-degrading bacterium that has shown the potential to provide anti-inflammatory and anti-obesity effects in mouse and man. We here focus on companion animals, specifically cats and dogs, and evaluate the microbial degradation of mucus and its health impact in the context of the worldwide epidemic of pet obesity. A literature survey revealed that the two presently known Akkermansia spp., A. muciniphila and A. glycaniphila, as well as other members of the phylum of Verrucomicrobia seem to be neither very prevalent nor abundant in the digestive tract of cats and dog. While this may be due to methodological aspects, it suggests that bacteria related to Akkermansia are not the major mucus degraders in these pets and hence other mucus-utilizing taxa may deserve attention. Hence, we will discuss the potential of these endogenous mucus utilizers and dietary interventions to boost these as well as the use of Akkermansia spp. related bacteria or their components as strategies to target feline and canine obesity.}, }
@article {pmid32243703, year = {2020}, author = {Adams, LA and Wang, Z and Liddle, C and Melton, PE and Ariff, A and Chandraratna, H and Tan, J and Ching, H and Coulter, S and de Boer, B and Christophersen, CT and O'Sullivan, TA and Morrison, M and Jeffrey, GP}, title = {Bile acids associate with specific gut microbiota, low-level alcohol consumption and liver fibrosis in patients with non-alcoholic fatty liver disease.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {}, number = {}, pages = {}, doi = {10.1111/liv.14453}, pmid = {32243703}, issn = {1478-3231}, support = {2016-17/031//Sir Charles Gairdner and Osborne Park Health Care Group Research Grant/ ; RF082//Hollywood Private Hospital Research Foundation Grant/ ; }, abstract = {BACKGROUND: Bile acids (BAs) are synthesized by the liver and modified by gut bacteria, and may play an intermediary role between the gut microbiome and liver in promoting fibrosis in non-alcoholic fatty liver disease (NAFLD). We investigated the associations between serum and faecal BAs, gut microbiome and fibrosis in patients with and without NAFLD and examined the impact of diet and alcohol consumption on these relationships.<br><br>METHODS: Adult patients (n = 122) underwent liver biopsy and BAs characterization by high-performance liquid chromatography/mass spectrometry. Gut microbiome composition was analysed using next-generation 16S rRNA sequencing. Diet and alcohol intake were determined by 3-day food diary.<br><br>RESULTS: Serum and faecal BA concentrations increased progressively among non-NAFLD controls (n = 55), NAFLD patients with no/mild fibrosis (F0-2, n = 58) and NAFLD with advanced fibrosis (F3/4, n = 9). Progressive increases in serum BAs were driven by primary conjugated BAs including glycocholic acid [GCA] and secondary conjugated BAs. In contrast, faecal BA increase was driven by secondary unconjugated BAs (predominately deoxycholic acid [DCA]). Serum GCA levels and faecal DCA levels correlated with the abundance of Bacteroidaceae and Lachnospiraceae, and stool secondary BAs with an unclassifiable family of the order Bacteroidales (Bacteroidales;other). These bacterial taxa were also associated with advanced fibrosis. Modest alcohol consumption was positively correlated with faecal DCA levels and relative abundance of Lachnospiracaea and Bacteroidales;other.<br><br>CONCLUSIONS: Higher serum and faecal BA levels are associated with advanced fibrosis in NAFLD. Specific gut bacteria link alterations in BA profiles and advanced fibrosis, and may be influenced by low-level alcohol consumption.}, }
@article {pmid32324967, year = {2020}, author = {Samples, RM and Balunas, MJ}, title = {Bridging the Gap: Plant-Endophyte Interactions as a Roadmap to Understanding Small Molecule Communication in Marine Microbiomes.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {}, number = {}, pages = {}, doi = {10.1002/cbic.202000064}, pmid = {32324967}, issn = {1439-7633}, abstract = {Probing the composition of the microbiome and its association with health and disease states is more accessible than ever due to the rise of affordable sequencing technology. Despite advances in our ability to identify members of symbiont communities, untangling the chemical signaling that they use to communicate with host organisms remains challenging. In order to gain a greater mechanistic understanding of how the microbiome impacts health, and how chemical ecology can be leveraged to advance small molecule drug discovery from microorganisms, the principals governing communication between host and symbiont must be elucidated. Herein, we review common modes of interkingdom small molecule communication in terrestrial and marine environments, describe the differences between these environments, and detail the advantages and disadvantages for studies focused on the marine environment. Finally, we propose the use of plant-endophyte interactions as a stepping stone to a greater understanding of similar interactions in marine invertebrates, and ultimately in humans.}, }
@article {pmid32319703, year = {2020}, author = {Vangoitsenhoven, R and Cresci, GAM}, title = {Role of Microbiome and Antibiotics in Autoimmune Diseases.}, journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/ncp.10489}, pmid = {32319703}, issn = {1941-2452}, support = {R00AA023266//GAC National Institutes of Health, NIAAA/ ; }, abstract = {The global rise in the incidence of autoimmune diseases has paralleled the widespread use of antibiotics. Recently, the gut microbiome has been shown to be key in the development and maturation of a normal immune system, and a range of microbial disturbances have been associated with the development and activity of several autoimmune diseases. Here, we aim to provide an overview of the mechanistic crosstalk between the human microbiome, the immune system, and antibiotics. The disease-associated microbial gut dysbiosis, the potential role of antibiotics in the development and treatment of autoimmune diseases, and the manipulation of the gut microbiome with prebiotics and probiotics is discussed using 2 key autoimmune diseases as an example: inflammatory bowel disease and type 1 diabetes. Although some data suggest that widespread use of antibiotics may facilitate autoimmunity through gut dysbiosis, there are also data to suggest antibiotics may hold the potential to improve disease activity. Currently, the effect of fecal microbiota transplantation on several autoimmune diseases is being studied in clinical trials, and several preclinical studies are revealing promising results with probiotic and prebiotic therapies.}, }
@article {pmid32318028, year = {2020}, author = {Eetemadi, A and Rai, N and Pereira, BMP and Kim, M and Schmitz, H and Tagkopoulos, I}, title = {The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {393}, doi = {10.3389/fmicb.2020.00393}, pmid = {32318028}, issn = {1664-302X}, abstract = {Food and human health are inextricably linked. As such, revolutionary impacts on health have been derived from advances in the production and distribution of food relating to food safety and fortification with micronutrients. During the past two decades, it has become apparent that the human microbiome has the potential to modulate health, including in ways that may be related to diet and the composition of specific foods. Despite the excitement and potential surrounding this area, the complexity of the gut microbiome, the chemical composition of food, and their interplay in situ remains a daunting task to fully understand. However, recent advances in high-throughput sequencing, metabolomics profiling, compositional analysis of food, and the emergence of electronic health records provide new sources of data that can contribute to addressing this challenge. Computational science will play an essential role in this effort as it will provide the foundation to integrate these data layers and derive insights capable of revealing and understanding the complex interactions between diet, gut microbiome, and health. Here, we review the current knowledge on diet-health-gut microbiota, relevant data sources, bioinformatics tools, machine learning capabilities, as well as the intellectual property and legislative regulatory landscape. We provide guidance on employing machine learning and data analytics, identify gaps in current methods, and describe new scenarios to be unlocked in the next few years in the context of current knowledge.}, }
@article {pmid32316935, year = {2020}, author = {Koliada, A and Moseiko, V and Romanenko, M and Piven, L and Lushchak, O and Kryzhanovska, N and Guryanov, V and Vaiserman, A}, title = {Seasonal variation in gut microbiota composition: cross-sectional evidence from Ukrainian population.}, journal = {BMC microbiology}, volume = {20}, number = {1}, pages = {100}, doi = {10.1186/s12866-020-01786-8}, pmid = {32316935}, issn = {1471-2180}, abstract = {BACKGROUND: Gut microbiota composition is known to depend on environmental (diet, day length, infections, xenobiotic exposure) and lifestyle (alcohol/drug intake, physical activity) factors. All these factors fluctuate seasonally, especially in areas with highly variable climatic conditions between seasons. Seasonal microbiota changes were reported in several previous studies. The purpose of our study was to investigate whether there is a seasonal variability in the gut microbiota composition in Ukrainian population. In contrast to previous studies performed on small-size samples using a longitudinal design, we used cross-sectional design with a large sample size (n = 769). Determination of microbial composition at the level of major microbial phyla was performed by qRT-PCR.<br><br>RESULTS: The relative abundance of major taxonomic groups of gut microbiota was found to be affected by month of sampling. Actinobacteria were more abundant and Bacteroidetes were less abundant in summer-derived samples compared to those obtained during other seasons, whereas Firmicutes content was seasonally independent. The Firmicutes to Bacteroidetes (F/B) ratio was significantly higher in summer-derived samples than in winter-derived ones. Odds to have F/B > 1 were 3.3 times higher in summer samples and 1.9 times higher in autumn samples than in winter ones; neither age, nor sex were significant confounding factors.<br><br>CONCLUSIONS: Seasonality of sampling could influence results of human microbiome research, thereby potentially biasing estimates. This factor must be taken into consideration in further microbiome research.}, }
@article {pmid32305861, year = {2020}, author = {Ma, ZS}, title = {Testing the Anna Karenina Principle in Human Microbiome-Associated Diseases.}, journal = {iScience}, volume = {23}, number = {4}, pages = {101007}, doi = {10.1016/j.isci.2020.101007}, pmid = {32305861}, issn = {2589-0042}, abstract = {The AKP (Anna Karenina principle), which refers to observations inspired by the opening line of Leo Tolstoy's Anna Karenina, &quot;all happy families are all alike; each unhappy family is unhappy in its own way,&quot; predicts that all &quot;healthy&quot; microbiomes are alike and each disease-associated microbiome is &quot;sick&quot; in its own way in human microbiome-associated diseases (MADs). The AKP hypothesis predicts the rise of heterogeneity/stochasticity in human microbiomes associated with dysbiosis due to MADs. We used the beta-diversity in Hill numbers and stochasticity analysis to detect AKP and anti-AKP effects. We tested the AKP with 27 human MAD studies and discovered that the AKP, anti-AKP, and non-AKP effects were exhibited in approximately 50%, 25%, and 25% of the MAD cases, respectively. Mechanistically, AKP effects are primarily influenced by highly dominant microbial species and less influenced by rare species. In contrast, all species appear to play equal roles in influencing anti-AKP effects.}, }
@article {pmid32298967, year = {2020}, author = {Otto, M}, title = {Staphylococci in the human microbiome: the role of host and interbacterial interactions.}, journal = {Current opinion in microbiology}, volume = {53}, number = {}, pages = {71-77}, doi = {10.1016/j.mib.2020.03.003}, pmid = {32298967}, issn = {1879-0364}, abstract = {Staphylococci are common commensals on human epithelial surfaces. Some species, most notably Staphylococcus aureus, have considerable pathogenic potential and can cause severe and sometimes fatal infections. Despite the long-known fact that staphylococcal infection arises from colonizing isolates, research on staphylococcal colonization has been limited, in particular regarding interactions with the colonizing microbiota. However, several recent studies are beginning to decipher such interactions, which range from bacteriocin-based or signaling interference-mediated inhibitory interactions to cooperation with host defenses to outcompete co-colonizers. This review will give an outline of recent research on the mechanistic underpinnings of staphylococcal interference with other members of the colonizing microbiota, some of which suggest new avenues for the development of novel anti-infectives or decolonization strategies.}, }
@article {pmid32298612, year = {2020}, author = {Ligthart, K and Belzer, C and de Vos, WM and Tytgat, HLP}, title = {Bridging Bacteria and the Gut: Functional Aspects of Type IV Pili.}, journal = {Trends in microbiology}, volume = {28}, number = {5}, pages = {340-348}, doi = {10.1016/j.tim.2020.02.003}, pmid = {32298612}, issn = {1878-4380}, abstract = {Cell-surface-located proteinaceous appendages, such as flagella and fimbriae or pili, are ubiquitous in bacterial communities. Here, we focus on conserved type IV pili (T4P) produced by bacteria in the intestinal tract, one of the most densely populated human ecosystems. Computational analysis revealed that approximately 30% of known intestinal bacteria are predicted to produce T4P. To rationalize how T4P allow intestinal bacteria to interact with their environment, other microbiota members, and host cells, we review their established role in gut commensals and pathogens with respect to adherence, motility, and biofilm formation, as well as protein secretion and DNA uptake. This work indicates that T4P are widely spread among the known members of the intestinal microbiota and that their contribution to human health might be underestimated.}, }
@article {pmid32294988, year = {2020}, author = {Tomaiuolo, R and Veneruso, I and Cariati, F and D'Argenio, V}, title = {Microbiota and Human Reproduction: The Case of Male Infertility.}, journal = {High-throughput}, volume = {9}, number = {2}, pages = {}, doi = {10.3390/ht9020010}, pmid = {32294988}, issn = {2571-5135}, support = {855720//H2020 Innovation In SMEs/ ; year 2016//EIT Health/ ; }, abstract = {The increasing interest in metagenomics is enhancing our knowledge regarding the composition and role of the microbiota in human physiology and pathology. Indeed, microbes have been reported to play a role in several diseases, including infertility. In particular, the male seminal microbiota has been suggested as an important factor able to influence couple's health and pregnancy outcomes, as well as offspring health. Nevertheless, few studies have been carried out to date to deeper investigate semen microbiome origins and functions, and its correlations with the partner's reproductive tract microbiome. Here, we report the state of the art regarding the male reproductive system microbiome and its alterations in infertility.}, }
@article {pmid32291445, year = {2020}, author = {Wu, K and Yuan, Y and Yu, H and Dai, X and Wang, S and Sun, Z and Wang, F and Fei, H and Lin, Q and Jiang, H and Chen, T}, title = {Gut microbial metabolite trimethylamine N-oxide aggravates GVHD by inducing M1 macrophage polarization in mice.}, journal = {Blood}, volume = {}, number = {}, pages = {}, doi = {10.1182/blood.2019003990}, pmid = {32291445}, issn = {1528-0020}, abstract = {The diversity of human microbiome heralds the difference of impact that gut microbial metabolites exert on allogenic graft-versus-host disease (GVHD), even though short-chain fatty acids and indole were demonstrated to reduce its severity. In this study, we dissected the role of choline-metabolized trimethylamine N-oxide (TMAO) in GVHD process. Either TMAO or high choline diet enhanced allogenic GVH reaction, while the analog of choline, 3,3-dimethyl-1-butanol reversed TMAO-induced GVHD severity. Interestingly, TMAO-induced alloreactive T cell proliferation and differentiation into T helper (Th) subtypes was seen in GVHD mice but not in in vitro cultures. We thus investigated the role of macrophage polarization which was absent from in vitro culture system. F4/80+CD11b+CD16/32+ M1 macrophage and signature genes, IL-1β, IL-6, TNF-α, CXCL9 and CXCL10 were increased in TMAO-induced GVHD tissues and in TMAO-cultured bone marrow derived macrophages (BMDMs). Inhibition of NLRP3 inflammosome reversed TMAO-stimulated M1 features, indicating that NLRP3 is the key proteolytic activator involved in macrophage's response to TMAO stimulation. Consistently, mitochondrial reactive oxygen species and enhanced NF-κB nuclear re-localization were investigated in TMAO-stimulated BMDMs. In vivo depletion of NLRP3 in GVHD recipients not only blocked M1 polarization but also reversed GVHD severity in the presence of TMAO treatment. In conclusion, our data revealed that TMAO-induced GVHD progression is resulted from Th1 and Th17 differentiation, which is mediated by polarized M1 macrophage requiring NLRP3 inflammasome activation. It provides the link among the host choline diet, microbial metabolites and GVH reaction, shedding light on alleviating GVHD by controlling choline diet.}, }
@article {pmid32278320, year = {2020}, author = {O'Mahony, L}, title = {Short Chain Fatty Acids Modulate Mast Cell Activation.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.14313}, pmid = {32278320}, issn = {1398-9995}, abstract = {Humans have evolved in an environmental and social context that enabled reliable transmissiosn and dispersal of symbionts, accompanied by appropriate nutritional support. However, recent changes in lifestyles, diet and social interactions have altered these metacommunity processes, disrupted the human microbiome and, as a consequence, increased risk of immune-mediated diseases such as allergy and asthma.}, }
@article {pmid32277534, year = {2020}, author = {Meng, X and Zhang, G and Cao, H and Yu, D and Fang, X and de Vos, WM and Wu, H}, title = {Gut Dysbacteriosis and Intestinal Disease: Mechanism and Treatment.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jam.14661}, pmid = {32277534}, issn = {1365-2672}, abstract = {The gut microbiome functions like an endocrine organ, generating bioactive metabolites, enzymes or small molecules that can impact host physiology. Gut dysbacteriosis is associated with many intestinal diseases including (but not limited to) IBD, PSC-IBD, IBS, chronic constipation, osmotic diarrhea and colorectal cancer. The potential pathogenic mechanism of gut dysbacteriosis associated with intestinal diseases includes the alteration of composition of gut microbiota as well as the gut microbiota-derived signaling molecules. The many correlations between the latter and the susceptibility for intestinal diseases has placed a spotlight on the gut microbiome as a potential novel target for therapeutics. Currently, fecal microbial transplantation, dietary interventions, use of probiotics, prebiotics and drugs are the major therapeutic tools utilized to impact dysbacteriosis and associated intestinal diseases. In this review, we systematically summarized the role of intestinal microbiome in the occurrence and development of intestinal diseases. The potential mechanism of the complex interplay between gut dysbacteriosis and intestinal diseases, and the treatment methods are also highlighted.}, }
@article {pmid32269511, year = {2020}, author = {Elmassry, MM and Piechulla, B}, title = {Volatilomes of Bacterial Infections in Humans.}, journal = {Frontiers in neuroscience}, volume = {14}, number = {}, pages = {257}, doi = {10.3389/fnins.2020.00257}, pmid = {32269511}, issn = {1662-4548}, abstract = {Sense of smell in humans has the capacity to detect certain volatiles from bacterial infections. Our olfactory senses were used in ancient medicine to diagnose diseases in patients. As humans are considered holobionts, each person's unique odor consists of volatile organic compounds (VOCs, volatilome) produced not only by the humans themselves but also by their beneficial and pathogenic micro-habitants. In the past decade it has been well documented that microorganisms (fungi and bacteria) are able to emit a broad range of olfactory active VOCs [summarized in the mVOC database (http://bioinformatics.charite.de/mvoc/)]. During microbial infection, the equilibrium between the human and its microbiome is altered, followed by a change in the volatilome. For several decades, physicians have been trying to utilize these changes in smell composition to develop fast and efficient diagnostic tools, particularly because volatiles detection is non-invasive and non-destructive, which would be a breakthrough in many therapies. Within this review, we discuss bacterial infections including gastrointestinal, respiratory or lung, and blood infections, focusing on the pathogens and their known corresponding volatile biomarkers. Furthermore, we cover the potential role of the human microbiota and their volatilome in certain diseases such as neurodegenerative diseases. We also report on discrete mVOCs that affect humans.}, }
@article {pmid32266088, year = {2020}, author = {Xu, J and Peng, JJ and Yang, W and Fu, K and Zhang, Y}, title = {Vaginal microbiomes and ovarian cancer: a review.}, journal = {American journal of cancer research}, volume = {10}, number = {3}, pages = {743-756}, pmid = {32266088}, issn = {2156-6976}, abstract = {The human microbiome, often termed as &quot;the forgotten organ&quot;, is an aggregation of microorganisms and their genomes that forms a mutualistic complex with the host. Recent research has shown the symbiotic merits of a microbiome ecosystem and its crucial role in the hosts' physiological functions. Disruption of this symbiotic relationship is prone to cause a broad spectrum of ailments, including cancer. The compositional and environmental factors that tip the scales from beneficial co-existence to the development of malignancy is actively investigated. Herein we review the latest research in knowledge regarding the association between the vaginal microbiomes and oncogenesis, with a particular focus on ovarian carcinoma.}, }
@article {pmid32257965, year = {2020}, author = {Fernández de Ullivarri, M and Arbulu, S and Garcia-Gutierrez, E and Cotter, PD}, title = {Antifungal Peptides as Therapeutic Agents.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {105}, doi = {10.3389/fcimb.2020.00105}, pmid = {32257965}, issn = {2235-2988}, abstract = {Fungi have been used since ancient times in food and beverage-making processes and, more recently, have been harnessed for the production of antibiotics and in processes of relevance to the bioeconomy. Moreover, they are starting to gain attention as a key component of the human microbiome. However, fungi are also responsible for human infections. The incidence of community-acquired and nosocomial fungal infections has increased considerably in recent decades. Antibiotic resistance development, the increasing number of immunodeficiency- and/or immunosuppression-related diseases and limited therapeutic options available are triggering the search for novel alternatives. These new antifungals should be less toxic for the host, with targeted or broader antimicrobial spectra (for diseases of known and unknown etiology, respectively) and modes of actions that limit the potential for the emergence of resistance among pathogenic fungi. Given these criteria, antimicrobial peptides with antifungal properties, i.e., antifungal peptides (AFPs), have emerged as powerful candidates due to their efficacy and high selectivity. In this review, we provide an overview of the bioactivity and classification of AFPs (natural and synthetic) as well as their mode of action and advantages over current antifungal drugs. Additionally, natural, heterologous and synthetic production of AFPs with a view to greater levels of exploitation is discussed. Finally, we evaluate the current and potential applications of these peptides, along with the future challenges relating to antifungal treatments.}, }
@article {pmid32255860, year = {2020}, author = {Yu, B and Yu, B and Yu, L}, title = {Commentary: Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome.}, journal = {Indian journal of microbiology}, volume = {60}, number = {2}, pages = {259-261}, doi = {10.1007/s12088-020-00863-w}, pmid = {32255860}, issn = {0046-8991}, abstract = {Human beings have co-evolved with the microorganisms in our environment for millions of years, and have developed into a symbiosis in a mutually beneficial/defensive way. Human beings have significant multifaceted relationships with the diverse microbial community. Apart from the important protective role of microbial community exposure in development of early immunity, millions of inimitable bacterial genes of the diverse microbial community are the indispensable source of essential nutrients like essential amino acids and essential fatty acids for human body. The essential nutrition from microbiome is harvested through xenophagy. As an immune effector, xenophagy will capture any microorganisms that touch the epithelial cells of our gastrointestinal tract, degrade them and turn them into nutrients for the use of our body.}, }
@article {pmid32247371, year = {2020}, author = {Keshavarzian, A and Engen, P and Bonvegna, S and Cilia, R}, title = {The gut microbiome in Parkinson's disease: A culprit or a bystander?.}, journal = {Progress in brain research}, volume = {252}, number = {}, pages = {357-450}, doi = {10.1016/bs.pbr.2020.01.004}, pmid = {32247371}, issn = {1875-7855}, abstract = {In recent years, large-scale metagenomics projects such as the Human Microbiome Project placed the gut microbiota under the spotlight of research on its role in health and in the pathogenesis several diseases, as it can be a target for novel therapeutical approaches. The emerging concept of a microbiota modulation of the gut-brain axis in the pathogenesis of neurodegenerative disorders has been explored in several studies in animal models, as well as in human subjects. Particularly, research on changes in the composition of gut microbiota as a potential trigger for alpha-synuclein (α-syn) pathology in Parkinson's disease (PD) has gained increasing interest. In the present review, we first provide the basis to the understanding of the role of gut microbiota in healthy subjects and the molecular basis of the gut-brain interaction, focusing on metabolic and neuroinflammatory factors that could trigger the alpha-synuclein conformational changes and aggregation. Then, we critically explored preclinical and clinical studies reporting on the changes in gut microbiota in PD, as compared to healthy subjects. Furthermore, we examined the relationship between the gut microbiota and PD clinical features, discussing data consistently reported across studies, as well as the potential sources of inconsistencies. As a further step toward understanding the effects of gut microbiota on PD, we discussed the relationship between dysbiosis and response to dopamine replacement therapy, focusing on Levodopa metabolism. We conclude that further studies are needed to determine whether the gut microbiota changes observed so far in PD patients is the cause or, instead, it is merely a consequence of lifestyle changes associated with the disease. Regardless, studies so far strongly suggest that changes in microbiota appears to be impactful in pathogenesis of neuroinflammation. Thus, dysbiotic microbiota in PD could influence the disease course and response to medication, especially Levodopa. Future research will assess the impact of microbiota-directed therapeutic intervention in PD patients.}, }
@article {pmid32246318, year = {2020}, author = {Chen, B and Wang, Z and Wang, J and Su, X and Yang, J and Zhang, Q and Zhang, L}, title = {The oral microbiome profile and biomarker in Chinese type 2 diabetes mellitus patients.}, journal = {Endocrine}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12020-020-02269-6}, pmid = {32246318}, issn = {1559-0100}, support = {31471202//National Natural Science Foundation of China/ ; 31471202//National Natural Science Foundation of China/ ; 31471202//National Natural Science Foundation of China/ ; 31471202//National Natural Science Foundation of China/ ; 31471202//National Natural Science Foundation of China/ ; 31471202//National Natural Science Foundation of China/ ; 31471202//National Natural Science Foundation of China/ ; 2016YYSP009//Shandong Provincial Key Research and Development Program/ ; }, abstract = {PURPOSE: Oral microbiota maintains a dynamic ecological balance with the host. However, a disruption in this balance can lead to oral diseases such as dental caries and periodontitis. Several studies suggest differences in microbial composition in the oral cavity between patients with T2DM and nondiabetic patients. However, there is inadequate oral microbiome-related data from Chinese patients with T2DM, and the difference in microbiome profile between Chinese patients with T2DM and other ethnicities needs to be investigated further.<br><br>METHOD: Oral swab samples were collected from 280 adult patients with T2DM and 162 healthy controls. Illumina sequencing was performed on oral samples targeting V1-V2 region of 16S rRNA gene and sequence analysis was carried in the QIIME.<br><br>RESULTS: Patients with T2DM and healthy cohorts exhibited distinct oral microbial clusters based on principal coordinate analysis (PCoA). The Firmicutes/Bacteroidetes ratio increased in T2DM and T2DM patients presented significantly higher numbers of Neisseria, Streptococcus, Haemophilus, and Pseudomonas genera, and lower numbers of Acinetobacteria compared with healthy controls. When compared with the available published data of oral and gut microbiome associated with T2DM patients, we found the ratio of Firmicutes/Bacteroidetes and the abundance of Haemophilus could be a specific microbial biomarker in Chinese patients with T2DM.<br><br>CONCLUSIONS: Our study revealed a significant difference in the oral microbiota between T2DM patients and healthy individuals. We identified 25 taxa, including 6 genera, with significant difference in abundance between T2DM and healthy controls.}, }
@article {pmid32246263, year = {2020}, author = {Swann, JR and Rajilic-Stojanovic, M and Salonen, A and Sakwinska, O and Gill, C and Meynier, A and Fança-Berthon, P and Schelkle, B and Segata, N and Shortt, C and Tuohy, K and Hasselwander, O}, title = {Considerations for the design and conduct of human gut microbiota intervention studies relating to foods.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-020-02232-1}, pmid = {32246263}, issn = {1436-6215}, abstract = {With the growing appreciation for the influence of the intestinal microbiota on human health, there is increasing motivation to design and refine interventions to promote favorable shifts in the microbiota and their interactions with the host. Technological advances have improved our understanding and ability to measure this indigenous population and the impact of such interventions. However, the rapid growth and evolution of the field, as well as the diversity of methods used, parameters measured and populations studied, make it difficult to interpret the significance of the findings and translate their outcomes to the wider population. This can prevent comparisons across studies and hinder the drawing of appropriate conclusions. This review outlines considerations to facilitate the design, implementation and interpretation of human gut microbiota intervention studies relating to foods based upon our current understanding of the intestinal microbiota, its functionality and interactions with the human host. This includes parameters associated with study design, eligibility criteria, statistical considerations, characterization of products and the measurement of compliance. Methodologies and markers to assess compositional and functional changes in the microbiota, following interventions are discussed in addition to approaches to assess changes in microbiota-host interactions and host responses. Last, EU legislative aspects in relation to foods and health claims are presented. While it is appreciated that the field of gastrointestinal microbiology is rapidly evolving, such guidance will assist in the design and interpretation of human gut microbiota interventional studies relating to foods.}, }
@article {pmid32240601, year = {2020}, author = {Yan, Y and Drew, DA and Markowitz, A and Lloyd-Price, J and Abu-Ali, G and Nguyen, LH and Tran, C and Chung, DC and Gilpin, KK and Meixell, D and Parziale, M and Schuck, M and Patel, Z and Richter, JM and Kelsey, PB and Garrett, WS and Chan, AT and Stadler, ZK and Huttenhower, C}, title = {Structure of the Mucosal and Stool Microbiome in Lynch Syndrome.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2020.03.005}, pmid = {32240601}, issn = {1934-6069}, abstract = {The gut microbiota has been associated with colorectal cancer (CRC), but causal alterations preceding CRC have not been elucidated. To prospectively assess microbiome changes prior to colorectal neoplasia, we investigated samples from 100 Lynch syndrome patients using 16S rRNA gene sequencing of colon biopsies, coupled with metagenomic and metatranscriptomic sequencing of feces. Colectomy and CRC history represented the largest effects on microbiome profiles. A subset of Clostridiaceae were depleted in stool corresponding with baseline adenomas, while Desulfovibrio was enriched both in stool and in mucosal biopsies. A classifier leveraging stool metatranscriptomes resulted in modest power to predict interval development of preneoplastic colonic adenoma. Predictive transcripts corresponded with a shift in flagellin contributors and oxidative metabolic microenvironment, potentially factors in local CRC pathogenesis. This suggests that the effectiveness of prospective microbiome monitoring for adenomas may be limited but supports the potential causality of these consistent, early microbial changes in colonic neoplasia.}, }
@article {pmid32239808, year = {2020}, author = {Kim, MH and Choi, JH}, title = {An Update on Sepsis Biomarkers.}, journal = {Infection &amp; chemotherapy}, volume = {52}, number = {1}, pages = {1-18}, doi = {10.3947/ic.2020.52.1.1}, pmid = {32239808}, issn = {2093-2340}, abstract = {Sepsis is a dysregulated systemic reaction to a common infection, that can cause life-threatening organ dysfunction. Over the last decade, the mortality rate of patients with sepsis has decreased as long as patients are treated according to the recommendations of the Surviving Sepsis Campaign, but is still unacceptably high. Patients at risk of sepsis should therefore be identified prior to the onset of organ dysfunction and this requires a rapid diagnosis and a prompt initiation of treatment. Unfortunately, there is no gold standard for the diagnosis of sepsis and traditional standard culture methods are time-consuming. Recently, in order to overcome these limitations, biomarkers which could help in predicting the diagnosis and prognosis of sepsis, as well as being useful for monitoring the response to treatments, have been identified. In addition, recent advances have led to the development of newly identified classes of biomarkers such as microRNAs, long-non-coding RNAs, and the human microbiome. This review focuses on the latest information on biomarkers that can be used to predict the diagnosis and prognosis of sepsis.}, }
@article {pmid32239603, year = {2020}, author = {Bruessow, F and Brüssow, H}, title = {Our Extended Genotype- an argument for the study of domesticated microbes.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.15001}, pmid = {32239603}, issn = {1462-2920}, abstract = {We interpret the domesticated organisms- plants, animals and the domesticated microbes used for food fermentation- as an extended genotype of humans due to their close relationship with our species. We propose to analyze the role of microbes in traditionally fermented food with the approaches used in the human microbiome project, and we expect to find associations with ethnic groups, explaining part of human (culinary) culture. This article is protected by copyright. All rights reserved.}, }
@article {pmid32236123, year = {2020}, author = {Stennett, CA and Dyer, TV and He, X and Robinson, CK and Ravel, J and Ghanem, KG and Brotman, RM}, title = {A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women.}, journal = {PloS one}, volume = {15}, number = {4}, pages = {e0228574}, doi = {10.1371/journal.pone.0228574}, pmid = {32236123}, issn = {1932-6203}, abstract = {Recent studies suggest that birth mode (Cesarean section [C-section] or vaginal delivery) is an important event in the initial colonization of the human microbiome and may be associated with long-term health outcomes. We sought to determine the association between a woman's birth mode and her vaginal microbiota in adulthood. We re-contacted 144 adult women from two U.S. studies and administered a brief survey. Vaginal microbiota was characterized on a single sample by amplicon sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene and clustered into community state types (CSTs). We evaluated the association between birth mode and a CST with low relative abundance of Lactobacillus spp. (&quot;molecular bacterial vaginosis&quot; [Molecular-BV]) compared to Lactobacillus-dominated CSTs in logistic regression modeling which adjusted for body mass index, a confounder in this analysis. Twenty-seven women (19%) reported C-section. Overall, C-section showed a non-significant trend towards increased odds of Molecular-BV (aOR = 1.22, 95% CI: 0.45, 3.32), and Prevotella bivia was the strongest single taxa associated with C-section. However, because the two archived studies had different inclusion criteria (interaction p = 0.048), we stratified the analysis by study site. In the study with a larger sample size (n = 88), women born by C-section had 3-fold higher odds of Molecular-BV compared to vaginally-delivered women (aOR = 3.55, p = 0.06, 95% CI: 0.97-13.02). No association was found in the smaller study (n = 56, aOR = 0.19, p = 0.14, 95% CI: 0.02-1.71). This pilot cross-sectional study suggests a possible association between C-section and Molecular-BV in adulthood. However, the analysis is limited by small sample size and lack of comparability in participant age and other characteristics between the study sites. Future longitudinal studies could recruit larger samples of women, address the temporal dynamics of vaginal microbiota, and explore other confounders, including maternal factors, breastfeeding history, and socioeconomic status, which may affect the relationship between birth mode and vaginal microbiota.}, }
@article {pmid32235279, year = {2020}, author = {Lundy, SD and Vij, SC and Rezk, AH and Cohen, JA and Bajic, P and Ramasamy, R}, title = {The microbiome of the infertile male.}, journal = {Current opinion in urology}, volume = {30}, number = {3}, pages = {355-362}, doi = {10.1097/MOU.0000000000000742}, pmid = {32235279}, issn = {1473-6586}, abstract = {PURPOSE OF REVIEW: Contrary to historic dogma, many tissues and organs in the human body contain a resident population of bacteria, fungi, and viruses collectively known as the microbiome. The microbiome plays a role in both homeostatic symbiosis and also pathogenic dysbiosis in a wide array of diseases. Our understanding of the relationship between the microbiome and male factor infertility is in its infancy but is slowly evolving.<br><br>RECENT FINDINGS: Recent literature indicates that semen (and likely the testis) is not sterile and contains a distinct microbiome, and these changes in its composition are associated with alterations in semen quality and fertility status. Preliminary investigation indicates that manipulating the human microbiome may have implications in improving semen parameters and fertility.<br><br>SUMMARY: In this review, we describe relationships between the microbiome and the genitourinary system, discuss the prior work on the relationship among bacteriospermia, leukocytospermia and male factor infertility, and summarize the current literature utilizing 16s rRNA-based next-generation sequencing on the seminal and testicular microbiome. We explore the specific microbial taxa implicated in various aspects of spermatic dysfunction and introduce preliminary evidence for therapeutic approaches to alter the microbiome and improve fertility status.}, }
@article {pmid32231681, year = {2020}, author = {Carter, KM and Lu, M and Jiang, H and An, L}, title = {An Information-Based Approach for Mediation Analysis on High-Dimensional Metagenomic Data.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {148}, doi = {10.3389/fgene.2020.00148}, pmid = {32231681}, issn = {1664-8021}, abstract = {The human microbiome plays a critical role in the development of gut-related illnesses such as inflammatory bowel disease and clinical pouchitis. A mediation model can be used to describe the interaction between host gene expression, the gut microbiome, and clinical/health situation (e.g., diseased or not, inflammation level) and may provide insights into underlying disease mechanisms. Current mediation regression methodology cannot adequately model high-dimensional exposures and mediators or mixed data types. Additionally, regression based mediation models require some assumptions for the model parameters, and the relationships are usually assumed to be linear and additive. With the microbiome being the mediators, these assumptions are violated. We propose two novel nonparametric procedures utilizing information theory to detect significant mediation effects with high-dimensional exposures and mediators and varying data types while avoiding standard regression assumptions. Compared with available methods through comprehensive simulation studies, the proposed method shows higher power and lower error. The innovative method is applied to clinical pouchitis data as well and interesting results are obtained.}, }
@article {pmid32231664, year = {2020}, author = {Al-Nasiry, S and Ambrosino, E and Schlaepfer, M and Morré, SA and Wieten, L and Voncken, JW and Spinelli, M and Mueller, M and Kramer, BW}, title = {The Interplay Between Reproductive Tract Microbiota and Immunological System in Human Reproduction.}, journal = {Frontiers in immunology}, volume = {11}, number = {}, pages = {378}, doi = {10.3389/fimmu.2020.00378}, pmid = {32231664}, issn = {1664-3224}, abstract = {In the last decade, the microbiota, i.e., combined populations of microorganisms living inside and on the surface of the human body, has increasingly attracted attention of researchers in the medical field. Indeed, since the completion of the Human Microbiome Project, insight and interest in the role of microbiota in health and disease, also through study of its combined genomes, the microbiome, has been steadily expanding. One less explored field of microbiome research has been the female reproductive tract. Research mainly from the past decade suggests that microbial communities residing in the reproductive tract represent a large proportion of the female microbial network and appear to be involved in reproductive failure and pregnancy complications. Microbiome research is facing technological and methodological challenges, as detection techniques and analysis methods are far from being standardized. A further hurdle is understanding the complex host-microbiota interaction and the confounding effect of a multitude of constitutional and environmental factors. A key regulator of this interaction is the maternal immune system that, during the peri-conceptional stage and even more so during pregnancy, undergoes considerable modulation. This review aims to summarize the current literature on reproductive tract microbiota describing the composition of microbiota in different anatomical locations (vagina, cervix, endometrium, and placenta). We also discuss putative mechanisms of interaction between such microbial communities and various aspects of the immune system, with a focus on the characteristic immunological changes during normal pregnancy. Furthermore, we discuss how abnormal microbiota composition, &quot;dysbiosis,&quot; is linked to a spectrum of clinical disorders related to the female reproductive system and how the maternal immune system is involved. Finally, based on the data presented in this review, the future perspectives in diagnostic approaches, research directions and therapeutic opportunities are explored.}, }
@article {pmid32231240, year = {2020}, author = {Chaudhari, DS and Dhotre, DP and Agarwal, DM and Gaike, AH and Bhalerao, D and Jadhav, P and Mongad, D and Lubree, H and Sinkar, VP and Patil, UK and Salvi, S and Bavdekar, A and Juvekar, SK and Shouche, YS}, title = {Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5685}, doi = {10.1038/s41598-020-62195-5}, pmid = {32231240}, issn = {2045-2322}, support = {BT/PR3461/BRB/10/968/2011//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; }, abstract = {The human microbiome plays a key role in maintaining host homeostasis and is influenced by age, geography, diet, and other factors. Traditionally, India has an established convention of extended family arrangements wherein three or more generations, bound by genetic relatedness, stay in the same household. In the present study, we have utilized this unique family arrangement to understand the association of age with the microbiome. We characterized stool, oral and skin microbiome of 54 healthy individuals from six joint families by 16S rRNA gene-based metagenomics. In total, 69 (1.03%), 293 (2.68%) and 190 (8.66%) differentially abundant OTUs were detected across three generations in the gut, skin and oral microbiome, respectively. Age-associated changes in the gut and oral microbiome of patrilineal families showed positive correlations in the abundance of phyla Proteobacteria and Fusobacteria, respectively. Genera Treponema and Fusobacterium showed a positive correlation with age while Granulicatella and Streptococcus showed a negative correlation with age in the oral microbiome. Members of genus Prevotella illustrated high abundance and prevalence as a core OTUs in the gut and oral microbiome. In conclusion, this study highlights that precise and perceptible association of age with microbiome can be drawn when other causal factors are kept constant.}, }
@article {pmid32230951, year = {2020}, author = {Hiippala, K and Kainulainen, V and Suutarinen, M and Heini, T and Bowers, JR and Jasso-Selles, D and Lemmer, D and Valentine, M and Barnes, R and Engelthaler, DM and Satokari, R}, title = {Isolation of Anti-Inflammatory and Epithelium Reinforcing Bacteroides and Parabacteroides Spp. from A Healthy Fecal Donor.}, journal = {Nutrients}, volume = {12}, number = {4}, pages = {}, doi = {10.3390/nu12040935}, pmid = {32230951}, issn = {2072-6643}, support = {304490//Academy of Finland/ ; 323156//Academy of Finland/ ; 285632//Academy of Finland/ ; Reetta Satokari//Sigrid Juséliuksen Säätiö/ ; }, abstract = {Altered intestinal microbiota is associated with systemic and intestinal diseases, such as inflammatory bowel disease (IBD). Dysbiotic microbiota with enhanced proinflammatory capacity is characterized by depletion of anaerobic commensals, increased proportion of facultatively anaerobic bacteria, as well as reduced diversity and stability. In this study, we developed a high-throughput in vitro screening assay to isolate intestinal commensal bacteria with anti-inflammatory capacity from a healthy fecal microbiota transplantation donor. Freshly isolated gut bacteria were screened for their capacity to attenuate Escherichia coli lipopolysaccharide (LPS)-induced interleukin 8 (IL-8) release from HT-29 cells. The screen yielded a number of Bacteroides and Parabacteroides isolates, which were identified as P.distasonis, B.caccae, B. intestinalis, B.uniformis, B. fragilis, B.vulgatus and B.ovatus using whole genome sequencing. We observed that a cell-cell contact with the epithelium was not necessary to alleviate in vitro inflammation as spent culture media from the isolates were also effective and the anti-inflammatory action did not correlate with the enterocyte adherence capacity of the isolates. The anti-inflammatory isolates also exerted enterocyte monolayer reinforcing action and lacked essential genes to synthetize hexa-acylated, proinflammatory lipid A, part of LPS. Yet, the anti-inflammatory effector molecules remain to be identified. The Bacteroides strains isolated and characterized in this study have potential to be used as so-called next-generation probiotics.}, }
@article {pmid32229436, year = {2020}, author = {Zheng, JS and Wahlqvist, ML}, title = {Regulobiosis: A regulatory and food system-sensitive role for fungal symbionts in human evolution and ecobiology.}, journal = {Asia Pacific journal of clinical nutrition}, volume = {29}, number = {1}, pages = {9-15}, doi = {10.6133/apjcn.202003_29(1).0002}, pmid = {32229436}, issn = {1440-6047}, abstract = {The role of microbiomes in human biology and health are being extensively investigated, yet how the fungal community or mycobiome contributes to an integral microbiome is unclear and probably underestimated. We review the roles of fungi from the perspectives of their functionality in human biology, their cross-kingdom talk with other human microbial organisms, their dependence on diet and their involvement in human health and diseases. We hypothesize that members of the fungal community may interact as necessary symbionts with members of other human microbiome communities, and play a key role in human biology, yet to be fully understood. We propose further that &quot;regulobiosis&quot;, whereby fungi play a regulatory role in human ecobiology, is operative in humans as probably obtains in other forms of life. Fungally-dependent regulobiosis would characterise, at first, microbiomes which include, but are not limited to, bacteria, archaea, and viruses; then, their human host; and, next, provide ecological connectedness.}, }
@article {pmid32221294, year = {2020}, author = {Gilijamse, PW and Hartstra, AV and Levin, E and Wortelboer, K and Serlie, MJ and Ackermans, MT and Herrema, H and Nederveen, AJ and Imangaliyev, S and Aalvink, S and Sommer, M and Levels, H and Stroes, ESG and Groen, AK and Kemper, M and de Vos, WM and Nieuwdorp, M and Prodan, A}, title = {Treatment with Anaerobutyricum soehngenii: a pilot study of safety and dose-response effects on glucose metabolism in human subjects with metabolic syndrome.}, journal = {NPJ biofilms and microbiomes}, volume = {6}, number = {1}, pages = {16}, doi = {10.1038/s41522-020-0127-0}, pmid = {32221294}, issn = {2055-5008}, support = {grant 2013 [016.146.327]//ZonMw (Netherlands Organisation for Health Research and Development)/ ; CVON IN CONTROL Young Talent Grant 2013//Hartstichting (Dutch Heart Foundation)/ ; GUT-MMM grant 2016//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, abstract = {Dysbiosis of the intestinal microbiota has been implicated in insulin resistance, although evidence regarding causality in humans is scarce. We performed a phase I/II dose-finding and safety study on the effect of oral intake of the anaerobic butyrogenic strain Anaerobutyricum soehngenii on glucose metabolism in 24 subjects with metabolic syndrome. We found that treatment with A. soehngenii was safe and observed a significant correlation between the measured fecal abundance of administered A. soehngenii and improvement in peripheral insulin sensitivity after 4 weeks of treatment. This was accompanied by an altered microbiota composition and a change in bile acid metabolism. Finally, we show that metabolic response upon administration of A. soehngenii (defined as improved insulin sensitivity 4 weeks after A. soehngenii intake) is dependent on microbiota composition at baseline. These data in humans are promising, but additional studies are needed to reproduce our findings and to investigate long-term effects, as well as other modes of delivery.}, }
@article {pmid32219339, year = {2020}, author = {Kyrgyzov, O and Prost, V and Gazut, S and Farcy, B and Brüls, T}, title = {Binning unassembled short reads based on k-mer abundance covariance using sparse coding.}, journal = {GigaScience}, volume = {9}, number = {4}, pages = {}, doi = {10.1093/gigascience/giaa028}, pmid = {32219339}, issn = {2047-217X}, abstract = {BACKGROUND: Sequence-binning techniques enable the recovery of an increasing number of genomes from complex microbial metagenomes and typically require prior metagenome assembly, incurring the computational cost and drawbacks of the latter, e.g., biases against low-abundance genomes and inability to conveniently assemble multi-terabyte datasets.<br><br>RESULTS: We present here a scalable pre-assembly binning scheme (i.e., operating on unassembled short reads) enabling latent genome recovery by leveraging sparse dictionary learning and elastic-net regularization, and its use to recover hundreds of metagenome-assembled genomes, including very low-abundance genomes, from a joint analysis of microbiomes from the LifeLines DEEP population cohort (n = 1,135, >1010 reads).<br><br>CONCLUSION: We showed that sparse coding techniques can be leveraged to carry out read-level binning at large scale and that, despite lower genome reconstruction yields compared to assembly-based approaches, bin-first strategies can complement the more widely used assembly-first protocols by targeting distinct genome segregation profiles. Read enrichment levels across 6 orders of magnitude in relative abundance were observed, indicating that the method has the power to recover genomes consistently segregating at low levels.}, }
@article {pmid32214138, year = {2020}, author = {Kummen, M and Solberg, OG and Storm-Larsen, C and Holm, K and Ragnarsson, A and Trøseid, M and Vestad, B and Skårdal, R and Yndestad, A and Ueland, T and Svardal, A and Berge, RK and Seljeflot, I and Gullestad, L and Karlsen, TH and Aaberge, L and Aukrust, P and Hov, JR}, title = {Rosuvastatin alters the genetic composition of the human gut microbiome.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {5397}, doi = {10.1038/s41598-020-62261-y}, pmid = {32214138}, issn = {2045-2322}, support = {2016067//Helse Sør-øst RHF/ ; 240787/F20//Norges Forskningsråd/ ; }, abstract = {The gut microbiome contributes to the variation of blood lipid levels, and secondary bile acids are associated with the effect of statins. Yet, our knowledge of how statins, one of our most common drug groups, affect the human microbiome is scarce. We aimed to characterize the effect of rosuvastatin on gut microbiome composition and inferred genetic content in stool samples from a randomized controlled trial (n = 66). No taxa were significantly altered by rosuvastatin during the study. However, rosuvastatin-treated participants showed a reduction in the collective genetic potential to transport and metabolize precursors of the pro-atherogenic metabolite trimethylamine-N-oxide (TMAO, p < 0.01), and an increase of related metabolites betaine and γ-butyrobetaine in plasma (p < 0.01). Exploratory analyses in the rosuvastatin group showed that participants with the least favorable treatment response (defined as < median change in high-density/low-density lipoprotein (HDL/LDL) ratio) showed a marked increase in TMAO-levels compared to those with a more favorable response (p < 0.05). Our data suggest that while rosuvastatin has a limited effect on gut microbiome composition, it could exert broader collective effects on the microbiome relevant to their function, providing a rationale for further studies of the influence of statins on the gut microbiome.}, }
@article {pmid32200333, year = {2020}, author = {Ben, Y and Hu, M and Zhang, X and Wu, S and Wong, MH and Wang, M and Andrews, CB and Zheng, C}, title = {Efficient detection and assessment of human exposure to trace antibiotic residues in drinking water.}, journal = {Water research}, volume = {175}, number = {}, pages = {115699}, doi = {10.1016/j.watres.2020.115699}, pmid = {32200333}, issn = {1879-2448}, abstract = {Human exposure to antibiotic residues in drinking water has not been well evaluated. This study is the first attempt to simultaneously and efficiently identify and quantify 92 antibiotic residues in filtered tap water (multistage filtration at the tap) (n = 36) collected from 10 areas of a large city in southern China, 10 Chinese brands of bottled/barreled water (n = 30) and six foreign brands of bottled water (n = 18) obtained from the Chinese market. The average and median concentrations of all the detected antibiotic compounds was 182 and 92 ng/L in filtered tap water, 180 and 105 ng/L in Chinese brands of bottled/barreled water, and 666 and 146 ng/L in foreign brands of bottled water, respectively. A total of 58 antibiotics were detected in the filtered tap water, and 45 and 36 antibiotics were detected in the Chinese and foreign brands of bottled water, respectively. More types of antibiotics were detected in Chinese brands of bottled water than in the other bottled waters. In addition, Chinese waters had high roxithromycin concentrations, while the foreign brands of bottled water had high concentrations of dicloxacillin. The average and median values of the estimated overall daily intake of all the detected antibiotics were 4.3 and 2.3 ng/kg/day when only filtered tap water was drunk, 4.0 and 2.5 ng/kg/day when Chinese brands of bottled water was drunk, and 16.0 and 4.9 ng/kg/day when foreign brands of bottled water was drunk. Further study is needed to develop a more comprehensive estimation of human exposure to antibiotic residues in the environment and a more in-depth understanding of the potential hazard of ingested antibiotic residues to the human microbiome.}, }
@article {pmid32199025, year = {2020}, author = {Puhlmann, ML and de Vos, WM}, title = {Back to the Roots: Revisiting the Use of the Fiber-Rich Cichorium intybusL. Taproots.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {}, number = {}, pages = {}, doi = {10.1093/advances/nmaa025}, pmid = {32199025}, issn = {2156-5376}, abstract = {Fibers are increasingly recognized as an indispensable part of our diet and vital for maintaining health. Notably, complex mixtures of fibers have been found to improve metabolic health. Following an analysis of the fiber content of plant-based products, we found the taproot of the chicory plant (Cichorium intybusL.) to be 1 of the vegetables with the highest fiber content, comprising nearly 90% of its dry weight. Chicory roots consist of a mixture of inulin, pectin, and (hemi-)cellulose and also contain complex phytochemicals, such as sesquiterpene lactones that have been characterized in detail. Nowaday, chicory roots are mainly applied as a source for the extraction of inulin, which is used as prebiotic fiber and food ingredient. Chicory roots, however, have long been consumed as a vegetable by humans. The whole root has been used for thousands of years for nutritional, medicinal, and other purposes, and it is still used in traditional dishes in various parts of the world. Here, we summarize the composition of chicory roots to explain their historic success in the human diet. We revisit the intake of chicory roots by humans and describe the different types of use along with their various methods of preparation. Hereby, we focus on the whole root in its complex, natural form, as well as in relation to its constituents, and discuss aspects regarding legal regulation and the safety of chicory root extracts for human consumption. Finally, we provide an overview of the current and future applications of chicory roots and their contribution to a fiber-rich diet.}, }
@article {pmid32194617, year = {2020}, author = {Jensen, CS and Norsigian, CJ and Fang, X and Nielsen, XC and Christensen, JJ and Palsson, BO and Monk, JM}, title = {Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {116}, doi = {10.3389/fgene.2020.00116}, pmid = {32194617}, issn = {1664-8021}, abstract = {The mitis group of streptococci (MGS) is a member of the healthy human microbiome in the oral cavity and upper respiratory tract. Troublingly, some MGS are able to escape this niche and cause infective endocarditis, a severe and devastating disease. Genome-scale models have been shown to be valuable in investigating metabolism of bacteria. Here we present the first genome-scale model, iCJ415, for Streptococcus oralis SK141. We validated the model using gene essentiality and amino acid auxotrophy data from closely related species. iCJ415 has 71-76% accuracy in predicting gene essentiality and 85% accuracy in predicting amino acid auxotrophy. Further, the phenotype of S. oralis was tested using the Biolog Phenotype microarrays, giving iCJ415 a 82% accuracy in predicting carbon sources. iCJ415 can be used to explore the metabolic differences within the MGS, and to explore the complicated metabolic interactions between different species in the human oral cavity.}, }
@article {pmid32186326, year = {2020}, author = {Fragiadakis, GK and Wastyk, HC and Robinson, JL and Sonnenburg, ED and Sonnenburg, JL and Gardner, CD}, title = {Long-term dietary intervention reveals resilience of the gut microbiota despite changes in diet and weight.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajcn/nqaa046}, pmid = {32186326}, issn = {1938-3207}, abstract = {BACKGROUND: With the rising rates of obesity and associated metabolic disorders, there is a growing need for effective long-term weight-loss strategies, coupled with an understanding of how they interface with human physiology. Interest is growing in the potential role of gut microbes as they pertain to responses to different weight-loss diets; however, the ways that diet, the gut microbiota, and long-term weight loss influence one another is not well understood.<br><br>OBJECTIVES: Our primary objective was to determine if baseline microbiota composition or diversity was associated with weight-loss success. A secondary objective was to track the longitudinal associations of changes to lower-carbohydrate or lower-fat diets and concomitant weight loss with the composition and diversity of the gut microbiota.<br><br>METHODS: We used 16S ribosomal RNA gene amplicon sequencing to profile microbiota composition over a 12-mo period in 49 participants as part of a larger randomized dietary intervention study of participants consuming either a healthy low-carbohydrate or a healthy low-fat diet.<br><br>RESULTS: While baseline microbiota composition was not predictive of weight loss, each diet resulted in substantial changes in the microbiota 3-mo after the start of the intervention; some of these changes were diet specific (14 taxonomic changes specific to the healthy low-carbohydrate diet, 12 taxonomic changes specific to the healthy low-fat diet) and others tracked with weight loss (7 taxonomic changes in both diets). After these initial shifts, the microbiota returned near its original baseline state for the remainder of the intervention, despite participants maintaining their diet and weight loss for the entire study.<br><br>CONCLUSIONS: These results suggest a resilience to perturbation of the microbiota's starting profile. When considering the established contribution of obesity-associated microbiotas to weight gain in animal models, microbiota resilience may need to be overcome for long-term alterations to human physiology. This trial was registered at clinicaltrials.gov as NCT01826591.}, }
@article {pmid32180472, year = {2020}, author = {Zou, Y and Wu, L and Xu, W and Zhou, X and Ye, K and Xiong, H and Song, C and Xie, Y}, title = {Correlation between antibiotic use in childhood and subsequent inflammatory bowel disease: a systematic review and meta-analysis.}, journal = {Scandinavian journal of gastroenterology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/00365521.2020.1737882}, pmid = {32180472}, issn = {1502-7708}, abstract = {Background: Antibiotic use leads to a cascade of inflammatory reaction in the gastrointestinal tract due to its association with a temporary disruption of human microbiome.Objectives: To explore the undetermined correlation between antibiotic use in childhood and subsequent inflammatory bowel disease (IBD).Methods: PUBMED, EMBASE and Cochrane Central Register of Controlled Trials were searched to identify related articles. We extracted and pooled the (adjusted) odds ratio (OR) and (adjusted) risk ratio (RR).Results: This systematic review and meta-analysis included 11 studies. The pooled OR of all 11 studies was 1.5 (95% confidence interval (CI): 1.22-1.85). The pooled ORs of the subsequent Crohn's disease and ulcerative colitis after antibiotic use in childhood were 1.59 (95% CI: 1.06-2.4) and 1.22 (95% CI: 0.82-1.8). The sensitivity analysis showed no change. The meta-regression showed there was not statistical significance for the publication year, research area and research methods. Egger's test showed publication bias in the IBD studies (p = .006 < .05) but no publication bias for the CD (p = .275>.05) and UC studies (p = .537>.05).Conclusions: There was a positive association between antibiotic use in childhood and the subsequently risk of Crohn's disease in non-European countries in the west during 2010-2013. Children in the United States taking antibiotics will have a higher risk of subsequently IBD than Europe, Asia and Australia. Registration number: CRD42019147648 (PROSPERO).}, }
@article {pmid32179736, year = {2019}, author = {El-Awady, A and de Sousa Rabelo, M and Meghil, MM and Rajendran, M and Elashiry, M and Stadler, AF and Foz, AM and Susin, C and Romito, GA and Arce, RM and Cutler, CW}, title = {Polymicrobial synergy within oral biofilm promotes invasion of dendritic cells and survival of consortia members.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {1}, pages = {11}, doi = {10.1038/s41522-019-0084-7}, pmid = {32179736}, issn = {2055-5008}, support = {R01 DE014328/DE/NIDCR NIH HHS/United States ; }, abstract = {Years of human microbiome research have confirmed that microbes rarely live or function alone, favoring diverse communities. Yet most experimental host-pathogen studies employ single species models of infection. Here, the influence of three-species oral microbial consortium on growth, virulence, invasion and persistence in dendritic cells (DCs) was examined experimentally in human monocyte-derived dendritic cells (DCs) and in patients with periodontitis (PD). Cooperative biofilm formation by Streptococcus gordonii, Fusobacterium nucleatum and Porphyromonas gingivalis was documented in vitro using growth models and scanning electron microscopy. Analysis of growth rates by species-specific 16s rRNA probes revealed distinct, early advantages to consortium growth for S. gordonii and F. nucleatum with P. gingivalis, while P. gingivalis upregulated its short mfa1 fimbriae, leading to increased invasion of DCs. F. nucleatum was only taken up by DCs when in consortium with P. gingivalis. Mature consortium regressed DC maturation upon uptake, as determined by flow cytometry. Analysis of dental plaques of PD and healthy subjects by 16s rRNA confirmed oral colonization with consortium members, but DC hematogenous spread was limited to P. gingivalis and F. nucleatum. Expression of P. gingivalis mfa1 fimbriae was increased in dental plaques and hematogenous DCs of PD patients. P. gingivalis in the consortium correlated with an adverse clinical response in the gingiva of PD subjects. In conclusion, we have identified polymicrobial synergy in a three-species oral consortium that may have negative consequences for the host, including microbial dissemination and adverse peripheral inflammatory responses.}, }
@article {pmid32179576, year = {2020}, author = {Tuompo, R and Lääveri, T and Hannu, T and Pakkanen, SH and Kirveskari, J and Leirisalo-Repo, M and Kantele, A}, title = {Reactive arthritis and other musculoskeletal symptoms associated with acquisition of diarrhoeagenic Escherichia coli (DEC).}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/annrheumdis-2019-216736}, pmid = {32179576}, issn = {1468-2060}, abstract = {OBJECTIVES: Using a prospective research design, we evaluated the association between acquisition of diarrhoeagenic Escherichia coli (DEC) and development of reactive arthritis (ReA) and other reactive musculoskeletal (MSK) symptoms among international travellers.<br><br>METHODS: A total of 526 study participants were asked to provide pretravel and post-travel stool samples and fill in questionnaires (pretravel, post-travel and 3-week follow-up). A multiplex quantitative PCR assay was deployed to detect five DEC comprising enteroaggregative E. coli, enteropathogenic E. coli, enterotoxigenic E. coli, enterohaemorrhagic E. coli and enteroinvasive E. coli and Salmonella, Shigella, Campylobacter, Yersinia, and Vibrio cholerae. Multivariate analysis was employed to identify factors predisposing to MSK symptoms. New post-travel MSK symptoms reported by participants with DEC were assessed by phone interviews and, if needed, clinically confirmed.<br><br>RESULTS: From among the total of 224 volunteers who returned all questionnaires and stool specimens, 38 (17.0%) reported MSK symptoms. Multivariate analysis revealed that acquisition of DEC was associated with MSK symptoms (OR 3.9; 95% CI 1.2 to 13.3). Of the 151 with only-DEC, four (2.6%) had ReA, two (1.3%) reactive tendinitis and three (2.0%) reactive arthralgia. ReA was mostly mild, and all patients with ReA were negative for human leucocyte antigen B27. Antibiotic treatment of travellers' diarrhoea did not prevent development of MSK symptoms.<br><br>CONCLUSION: A total of 17% of volunteers reported post-travel MSK symptoms. DEC acquisition was associated with an increased risk of developing them, yet the ReA incidence remained low and the clinical picture mild. Antibiotic treatment did not protect against development of MSK symptoms.}, }
@article {pmid32174900, year = {2020}, author = {Sarra, A and Celluzzi, A and Bruno, SP and Ricci, C and Sennato, S and Ortore, MG and Casciardi, S and Del Chierico, F and Postorino, P and Bordi, F and Masotti, A}, title = {Biophysical Characterization of Membrane Phase Transition Profiles for the Discrimination of Outer Membrane Vesicles (OMVs) From Escherichia coli Grown at Different Temperatures.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {290}, doi = {10.3389/fmicb.2020.00290}, pmid = {32174900}, issn = {1664-302X}, abstract = {Dynamic Light Scattering (DLS), Small Angle X-ray Scattering (SAXS) and Transmission Electron Microscopy (TEM) are physical techniques widely employed to characterize the morphology and the structure of vesicles such as liposomes or human extracellular vesicles (exosomes). Bacterial extracellular vesicles are similar in size to human exosomes, although their function and membrane properties have not been elucidated in such detail as in the case of exosomes. Here, we applied the above cited techniques, in synergy with the thermotropic characterization of the vesicles lipid membrane using a turbidimetric technique to the study of vesicles produced by Gram-negative bacteria (Outer Membrane Vesicles, OMVs) grown at different temperatures. This study demonstrated that our combined approach is useful to discriminate vesicles of different origin or coming from bacteria cultured under different experimental conditions. We envisage that in a near future the techniques employed in our work will be further implemented to discriminate complex mixtures of bacterial vesicles, thus showing great promises for biomedical or diagnostic applications.}, }
@article {pmid32170007, year = {2020}, author = {Bhatt, AP and Pellock, SJ and Biernat, KA and Walton, WG and Wallace, BD and Creekmore, BC and Letertre, MM and Swann, JR and Wilson, ID and Roques, JR and Darr, DB and Bailey, ST and Montgomery, SA and Roach, JM and Azcarate-Peril, MA and Sartor, RB and Gharaibeh, RZ and Bultman, SJ and Redinbo, MR}, title = {Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {}, number = {}, pages = {}, doi = {10.1073/pnas.1918095117}, pmid = {32170007}, issn = {1091-6490}, abstract = {Irinotecan treats a range of solid tumors, but its effectiveness is severely limited by gastrointestinal (GI) tract toxicity caused by gut bacterial β-glucuronidase (GUS) enzymes. Targeted bacterial GUS inhibitors have been shown to partially alleviate irinotecan-induced GI tract damage and resultant diarrhea in mice. Here, we unravel the mechanistic basis for GI protection by gut microbial GUS inhibitors using in vivo models. We use in vitro, in fimo, and in vivo models to determine whether GUS inhibition alters the anticancer efficacy of irinotecan. We demonstrate that a single dose of irinotecan increases GI bacterial GUS activity in 1 d and reduces intestinal epithelial cell proliferation in 5 d, both blocked by a single dose of a GUS inhibitor. In a tumor xenograft model, GUS inhibition prevents intestinal toxicity and maintains the antitumor efficacy of irinotecan. Remarkably, GUS inhibitor also effectively blocks the striking irinotecan-induced bloom of Enterobacteriaceae in immune-deficient mice. In a genetically engineered mouse model of cancer, GUS inhibition alleviates gut damage, improves survival, and does not alter gut microbial composition; however, by allowing dose intensification, it dramatically improves irinotecan's effectiveness, reducing tumors to a fraction of that achieved by irinotecan alone, while simultaneously promoting epithelial regeneration. These results indicate that targeted gut microbial enzyme inhibitors can improve cancer chemotherapeutic outcomes by protecting the gut epithelium from microbial dysbiosis and proliferative crypt damage.}, }
@article {pmid32169076, year = {2020}, author = {Murugesan, S and Al Ahmad, SF and Singh, P and Saadaoui, M and Kumar, M and Al Khodor, S}, title = {Profiling the Salivary microbiome of the Qatari population.}, journal = {Journal of translational medicine}, volume = {18}, number = {1}, pages = {127}, doi = {10.1186/s12967-020-02291-2}, pmid = {32169076}, issn = {1479-5876}, abstract = {BACKGROUND: The role of the human microbiome in human health and disease has been studied in various body sites. However, compared to the gut microbiome, where most of the research focus is, the salivary microbiome still bears a vast amount of information that needs to be revealed. This study aims to characterize the salivary microbiome composition in the Qatari population, and to explore specific microbial signatures that can be associated with various lifestyles and different oral conditions.<br><br>MATERIALS AND METHODS: We characterized the salivary microbiome of 997 Qatari adults using high-throughput sequencing of the V1-V3 region of the 16S rRNA gene.<br><br>RESULTS: In this study, we have characterized the salivary microbiome of 997 Qatari participants. Our data show that Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria are the common phyla isolated from the saliva samples, with Bacteroidetes being the most predominant phylum. Bacteroidetes was also more predominant in males versus females in the study cohort, although differences in the microbial diversity were not statistically significant. We also show that, a lower diversity of the salivary microbiome is observed in the elderly participants, with Prevotella and Treponema being the most significant genera. In participants with oral conditions such as mouth ulcers, bleeding or painful gum, our data show that Prevotella and Capnocytophaga are the most dominant genera as compared to the controls. Similar patterns were observed in participants with various smoking habits as compared to the non-smoking participants. Our data show that Streptococcus and Neisseria are more dominant among denture users, as compared to the non-denture users. Our data also show that, abnormal oral conditions are associated with a reduced microbial diversity and microbial richness. Moreover, in this study we show that frequent coffee drinkers have higher microbial diversity compared to the non-drinkers, indicating that coffee may cause changes to the salivary microbiome. Furthermore, tea drinkers show higher microbial richness as compared to the non-tea drinkers.<br><br>CONCLUSION: This is the first study to assess the salivary microbiome in an Arab population, and one of the largest population-based studies aiming to the characterize the salivary microbiome composition and its association with age, oral health, denture use, smoking and coffee-tea consumption.}, }
@article {pmid32167855, year = {2020}, author = {Belmok, A and de Cena, JA and Kyaw, CM and Damé-Teixeira, N}, title = {The Oral Archaeome: A Scoping Review.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {22034520910435}, doi = {10.1177/0022034520910435}, pmid = {32167855}, issn = {1544-0591}, abstract = {The Archaea domain was recognized as a separate phylogenetic lineage in the tree of life nearly 3 decades ago. It is now known as part of the human microbiome; however, given that its roles in oral sites are still poorly understood, this review aimed to establish the current level of evidence regarding archaea in the oral cavity to guide future research, providing insights on the present knowledge about the human oral archaeome. A scoping review was conducted with the PRISMA Extension for Scoping Reviews checklist. Five electronic databases were searched, as well as gray literature. Two independent reviewers performed the selection and characterization of the studies. Clinical studies were included when the target population consisted of humans of any age who were donors of samples from the oral cavity. A qualitative analysis was performed, based on the type of oral site and by considering the methods employed for archaeal identification and taxonomy, including the DNA extraction protocols, primers, and probes used. Fifty articles were included in the final scoping review, published from 1987 to 2019. Most studies sampled periodontal sites. Methanogens were the most abundant archaea in those sites, and their presence could be associated with other periodontal pathogens. No consistent relationship with different disease conditions was observed in studies that evaluated the microbiota surviving in endodontic sites. Few articles analyzed the presence of archaea in dental caries, saliva, or tongue microbiota, as well as in archaeologic samples, also showing a relationship with healthy microbiota. Archaea have been detected in different oral niches of individuals from diverse geographic locations and clinical conditions, suggesting potential roles in oral diseases. Methodological limitations may hamper our current knowledge about archaeal diversity and prevalence in oral samples, and future research with diversified methodological approaches may lead to a better comprehension of the human oral archaeome.}, }
@article {pmid32167023, year = {2020}, author = {Depommier, C and Van Hul, M and Everard, A and Delzenne, NM and De Vos, WM and Cani, PD}, title = {Pasteurized Akkermansia muciniphila increases whole-body energy expenditure and fecal energy excretion in diet-induced obese mice.}, journal = {Gut microbes}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/19490976.2020.1737307}, pmid = {32167023}, issn = {1949-0984}, abstract = {Accumulating evidence points to Akkermansia muciniphila as a novel candidate to prevent or treat obesity-related metabolic disorders. We recently observed, in mice and in humans, that pasteurization of A. muciniphila increases its beneficial effects on metabolism. However, it is currently unknown if the observed beneficial effects on body weight and fat mass gain are due to specific changes in energy expenditure. Therefore, we investigated the effects of pasteurized A. muciniphila on whole-body energy metabolism during high-fat diet feeding by using metabolic chambers. We confirmed that daily oral administration of pasteurized A. muciniphila alleviated diet-induced obesity and decreased food energy efficiency. We found that this effect was associated with an increase in energy expenditure and spontaneous physical activity. Strikingly, we discovered that energy expenditure was enhanced independently from changes in markers of thermogenesis or beiging of the white adipose tissue. However, we found in brown and white adipose tissues that perilipin2, a factor associated with lipid droplet and known to be altered in obesity, was decreased in expression by pasteurized A. muciniphila. Finally, we observed that treatment with pasteurized A. muciniphila increased energy excretion in the feces. Interestingly, we demonstrated that this effect was not due to the modulation of intestinal lipid absorption or chylomicron synthesis but likely involved a reduction of carbohydrates absorption and enhanced intestinal epithelial turnover.In conclusion, this study further dissects the mechanisms by which pasteurized A. muciniphila reduces body weight and fat mass gain. These data also further support the impact of targeting the gut microbiota by using specific bacteria to control whole-body energy metabolism.}, }
@article {pmid32166902, year = {2020}, author = {Antosca, K and Hoen, AG and Palys, T and Hilliard, M and Morrison, HG and Coker, M and Madan, J and Karagas, MR}, title = {Reliability of stool microbiome methods for DNA yields and sequencing among infants and young children.}, journal = {MicrobiologyOpen}, volume = {}, number = {}, pages = {e1018}, doi = {10.1002/mbo3.1018}, pmid = {32166902}, issn = {2045-8827}, support = {P01ES022832//U.S. National Institutes of Environmental Health Sciences/ ; P20GM104416//U.S. National Institutes of General Medicine/ ; RD 83544201//U.S. EPA/ ; 5T32HL134598, UH3OD023275/GF/NIH HHS/United States ; }, abstract = {With the emergence of large-scale epidemiologic human microbiome studies, there is a need to understand the reproducibility of microbial DNA sequencing and the impact of specimen collection and processing methods on measures of microbial community composition and structure, with reproducibility studies in infants and young children particularly lacking. Here, we examined batch-to-batch variability and reliability of collection, handling, and processing protocols, testing replicate stool samples from infants and young children using Illumina MiSeq sequencing of the bacterial 16S rRNA gene V4-V5 hypervariable region, evaluating 33 conditions with different protocols and extraction methods. We detected no evidence of batch effects in replicate DNA samples or extractions from the same stool sample. Variability in DNA yield and alpha diversity was observed between the different collection, handling, and processing protocols. However, across all protocols, subject variability was the dominant contributor to microbiome structure, with comparatively little impact of the protocol used. While collection method and DNA extraction kit may affect DNA yield, and correspondingly alpha diversity, our findings suggest that characterization of the structure and composition of the fecal microbiome of infants and young children are reliably measurable by standardized collection, handling, and processing protocols and DNA extraction methods within an individual longitudinal study.}, }
@article {pmid32158700, year = {2020}, author = {Romani, L and Del Chierico, F and Chiriaco, M and Foligno, S and Reddel, S and Salvatori, G and Cifaldi, C and Faraci, S and Finocchi, A and Rossi, P and Bagolan, P and D'Argenio, P and Putignani, L and Fusaro, F}, title = {Gut Mucosal and Fecal Microbiota Profiling Combined to Intestinal Immune System in Neonates Affected by Intestinal Ischemic Injuries.}, journal = {Frontiers in cellular and infection microbiology}, volume = {10}, number = {}, pages = {59}, doi = {10.3389/fcimb.2020.00059}, pmid = {32158700}, issn = {2235-2988}, abstract = {Background and Purpose: Early life microbiota plays a crucial role in human health by acting as a barrier from pathogens' invasion and maintaining the intestinal immune homoeostasis. Altered fecal microbiota (FM) ecology was reported in newborns affected by intestinal ischemia. Our purpose was to describe, in these patients, the FM, the mucosal microbiota (MM) and the mucosal immunity. Methods: Fourteen newborns underwent intestinal resection because of intestinal ischemia. FM and MM were determined through targeted-metagenomics, diversity assignment and Kruskal-Wallis analyses of Operational taxonomic units (OTUs). The mucosal immune cells were analyzed through cytofluorimetry. Results and Conclusion: Based on the severity intestinal injueris we identified two groups: extensive (EII) and focal intestinal ischemia (FII). FM and MM varied in EII and FII groups, showing in the EII group the predominance of Proteobacteria and Enterobacteriaceae and the reduction of Bacteroidetes and Verrucomicrobia for both microbiota. The MM was characterized by a statistically significant reduction of Bacteroides, Lachnospiraceae and Ruminococcaceae and by a higher diversity in the EII compared to FII group. FM showed a prevalence of Proteobacteria, while the Shannon index was lower in the EII compared to FII group. An overall increment in B- and T-lymphocytes and Natural killer (NK) T-like cells was found for EII mucosal samples associated to an increment of TNF-α and INF-γ expressing cells, compared to FII group. FM and MM carry specific signatures of intestinal ischemic lesions. Further research may be crucial to address the role of specific taxa in EII, expecially with reference to inflammation grade and ischemia extension.}, }
@article {pmid32156071, year = {2020}, author = {Pan, S and Hullar, MAJ and Lai, LA and Peng, H and May, DH and Noble, WS and Raftery, D and Navarro, SL and Neuhouser, ML and Lampe, PD and Lampe, JW and Chen, R}, title = {Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, doi = {10.3390/microorganisms8030379}, pmid = {32156071}, issn = {2076-2607}, support = {R01 CA192222/NH/NIH HHS/United States ; U54 CA116847/NH/NIH HHS/United States ; P30 CA015704/NH/NIH HHS/United States ; R01 CA211892/NH/NIH HHS/United States ; }, abstract = {Although the gut microbiome has been associated with dietary patterns linked to health, microbial metabolism is not well characterized. This ancillary study was a proof of principle analysis for a novel application of metaproteomics to study microbial protein expression in a controlled dietary intervention. We measured the response of the microbiome to diet in a randomized crossover dietary intervention of a whole-grain, low glycemic load diet (WG) and a refined-grain, high glycemic load diet (RG). Total proteins in stools from 9 participants at the end of each diet period (n = 18) were analyzed by LC MS/MS and proteins were identified using the Human Microbiome Project (HMP) human gut microbiome database and UniProt human protein databases. T-tests, controlling for false discovery rate (FDR) <10%, were used to compare the Gene Ontology (GO) biological processes and bacterial enzymes between the two interventions. Using shotgun proteomics, more than 53,000 unique peptides were identified including microbial (89%) and human peptides (11%). Forty-eight bacterial enzymes were statistically different between the diets, including those implicated in SCFA production and degradation of fatty acids. Enzymes associated with degradation of human mucin were significantly enriched in the RG diet. These results illustrate that the metaproteomic approach is a valuable tool to study the microbial metabolism of diets that may influence host health.}, }
@article {pmid32153643, year = {2020}, author = {Ma, Y and Liu, G and Ma, Y and Chen, Q}, title = {Integrative Analysis for Identifying Co-Modules of Microbe-Disease Data by Matrix Tri-Factorization With Phylogenetic Information.}, journal = {Frontiers in genetics}, volume = {11}, number = {}, pages = {83}, doi = {10.3389/fgene.2020.00083}, pmid = {32153643}, issn = {1664-8021}, abstract = {Microbe-disease association relationship mining is drawing more and more attention due to its potential in capturing disease-related microbes. Hence, it is essential to develop new tools or algorithms to study the complex pathogenic mechanism of microbe-related diseases. However, previous research studies mainly focused on the paradigm of &quot;one disease, one microbe,&quot; rarely investigated the cooperation and associations between microbes, diseases or microbe-disease co-modules from system level. In this study, we propose a novel two-level module identifying algorithm (MDNMF) based on nonnegative matrix tri-factorization which integrates two similarity matrices (disease and microbe similarity matrices) and one microbe-disease association matrix into the objective of MDNMF. MDNMF can identify the modules from different levels and reveal the connections between these modules. In order to improve the efficiency and effectiveness of MDNMF, we also introduce human symptoms-disease network and microbial phylogenetic distance into this model. Furthermore, we applied it to HMDAD dataset and compared it with two NMF-based methods to demonstrate its effectiveness. The experimental results show that MDNMF can obtain better performance in terms of enrichment index (EI) and the number of significantly enriched taxon sets. This demonstrates the potential of MDNMF in capturing microbial modules that have significantly biological function implications.}, }
@article {pmid32133297, year = {2020}, author = {Cheng, H and Wang, Z and Cui, L and Wen, Y and Chen, X and Gong, F and Yi, H}, title = {Opportunities and Challenges of the Human Microbiome in Ovarian Cancer.}, journal = {Frontiers in oncology}, volume = {10}, number = {}, pages = {163}, pmid = {32133297}, issn = {2234-943X}, abstract = {Ovarian cancer is the most lethal malignancy among gynecological cancers worldwide. Most ovarian cancer patients are diagnosed at an advanced stage because of non-specific clinical symptoms. The human microbiome plays a crucial role in maintaining the normal physiological and pathological state of the body. With the development of technologies such as DNA and 16S rRNA sequencing, an increasing number of findings on the role of microbiome in cancers are being reported. Microbiome abnormalities are increasingly associated with diseases, including cancer development, and response to therapies. Some studies have shown the relationship between microbiome changes and ovarian cancer. However, the mechanisms underlying this relationship are not yet fully understood. Here, we summarize the key findings in this regard by focusing on estrogen metabolism and host recognition receptors in microorganisms and changes in the gut or pelvic microbiome in patients with ovarian cancer. We further discuss the potential of using the microbiome as a novel biomarker for cancers. We also highlight the possibility to use microorganisms as a treatment modality to enhance the immune system, activate anti-tumor response, mediate chemotherapy resistance, and ameliorate the adverse effects of the treatment.}, }
@article {pmid32132244, year = {2020}, author = {Bellone, M and Brevi, A and Huber, S}, title = {Microbiota-Propelled T Helper 17 Cells in Inflammatory Diseases and Cancer.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {84}, number = {2}, pages = {}, doi = {10.1128/MMBR.00064-19}, pmid = {32132244}, issn = {1098-5557}, abstract = {SUMMARYTechnologies allowing genetic sequencing of the human microbiome are opening new realms to discovery. The host microbiota substantially impacts immune responses both in immune-mediated inflammatory diseases (IMIDs) and in tumors affecting tissues beyond skin and mucosae. However, a mechanistic link between host microbiota and cancer or IMIDs has not been well established. Here, we propose T helper 17 (TH17) lymphocytes as the connecting factor between host microbiota and rheumatoid or psoriatic arthritides, multiple sclerosis, breast or ovarian cancer, and multiple myeloma. We theorize that similar mechanisms favor the expansion of gut-borne TH17 cells and their deployment at the site of inflammation in extraborder IMIDs and tumors, where TH17 cells are driving forces. Thus, from a pathogenic standpoint, tumors may share mechanistic routes with IMIDs. A review of similarities and divergences in microbiota-TH17 cell interactions in IMIDs and cancer sheds light on previously ignored pathways in either one of the two groups of pathologies and identifies novel therapeutic avenues.}, }
@article {pmid32129192, year = {2020}, author = {Vairakkani, R and Fernando, ME and Raj, TY}, title = {Metabolome and microbiome in kidney diseases.}, journal = {Saudi journal of kidney diseases and transplantation : an official publication of the Saudi Center for Organ Transplantation, Saudi Arabia}, volume = {31}, number = {1}, pages = {1-9}, doi = {10.4103/1319-2442.279927}, pmid = {32129192}, issn = {1319-2442}, abstract = {Despite several decades of intensive research and hard work in nephrology, a void exists in the availability of markers for identifying at-risk individuals, diagnosing diseases at incipient stage, and predicting treatment response. Most of the current widely available diagnostic tools such as creatinine, urine analysis, and imaging studies are quite insensitive such that about half of the kidney function is lost before perceivable changes are observed with these tests. In addition, these parameters are affected by factors other than renal, questioning their specificity. Renal biopsy, though specific, is quite expensive, risky, and invasive. The recent surge in the knowledge of small molecules in the tissue and body fluids, &quot;metabolomics,&quot; thanks to the Human Metabolome Database created by the Human Metabolome Project, has opened a new avenue for better understanding the disease pathogenesis and, in parallel, to identify novel biomarkers and druggable targets. Kidney, by virtue of its metabolic machinery and also being a major handler of metabolites generated by other tissues, is very much amenable to the metabolomic approach of studying its various perturbations. The gut microbiome, characterized by the Human Microbiome Project, is one of the principal players in metabolomics. Changes in metabolite profile due to alterations in gut microbiome can occur either as a cause or consequence of renal diseases. Unmasking the renal-metabolome-microbiome link has a great potential to script a new era in the diagnosis and management of renal diseases.}, }
@article {pmid32121205, year = {2020}, author = {Sare, AR and Stouvenakers, G and Eck, M and Lampens, A and Goormachtig, S and Jijakli, MH and Massart, S}, title = {Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested?.}, journal = {Microorganisms}, volume = {8}, number = {3}, pages = {}, doi = {10.3390/microorganisms8030342}, pmid = {32121205}, issn = {2076-2607}, support = {FIRA 5200818F//Fonds De La Recherche Scientifique - FNRS/ ; }, abstract = {Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.}, }
@article {pmid32117102, year = {2020}, author = {Tsigalou, C and Konstantinidis, T and Stavropoulou, E and Bezirtzoglou, EE and Tsakris, A}, title = {Potential Elimination of Human Gut Resistome by Exploiting the Benefits of Functional Foods.}, journal = {Frontiers in microbiology}, volume = {11}, number = {}, pages = {50}, pmid = {32117102}, issn = {1664-302X}, abstract = {Recent advances in technology over the last decades have strived to elucidate the diverse and abundant ecosystem of the human microbiome. The intestinal microbiota represents a densely inhabited environment that offers a plethora of beneficial effects to the host's wellbeing. On the other hand, it can serve as a potential reservoir of Multi-Drug Resistant (MDR) bacteria and their antibiotic-resistant genes (ARgenes), which comprise the &quot;gut resistome.&quot; ARgenes, like antibiotics, have been omnipresent in the environment for billions of years. In the context of the gut microbiome, these genes may conflate into exogenous MDR or emerge in commensals due to mutations or gene transfers. It is currently generally accepted that Antimicrobial Resistance (AMR) poses a serious threat to public health worldwide. It is of paramount importance that researchers focus on, amongst other parameters, elaborating strategies to manage the gut resistome, particularly focusing on the diminution of AMR. Potential interventions in the gut microbiome field by Fecal Microbiota Transplant (FMT) or functional foods are newly emerged candidates for the uprooting of MDR strains and restoring dysbiosis and resilience. Probiotic nutrition is thought to diminish gut colonization from pathobionts. Yet only a few studies have explored the effects of antibiotics use on the reservoir of AR genes and the demanding time for return to normal by gut microbiota-targeted strategies. Regular administration of probiotic bacteria has recently been linked to restoration of the gut ecosystem and decrease of the gut resistome and AR genes carriers. This review summarizes the latest information about the intestinal resistome and the intriguing methods of fighting against AMR through probiotic-based methods and gut microbial shifts that have been proposed. This study contains some key messages: (1) AMR currently poses a lethal threat to global health, and it is pivotal for the scientific community to do its utmost in fighting against it; (2) human gut microbiome research, within the last decade especially, seems to be preoccupied with the interface of numerous diseases and identifying a potential target for a variety of interventions; (3) the gut resistome, comprised of AR genesis, presents very early on in life and is prone to shifts due to the use of antibiotics or dietary supplements; and (4) future strategies involving functional foods seem promising for the battle against AMR through intestinal resistome diminution.}, }
@article {pmid32112046, year = {2020}, author = {Domingue, JC and Drewes, JL and Merlo, CA and Housseau, F and Sears, CL}, title = {Host responses to mucosal biofilms in the lung and gut.}, journal = {Mucosal immunology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41385-020-0270-1}, pmid = {32112046}, issn = {1935-3456}, abstract = {The impact of the human microbiome on health and disease is of utmost importance and has been studied intensively in recent years. Microbes promote immune system development and are essential to the production and absorption of nutrients for the host but are also implicated in disease pathogenesis. Particularly, bacterial biofilms have long been recognized as contributors to chronic infections and diseases in humans. However, our understanding of how the host responds to the presence of biofilms, specifically the immune response to biofilms, and how this contributes to disease pathogenesis is limited. This review aims to highlight what is known about biofilm formation and in vivo models available for the biofilm study. We critique the contribution of biofilms to human diseases, focusing on the lung diseases, cystic fibrosis and chronic obstructive pulmonary disease, and the gut diseases, inflammatory bowel disease and colorectal cancer.}, }
@article {pmid32109571, year = {2020}, author = {Tarsillo, B and Priefer, R}, title = {Proteobiotics as a new antimicrobial therapy.}, journal = {Microbial pathogenesis}, volume = {142}, number = {}, pages = {104093}, doi = {10.1016/j.micpath.2020.104093}, pmid = {32109571}, issn = {1096-1208}, abstract = {Antibiotic resistance is a major concern for healthcare. The emergence of resistant bacteria has contributed to an increase in cost, morbidity, and mortality rates of patients. There is evidence to suggest that the inhibition of bacteria's virulence strategies would downregulate their pathogenesis and stop infections while also preventing more resistance. This concept became the backbone of many studies in the arena of human microbiome. Through probiotic studies, novel compounds were discovered that possessed antimicrobial activity. These have become labeled as proteobiotics, i.e. metabolites from probiotics. Proteobiotics have demonstrated the ability to interrupt bacteria cell-to-cell communication. Currently, there is one approved product containing proteobiotic technologies for swine showing positive outcomes.}, }
@article {pmid32109360, year = {2020}, author = {de Jesus, VC and Shikder, R and Oryniak, D and Mann, K and Alamri, A and Mittermuller, B and Duan, K and Hu, P and Schroth, RJ and Chelikani, P}, title = {Sex-Based Diverse Plaque Microbiota in Children with Severe Caries.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {22034520908595}, doi = {10.1177/0022034520908595}, pmid = {32109360}, issn = {1544-0591}, abstract = {Severe early childhood caries (S-ECC) is a multifactorial disease that can lead to suffering and reduced oral health-related quality of life in young children. The bacterial and fungal composition of dental plaque and how children's sex is associated with S-ECC are largely unknown. In this study, V4-16S rRNA and ITS1 rRNA gene amplicon sequencing was used to compare the plaque bacteriome and mycobiome of children <72 mo of age: 40 with S-ECC (15 males, 25 females) and 40 caries-free (19 males, 21 females). Health- and nutrition-related questionnaire data were also investigated. This study aimed to analyze potential sex-based differences in the supragingival plaque microbiota of young children with S-ECC and those caries-free. Behavioral and nutritional habit differences were observed between children with S-ECC and those caries-free and between male and female children. Overall, higher levels of Veillonella dispar, Streptococcus mutans, and other bacterial species were found in the S-ECC group as compared with caries-free controls (P < 0.05). A significant difference in the abundance of Neisseria was observed between males and females with S-ECC (P < .05). Fungal taxonomic analysis showed significantly higher levels of Candida dubliniensis in the plaque of children with S-ECC as compared with those caries-free (P < 0.05), but no differences were observed with Candida albicans (P > 0.05). Significant differences in the relative abundance of Mycosphaerella, Cyberlindnera, and Trichosporon fungal species were also observed between the caries-free and S-ECC groups (P < 0.05). Machine learning analysis revealed the most important bacterial and fungal species for classifying S-ECC versus caries-free. Different patterns of crosstalk between microbial species were observed between male and female children. Our work demonstrates that plaque microbiota and sex may be important determinants for S-ECC and could be factors to consider for inclusion in caries risk assessment tools.}, }
@article {pmid32108360, year = {2020}, author = {Ruokolainen, L and Parkkola, A and Karkman, A and Sinkko, H and Peet, A and Hämäläinen, AM and von Hertzen, L and Tillmann, V and Koski, K and Virtanen, SM and Niemelä, O and Haahtela, T and Knip, M}, title = {Contrasting microbiotas between Finnish and Estonian infants: exposure to Acinetobacter may contribute to the allergy gap.}, journal = {Allergy}, volume = {}, number = {}, pages = {}, doi = {10.1111/all.14250}, pmid = {32108360}, issn = {1398-9995}, abstract = {BACKGROUND: Allergic diseases are more common in Finland than in Estonia, which-according to the biodiversity hypothesis-could relate to differences in early microbial exposures.<br><br>METHODS: We aimed at defining possible microbial perturbations preceding early atopic sensitisation. Stool, nasal, and skin samples of 6-month-old DIABIMMUNE study participants with HLA susceptibility to type 1 diabetes were collected. We compared microbiotas of sensitised (determined by specific IgE-results at 18 months of age) and unsensitised Estonian and Finnish children.<br><br>RESULTS: Sensitisation was differentially targeted between populations, as egg- and birch pollen-specific IgE was more common in Finland. Microbial diversity and community composition also differed; the genus Acinetobacter was more abundant in Estonian skin- and nasal samples. Particularly, the strain level profile of Acinetobacter lwoffii was more diverse in Estonian samples. Early microbiota was not generally associated with later sensitisation. Microbial composition tended to differ between children with or without IgE-related sensitisation, but only in Finland. While land-use pattern (i.e. green areas vs. urban landscapes around the children's homes) was not associated with microbiota as a whole, it associated with the composition of the genus Acinetobacter. Breastfeeding affected gut microbial composition and seemed to protect from sensitisation.<br><br>CONCLUSIONS: In accordance with the biodiversity hypothesis, our results support disparate early exposure to environmental microbes between Finnish and Estonian children and suggest a significant role of the genus Acinetobacter in the allergy gap between the two populations. The significance of the observed differences for later allergic sensitisation remains open.}, }
@article {pmid32107336, year = {2020}, author = {Merli, P and Putignani, L and Ruggeri, A and Del Chierico, F and Gargiullo, L and Galaverna, F and Gaspari, S and Pagliara, D and Russo, A and Pane, S and Strocchio, L and Algeri, M and Rea, F and Romeo, EF and Bernaschi, P and Onetti Muda, A and Dallapiccola, B and Locatelli, F}, title = {Decolonization of multi-drug resistant bacteria by fecal microbiota transplantation in five pediatric patients before allogeneic hematopoietic stem cell transplantation: gut microbiota profiling, infectious and clinical outcomes.}, journal = {Haematologica}, volume = {}, number = {}, pages = {}, doi = {10.3324/haematol.2019.244210}, pmid = {32107336}, issn = {1592-8721}, }
@article {pmid32103766, year = {2020}, author = {Shen, L}, title = {Gut, oral and nasal microbiota and Parkinson's disease.}, journal = {Microbial cell factories}, volume = {19}, number = {1}, pages = {50}, pmid = {32103766}, issn = {1475-2859}, abstract = {Parkinson's disease (PD) is the second most prevalent neurodegenerative disease, and in an effort to identify novel therapeutic target for this disease in recent years, human microbiota has attracted much interest. This paper briefly summarizes the main findings concerning the differences of human microbiome across several important mucosal interfaces, including nose, mouth, and gut between PD patients and controls as obtained from a total of 13 studies published since 2015, which covered a total of 943 PD patients and 831 matched controls from 6 countries. Overall, these studies supported the differences of gut microbiota between PD patients and matched controls, while significantly altered bacterial taxa among studies were not identical. Due to relatively limited number of available studies and covered patients, the associations between oral and nasal microbiota and PD remain inconclusive. The therapeutic and diagnostic potentials of gut microbiota for PD are discussed. More well-designed clinical studies recruiting large-scale PD patients are encouraged in future.}, }
@article {pmid32103319, year = {2020}, author = {Ulaszewska, MM and Koutsos, A and Trošt, K and Stanstrup, J and Garcia-Aloy, M and Scholz, M and Fava, F and Natella, F and Scaccini, C and Vrhovsek, U and Tuohy, K and Lovegrove, J and Mattivi, F}, title = {Two apples a day modulate human:microbiome co-metabolic processing of polyphenols, tyrosine and tryptophan.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00394-020-02201-8}, pmid = {32103319}, issn = {1436-6215}, support = {FOODBALL//Joint Programming Initiative A healthy diet for a healthy life/ ; CABALA_DIET&amp;HEALTH//Joint Programming Initiative A healthy diet for a healthy life/ ; }, abstract = {PURPOSE: Validated biomarkers of food intake (BFIs) have recently been suggested as a useful tool to assess adherence to dietary guidelines or compliance in human dietary interventions. Although many new candidate biomarkers have emerged in the last decades for different foods from metabolic profiling studies, the number of comprehensively validated biomarkers of food intake is limited. Apples are among the most frequently consumed fruits and a rich source of polyphenols and fibers, an important mediator for their health-protective properties.<br><br>METHODS: Using an untargeted metabolomics approach, we aimed to identify biomarkers of long-term apple intake and explore how apples impact on the human plasma and urine metabolite profiles. Forty mildly hypercholesterolemic volunteers consumed two whole apples or a sugar and energy-matched control beverage, daily for 8 weeks in a randomized, controlled, crossover intervention study. The metabolome in plasma and urine samples was analyzed via untargeted metabolomics.<br><br>RESULTS: We found 61 urine and 9 plasma metabolites being statistically significant after the whole apple intake compared to the control beverage, including several polyphenol metabolites that could be used as BFIs. Furthermore, we identified several endogenous indole and phenylacetyl-glutamine microbial metabolites significantly increasing in urine after apple consumption. The multiomic dataset allowed exploration of the correlations between metabolites modulated significantly by the dietary intervention and fecal microbiota species at genus level, showing interesting interactions between Granulicatella genus and phenyl-acetic acid metabolites. Phloretin glucuronide and phloretin glucuronide sulfate appeared promising biomarkers of apple intake; however, robustness, reliability and stability data are needed for full BFI validation.<br><br>CONCLUSION: The identified apple BFIs can be used in future studies to assess compliance and to explore their health effects after apple intake. Moreover, the identification of polyphenol microbial metabolites suggests that apple consumption mediates significant gut microbial metabolic activity which should be further explored.}, }
@article {pmid32103176, year = {2020}, author = {Quinn, RA and Melnik, AV and Vrbanac, A and Fu, T and Patras, KA and Christy, MP and Bodai, Z and Belda-Ferre, P and Tripathi, A and Chung, LK and Downes, M and Welch, RD and Quinn, M and Humphrey, G and Panitchpakdi, M and Weldon, KC and Aksenov, A and da Silva, R and Avila-Pacheco, J and Clish, C and Bae, S and Mallick, H and Franzosa, EA and Lloyd-Price, J and Bussell, R and Thron, T and Nelson, AT and Wang, M and Leszczynski, E and Vargas, F and Gauglitz, JM and Meehan, MJ and Gentry, E and Arthur, TD and Komor, AC and Poulsen, O and Boland, BS and Chang, JT and Sandborn, WJ and Lim, M and Garg, N and Lumeng, JC and Xavier, RJ and Kazmierczak, BI and Jain, R and Egan, M and Rhee, KE and Ferguson, D and Raffatellu, M and Vlamakis, H and Haddad, GG and Siegel, D and Huttenhower, C and Mazmanian, SK and Evans, RM and Nizet, V and Knight, R and Dorrestein, PC}, title = {Global chemical effects of the microbiome include new bile-acid conjugations.}, journal = {Nature}, volume = {579}, number = {7797}, pages = {123-129}, doi = {10.1038/s41586-020-2047-9}, pmid = {32103176}, issn = {1476-4687}, support = {P01 HL088093/HL/NHLBI NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; R01 HL105278/HL/NHLBI NIH HHS/United States ; R37 DK057978/DK/NIDDK NIH HHS/United States ; 5U01AI124316-03/NH/NIH HHS/United States ; 1R03CA211211-01/NH/NIH HHS/United States ; 1R01HL116235/NH/NIH HHS/United States ; U54DE023798/NH/NIH HHS/United States ; R24DK110499/NH/NIH HHS/United States ; GMS10RR029121/NH/NIH HHS/United States ; 1 DP1 AT010885/NH/NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 HD084163/HD/NICHD NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; CA014195/CA/NCI NIH HHS/United States ; }, abstract = {A mosaic of cross-phylum chemical interactions occurs between all metazoans and their microbiomes. A number of molecular families that are known to be produced by the microbiome have a marked effect on the balance between health and disease1-9. Considering the diversity of the human microbiome (which numbers over 40,000 operational taxonomic units10), the effect of the microbiome on the chemistry of an entire animal remains underexplored. Here we use mass spectrometry informatics and data visualization approaches11-13 to provide an assessment of the effects of the microbiome on the chemistry of an entire mammal by comparing metabolomics data from germ-free and specific-pathogen-free mice. We found that the microbiota affects the chemistry of all organs. This included the amino acid conjugations of host bile acids that were used to produce phenylalanocholic acid, tyrosocholic acid and leucocholic acid, which have not previously been characterized despite extensive research on bile-acid chemistry14. These bile-acid conjugates were also found in humans, and were enriched in patients with inflammatory bowel disease or cystic fibrosis. These compounds agonized the farnesoid X receptor in vitro, and mice gavaged with the compounds showed reduced expression of bile-acid synthesis genes in vivo. Further studies are required to confirm whether these compounds have a physiological role in the host, and whether they contribute to gut diseases that are associated with microbiome dysbiosis.}, }
@article {pmid32102941, year = {2020}, author = {Wu, L and Zeng, T and Deligios, M and Milanesi, L and Langille, MGI and Zinellu, A and Rubino, S and Carru, C and Kelvin, DJ}, title = {Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {32102941}, issn = {2379-5042}, abstract = {Human body microbes interact with the host, forming microbial communities that are in continual flux during the aging process. Previous studies have mostly focused on surveying a single body habitat to determine the age-related variation in the bacterial and fungal communities. A more comprehensive understanding of the variation in the human microbiota and mycobiota across multiple body habitats related to aging is still unclear. To obtain an integrated view of the spatial distribution of microbes in a specific Mediterranean population across a wide age range, we surveyed the bacterial and fungal communities in the skin, oral cavity, and gut in the young, elderly, and centenarians in Sardinia using 16S rRNA gene and internal transcribed spacer 1 (ITS1) sequencing. We found that the distribution and correlation of bacterial and fungal communities in Sardinians were largely determined by body site. In each age group, the bacterial and fungal communities found in the skin were significantly different in structure. In the oral cavity, age had a marginal impact on the structures of the bacterial and fungal communities. Furthermore, the gut bacterial communities in centenarians clustered separately from those of the young and elderly, while the fungal communities in the gut habitat could not be separated by host age.IMPORTANCE Site-specific microbial communities are recognized as important factors in host health and disease. To better understand how the human microbiota potentially affects and is affected by its host during the aging process, the fundamental issue to address is the distribution of microbiota related to age. Here, we show an integrated view of the spatial distribution of microbes in a specific Mediterranean population (Sardinians) across a wide age range. Our study indicates that age plays a critical role in shaping the human microbiota in a habitat-dependent manner. The dynamic age-related microbiota changes we observed across multiple body sites may provide possibilities for modulating microbe communities to maintain or improve health during aging.}, }
@article {pmid32102343, year = {2020}, author = {Lopez-Santamarina, A and Miranda, JM and Mondragon, ADC and Lamas, A and Cardelle-Cobas, A and Franco, CM and Cepeda, A}, title = {Potential Use of Marine Seaweeds as Prebiotics: A Review.}, journal = {Molecules (Basel, Switzerland)}, volume = {25}, number = {4}, pages = {}, doi = {10.3390/molecules25041004}, pmid = {32102343}, issn = {1420-3049}, abstract = {Human gut microbiota plays an important role in several metabolic processes and human diseases. Various dietary factors, including complex carbohydrates, such as polysaccharides, provide abundant nutrients and substrates for microbial metabolism in the gut, affecting the members and their functionality. Nowadays, the main sources of complex carbohydrates destined for human consumption are terrestrial plants. However, fresh water is an increasingly scarce commodity and world agricultural productivity is in a persistent decline, thus demanding the exploration of other sources of complex carbohydrates. As an interesting option, marine seaweeds show rapid growth and do not require arable land, fresh water or fertilizers. The present review offers an objective perspective of the current knowledge surrounding the impacts of seaweeds and their derived polysaccharides on the human microbiome and the profound need for more in-depth investigations into this topic. Animal experiments and in vitro colonic-simulating trials investigating the effects of seaweed ingestion on human gut microbiota are discussed.}, }
@article {pmid32101723, year = {2020}, author = {Xavier, JB and Young, VB and Skufca, J and Ginty, F and Testerman, T and Pearson, AT and Macklin, P and Mitchell, A and Shmulevich, I and Xie, L and Caporaso, JG and Crandall, KA and Simone, NL and Godoy-Vitorino, F and Griffin, TJ and Whiteson, KL and Gustafson, HH and Slade, DJ and Schmidt, TM and Walther-Antonio, MRS and Korem, T and Webb-Robertson, BM and Styczynski, MP and Johnson, WE and Jobin, C and Ridlon, JM and Koh, AY and Yu, M and Kelly, L and Wargo, JA}, title = {The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.}, journal = {Trends in cancer}, volume = {6}, number = {3}, pages = {192-204}, doi = {10.1016/j.trecan.2020.01.004}, pmid = {32101723}, issn = {2405-8025}, abstract = {The collection of microbes that live in and on the human body - the human microbiome - can impact on cancer initiation, progression, and response to therapy, including cancer immunotherapy. The mechanisms by which microbiomes impact on cancers can yield new diagnostics and treatments, but much remains unknown. The interactions between microbes, diet, host factors, drugs, and cell-cell interactions within the cancer itself likely involve intricate feedbacks, and no single component can explain all the behavior of the system. Understanding the role of host-associated microbial communities in cancer systems will require a multidisciplinary approach combining microbial ecology, immunology, cancer cell biology, and computational biology - a systems biology approach.}, }
@article {pmid32099373, year = {2020}, author = {Michael, H and Mpofana, T and Ramlall, S and Oosthuizen, F}, title = {The Role of Brain Derived Neurotrophic Factor in HIV-Associated Neurocognitive Disorder: From the Bench-Top to the Bedside.}, journal = {Neuropsychiatric disease and treatment}, volume = {16}, number = {}, pages = {355-367}, pmid = {32099373}, issn = {1176-6328}, abstract = {Human immunodeficiency virus (HIV)-associated neurocognitive disorder (HAND) remains prevalent in the anti-retroviral (ART) era. While there is a complex interplay of many factors in the neuropathogenesis of HAND, decreased neurotrophic synthesis has been shown to contribute to synaptic degeneration which is a hallmark of HAND neuropathology. Brain derived neurotrophic factor (BDNF) is the most abundant and synaptic-promoting neurotrophic factor in the brain and plays a critical role in both learning and memory. Reduced BDNF levels can worsen neurocognitive impairment in HIV-positive individuals across several domains. In this paper, we review the evidence from pre-clinical and clinical studies showing the neuroprotective roles of BDNF against viral proteins, effect on co-morbid mental health disorders, altered human microbiome and ART in HAND management. Potential applications of BDNF modulation in pharmacotherapeutic, cognitive and behavioral interventions in HAND are also discussed. Finally, research gaps and future research direction are identified with the aim of helping researchers to direct efforts to make these BDNF driven interventions improve the quality of life of patients living with HAND.}, }
@article {pmid32098835, year = {2020}, author = {Rosa, BA and Mihindukulasuriya, K and Hallsworth-Pepin, K and Wollam, A and Martin, J and Snowden, C and Dunne, WM and Weinstock, GM and Burnham, CA and Mitreva, M}, title = {Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {32098835}, issn = {2379-5077}, abstract = {Whole-genome bacterial sequences are required to better understand microbial functions, niche-specific bacterial metabolism, and disease states. Although genomic sequences are available for many of the human-associated bacteria from commonly tested body habitats (e.g., feces), as few as 13% of bacterium-derived reads from other sites such as the skin map to known bacterial genomes. To facilitate a better characterization of metagenomic shotgun reads from underrepresented body sites, we collected over 10,000 bacterial isolates originating from 14 human body habitats, identified novel taxonomic groups based on full-length 16S rRNA gene sequences, clustered the sequences to ensure that no individual taxonomic group was overselected for sequencing, prioritized bacteria from underrepresented body sites (such as skin and respiratory and urinary tracts), and sequenced and assembled genomes for 665 new bacterial strains. Here, we show that addition of these genomes improved read mapping rates of Human Microbiome Project (HMP) metagenomic samples by nearly 30% for the previously underrepresented phylum Fusobacteria, and 27.5% of the novel genomes generated here had high representation in at least one of the tested HMP samples, compared to 12.5% of the sequences in the public databases, indicating an enrichment of useful novel genomic sequences resulting from the prioritization procedure. As our understanding of the human microbiome continues to improve and to enter the realm of therapy developments, targeted approaches such as this to improve genomic databases will increase in importance from both an academic and a clinical perspective.IMPORTANCE The human microbiome plays a critically important role in health and disease, but current understanding of the mechanisms underlying the interactions between the varying microbiome and the different host environments is lacking. Having access to a database of fully sequenced bacterial genomes provides invaluable insights into microbial functions, but currently sequenced genomes for the human microbiome have largely come from a limited number of body sites (primarily feces), while other sites such as the skin, respiratory tract, and urinary tract are underrepresented, resulting in as little as 13% of bacterium-derived reads mapping to known bacterial genomes. Here, we sequenced and assembled 665 new bacterial genomes, prioritized from a larger database to select underrepresented body sites and bacterial taxa in the existing databases. As a result, we substantially improve mapping rates for samples from the Human Microbiome Project and provide an important contribution to human bacterial genomic databases for future studies.}, }
@article {pmid32094388, year = {2020}, author = {Marsland, R and Cui, W and Mehta, P}, title = {A minimal model for microbial biodiversity can reproduce experimentally observed ecological patterns.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {3308}, pmid = {32094388}, issn = {2045-2322}, support = {1R35GM119461//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Mathematical Modeling of Living Systems//Simons Foundation/ ; }, abstract = {Surveys of microbial biodiversity such as the Earth Microbiome Project (EMP) and the Human Microbiome Project (HMP) have revealed robust ecological patterns across different environments. A major goal in ecology is to leverage these patterns to identify the ecological processes shaping microbial ecosystems. One promising approach is to use minimal models that can relate mechanistic assumptions at the microbe scale to community-level patterns. Here, we demonstrate the utility of this approach by showing that the Microbial Consumer Resource Model (MiCRM) - a minimal model for microbial communities with resource competition, metabolic crossfeeding and stochastic colonization - can qualitatively reproduce patterns found in survey data including compositional gradients, dissimilarity/overlap correlations, richness/harshness correlations, and nestedness of community composition. By using the MiCRM to generate synthetic data with different environmental and taxonomical structure, we show that large scale patterns in the EMP can be reproduced by considering the energetic cost of surviving in harsh environments and HMP patterns may reflect the importance of environmental filtering in shaping competition. We also show that recently discovered dissimilarity-overlap correlations in the HMP likely arise from communities that share similar environments rather than reflecting universal dynamics. We identify ecologically meaningful changes in parameters that alter or destroy each one of these patterns, suggesting new mechanistic hypotheses for further investigation. These findings highlight the promise of minimal models for microbial ecology.}, }
@article {pmid32089572, year = {2020}, author = {Gupta, V and Kumar, R and Sood, U and Singhvi, N}, title = {Reconciling Hygiene and Cleanliness: A New Perspective from Human Microbiome.}, journal = {Indian journal of microbiology}, volume = {60}, number = {1}, pages = {37-44}, pmid = {32089572}, issn = {0046-8991}, abstract = {The term hygiene is deeply rooted with the concept of maintaining sound health and alertness towards cleanliness, while &quot;hygiene hypothesis&quot; depicts the protective role of microbial community exposure in development of early immunity and initial allergic and aesthetic reactions. The tug-of-war has now been pushed toward the literal term &quot;hygiene&quot; over the &quot;hygiene hypothesis&quot; and has continued with disinfection of all microbial loads from the related environments to avoid infections in humans. With the advancement in the microbiome studies, it became clear that humans possess warm, and significant relationships with diverse microbial community. With this opinion article, we have emphasized on the importance of hygiene hypothesis in immunological responses. We also propose the individual/targeted hygiene instead of application of unanimous hygiene hypothesis. This review also elaborates the common practices that should be employed to maintain hygiene along with the balanced microbiome.}, }
@article {pmid32089571, year = {2020}, author = {Singhvi, N and Gupta, V and Gaur, M and Sharma, V and Puri, A and Singh, Y and Dubey, GP and Lal, R}, title = {Interplay of Human Gut Microbiome in Health and Wellness.}, journal = {Indian journal of microbiology}, volume = {60}, number = {1}, pages = {26-36}, pmid = {32089571}, issn = {0046-8991}, abstract = {The gut microbiome analysis, with specific interest on their direct impact towards the human health, is currently revolutionizing the unexplored frontiers of the pathogenesis and wellness. Although in-depth investigations of gut microbiome, 'the Black Boxes', complexities and functionalities are yet at its infancy, profound evidences are being reported for their concurrent involvement in disease etiology and its treatment. Interestingly, studies from the 'minimal murine' (Oligo-MM12), 'humanized' microbiota gnotobiotic mice models and patient samples, combined with multi-omics and cell biology approaches, have been revealing the implications of these findings in the treatment of gut dysbiosis associated diseases. Nonetheless, due to the inherent heterogeneity of the gut commensals and their unified co-existence with opportunistic pathobionts, it is utmost essential to highlight their functionalities in 'good or bad' gut in human wellness. We have specifically reviewed dietary lifestyle and infectious diseases linked with the gut bacterial consortia to delineate the ecobiotic approaches towards their treatment. This notably includes gut mucosal immunity mediated diseases such as Tuberculosis, IBD, CDI, Type 2 Diabetes, etc. Alongside of each dysbiosis, we have described the current therapeutic advancements of the pre- and probiotics derived from human microbiome studies to restore gut microbial homeostasis. With a continuous running debate on the role of microbiota in above mentioned diseases, we have collected numerous scientific evidences highlighting a previously unanticipated complex involvement of gut microbiome in the potential of human health.}, }
@article {pmid32080334, year = {2020}, author = {Piersigilli, F and Syed, M and Lam, TT and Dotta, A and Massoud, M and Vernocchi, P and Quagliariello, A and Putignani, L and Auriti, C and Salvatori, G and Bagolan, P and Bhandari, V}, title = {An omic approach to congenital diaphragmatic hernia: a pilot study of genomic, microRNA, and metabolomic profiling.}, journal = {Journal of perinatology : official journal of the California Perinatal Association}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41372-020-0623-3}, pmid = {32080334}, issn = {1476-5543}, abstract = {INTRODUCTION: The omic approach can help identify a signature that can be potentially used as biomarkers in babies with congenital diaphragmatic hernia (CDH).<br><br>OBJECTIVES: To find a specific microRNA (miR) and metabolic fingerprint of the tracheal aspirates (TA) of CDH patients. We conducted a genetic analysis from blood samples.<br><br>METHODS: TA samples collected in the first 48 h of life in patients with CDH, compared with age-matched controls. Metabolomics done by a mass spectroscopy-based assay. Genomics done using chromosomal microarray analysis.<br><br>RESULTS: CDH (n = 17) and 16 control neonates enrolled. miR-16, miR-17, miR-18, miR-19b, and miR-20a had an increased expression, while miR-19a had a twofold decreased expression in CDH patients, compared with age-matched control patients. Specific metabolites separated neonates with CDH from controls. A genetic mutation found in a small subset of patients.<br><br>CONCLUSIONS: Specific patterns of metabolites and miR expression can be discerned in TA samples in infants with CDH.}, }
@article {pmid32077339, year = {2020}, author = {Grosse, CSJ and Christophersen, CT and Devine, A and Lawrance, IC}, title = {The role of a plant-based diet in the pathogenesis, etiology and management of the inflammatory bowel diseases.}, journal = {Expert review of gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/17474124.2020.1733413}, pmid = {32077339}, issn = {1747-4132}, abstract = {Introduction: Inflammatory Bowel Disease (IBD) carries a significant burden on an individual's quality-of-life and on the healthcare system. The majority of patients use dietary modifications to manage their symptoms, despite limited research to support these changes. There is emerging data that a plant-based diet will be of benefit to IBD patients.Areas covered: A literature review on the pathogenesis and potential benefits of dietary management of IBD.Expert opinion: A Westernized diet has been associated with IBD risk and relapse; hence a plant-based diet may be of benefit to IBD patients through reducing inflammation and restoring symbiosis. Dietary therapy can be an important adjunct therapy, however, better quality studies are still required.}, }
@article {pmid32076932, year = {2020}, author = {Bresalier, RS and Chapkin, RS}, title = {Human Microbiome in Health and Disease: The Good, the Bad, and the Bugly.}, journal = {Digestive diseases and sciences}, volume = {65}, number = {3}, pages = {671-673}, doi = {10.1007/s10620-020-06059-y}, pmid = {32076932}, issn = {1573-2568}, }
@article {pmid32076128, year = {2020}, author = {Darcy, JL and Washburne, AD and Robeson, MS and Prest, T and Schmidt, SK and Lozupone, CA}, title = {A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41396-020-0613-7}, pmid = {32076128}, issn = {1751-7370}, support = {DEB-1258160//National Science Foundation (NSF)/ ; 5 T15 LM009451-12//U.S. Department of Health &amp; Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; }, abstract = {Understanding when and why new species are recruited into microbial communities is a formidable problem with implications for managing microbial systems, for instance by helping us better understand whether a probiotic or pathogen would be expected to colonize a human microbiome. Much theory in microbial temporal dynamics is focused on how phylogenetic relationships between microbes impact the order in which those microbes are recruited; for example, species that are closely related may competitively exclude each other. However, several recent human microbiome studies have observed closely related bacteria being recruited into microbial communities in short succession, suggesting that microbial community assembly is historically contingent, but competitive exclusion of close relatives may not be important. To address this, we developed a mathematical model that describes the order in which new species are detected in microbial communities over time within a phylogenetic framework. We use our model to test three hypothetical assembly modes: underdispersion (species recruitment is more likely if a close relative was previously detected), overdispersion (recruitment is more likely if a close relative has not been previously detected), and the neutral model (recruitment likelihood is not related to phylogenetic relationships among species). We applied our model to longitudinal human microbiome data, and found that for the individuals we analyzed, the human microbiome generally follows the underdispersion (i.e., nepotism) hypothesis. Exceptions were oral communities and the fecal communities of two infants that had undergone heavy antibiotic treatment. None of the datasets we analyzed showed statistically significant phylogenetic overdispersion.}, }
@article {pmid32075244, year = {2020}, author = {Benedetti, F and Cocchi, F and Latinovic, OS and Curreli, S and Krishnan, S and Munawwar, A and Gallo, RC and Zella, D}, title = {Role of Mycoplasma Chaperone DnaK in Cellular Transformation.}, journal = {International journal of molecular sciences}, volume = {21}, number = {4}, pages = {}, doi = {10.3390/ijms21041311}, pmid = {32075244}, issn = {1422-0067}, abstract = {Studies of the human microbiome have elucidated an array of complex interactions between prokaryotes and their hosts. However, precise bacterial pathogen-cancer relationships remain largely elusive, although several bacteria, particularly those establishing persistent intra-cellular infections, like mycoplasmas, can alter host cell cycles, affect apoptotic pathways, and stimulate the production of inflammatory substances linked to DNA damage, thus potentially promoting abnormal cell growth and transformation. Consistent with this idea, in vivo experiments in several chemically induced or genetically deficient mouse models showed that germ-free conditions reduce colonic tumor formation. We demonstrate that mycoplasma DnaK, a chaperone protein belonging to the Heath shock protein (Hsp)-70 family, binds Poly-(ADP-ribose) Polymerase (PARP)-1, a protein that plays a critical role in the pathways involved in recognition of DNA damage and repair, and reduces its catalytic activity. It also binds USP10, a key p53 regulator, reducing p53 stability and anti-cancer functions. Finally, we showed that bystander, uninfected cells take up exogenous DnaK-suggesting a possible paracrine function in promoting cellular transformation, over and above direct mycoplasma infection. We propose that mycoplasmas, and perhaps certain other bacteria with closely related DnaK, may have oncogenic activity, mediated through the inhibition of DNA repair and p53 functions, and may be involved in the initiation of some cancers but not necessarily involved nor necessarily even be present in later stages.}, }
@article {pmid32073295, year = {2020}, author = {Swanson, KS and de Vos, WM and Martens, EC and Gilbert, JA and Menon, RS and Soto-Vaca, A and Hautvast, J and Meyer, PD and Borewicz, K and Vaughan, EE and Slavin, JL}, title = {Effect of fructans, prebiotics and fibres on the human gut microbiome assessed by 16S rRNA-based approaches: a review.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-30}, doi = {10.3920/BM2019.0082}, pmid = {32073295}, issn = {1876-2891}, abstract = {The inherent and diverse capacity of dietary fibres, nondigestible oligosaccharides (NDOs) and prebiotics to modify the gut microbiota and markedly influence health status of the host has attracted rising interest. Research and collective initiatives to determine the composition and diversity of the human gut microbiota have increased over the past decade due to great advances in high-throughput technologies, particularly the 16S ribosomal RNA (rRNA) sequencing. Here we reviewed the application of 16S rRNA-based molecular technologies, both community wide (sequencing and phylogenetic microarrays) and targeted methodologies (quantitative PCR, fluorescent in situ hybridisation) to study the effect of chicory inulin-type fructans, NDOs and specific added fibres, such as resistant starches, on the human intestinal microbiota. Overall, such technologies facilitated the monitoring of microbiota shifts due to prebiotic/fibre consumption, though there are limited community-wide sequencing studies so far. Molecular studies confirmed the selective bifidogenic effect of fructans and galactooligosaccharides (GOS) in human intervention studies. Fructans only occasionally decreased relative abundance of Bacteroidetes or stimulated other groups. The sequencing studies for various resistant starches, polydextrose and beta-glucan showed broader effects with more and different types of gut microbial species being enhanced, often including phylotypes of Ruminococcaceae. There was substantial variation in terms of magnitude of response and in individual responses to a specific fibre or NDO which may be due to numerous factors, such as initial presence and relative abundance of a microbial type, diet, genetics of the host, and intervention parameters, such as intervention duration and fibre dose. The field will clearly benefit from a more systematic approach that will support defining the impact of prebiotics and fibres on the gut microbiome, identify biomarkers that link gut microbes to health, and address the personalised response of an individual's microbiota to prebiotics and dietary fibres.}, }
@article {pmid32066625, year = {2020}, author = {Ghosh, TS and Rampelli, S and Jeffery, IB and Santoro, A and Neto, M and Capri, M and Giampieri, E and Jennings, A and Candela, M and Turroni, S and Zoetendal, EG and Hermes, GDA and Elodie, C and Meunier, N and Brugere, CM and Pujos-Guillot, E and Berendsen, AM and De Groot, LCPGM and Feskins, EJM and Kaluza, J and Pietruszka, B and Bielak, MJ and Comte, B and Maijo-Ferre, M and Nicoletti, C and De Vos, WM and Fairweather-Tait, S and Cassidy, A and Brigidi, P and Franceschi, C and O'Toole, PW}, title = {Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2019-319654}, pmid = {32066625}, issn = {1468-3288}, abstract = {OBJECTIVE: Ageing is accompanied by deterioration of multiple bodily functions and inflammation, which collectively contribute to frailty. We and others have shown that frailty co-varies with alterations in the gut microbiota in a manner accelerated by consumption of a restricted diversity diet. The Mediterranean diet (MedDiet) is associated with health. In the NU-AGE project, we investigated if a 1-year MedDiet intervention could alter the gut microbiota and reduce frailty.<br><br>DESIGN: We profiled the gut microbiota in 612 non-frail or pre-frail subjects across five European countries (UK, France, Netherlands, Italy and Poland) before and after the administration of a 12-month long MedDiet intervention tailored to elderly subjects (NU-AGE diet).<br><br>RESULTS: Adherence to the diet was associated with specific microbiome alterations. Taxa enriched by adherence to the diet were positively associated with several markers of lower frailty and improved cognitive function, and negatively associated with inflammatory markers including C-reactive protein and interleukin-17. Analysis of the inferred microbial metabolite profiles indicated that the diet-modulated microbiome change was associated with an increase in short/branch chained fatty acid production and lower production of secondary bile acids, p-cresols, ethanol and carbon dioxide. Microbiome ecosystem network analysis showed that the bacterial taxa that responded positively to the MedDiet intervention occupy keystone interaction positions, whereas frailty-associated taxa are peripheral in the networks.<br><br>CONCLUSION: Collectively, our findings support the feasibility of improving the habitual diet to modulate the gut microbiota which in turn has the potential to promote healthier ageing.}, }
@article {pmid32065252, year = {2020}, author = {Peñalver Bernabé, B and Maki, PM and Dowty, SM and Salas, M and Cralle, L and Shah, Z and Gilbert, JA}, title = {Precision medicine in perinatal depression in light of the human microbiome.}, journal = {Psychopharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00213-019-05436-4}, pmid = {32065252}, issn = {1432-2072}, support = {Arnold O Beckman Postdoctoral Award//Arnold and Mabel Beckman Foundation (US)/ ; }, abstract = {Perinatal depression is the most common complication of pregnancy and affects the mother, fetus, and infant. Recent preclinical studies and a limited number of clinical studies have suggested an influence of the gut microbiome on the onset and course of mental health disorders. In this review, we examine the current state of knowledge regarding genetics, epigenetics, heritability, and neuro-immuno-endocrine systems biology in perinatal mood disorders, with a particular focus on the interaction between these factors and the gut microbiome, which is mediated via the gut-brain axis. We also provide an overview of experimental and analytical methods that are currently available to researchers interested in elucidating the influence of the gut microbiome on mental health disorders during pregnancy and postpartum.}, }
@article {pmid32060812, year = {2020}, author = {Wilson, AS and Koller, KR and Ramaboli, MC and Nesengani, LT and Ocvirk, S and Chen, C and Flanagan, CA and Sapp, FR and Merritt, ZT and Bhatti, F and Thomas, TK and O'Keefe, SJD}, title = {Diet and the Human Gut Microbiome: An International Review.}, journal = {Digestive diseases and sciences}, volume = {65}, number = {3}, pages = {723-740}, pmid = {32060812}, issn = {1573-2568}, abstract = {This review summarizes the key results of recently published studies on the effects of dietary change and nutritional intervention on the human microbiome from around the world, focusing on the USA, Canada, Europe, Asia, and Africa. It first explores mechanisms that might explain the ability of fiber-rich foods to suppress the incidence and mortality from westernized diseases, notably cancers of the colon, breast, liver, cardiovascular, infectious, and respiratory diseases, diabetes, and obesity (O'Keefe in Lancet Gastroenterol Hepatol 4(12):984-996, 2019; Am J Clin Nutr 110:265-266, 2019). It summarizes studies from Africa which suggest that disturbance of the colonic microbiome may exacerbate chronic malnutrition and growth failure in impoverished communities and highlights the importance of breast feeding. The American section discusses the role of the microbiome in the swelling population of patients with obesity and type 2 diabetes and examines the effects of race, ethnicity, geography, and climate on microbial diversity and metabolism. The studies from Europe and Asia extoll the benefits of whole foods and plant-based diets. The Asian studies examine the worrying changes from low-fat, high-carbohydrate diets to high-fat, low-carbohydrate ones and the increasing appearance of westernized diseases as in Africa and documents the ability of high-fiber traditional Chinese diets to reverse type 2 diabetes and control weight loss. In conclusion, most of the studies reviewed demonstrate clear changes in microbe abundances and in the production of fermentation products, such as short-chain fatty acids and phytochemicals following dietary change, but the significance of the microbiota changes to human health, with the possible exception of the stimulation of butyrogenic taxa by fiber-rich foods, is generally implied and not measured. Further studies are needed to determine how these changes in microbiota composition and metabolism can improve our health and be used to prevent and treat disease.}, }
@article {pmid32055399, year = {2020}, author = {Garza, DR and Taddese, R and Wirbel, J and Zeller, G and Boleij, A and Huynen, MA and Dutilh, BE}, title = {Metabolic models predict bacterial passengers in colorectal cancer.}, journal = {Cancer &amp; metabolism}, volume = {8}, number = {}, pages = {3}, pmid = {32055399}, issn = {2049-3002}, abstract = {Background: Colorectal cancer (CRC) is a complex multifactorial disease. Increasing evidence suggests that the microbiome is involved in different stages of CRC initiation and progression. Beyond specific pro-oncogenic mechanisms found in pathogens, metagenomic studies indicate the existence of a microbiome signature, where particular bacterial taxa are enriched in the metagenomes of CRC patients. Here, we investigate to what extent the abundance of bacterial taxa in CRC metagenomes can be explained by the growth advantage resulting from the presence of specific CRC metabolites in the tumor microenvironment.<br><br>Methods: We composed lists of metabolites and bacteria that are enriched on CRC samples by reviewing metabolomics experimental literature and integrating data from metagenomic case-control studies. We computationally evaluated the growth effect of CRC enriched metabolites on over 1500 genome-based metabolic models of human microbiome bacteria. We integrated the metabolomics data and the mechanistic models by using scores that quantify the response of bacterial biomass production to CRC-enriched metabolites and used these scores to rank bacteria as potential CRC passengers.<br><br>Results: We found that metabolic networks of bacteria that are significantly enriched in CRC metagenomic samples either depend on metabolites that are more abundant in CRC samples or specifically benefit from these metabolites for biomass production. This suggests that metabolic alterations in the cancer environment are a major component shaping the CRC microbiome.<br><br>Conclusion: Here, we show with in sillico models that supplementing the intestinal environment with CRC metabolites specifically predicts the outgrowth of CRC-associated bacteria. We thus mechanistically explain why a range of CRC passenger bacteria are associated with CRC, enhancing our understanding of this disease. Our methods are applicable to other microbial communities, since it allows the systematic investigation of how shifts in the microbiome can be explained from changes in the metabolome.}, }
@article {pmid32054471, year = {2020}, author = {Nazareth, R and Chasqueira, MJ and Rodrigues, ML and Paulino, C and Conceição, C and Lêdo, L and Segura, Ú and Santos, M and Messias, A and Póvoa, P and Paixão, P}, title = {Respiratory viruses in mechanically ventilated patients: a pilot study.}, journal = {BMC pulmonary medicine}, volume = {20}, number = {1}, pages = {39}, pmid = {32054471}, issn = {1471-2466}, abstract = {BACKGROUND: Respiratory virome is an integral part of the human microbiome and its characterization may contribute to a better understanding of the changes that arise in the disease and, consequently, influence the approach and treatment of patients with acute lower respiratory infections. The aim of this study was to evaluate the presence of respiratory viruses in the lower airways of individuals undergoing invasive mechanical ventilation, with and without acute lower respiratory infection (respectively WRI and WORI groups).<br><br>METHODS: We studied 44 mini-bronchoalveolar lavage samples (collected with a double catheter, Combicath® kit) from patients with mean age in the seventh decade, 20 from WORI group and 24 from WRI group, who were hospitalized for acute respiratory failure in Intensive Care Units of two hospitals in the Lisbon area. Real-time PCR was applied to verify analyse the presence of 15 common respiratory viruses (adenovirus, human bocavirus, influenza virus A and B, repiratory syncytial virus, human parainfluenza virus types 1, 2, 3 and 4, human enterovirus, human rhinovirus, human metapneumovirus, human coronavirus group 1 (229E, NL63) and 2 (OC43, HKU1).<br><br>RESULTS: Respiratory viruses were detected in six of the 20 patients in the WORI group: influenza AH3 (n = 2), parainfluenza virus 1/3 (n = 2), human rhinovirus (n = 2), respiratory syncytial virus (n = 1) and human metapneumovirus (n = 1). In the WRI group, respiratory viruses were detected in 12 of the 24 patients: influenza AH3 (n = 3), human rhinovirus (n = 3), respiratory syncytial virus (n = 3), human metapneumovirus (n = 3), human bocavirus (n = 2) and human enterovirus (n = 1). Simultaneous detection of two viruses was recorded in two samples in both groups.<br><br>CONCLUSIONS: The results of this study suggest the presence of common respiratory viruses in the lower respiratory tract without causing symptomatic infection, even in carefully collected lower samples. This may have important implications on the interpretation of the results on the diagnostic setting.}, }
@article {pmid32040665, year = {2020}, author = {Engstrand, L and Graham, DY}, title = {Microbiome and Gastric Cancer.}, journal = {Digestive diseases and sciences}, volume = {65}, number = {3}, pages = {865-873}, pmid = {32040665}, issn = {1573-2568}, abstract = {The late 1800s Louis Pasteur and Robert Koch introduced and popularized the germ theory of disease. At that time, gastric cancer was the most common cause of cancer deaths in most countries making the stomach an early site of microbial research with a focus on gastric luminal and mucosal bacteria and the role of Boas-Oppler bacillus (Lactobacillus) in the diagnosis of gastric cancer. In the 1970s, the research focus evolved to studies of the gastric microbiome in the production of nitrosamines and included development of the Correa cascade. Interest in nitrosamine production peaked in the late 1980s and was replaced by studies of the newly described Helicobacter pylori and studies of its role in gastritis, gastric atrophy, and gastric cancer. The last decade has witnessed a rebirth in interest in the gastric microbiota as part of worldwide interest in the human microbiome. Although fungi were prominent in the studies of gastric microbiology in the nineteenth century, their potential role in disease pathogenesis has yet to be addressed using modern techniques. Overall, current studies of the gastric bacterial microbiome do not provide convincing evidence to expand the role of the gastric microbiome in cancer pathogenesis beyond what is directly attributable to the oncogenic potential of H. pylori and its role in persisting acute-on-chronic inflammation.}, }
@article {pmid32040250, year = {2020}, author = {Guo, XY and Liu, XJ and Hao, JY}, title = {Gut Microbiota in Ulcerative Colitis: Insights on Pathogenesis and Treatment.}, journal = {Journal of digestive diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-2980.12849}, pmid = {32040250}, issn = {1751-2980}, abstract = {Gut microbiota constitute the largest reservoir of the human microbiome, and is an abundant and stable ecosystem - based on its diversity, complexity, redundancy, and host interactions. This ecosystem is indispensable for human development and health. The integrity of the intestinal mucosal barrier depends on its interactions with gut microbiota. The commensal bacterial community is implicated in the pathogenesis of inflammatory bowel disease(IBD), including ulcerative colitis (UC). The dysbiosis of microbes is characterized by reduced biodiversity, abnormal composition, altered spatial distribution, as well as interactions among microbiota, between different strains of microbiota, and with the host. The defects in microecology, with the related metabolic pathways and molecular mechanisms, play a critical role in the innate immunity of the intestinal mucosa in UC. Fecal microbiota transplantation (FMT) has been used to treat many diseases related to gut microbiota, with the most promising outcome reported in antibiotic-associated diarrhea, followed by IBD. This review evaluated the results of various reports of FMT in UC. The efficacy of FMT remains highly controversial, and needs to be regularized by integrated management, standardization of procedures, and individualization of treatment.}, }
@article {pmid32037278, year = {2020}, author = {Rao, BC and Lou, JM and Wang, WJ and Li, A and Cui, GY and Yu, ZJ and Ren, ZG}, title = {Human microbiome is a diagnostic biomarker in hepatocellular carcinoma.}, journal = {Hepatobiliary &amp; pancreatic diseases international : HBPD INT}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.hbpd.2020.01.003}, pmid = {32037278}, issn = {1499-3872}, abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) is the third leading cause of cancer mortality worldwide. Increasing evidence indicates a close relationship between HCC and the human microbiota. Herein, we reviewed the important potential of the human microbiota as a diagnostic biomarker of HCC.<br><br>DATA SOURCES: Several innovative studies have investigated the characteristics of the gut and oral microbiomes in patients with HCC and proposed that the human microbiome has the potential to be a diagnostic biomarker of HCC. Literature from February 1999 to February 2019 was searched in the PubMed database using the keywords &quot;microbiota&quot; or &quot;microbiome&quot; or &quot;microbe&quot; and &quot;liver cancer&quot; or &quot;hepatocellular carcinoma&quot;, and the results of clinical and experimental studies were analyzed.<br><br>RESULTS: Specific changes occur in the human microbiome of patients with HCC. Moreover, the gut microbiome and oral microbiome can be used as non-invasive diagnostic biomarkers for HCC. Furthermore, they also have certain diagnostic potential for precancerous diseases of HCC. The diagnostic potential of the blood microbiota and ascites microbiota in HCC will be gradually discovered in the future.<br><br>CONCLUSIONS: The human microbiome is valuable to the diagnosis of HCC and provides a novel strategy for targeted therapy of HCC. The human microbiome may be widely used in the diagnosis, treatment and prognosis for multiple system diseases or cancers in the future.}, }
@article {pmid32023941, year = {2020}, author = {Chowdhury, S and Fong, SS}, title = {Computational Modeling of the Human Microbiome.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, doi = {10.3390/microorganisms8020197}, pmid = {32023941}, issn = {2076-2607}, support = {U54HD080784//Office of Extramural Research, National Institutes of Health/ ; }, abstract = {The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.}, }
@article {pmid32023871, year = {2020}, author = {Panyukov, VV and Kiselev, SS and Ozoline, ON}, title = {Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling.}, journal = {International journal of molecular sciences}, volume = {21}, number = {3}, pages = {}, doi = {10.3390/ijms21030944}, pmid = {32023871}, issn = {1422-0067}, support = {18-14-00348//Russian Science Foundation/ ; 18-07-00899//Российский Фонд Фундаментальных Исследований (РФФИ)/ ; }, abstract = {The need for a comparative analysis of natural metagenomes stimulated the development of new methods for their taxonomic profiling. Alignment-free approaches based on the search for marker k-mers turned out to be capable of identifying not only species, but also strains of microorganisms with known genomes. Here, we evaluated the ability of genus-specific k-mers to distinguish eight phylogroups of Escherichia coli (A, B1, C, E, D, F, G, B2) and assessed the presence of their unique 22-mers in clinical samples from microbiomes of four healthy people and four patients with Crohn's disease. We found that a phylogenetic tree inferred from the pairwise distance matrix for unique 18-mers and 22-mers of 124 genomes was fully consistent with the topology of the tree, obtained with concatenated aligned sequences of orthologous genes. Therefore, we propose strain-specific &quot;barcodes&quot; for rapid phylotyping. Using unique 22-mers for taxonomic analysis, we detected microbes of all groups in human microbiomes; however, their presence in the five samples was significantly different. Pointing to the intraspecies heterogeneity of E. coli in the natural microflora, this also indicates the feasibility of further studies of the role of this heterogeneity in maintaining population homeostasis.}, }
@article {pmid32014010, year = {2020}, author = {Botticelli, A and Vernocchi, P and Marini, F and Quagliariello, A and Cerbelli, B and Reddel, S and Del Chierico, F and Di Pietro, F and Giusti, R and Tomassini, A and Giampaoli, O and Miccheli, A and Zizzari, IG and Nuti, M and Putignani, L and Marchetti, P}, title = {Gut metabolomics profiling of non-small cell lung cancer (NSCLC) patients under immunotherapy treatment.}, journal = {Journal of translational medicine}, volume = {18}, number = {1}, pages = {49}, pmid = {32014010}, issn = {1479-5876}, support = {Ricerca Corrente 201802G004314//Ministry of Health/ ; }, abstract = {BACKGROUND: Despite the efficacy of immune checkpoint inhibitors (ICIs) only the 20-30% of treated patients present long term benefits. The metabolic changes occurring in the gut microbiota metabolome are herein proposed as a factor potentially influencing the response to immunotherapy.<br><br>METHODS: The metabolomic profiling of gut microbiota was characterized in 11 patients affected by non-small cell lung cancer (NSCLC) treated with nivolumab in second-line treatment with anti-PD-1 nivolumab. The metabolomics analyses were performed by GC-MS/SPME and 1H-NMR in order to detect volatile and non-volatile metabolites. Metabolomic data were processed by statistical profiling and chemometric analyses.<br><br>RESULTS: Four out of 11 patients (36%) presented early progression, while the remaining 7 out of 11 (64%) presented disease progression after 12 months. 2-Pentanone (ketone) and tridecane (alkane) were significantly associated with early progression, and on the contrary short chain fatty acids (SCFAs) (i.e., propionate, butyrate), lysine and nicotinic acid were significantly associated with long-term beneficial effects.<br><br>CONCLUSIONS: Our preliminary data suggest a significant role of gut microbiota metabolic pathways in affecting response to immunotherapy. The metabolic approach could be a promising strategy to contribute to the personalized management of cancer patients by the identification of microbiota-linked &quot;indicators&quot; of early progressor and long responder patients.}, }
@article {pmid32011231, year = {2020}, author = {Cepko, LCS and Garling, EE and Dinsdale, MJ and Scott, WP and Bandy, L and Nice, T and Faber-Hammond, J and Mellies, JL}, title = {Myoviridae phage PDX kills enteroaggregative Escherichia coli without human microbiome dysbiosis.}, journal = {Journal of medical microbiology}, volume = {69}, number = {2}, pages = {309-323}, doi = {10.1099/jmm.0.001162}, pmid = {32011231}, issn = {1473-5644}, abstract = {Introduction. Bacteriophage therapy can be developed to target emerging diarrhoeal pathogens, but doing so in the absence of microbiome disruption, which occurs with antibiotic treatment, has not been established.Aim. Identify a therapeutic bacteriophage that kills diarrhoeagenic enteroaggregative Escherichia coli (EAEC) while leaving the human microbiome intact.Methodology. Phages from wastewater in Portland, OR, USA were screened for bacteriolytic activity by overlay assay. One isolated phage, PDX, was classified by electron microscopy and genome sequencing. A mouse model of infection determined whether the phage was therapeutic against EAEC. 16S metagenomic analysis of anaerobic cultures determined whether a normal human microbiome was altered by treatment.Results.Escherichia virus PDX, a member of the strictly lytic family Myoviridae, killed a case-associated EAEC isolate from a child in rural Tennessee in a dose-dependent manner, and killed EAEC isolates from Columbian children. A single dose of PDX (multiplicity of infection: 100) 1 day post-infection reduced EAEC recovered from mouse faeces. PDX also killed EAEC when cultured anaerobically in the presence of human faecal bacteria. While the addition of EAEC reduced the β-diversity of the human microbiota, that of the cultures with either faeces alone, faeces with EAEC and PDX, or with just PDX phage was not different statistically.Conclusion.PDX killed EAEC isolate EN1E-0007 in vivo and in vitro, while not altering the diversity of normal human microbiota in anaerobic culture, and thus could be part of an effective therapy for children in developing countries and those suffering from EAEC-mediated traveller's diarrhoea without causing dysbiosis.}, }
@article {pmid32010645, year = {2019}, author = {Zhang, L and Liu, Y and Zheng, HJ and Zhang, CP}, title = {The Oral Microbiota May Have Influence on Oral Cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {476}, pmid = {32010645}, issn = {2235-2988}, abstract = {The oral microbiota plays an important role in the human microbiome and human health, and imbalances between microbes and their hosts can lead to oral and systemic diseases and chronic inflammation, which is usually caused by bacteria and contributes to cancer. There may be a relationship between oral bacteria and oral squamous cell carcinoma (OSCC); however, this relationship has not been thoroughly characterized. Therefore, in this study, we compared the microbiota compositions between tumor sites and opposite normal tissues in buccal mucosal of 50 patients with OSCC using the 16S rDNA sequencing. Richness and diversity of bacteria were significantly higher in tumor sites than in the control tissues. Cancer tissues were enriched in six families (Prevotellaceae, Fusobacteriaceae, Flavobacteriaceae, Lachnospiraceae, Peptostreptococcaceae, and Campylobacteraceae) and 13 genera, including Fusobacterium, Alloprevotella and Porphyromonas. At the species level, the abundances of Fusobacterium nucleatum, Prevotella intermedia, Aggregatibacter segnis, Capnocytophaga leadbetteri, Peptostreptococcus stomatis, and another five species were significantly increased, suggesting a potential association between these bacteria and OSCC. Furthermore, the functional prediction revealed that genes involved in bacterial chemotaxis, flagellar assembly and lipopolysaccharide (LPS) biosynthesis which are associated with various pathological processes, were significantly increased in the OSCC group. Overall, oral bacterial profiles showed significant difference between cancer sites and normal tissue of OSCC patients, which might be onsidered diagnostic markers and treatment targets. Our study has been registered in the Chinese clinical trial registry (ChiCTR1900025253, http://www.chictr.org.cn/index.aspx).}, }
@article {pmid31996419, year = {2020}, author = {Ghannam, RB and Schaerer, LG and Butler, TM and Techtmann, SM}, title = {Biogeographic Patterns in Members of Globally Distributed and Dominant Taxa Found in Port Microbial Communities.}, journal = {mSphere}, volume = {5}, number = {1}, pages = {}, pmid = {31996419}, issn = {2379-5042}, abstract = {We conducted a global characterization of the microbial communities of shipping ports to serve as a novel system to investigate microbial biogeography. The community structures of port microbes from marine and freshwater habitats house relatively similar phyla, despite spanning large spatial scales. As part of this project, we collected 1,218 surface water samples from 604 locations across eight countries and three continents to catalogue a total of 20 shipping ports distributed across the East and West Coast of the United States, Europe, and Asia to represent the largest study of port-associated microbial communities to date. Here, we demonstrated the utility of machine learning to leverage this robust system to characterize microbial biogeography by identifying trends in biodiversity across broad spatial scales. We found that for geographic locations sharing similar environmental conditions, subpopulations from the dominant phyla of these habitats (Actinobacteria, Bacteroidetes, Cyanobacteria, and Proteobacteria) can be used to differentiate 20 geographic locations distributed globally. These results suggest that despite the overwhelming diversity within microbial communities, members of the most abundant and ubiquitous microbial groups in the system can be used to differentiate a geospatial location across global spatial scales. Our study provides insight into how microbes are dispersed spatially and robust methods whereby we can interrogate microbial biogeography.IMPORTANCE Microbes are ubiquitous throughout the world and are highly diverse. Characterizing the extent of variation in the microbial diversity across large geographic spatial scales is a challenge yet can reveal a lot about what biogeography can tell us about microbial populations and their behavior. Machine learning approaches have been used mostly to examine the human microbiome and, to some extent, microbial communities from the environment. Here, we display how supervised machine learning approaches can be useful to understand microbial biodiversity and biogeography using microbes from globally distributed shipping ports. Our findings indicate that the members of globally dominant phyla are important for differentiating locations, which reduces the reliance on rare taxa to probe geography. Further, this study displays how global biogeographic patterning of aquatic microbial communities (and other systems) can be assessed through populations of the highly abundant and ubiquitous taxa that dominant the system.}, }
@article {pmid31993418, year = {2019}, author = {Kang, W and Sun, T and Tang, D and Zhou, J and Feng, Q}, title = {Time-Course Transcriptome Analysis of Gingiva-Derived Mesenchymal Stem Cells Reveals That Fusobacterium nucleatum Triggers Oncogene Expression in the Process of Cell Differentiation.}, journal = {Frontiers in cell and developmental biology}, volume = {7}, number = {}, pages = {359}, pmid = {31993418}, issn = {2296-634X}, abstract = {Fusobacterium nucleatum has pathogenic effects on oral squamous cell carcinoma and colon cancer, while the effects of continuously altered gene expression in normal human cells, as induced by persistent exposure to F. nucleatum, remain unclear. In this study, a microarray Significant Profiles (maSigPro) analysis was used to obtain the transcriptome profile of gingiva-derived mesenchymal stem cells (GMSCs) stimulated by F. nucleatum for 3, 7, 14, and 21 day, and the results revealed 790 (nine clusters) differentially expressed genes (DEGs), which were significantly enriched in cell adherens junctions and cancer-related pathways. On the basis of a short time-series expression miner (STEM) analysis, all the expressed genes in the GMSCs were grouped into 50 clusters according to dynamic gene expression patterns, and the expression levels of three gene clusters in the F. nucleatum-treated GMSCs were significantly different than the predicted values. Among the 790 DEGs, 50 tumor-associated genes (TAGs; such as L3MBTL4, CD163, CCCND2, CADM1, BCL7A, and IGF1) and five core dynamic DEGs (PLCG2, CHI3L2, L3MBTL4, SH2D2A, and NLRP3) were identified during F. nucleatum stimulation. Results from a GeneMANIA database analysis showed that PLCG2, CHI3L2, SH2D2A, and NLRP3 and 20 other proteins formed a complex network of which 12 genes were enriched in cancer-related pathways. Based on the five core dynamic DEGs, the related microRNAs (miRNAs) and transcription factors (TFs) were obtained from public resources, and an integrated network composed of the related TFs, miRNAs, and mRNAs was constructed. The results indicated that these genes were regulated by several miRNAs, such as miR-372-3p, miR-603, and miR-495-3p, and several TFs, including CREB3, GATA2, and SOX4. Our study suggests that long-term stimulation by F. nucleatum may trigger the expression of cancer-related genes in normal gingiva-derived stem cells.}, }
@article {pmid31991821, year = {2020}, author = {Simões-Silva, L and Araujo, R and Pestana, M and Soares-Silva, I and Sampaio-Maia, B}, title = {Peritoneal Microbiome in End-Stage Renal Disease Patients and the Impact of Peritoneal Dialysis Therapy.}, journal = {Microorganisms}, volume = {8}, number = {2}, pages = {}, doi = {10.3390/microorganisms8020173}, pmid = {31991821}, issn = {2076-2607}, support = {Research Grant 2014 to ISS//European Society of Clinical Microbiology and Infectious Diseases/ ; SFRH/BPD/101016/2014//Fundação para a Ciência e a Tecnologia/ ; POCI-01-0145-FEDER-029777//Fundação para a Ciência e a Tecnologia/ ; PTDC/MEC-MCI/29777/2017//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/04050/2019//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {Factors influencing the occurrence of peritoneal dialysis (PD)-related infections are still far from fully understood. Recent studies described the existence of specific microbiomes in body sites previously considered microbiome-free, unravelling new microbial pathways in the human body. In the present study, we analyzed the peritoneum of end-stage kidney disease (ESKD) patients to determine if they harbored a specific microbiome and if it is altered in patients on PD therapy. We conducted a cross-sectional study where the peritoneal microbiomes from ESKD patients with intact peritoneal cavities (ESKD non-PD, n = 11) and ESKD patients undergoing PD therapy (ESKD PD, n = 9) were analyzed with a 16S rRNA approach. Peritoneal tissue of ESKD patients contained characteristically low-abundance microbiomes dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Patients undergoing PD therapy presented lower species richness, with dominance by the Pseudomonadaceae and Prevotelaceae families. This study provides the first characterization of the peritoneal microbiome in ESKD patients, bringing new insight to the human microbiome. Additionally, PD therapy may induce changes in this unique microbiome. The clinical relevance of these observations should be further explored to uncover the role of the peritoneal microbiome as a key element in the onset or aggravation of infection in ESKD patients, especially those undergoing PD.}, }
@article {pmid31988008, year = {2020}, author = {Zhang, Y and Ying, X and He, Y and Jiang, L and Zhang, S and Bartra, SS and Plano, GV and Klena, JD and Skurnik, M and Chen, H and Cai, H and Chen, T}, title = {Invasiveness of the Yersinia pestis ail protein contributes to host dissemination in pneumonic and oral plague.}, journal = {Microbial pathogenesis}, volume = {141}, number = {}, pages = {103993}, doi = {10.1016/j.micpath.2020.103993}, pmid = {31988008}, issn = {1096-1208}, abstract = {Yersinia pestis, a Gram-negative bacterium, is the etiologic agent of plague. A hallmark of Y. pestis infection is the organism's ability to rapidly disseminate through an animal host. Y. pestis expresses the outer membrane protein, Ail (Attachment invasion locus), which is associated with host invasion and serum resistance. However, whether Ail plays a role in host dissemination remains unclear. In this study, C57BL/6J mice were challenged with a defined Y. pestis strain, KimD27, or an isogenic ail-deleted mutant derived from KimD27 via metacarpal paw pad inoculation, nasal drops, orogastric infection, or tail vein injection to mimic bubonic, pneumonic, oral, or septicemic plague, respectively. Our results showed that ail-deleted Y. pestis KimD27 lost the ability to invade host cells, leading to failed host dissemination in the pneumonic and oral plague models but not in the bubonic or septicemic plague models, which do not require invasiveness. Therefore, this study demonstrated that whether Ail plays a role in Y. pestis pathogenesis depends on the infection route.}, }
@article {pmid31979276, year = {2020}, author = {Oduor, JMO and Kadija, E and Nyachieo, A and Mureithi, MW and Skurnik, M}, title = {Bioprospecting Staphylococcus Phages with Therapeutic and Bio-Control Potential.}, journal = {Viruses}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/v12020133}, pmid = {31979276}, issn = {1999-4915}, support = {288701//Academy of Finland/ ; Decision 2016//Jane ja Aatos Erkon Säätiö/ ; TM-18-10752//Opetushallitus/ ; TM-16-10301//Opetushallitus/ ; Decision June28, 2017//European Society of Clinical Microbiology and Infectious Diseases/ ; }, abstract = {Emergence of antibiotic-resistant bacteria is a serious threat to the public health. This is also true for Staphylococcus aureus and other staphylococci. Staphylococcus phages Stab20, Stab21, Stab22, and Stab23, were isolated in Albania. Based on genomic and phylogenetic analysis, they were classified to genus Kayvirus of the subfamily Twortvirinae. In this work, we describe the in-depth characterization of the phages that electron microscopy confirmed to be myoviruses. These phages showed tolerance to pH range of 5.4 to 9.4, to maximum UV radiation energy of 25 µJ/cm2, to temperatures up to 45 °C, and to ethanol concentrations up to 25%, and complete resistance to chloroform. The adsorption rate constants of the phages ranged between 1.0 × 10-9 mL/min and 4.7 × 10-9 mL/min, and the burst size was from 42 to 130 plaque-forming units. The phages Stab20, 21, 22, and 23, originally isolated using Staphylococcusxylosus as a host, demonstrated varied host ranges among different Staphylococcus strains suggesting that they could be included in cocktail formulations for therapeutic or bio-control purpose. Phage particle proteomes, consisting on average of ca 60-70 gene products, revealed, in addition to straight-forward structural proteins, also the presence of enzymes such DNA polymerase, helicases, recombinases, exonucleases, and RNA ligase polymer. They are likely to be injected into the bacteria along with the genomic DNA to take over the host metabolism as soon as possible after infection.}, }
@article {pmid31977194, year = {2020}, author = {Chevrette, MG and Handelsman, J}, title = {From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome.}, journal = {Biochemistry}, volume = {59}, number = {6}, pages = {729-730}, doi = {10.1021/acs.biochem.0c00033}, pmid = {31977194}, issn = {1520-4995}, }
@article {pmid31975449, year = {2020}, author = {Megrian, D and Taib, N and Witwinowski, J and Beloin, C and Gribaldo, S}, title = {One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide.}, journal = {Molecular microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mmi.14469}, pmid = {31975449}, issn = {1365-2958}, abstract = {How, when, and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.}, }
@article {pmid31967708, year = {2020}, author = {Napoli, E and Siracusa, L and Ruberto, G}, title = {New Tricks for Old Guys: Recent Developments in the Chemistry, Biochemistry, Applications and Exploitation of Selected Species from the Lamiaceae Family.}, journal = {Chemistry &amp; biodiversity}, volume = {}, number = {}, pages = {}, doi = {10.1002/cbdv.201900677}, pmid = {31967708}, issn = {1612-1880}, abstract = {Lamiaceae is one of the largest families of flowering plants comprising about 250 genera and over 7,000 species. Most of the plants of this family are aromatic and therefore important source of essential oils. Lamiaceae are widely used as culinary herbs and reported as medicinal plants in several folk traditions. In the Mediterranean area oregano, sage, rosemary, thyme and lavender stand out for geographical diffusion and variety of uses. The aim of this review is to provide recent data dealing with the phytochemical and pharmacological studies, and the more recent applications of the essential oils and the non-volatile phytocomplexes. This literature survey suggests how the deeper understanding of biomolecular processes in the health and food sectors as per as pest control bioremediation of cultural heritage, or interaction with human microbiome, fields, leads to the rediscovery and new potential applications of well-known plants.}, }
@article {pmid31964769, year = {2020}, author = {Jia, Z and Zhao, X and Liu, X and Zhao, L and Jia, Q and Shi, J and Xu, X and Hao, L and Xu, Z and Zhong, Q and Yu, K and Cui, S and Chen, H and Guo, J and Li, X and Han, Y and Song, X and Zhao, C and Bo, X and Tian, Y and Wang, W and Xie, G and Feng, Q and He, K}, title = {Impacts of the Plateau Environment on the Gut Microbiota and Blood Clinical Indexes in Han and Tibetan Individuals.}, journal = {mSystems}, volume = {5}, number = {1}, pages = {}, pmid = {31964769}, issn = {2379-5077}, abstract = {The intestinal microbiota is significantly affected by the external environment, but our understanding of the effects of extreme environments such as plateaus is far from adequate. In this study, we systematically analyzed the variation in the intestinal microbiota and 76 blood clinical indexes among 393 healthy adults with different plateau living durations (Han individuals with no plateau living, with plateau living for 4 to 6 days, with plateau living for >3 months, and who returned to the plain for 3 months, as well as plateau-living Tibetans). The results showed that the high-altitude environment rapidly (4 days) and continually (more than 3 months) shaped both the intestinal microbiota and clinical indexes of the Han population. With prolongation of plateau living, the general characteristics of the intestinal microbiota and clinical indexes of the Han population were increasingly similar to those of the Tibetan population. The intestinal microbiota of the Han population that returned to the plain area for 3 months still resembled that of the plateau-living Han population rather than that of the Han population on the plain. Moreover, clinical indexes such as blood glucose were significantly lower in the plateau groups than in the nonplateau groups, while the opposite result was obtained for testosterone. Interestingly, there were Tibetan-specific correlations between glucose levels and Succinivibrio and Sarcina abundance in the intestine. The results of this study suggest that a hypoxic environment could rapidly and lastingly affect both the human intestinal microbiota and blood clinical indexes, providing new insights for the study of plateau adaptability.IMPORTANCE The data presented in the present study demonstrate that the hypoxic plateau environment has a profound impact on the gut microbiota and blood clinical indexes in Han and Tibetan individuals. The plateau-changed signatures of the gut microbiota and blood clinical indexes were not restored to the nonplateau status in the Han cohorts, even when the individuals returned to the plain from the plateau for several months. Our study will improve the understanding of the great impact of hypoxic environments on the gut microbiota and blood clinical indexes as well as the adaptation mechanism and intervention targets for plateau adaptation.}, }
@article {pmid31961709, year = {2020}, author = {Lawenius, L and Scheffler, JM and Gustafsson, KL and Henning, P and Nilsson, KH and Colldén, H and Islander, U and Plovier, H and Cani, PD and de Vos, WM and Ohlsson, C and Sjögren, K}, title = {Pasteurized Akkermansia muciniphila protects from fat mass gain but not from bone loss.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00425.2019}, pmid = {31961709}, issn = {1522-1555}, abstract = {Probiotic bacteria can protect from ovariectomy (ovx)-induced bone loss in mice. Akkermansia muciniphila is considered to have probiotic potential due to its beneficial effect on obesity and insulin resistance. The purpose of the present study was to determine if treatment with pasteurized Akkermansia muciniphila (pAkk) could prevent ovx-induced bone loss. Mice were treated with vehicle or pAkk for 4 weeks, starting 3 days before ovx or sham surgery. Treatment with pAkk reduced fat mass accumulation confirming earlier findings. However, treatment with pAkk decreased trabecular and cortical bone mass in femur and vertebra of gonadal intact mice and did not protect from ovx-induced bone loss. Treatment with pAkk increased serum parathyroid hormone (PTH) levels and increased expression of calcium transporter Trpv5 in kidney suggesting increased reabsorption of calcium in the kidneys. Serum amyloid A 3 (SAA3) can suppress bone formation and mediate the effects of PTH on bone resorption and bone loss in mice and treatment with pAkk increased serum levels of SAA3 and gene expression of Saa3 in colon. Moreover, regulatory T cells can be protective of bone and pAkk treated mice had decreased number of regulatory T cells in mesenteric lymph nodes and bone marrow. In conclusion, treatment with pAkk protected from ovx-induced fat mass gain but not from bone loss and reduced bone mass in gonadal intact mice. Our findings with pAkk differ from some probiotics that have been shown to protect bone mass, demonstrating that not all prebiotic and probiotic factors have the same effect on bone.}, }
@article {pmid31961674, year = {2020}, author = {Chang, PT and Rao, K and Longo, LO and Lawton, ES and Scherer, G and Van Arnam, EB}, title = {Thiopeptide Defense by an Ant's Bacterial Symbiont.}, journal = {Journal of natural products}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jnatprod.9b00897}, pmid = {31961674}, issn = {1520-6025}, abstract = {Fungus-growing ants and their microbial symbionts have emerged as a model system for understanding antibiotic deployment in an ecological context. Here we establish that bacterial symbionts of the ant Trachymyrmex septentrionalis antagonize their most likely competitors, other strains of ant-associated bacteria, using the thiopeptide antibiotic GE37468. Genomic analysis suggests that these symbionts acquired the GE37468 gene cluster from soil bacteria. This antibiotic, with known activity against human pathogens, was previously identified in a biochemical screen but had no known ecological role. GE37468's host-associated defense role in this insect niche intriguingly parallels the function of similar thiopeptides in the human microbiome.}, }
@article {pmid31954376, year = {2020}, author = {Korpela, K and Salonen, A and Saxen, H and Nikkonen, A and Peltola, V and Jaakkola, T and de Vos, W and Kolho, KL}, title = {Antibiotics in early life associate with specific gut microbiota signatures in a prospective longitudinal infant cohort.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41390-020-0761-5}, pmid = {31954376}, issn = {1530-0447}, abstract = {BACKGROUND: The effects of antibiotics on infant gut microbiota are unclear. We hypothesized that the use of common antibiotics results in long-term aberration in gut microbiota.<br><br>METHODS: Antibiotic-naive infants were prospectively recruited when hospitalized because of a respiratory syncytial virus infection. Composition of fecal microbiota was compared between those receiving antibiotics during follow-up (prescribed at clinicians' discretion because of complications such as otitis media) and those with no antibiotic exposure. Fecal sampling started on day 1, then continued at 2-day intervals during the hospital stay, and at 1, 3 and 6 months at home.<br><br>RESULTS: One hundred and sixty-three fecal samples from 40 patients (median age 2.3 months at baseline; 22 exposed to antibiotics) were available for microbiota analyses. A single course of amoxicillin or macrolide resulted in aberration of infant microbiota characterized by variation in the abundance of bifidobacteria, enterobacteria and clostridia, lasting for several months. Recovery from the antibiotics was associated with an increase in clostridia. Occasionally, antibiotic use resulted in microbiota profiles associated with inflammatory conditions.<br><br>CONCLUSIONS: Antibiotic use in infants modifies especially bifidobacterial levels. Further studies are warranted whether administration of bifidobacteria will provide health benefits by normalizing the microbiota in infants receiving antibiotics.}, }
@article {pmid31949191, year = {2020}, author = {Husso, A and Jalanka, J and Alipour, MJ and Huhti, P and Kareskoski, M and Pessa-Morikawa, T and Iivanainen, A and Niku, M}, title = {The composition of the perinatal intestinal microbiota in horse.}, journal = {Scientific reports}, volume = {10}, number = {1}, pages = {441}, pmid = {31949191}, issn = {2045-2322}, abstract = {The establishment of the intestinal microbiota is critical for the digestive and immune systems. We studied the early development of the rectal microbiota in horse, a hindgut fermenter, from birth until 7 days of age, by qPCR and 16S rRNA gene amplicon sequencing. To evaluate initial sources of the foal microbiota, we characterised dam fecal, vaginal and oral microbiotas. We utilised an amplicon sequence variant (ASV) pipeline to maximise resolution and reproducibility. Stringent ASV filtering based on prevalence and abundance in samples and controls purged contaminants while preserving intestinal taxa. Sampled within 20 minutes after birth, rectal meconium contained small amounts of diverse bacterial DNA, with a profile closer to mare feces than mouth. 24 hours after birth, rectum was colonised by Firmicutes and Proteobacteria, some foals dominated by single genera. At day 7, the rectal genera were still different from adult feces. The mare vaginal microbiota contributed to 24 h and 7 day microbiotas. It contained few lactobacilli, with Corynebacterium, Porphyromonas, Campylobacter and Helcococcus as the most abundant genera. In the oral mucosa, Gemella was extremely abundant. Our observations indicate that bacteria or bacterial components are present in the intestine immediately after birth, but the newborn microbiota changes rapidly.}, }
@article {pmid31944633, year = {2020}, author = {Selway, CA and Eisenhofer, R and Weyrich, LS}, title = {Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing.}, journal = {The journal of pathology. Clinical research}, volume = {}, number = {}, pages = {}, doi = {10.1002/cjp2.151}, pmid = {31944633}, issn = {2056-4538}, abstract = {The human microbiome can play key roles in disease, and diagnostic testing will soon have the ability to examine these roles in the context of clinical applications. Currently, most diagnostic testing in pathology applications focuses on a small number of disease-causing microbes and dismisses the whole microbial community that causes or is modulated by disease. Microbiome modifications have already provided clinically relevant insights in gut and oral diseases, such as irritable bowel disease, but there are currently limitations when clinically examining microbiomes outside of these body sites. This is critical, as the majority of microbial samples used in pathology originate from body sites that contain low concentrations of microbial DNA, including skin, tissue, blood, and urine. These samples, also known as low microbial biomass samples, are difficult to examine without careful consideration and precautions to mitigate contamination and biases. Here, we present the limitations when analysing low microbial biomass samples using current protocols and techniques and highlight the advantages that microbiome testing can offer diagnostics in the future, if the proper precautions are implemented. Specifically, we discuss the sources of contamination and biases that may result in false assessments for these sample types. Finally, we provide recommendations to mitigate contamination and biases from low microbial biomass samples during diagnostic testing, which will be especially important to effectively diagnose and treat patients using microbiome analyses.}, }
@article {pmid31940382, year = {2020}, author = {Jian, C and Luukkonen, P and Yki-Järvinen, H and Salonen, A and Korpela, K}, title = {Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling.}, journal = {PloS one}, volume = {15}, number = {1}, pages = {e0227285}, pmid = {31940382}, issn = {1932-6203}, abstract = {The use of relative abundance data from next generation sequencing (NGS) can lead to misinterpretations of microbial community structures, as the increase of one taxon leads to the concurrent decrease of the other(s) in compositional data. Although different DNA- and cell-based methods as well as statistical approaches have been developed to overcome the compositionality problem, and the biological relevance of absolute bacterial abundances has been demonstrated, the human microbiome research has not yet adopted these methods, likely due to feasibility issues. Here, we describe how quantitative PCR (qPCR) done in parallel to NGS library preparation provides an accurate estimation of absolute taxon abundances from NGS data and hence provides an attainable solution to compositionality in high-throughput microbiome analyses. The advantages and potential challenges of the method are also discussed.}, }
@article {pmid31921929, year = {2019}, author = {Zangl, I and Pap, IJ and Aspöck, C and Schüller, C}, title = {The role of Lactobacillus species in the control of Candida via biotrophic interactions.}, journal = {Microbial cell (Graz, Austria)}, volume = {7}, number = {1}, pages = {1-14}, pmid = {31921929}, issn = {2311-2638}, abstract = {Microbial communities have an important role in health and disease. Candida spp. are ubiquitous commensals and sometimes opportunistic fungal pathogens of humans, colonizing mucosal surfaces of the genital, urinary, respiratory and gastrointestinal tracts and the oral cavity. They mainly cause local mucosal infections in immune competent individuals. However, in the case of an ineffective immune defense, Candida infections may become a serious threat. Lactobacillus spp. are part of the human microbiome and are natural competitors of Candida in the vaginal environment. Lactic acid, low pH and other secreted metabolites are environmental signals sensed by fungal species present in the microbiome. This review briefly discusses the ternary interaction between host, Lactobacillus species and Candida with regard to fungal infections and the potential antifungal and fungistatic effect of Lactobacillus species. Our understanding of these interactions is incomplete due to the variability of the involved species and isolates and the complexity of the human host.}, }
@article {pmid31921705, year = {2019}, author = {Kang, W and Ji, X and Zhang, X and Tang, D and Feng, Q}, title = {Persistent Exposure to Fusobacterium nucleatum Triggers Chemokine/Cytokine Release and Inhibits the Proliferation and Osteogenic Differentiation Capabilities of Human Gingiva-Derived Mesenchymal Stem Cells.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {429}, pmid = {31921705}, issn = {2235-2988}, abstract = {Fusobacterium nucleatum is one of the most frequent pathogenic bacteria causing periodontitis. The direct effect of Fusobacterium nucleatum (F. nucleatum) on oral stem cells has rarely been reported. In this study, we aimed to evaluate how gingiva-derived mesenchymal stem cells (GMSCs) respond to a direct challenge with F. nucleatum. GMSCs were isolated by the limiting dilution method and exposed to F. nucleatum at various multiplicities of infection (MOIs; F. nucleatum:cell ratios of 10:1, 50:1, and 100:1) for 24 h to 4 weeks. Our results indicated that F. nucleatum significantly inhibited cell proliferation in a dose-dependent manner and promoted cell migration and the release of chemokines/cytokines, such as CCL2, CXCL1, and IL-6. Additionally, F. nucleatum inhibited GMSC osteogenic differentiation partly by decreasing alkaline phosphatase (ALP) activity, mineralized nodule formation, and osteogenesis-related gene and protein expression. RNA-sequencing analyses indicated that F. nucleatum time-dependently activated cellular signaling pathways during the process of osteogenic differentiation. A total of 64 cell differentiation-related genes were found to be differentially expressed between non-infected and F. nucleatum-infected GMSCs at 3, 7, 14, and 21 d. Intriguingly, we discovered that the 64 cell differentiation-related differentially expressed genes (DEGs) were significantly enriched in cancer-related pathways, such as bone cancer, osteosarcoma and bone marrow cancer, which provides new insight into tumorigenesis during the process of GMSC osteogenic differentiation. In conclusion, this study demonstrates that persistent exposure to F. nucleatum promotes cell migration and chemokine/cytokine release and inhibits the proliferation and osteogenic differentiation of GMSCs. Our study provides a novel and long-time bacteria-cell co-culture in vitro model and makes a foundation for the future mechanistic studies of GMSCs under F. nucleatum infection.}, }
@article {pmid31919630, year = {2020}, author = {Nobile, V and Palumbo, F and Lanni, S and Ghisio, V and Vitali, A and Castagnola, M and Marzano, V and Maulucci, G and De Angelis, C and De Spirito, M and Pacini, L and D'Andrea, L and Ragno, R and Stazi, G and Valente, S and Mai, A and Chiurazzi, P and Genuardi, M and Neri, G and Tabolacci, E}, title = {Altered mitochondrial function in cells carrying a premutation or unmethylated full mutation of the FMR1 gene.}, journal = {Human genetics}, volume = {139}, number = {2}, pages = {227-245}, pmid = {31919630}, issn = {1432-1203}, support = {GGP15257A//Fondazione Telethon/ ; Prot. 201789LFKB//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, mesh = {Ataxia/genetics/metabolism/*pathology ; Case-Control Studies ; Cells, Cultured ; *DNA Methylation ; Fibroblasts/metabolism/pathology ; Fragile X Mental Retardation Protein/genetics/*metabolism ; Fragile X Syndrome/genetics/metabolism/*pathology ; Humans ; Male ; Mitochondria/metabolism/*pathology ; Mitochondrial Proteins/genetics/*metabolism ; *Mutation ; Proteome/*analysis ; RNA, Small Interfering/genetics ; Superoxide Dismutase/antagonists &amp; inhibitors/genetics/metabolism ; Tremor/genetics/metabolism/*pathology ; }, abstract = {Fragile X-related disorders are due to a dynamic mutation of the CGG repeat at the 5' UTR of the FMR1 gene, coding for the RNA-binding protein FMRP. As the CGG sequence expands from premutation (PM, 56-200 CGGs) to full mutation (> 200 CGGs), FMRP synthesis decreases until it is practically abolished in fragile X syndrome (FXS) patients, mainly due to FMR1 methylation. Cells from rare individuals with no intellectual disability and carriers of an unmethylated full mutation (UFM) produce slightly elevated levels of FMR1-mRNA and relatively low levels of FMRP, like in PM carriers. With the aim of clarifying how UFM cells differ from CTRL and FXS cells, a comparative proteomic approach was undertaken, from which emerged an overexpression of SOD2 in UFM cells, also confirmed in PM but not in FXS. The SOD2-mRNA bound to FMRP in UFM more than in the other cell types. The high SOD2 levels in UFM and PM cells correlated with lower levels of superoxide and reactive oxygen species (ROS), and with morphological anomalies and depolarization of the mitochondrial membrane detected through confocal microscopy. The same effect was observed in CTRL and FXS after treatment with MC2791, causing SOD2 overexpression. These mitochondrial phenotypes reverted after knock-down with siRNA against SOD2-mRNA and FMR1-mRNA in UFM and PM. Overall, these data suggest that in PM and UFM carriers, which have high levels of FMR1 transcription and may develop FXTAS, SOD2 overexpression helps to maintain low levels of both superoxide and ROS with signs of mitochondrial degradation.}, }
@article {pmid31918033, year = {2020}, author = {Marzano, V and Tilocca, B and Fiocchi, AG and Vernocchi, P and Levi Mortera, S and Urbani, A and Roncada, P and Putignani, L}, title = {Perusal of food allergens analysis by mass spectrometry-based proteomics.}, journal = {Journal of proteomics}, volume = {215}, number = {}, pages = {103636}, doi = {10.1016/j.jprot.2020.103636}, pmid = {31918033}, issn = {1876-7737}, abstract = {Food allergy is the disease where the immune system is elicited by antigens in food. Although innocuous for immune-tolerant individuals, an ever-growing number of food allergenic people are being registered worldwide. To date, no treatment to cure food allergy is available and the disease management relies on the careful exclusion of the allergenic food from the diet of the allergic individuals. Great efforts are ongoing to clarify the allergenic mechanisms of the diverse allergenic proteins of food origin, aimed to both designing suitable therapies and for a timely and precise diagnosis of the allergic condition. Among the other omics sciences, mass spectrometry (MS)-based proteomics is gaining a steadily increasing interest by the whole scientific community acknowledged its high versatility. In the present work, the latest proteomics based-studies on allergenic proteins are reviewed to provide guidance on the different MS-based methodologies adopted in the research on food allergens. Our review points to highlight the strengths of the MS-based proteomics and how these have been exploited to address specific research questions. Also, the most common drawbacks encountered in a proteomic study are discussed, providing an overview that helps novel researchers in choosing the more suitable experimental workflow. SIGNIFICANCE: Wide wealth of knowledge arising from the various MS-based proteomic investigations is improving our understanding of food allergy through molecular characterization of food allergens. The present work reviews the key aspects to be evaluated while investigating food allergens by means of MS-based proteomics and provide guidance to the novel research groups approaching to the fascinating world of MS-based food allergens detection.}, }
@article {pmid31905733, year = {2019}, author = {Signore, F and Gulìa, C and Votino, R and De Leo, V and Zaami, S and Putignani, L and Gigli, S and Santini, E and Bertacca, L and Porrello, A and Piergentili, R}, title = {The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility.}, journal = {Genes}, volume = {11}, number = {1}, pages = {}, pmid = {31905733}, issn = {2073-4425}, abstract = {The World Health Organization (WHO) defines infertility as the inability of a sexually active, non-contracepting couple to achieve spontaneous pregnancy within one year. Statistics show that the two sexes are equally at risk. Several causes may be responsible for male infertility; however, in 30-40% of cases a diagnosis of idiopathic male infertility is made in men with normal urogenital anatomy, no history of familial fertility-related diseases and a normal panel of values as for endocrine, genetic and biochemical markers. Idiopathic male infertility may be the result of gene/environment interactions, genetic and epigenetic abnormalities. Numerical and structural anomalies of the Y chromosome represent a minor yet significant proportion and are the topic discussed in this review. We searched the PubMed database and major search engines for reports about Y-linked male infertility. We present cases of Y-linked male infertility in terms of (i) anomalies of the Y chromosome structure/number; (ii) Y chromosome misbehavior in a normal genetic background; (iii) Y chromosome copy number variations (CNVs). We discuss possible explanations of male infertility caused by mutations, lower or higher number of copies of otherwise wild type, Y-linked sequences. Despite Y chromosome structural anomalies are not a major cause of male infertility, in case of negative results and of normal DNA sequencing of the ascertained genes causing infertility and mapping on this chromosome, we recommend an analysis of the karyotype integrity in all cases of idiopathic fertility impairment, with an emphasis on the structure and number of this chromosome.}, }
@article {pmid31904815, year = {2020}, author = {Zhang, X and Yi, N}, title = {Fast Zero-Inflated Negative Binomial Mixed Modeling Approach for Analyzing Longitudinal Metagenomics Data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btz973}, pmid = {31904815}, issn = {1367-4811}, abstract = {MOTIVATION: Longitudinal metagenomics data, including both 16S rRNA and whole-metagenome shotgun sequencing data, enhanced our abilities to understand the dynamic associations between the human microbiome and various diseases. However, analytic tools have not been fully developed to simultaneously address the main challenges of longitudinal metagenomics data, i.e. high-dimensionality, dependence among samples and zero-inflation of observed counts.<br><br>RESULTS: We propose a fast zero-inflated negative binomial mixed modeling (FZINBMM) approach to analyze high-dimensional longitudinal metagenomic count data. The FZINBMM approach is based on zero-inflated negative binomial mixed models (ZINBMMs) for modeling longitudinal metagenomic count data and a fast EM-IWLS algorithm for fitting ZINBMMs. FZINBMM takes advantage of a commonly used procedure for fitting linear mixed models (LMMs), which allows us to include various types of fixed and random effects and within-subject correlation structures and quickly analyze many taxa. We found that FZINBMM remarkably outperformed in computational efficiency and was statistically comparable with two R packages, GLMMadaptive and glmmTMB, that use numerical integration to fit ZINBMMs. Extensive simulations and real data applications showed that FZINBMM outperformed other previous methods, including LMMs, negative binomial mixed models and zero-inflated Gaussian mixed models.<br><br>AVAILABILITY: FZINBMM has been implemented in the R package NBZIMM, available in the public GitHub repository http://github.com//nyiuab//NBZIMM.}, }
@article {pmid31904155, year = {2020}, author = {Cui, JJ and Wang, LY and Tan, ZR and Zhou, HH and Zhan, X and Yin, JY}, title = {MASS SPECTROMETRY-BASED PERSONALIZED DRUG THERAPY.}, journal = {Mass spectrometry reviews}, volume = {}, number = {}, pages = {}, doi = {10.1002/mas.21620}, pmid = {31904155}, issn = {1098-2787}, abstract = {Personalized drug therapy aims to provide tailored treatment for individual patient. Mass spectrometry (MS) is revolutionarily involved in this area because MS is a rapid, customizable, cost-effective, and easy to be used high-throughput method with high sensitivity, specificity, and accuracy. It is driving the formation of a new field, MS-based personalized drug therapy, which currently mainly includes five subfields: therapeutic drug monitoring (TDM), pharmacogenomics (PGx), pharmacomicrobiomics, pharmacoepigenomics, and immunopeptidomics. Gas chromatography-MS (GC-MS) and liquid chromatography-MS (LC-MS) are considered as the gold standard for TDM, which can be used to optimize drug dosage. Matrix-assisted laser desorption ionization-time of flight-MS (MALDI-TOF-MS) significantly improves the capability of detecting biomacromolecule, and largely promotes the application of MS in PGx. It is becoming an indispensable tool for genotyping, which is used to discover and validate genetic biomarkers. In addition, MALDI-TOF-MS also plays important roles in identity of human microbiome whose diversity can explain interindividual differences of drug response. Pharmacoepigenetics is to study the role of epigenetic factors in individualized drug treatment. MS can be used to discover and validate pharmacoepigenetic markers (DNA methylation, histone modification, and noncoding RNA). For the emerging cancer immunotherapy, personalized cancer vaccine has effective immunotherapeutic activity in the clinic. MS-based immunopeptidomics can effectively discover and screen neoantigens. This article systematically reviewed MS-based personalized drug therapy in the above mentioned five subfields. © 2020 Wiley Periodicals, Inc. Mass Spec Rev.}, }
@article {pmid31894374, year = {2020}, author = {Yang, J and Zhang, J and Zhao, C and Gai, Z and Mu, X and Wang, Y and Zhang, C and Su, Z and Gao, L and Zhu, D and Zuo, Z and Heng, X and Zhang, L}, title = {Blood Loss Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Gut Microbiome of Rabbits.}, journal = {Current microbiology}, volume = {77}, number = {3}, pages = {415-424}, pmid = {31894374}, issn = {1432-0991}, support = {81671362//The National Natural Science Foundation of China/ ; 31471202//The National Natural Science Foundation of China/ ; 2018CXGC1219//The Shandong Provincial Key Research and Development Program/ ; 2016YYSP009//The Shandong Provincial Key Research and Development Program/ ; 2016GNS023//Weihai Technique Extension Project/ ; tshw20120206//The Taishan Scholars Program of Shandong Province/ ; }, abstract = {Massive blood loss, a common pathological complication in the clinic, is often accompanied by altered gut integrity and intestinal wall damage. Little is known to what extent the gut microbiome could be correlated with this process. The gut microbiome plays a crucial role in human health, especially in immune and inflammatory responses. This study aims to determine whether acute blood loss affects the gut microbiome and the dynamic variation of the gut microbiome following the loss of blood. We used New Zealand rabbits to mimic the blood loss complication and designed a five-time-point fecal sampling strategy including 24-h pre-blood loss procedure, 24 h, 36 h, 48 h, and 1-week post-blood loss procedure. Gut microbiome composition and diversity were analyzed using 16S rRNA gene sequencing and downstream α-diversity, β-diversity, and taxonomy analysis. The gut microbiome changed dramatically after blood loss procedure. There was a significant increase in diversity and richness of the gut microbiome at 24-h post-procedure (P = 0.038). Based on an analysis of similarities, the composition of gut microbiome in the samples collected at 24-h post-procedure was significantly different from that of pre-procedure samples (r = 0.79, P = 0.004 weighted unifrac distance; r = 0.99, P = 0.002, unweighted unifrac distance). The relative abundance of Lactobacillus was significantly decreased in the post-procedure samples (P = 0.0006), while the relative abundance of Clostridiales (P = 0.018) and Bacteroidales (P = 0.015) was significantly increased after procedure. We also found the relative abundance of Bacilli, Lactobacillus, Myroides, and Prevotella decreased gradually at different time points after blood loss. The relative abundance of the Clostridia, Alphaproteobacteria, and Sporosarcina increased at 24-h post-procedure and decreased thereafter. This preliminary study discovered potential connections between blood loss and dysbiosis of gut microbiome. The diversity and abundance of the gut microbiome was affected to various extents after acute blood loss and unable to be restored to the original microbiome profile even after one week. The increase in relative abundance of opportunistic pathogens after blood loss could be an important indication to reconsider immune and inflammatory responses after acute blood loss from the perspective of gut microbiome.}, }
@article {pmid31889089, year = {2019}, author = {Gavin, DP and Reen, FJ and Rocha-Martin, J and Abreu-Castilla, I and Woods, DF and Foley, AM and Sánchez-Murcia, PA and Schwarz, M and O'Neill, P and Maguire, AR and O'Gara, F}, title = {Genome mining and characterisation of a novel transaminase with remote stereoselectivity.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {20285}, pmid = {31889089}, issn = {2045-2322}, abstract = {Microbial enzymes from pristine niches can potentially deliver disruptive opportunities in synthetic routes to Active Pharmaceutical Ingredients and intermediates in the Pharmaceutical Industry. Advances in green chemistry technologies and the importance of stereochemical control, further underscores the application of enzyme-based solutions in chemical synthesis. The rich tapestry of microbial diversity in the oceanic ecosystem encodes a capacity for novel biotransformations arising from the chemical complexity of this largely unexplored bioactive reservoir. Here we report a novel ω-transaminase discovered in a marine sponge Pseudovibrio sp. isolate. Remote stereoselection using a transaminase has been demonstrated for the first time using this novel protein. Application to the resolution of an intermediate in the synthesis of sertraline highlights the synthetic potential of this novel biocatalyst discovered through genomic mining. Integrated chemico-genomics revealed a unique substrate profile, while molecular modelling provided structural insights into this 'first in class' selectivity at a remote chiral centre.}, }
@article {pmid31887978, year = {2019}, author = {Picca, A and Ponziani, FR and Calvani, R and Marini, F and Biancolillo, A and Coelho-Junior, HJ and Gervasoni, J and Primiano, A and Putignani, L and Del Chierico, F and Reddel, S and Gasbarrini, A and Landi, F and Bernabei, R and Marzetti, E}, title = {Gut Microbial, Inflammatory and Metabolic Signatures in Older People with Physical Frailty and Sarcopenia: Results from the BIOSPHERE Study.}, journal = {Nutrients}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/nu12010065}, pmid = {31887978}, issn = {2072-6643}, support = {IMI-JU #115621//Innovative Medicines Initiative/ ; D3.2 2013//Intramural Research Grants from the Università Cattolica del Sacro Cuore/ ; D3.2 2015//Intramural Research Grants from the Università Cattolica del Sacro Cuore/ ; NA//Nonprofit research foundation &quot;Centro Studi Achille e Linda Lorenzon&quot;/ ; CAPES; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Physical frailty and sarcopenia (PF&amp;S) share multisystem derangements, including variations in circulating amino acids and chronic low-grade inflammation. Gut microbiota balances inflammatory responses in several conditions and according to nutritional status. Therefore, an altered gut-muscle crosstalk has been hypothesized in PF&amp;S. We analyzed the gut microbial taxa, systemic inflammation, and metabolic characteristics of older adults with and without PF&amp;S. An innovative multi-marker analytical approach was applied to explore the classification performance of potential biomarkers for PF&amp;S. Thirty-five community dwellers aged 70+, 18 with PF&amp;S, and 17 nonPF&amp;S controls were enrolled. Sequential and Orthogonalized Covariance Selection (SO-CovSel), a multi-platform regression method developed to handle highly correlated variables, was applied. The SO-CovSel model with the best prediction ability using the smallest number of variables was built using seven mediators. The model correctly classified 91.7% participants with PF&amp;S and 87.5% nonPF&amp;S controls. Compared with the latter group, PF&amp;S participants showed higher serum concentrations of aspartic acid, lower circulating levels of concentrations of threonine and macrophage inflammatory protein 1α, increased abundance of Oscillospira and Ruminococcus microbial taxa, and decreased abundance of Barnesiellaceae and Christensenellaceae. Future investigations are warranted to determine whether these biomediators are involved in PF&amp;S pathophysiology and may, therefore, provide new targets for interventions.}, }
@article {pmid31886477, year = {2019}, author = {Tomassi, D and Forzani, L and Duarte, S and Pfeiffer, RM}, title = {Sufficient dimension reduction for compositional data.}, journal = {Biostatistics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/biostatistics/kxz060}, pmid = {31886477}, issn = {1468-4357}, abstract = {Recent efforts to characterize the human microbiome and its relation to chronic diseases have led to a surge in statistical development for compositional data. We develop likelihood-based sufficient dimension reduction methods (SDR) to find linear combinations that contain all the information in the compositional data on an outcome variable, i.e., are sufficient for modeling and prediction of the outcome. We consider several models for the inverse regression of the compositional vector or transformations of it, as a function of outcome. They include normal, multinomial, and Poisson graphical models that allow for complex dependencies among observed counts. These methods yield efficient estimators of the reduction and can be applied to continuous or categorical outcomes. We incorporate variable selection into the estimation via penalties and address important invariance issues arising from the compositional nature of the data. We illustrate and compare our methods and some established methods for analyzing microbiome data in simulations and using data from the Human Microbiome Project. Displaying the data in the coordinate system of the SDR linear combinations allows visual inspection and facilitates comparisons across studies.}, }
@article {pmid31883524, year = {2019}, author = {Manara, S and Asnicar, F and Beghini, F and Bazzani, D and Cumbo, F and Zolfo, M and Nigro, E and Karcher, N and Manghi, P and Metzger, MI and Pasolli, E and Segata, N}, title = {Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {299}, pmid = {31883524}, issn = {1474-760X}, abstract = {BACKGROUND: Humans have coevolved with microbial communities to establish a mutually advantageous relationship that is still poorly characterized and can provide a better understanding of the human microbiome. Comparative metagenomic analysis of human and non-human primate (NHP) microbiomes offers a promising approach to study this symbiosis. Very few microbial species have been characterized in NHP microbiomes due to their poor representation in the available cataloged microbial diversity, thus limiting the potential of such comparative approaches.<br><br>RESULTS: We reconstruct over 1000 previously uncharacterized microbial species from 6 available NHP metagenomic cohorts, resulting in an increase of the mappable fraction of metagenomic reads by 600%. These novel species highlight that almost 90% of the microbial diversity associated with NHPs has been overlooked. Comparative analysis of this new catalog of taxa with the collection of over 150,000 genomes from human metagenomes points at a limited species-level overlap, with only 20% of microbial candidate species in NHPs also found in the human microbiome. This overlap occurs mainly between NHPs and non-Westernized human populations and NHPs living in captivity, suggesting that host lifestyle plays a role comparable to host speciation in shaping the primate intestinal microbiome. Several NHP-specific species are phylogenetically related to human-associated microbes, such as Elusimicrobia and Treponema, and could be the consequence of host-dependent evolutionary trajectories.<br><br>CONCLUSIONS: The newly reconstructed species greatly expand the microbial diversity associated with NHPs, thus enabling better interrogation of the primate microbiome and empowering in-depth human and non-human comparative and co-diversification studies.}, }
@article {pmid31876898, year = {2019}, author = {Harkins, CP and Kong, HH and Segre, JA}, title = {Manipulating the Human Microbiome to Manage Disease.}, journal = {JAMA}, volume = {}, number = {}, pages = {}, doi = {10.1001/jama.2019.19602}, pmid = {31876898}, issn = {1538-3598}, }
@article {pmid31875448, year = {2019}, author = {Zhou, ZY and Xu, X and Zhou, Y}, title = {[Research progress on carbohydrate active enzymes of human microbiome].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {37}, number = {6}, pages = {666-670}, doi = {10.7518/hxkq.2019.06.017}, pmid = {31875448}, issn = {2618-0456}, mesh = {Carbohydrates ; *Gastrointestinal Tract ; Humans ; *Microbiota ; }, abstract = {A massive variety of microorganisms live in and on the human body, especially at oral, skin, vaginal, gastroin-testinal, and respiratory sites. The complicated metabolic activities of microorganisms assist human digestive function and participate in a series of physiological and pathogenetic processes. Carbohydrate-active enzymes (CAZymes) are a series of enzymes that function in degradation, modification, and formation of glycoside bonds. Microbes regulate the physiological and pathogenetic processes of human body by producing various CAZymes to degrade and modify complex carbohydrates and generate signal molecules for further utilization in human cells. Here, we reviewed the mechanisms of complex carbohy-drate metabolism and related microbial CAZymes, especially in digestive tract and oral cavity. We also summarized the rela-tionship between microbial CAZymes and human health, and proposed potential applications.}, }
@article {pmid31874963, year = {2019}, author = {Majid, M and Andleeb, S}, title = {Designing a multi-epitopic vaccine against the enterotoxigenic Bacteroides fragilis based on immunoinformatics approach.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {19780}, pmid = {31874963}, issn = {2045-2322}, abstract = {Enterotoxigenic Bacteroides fragilis is an enteric pathogen which is described as a causative agent of various intestinal infections and inflammatory diseases. Moreover, various research studies have reported it to be a leading factor in the development of colorectal cancer. As a part of the normal human microbiome, its treatment has become quite a challenge due to the alarming resistance against the available antibiotics. Although, this particular strain of B. fragilis shows susceptibility to few antibiotics, it is pertinent to devise an effective vaccine strategy for its elimination. There is no vaccine available against this pathogen up to date; therefore, we systematically ventured the outer membrane toxin producing proteins found exclusively in the toxigenic B. fragilis through the in-silico approaches to predict a multi-epitopic chimeric vaccine construct. The designed protein constitutes of epitopes which are predicted for linear B cells, Helper and T cells of outer membrane proteins expected to be putative vaccine candidates. The finalized proteins are only expressed in the enterotoxigenic B. fragilis, thus proving them to be exclusive. The 3D structure of the protein was first predicted followed by its refinement and validation via utilizing the bioinformatic approaches. Docking of the designed protein with the TLR2 receptor forecasted apt binding. Upon immune simulation, notable levels were observed in the expression of the immune cells.}, }
@article {pmid31872558, year = {2019}, author = {Grosicki, GJ and Durk, RP and Bagley, JR}, title = {Rapid gut microbiome changes in a world-class ultramarathon runner.}, journal = {Physiological reports}, volume = {7}, number = {24}, pages = {e14313}, pmid = {31872558}, issn = {2051-817X}, support = {//Rossi Family Foundation/ ; }, abstract = {The human gut microbiome is a dynamic ecosystem with prolific health connotations. Physical activity is emerging as a potent regulator of human microbiome composition. This study examined changes in the gut microbiome of a world-class ultramarathon runner before and after competing in the Western States Endurance Run (WSER), a 163 km mountain footrace. Anthropometrics and body composition were assessed and the ultramarathoner's submaximal and maximal performance profiles were evaluated. Gut microbiome analyses were performed at four time-points: 21 weeks and 2 weeks before and 2 hours and 10 days after WSER. Aerobic power (VO2 max) was 4.24 L/min (66.7 ml kg-1 min-1), and running economy (51.1 ml kg-1 min-1 at 268 m/min) and lactate threshold (~83% VO2 max) values were comparable to that of highly trained distance runners. Two hours post-race, considerable changes in the ultrarunners' gut microbiome were observed. Alpha diversity (Shannon Diversity Index) increased from 2.73 to 2.80 and phylum-level bacterial composition (Firmicutes/Bacteroidetes ratio) rose from 4.4 to 14.2. Underlying these macro-level microbial alterations were demonstrable increases in select bacterial genera such as Veillonella (+14,229%) and Streptococcus (+438%) concomitant with reductions in Alloprevotella (-79%) and Subdolingranulum (-50%). To our knowledge, this case study shows the most rapid and pronounced shifts in human gut microbiome composition after acute exercise in the human literature. These findings provide yet another example of how exercise can be a powerful modulator of human health.}, }
@article {pmid31870912, year = {2019}, author = {Ly, LK and Rowles, JL and Paul, HM and Alves, JMP and Yemm, C and Wolf, PM and Devendran, S and Hudson, ME and Morris, DJ and Erdman, JW and Ridlon, JM}, title = {Bacterial steroid-17,20-desmolase is a taxonomically rare enzymatic pathway that converts prednisone to 1,4-androstanediene-3,11,17-trione, a metabolite that causes proliferation of prostate cancer cells.}, journal = {The Journal of steroid biochemistry and molecular biology}, volume = {199}, number = {}, pages = {105567}, doi = {10.1016/j.jsbmb.2019.105567}, pmid = {31870912}, issn = {1879-1220}, support = {T32 CA057699/CA/NCI NIH HHS/United States ; }, abstract = {The adrenal gland has traditionally been viewed as a source of &quot;weak androgens&quot;; however, emerging evidence indicates 11-oxy-androgens of adrenal origin are metabolized in peripheral tissues to potent androgens. Also emerging is the role of gut bacteria in the conversion of C21 glucocorticoids to 11-oxygenated C19 androgens. Clostridium scindens ATCC 35,704 is a gut microbe capable of converting cortisol into 11-oxy-androgens by cleaving the side-chain. The desA and desB genes encode steroid-17,20-desmolase. Our prior study indicated that the urinary tract bacterium, Propionimicrobium lymphophilum ACS-093-V-SCH5 encodes desAB and converts cortisol to 11β-hydroxyandrostenedione. We wanted to determine how widespread this function occurs in the human microbiome. Phylogenetic and sequence similarity network analyses indicated that the steroid-17,20-desmolase pathway is taxonomically rare and located in gut and urogenital microbiomes. Two microbes from each of these niches, C. scindens and Propionimicrobium lymphophilum, respectively, were screened for activity against endogenous (cortisol, cortisone, and allotetrahydrocortisol) and exogenous (prednisone, prednisolone, dexamethasone, and 9-fluorocortisol) glucocorticoids. LC/MS analysis showed that both microbes were able to side-chain cleave all glucocorticoids, forming 11-oxy-androgens. Pure recombinant DesAB from C. scindens showed the highest activity against prednisone, a commonly prescribed glucocorticoid. In addition, 0.1 nM 1,4-androstadiene-3,11,17-trione, bacterial side-chain cleavage product of prednisone, showed significant proliferation relative to vehicle in androgen-dependent growth LNCaP prostate cancer cells after 24 h (2.3 fold; P < 0.01) and 72 h (1.6 fold; P < 0.01). Taken together, DesAB-expressing microbes may be an overlooked source of androgens in the body, potentially contributing to various disease states, such as prostate cancer.}, }
@article {pmid31866425, year = {2020}, author = {Liu, Q and Liu, Q and Meng, H and Lv, H and Liu, Y and Liu, J and Wang, H and He, L and Qin, J and Wang, Y and Dai, Y and Otto, M and Li, M}, title = {Staphylococcus epidermidis Contributes to Healthy Maturation of the Nasal Microbiome by Stimulating Antimicrobial Peptide Production.}, journal = {Cell host &amp; microbe}, volume = {27}, number = {1}, pages = {68-78.e5}, doi = {10.1016/j.chom.2019.11.003}, pmid = {31866425}, issn = {1934-6069}, support = {ZIA AI000904/AI/NIAID NIH HHS/United States ; }, abstract = {The composition of the human microbiome profoundly impacts human well-being. However, the mechanisms underlying microbiome maturation are poorly understood. The nasal microbiome is of particular importance as a source of many respiratory infections. Here, we performed a large sequencing and culture-based analysis of the human nasal microbiota from different age groups. We observed a significant decline of pathogenic bacteria before adulthood, with an increase of the commensal Staphylococcus epidermidis. In seniors, this effect was partially reversed. In vitro, many S. epidermidis isolates stimulated nasal epithelia to produce antimicrobial peptides, killing pathogenic competitors, while S. epidermidis itself proved highly resistant owing to its exceptional capacity to form biofilms. Furthermore, S. epidermidis isolates with high antimicrobial peptide-inducing and biofilm-forming capacities outcompeted pathogenic bacteria during nasal colonization in vivo. Our study identifies a pivotal role of S. epidermidis in healthy maturation of the nasal microbiome, which is achieved at least in part by symbiotic cooperation with innate host defense.}, }
@article {pmid31861722, year = {2019}, author = {Deering, KE and Devine, A and O'Sullivan, TA and Lo, J and Boyce, MC and Christophersen, CT}, title = {Characterizing the Composition of the Pediatric Gut Microbiome: A Systematic Review.}, journal = {Nutrients}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/nu12010016}, pmid = {31861722}, issn = {2072-6643}, support = {NA//Edith Cowan University/ ; }, abstract = {The consortium of trillions of microorganisms that live inside the human gut are integral to health. Little has been done to collate and characterize the microbiome of children. A systematic review was undertaken to address this gap (PROSPERO ID: CRD42018109599). MEDLINE and EMBASE were searched using the keywords: &quot;healthy preadolescent children&quot; and &quot;gut microbiome&quot; to 31 August 2018. Of the 815 journal articles, 42 met the inclusion criteria. The primary outcome was the relative abundance of bacteria at the phylum, family, and genus taxonomic ranks. α-diversity, short chain fatty acid concentrations, diet, 16S rRNA sequencing region, and geographical location were documented. The preadolescent gut microbiome is dominated at the phylum level by Firmicutes (weighted overall average relative abundance = 51.1%) and Bacteroidetes (36.0%); genus level by Bacteroides (16.0%), Prevotella (8.69%), Faecalibacterium (7.51%), and Bifidobacterium (5.47%). Geographic location and 16S rRNA sequencing region were independently associated with microbial proportions. There was limited consensus between studies that reported α-diversity and short chain fatty acids. Broadly speaking, participants from non-Western locations, who were less likely to follow a Westernized dietary pattern, had higher α-diversity and SCFA concentrations. Confirmatory studies will increase the understanding of the composition and functional capacity of the preadolescent gut microbiome.}, }
@article {pmid31857734, year = {2020}, author = {Martiny, JBH and Whiteson, KL and Bohannan, BJM and David, LA and Hynson, NA and McFall-Ngai, M and Rawls, JF and Schmidt, TM and Abdo, Z and Blaser, MJ and Bordenstein, S and Bréchot, C and Bull, CT and Dorrestein, P and Eisen, JA and Garcia-Pichel, F and Gilbert, J and Hofmockel, KS and Holtz, ML and Knight, R and Mark Welch, DB and McDonald, D and Methé, B and Mouncey, NJ and Mueller, NT and Pfister, CA and Proctor, L and Sachs, JL}, title = {The emergence of microbiome centres.}, journal = {Nature microbiology}, volume = {5}, number = {1}, pages = {2-3}, doi = {10.1038/s41564-019-0644-x}, pmid = {31857734}, issn = {2058-5276}, support = {K01 HL141589/HL/NHLBI NIH HHS/United States ; DEB-1925761//NSF | BIO | Division of Environmental Biology (DEB)/ ; N00014-19-1-2313//United States Department of Defense | United States Navy | Office of Naval Research (ONR)/ ; }, }
@article {pmid31850811, year = {2019}, author = {Lo Presti, A and Del Chierico, F and Altomare, A and Zorzi, F and Cella, E and Putignani, L and Guarino, MPL and Monteleone, G and Cicala, M and Angeletti, S and Ciccozzi, M}, title = {Exploring the genetic diversity of the 16S rRNA gene of Akkermansia muciniphila in IBD and IBS.}, journal = {Future microbiology}, volume = {14}, number = {}, pages = {1497-1509}, doi = {10.2217/fmb-2019-0175}, pmid = {31850811}, issn = {1746-0921}, abstract = {Aim: The human gastrointestinal tract harbors diverse, abundant microbiota and Akkermansia muciniphila is involved in this community. The aim of this study is to characterize 16 new A. muciniphila 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. Materials &amp; methods: A phylogenetic approach was used to study the genetic diversity and SNPs in 16 A. muciniphila 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which were patients affected by IBS, 30 by inflammatory bowel disease and 41 were CTRLs. Results: Phylogenetic analysis confirmed the subdivision into different supported clusters. An increase of variability in IBS has been identified. Conclusion: The genetic variation combined to the relative abundance, contribute to the protective role of A. muciniphila. Phylogenesis represent an additional approach to investigate genetic variability.}, }
@article {pmid31850333, year = {2019}, author = {Song, N and Liu, X and Feng, Q and Xu, M and Lan, X and Li, M and Liu, R and Li, C and Dong, T and Wang, D and Liu, S}, title = {Whole Body Vibration Triggers a Change in the Mutual Shaping State of Intestinal Microbiota and Body's Immunity.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {7}, number = {}, pages = {377}, pmid = {31850333}, issn = {2296-4185}, abstract = {Whole body vibration (WBV) is a non-invasive physical therapy that has recently been included in the hospital's patient rehabilitation training catalog, but its health effects have not been sufficiently studied. In the present study, to examine the possible effects of WBV on immune cell differentiation, the IFN, IL-4,-17, F4/80 and CD3,-4,-8,-11b,-11c,-19 markers were used to characterizing the cells in mouse spleen. The results showed that the CD4 and CD25 positive lymphocytes in the spleen were significantly increased in the WBV group, and the population of Treg cells was enhanced significantly in response to WBV. Since the differentiation in immune cells is usually associated with microbiota, therefore the intestinal flora was characterized in mice and human individuals. The results indicated that WBV significantly reduced the α-diversity of mouse intestinal microbiota. Moreover, the principal coordinate analysis (PCoA) results indicated that the β-diversities of both mice and human fecal microbiota increased after WBV. Analysis of the bacterial composition indicated that the contents of a variety of bacteria changed in mice upon the stimulation of vibration, such as Lactobacillus animalis in mice, and Lactobacillus paraplantarum and Lactobacillus sanfranciscensis in human. The succeeding correlation analysis revealed that some bacteria with significant content variations were correlated to the regulatory T cell differentiation in mice and physical characteristics in human. Our research will provide the basis for future non-invasive treatment of microbial and immune related diseases.}, }
@article {pmid31849833, year = {2019}, author = {Sutton, TDS and Hill, C}, title = {Gut Bacteriophage: Current Understanding and Challenges.}, journal = {Frontiers in endocrinology}, volume = {10}, number = {}, pages = {784}, pmid = {31849833}, issn = {1664-2392}, abstract = {The gut microbiome is widely accepted to have a significant impact on human health yet, despite years of research on this complex ecosystem, the contributions of different forces driving microbial population structure remain to be fully elucidated. The viral component of the human gut microbiome is dominated by bacteriophage, which are known to play crucial roles in shaping microbial composition, driving bacterial diversity, and facilitating horizontal gene transfer. Bacteriophage are also one of the most poorly understood components of the human gut microbiome, with the vast majority of viral sequences sharing little to no homology to reference databases. If we are to understand the dynamics of bacteriophage populations, their interaction with the human microbiome and ultimately their influence on human health, we will depend heavily on sequence based approaches and in silico tools. This is complicated by the fact that, as with any research field in its infancy, methods of analyses vary and this can impede our ability to compare the outputs of different studies. Here, we discuss the major findings to date regarding the human virome and reflect on our current understanding of how gut bacteriophage shape the microbiome. We consider whether or not the virome field is built on unstable foundations and if so, how can we provide a solid basis for future experimentation. The virome is a challenging yet crucial piece of the human microbiome puzzle. In order to develop our understanding, we will discuss the need to underpin future studies with robust research methods and suggest some solutions to existing challenges.}, }
@article {pmid31848308, year = {2019}, author = {Wang, C and Li, P and Yan, Q and Chen, L and Li, T and Zhang, W and Li, H and Chen, C and Han, X and Zhang, S and Xu, M and Li, B and Zhang, X and Ni, H and Ma, Y and Dong, B and Li, S and Liu, S}, title = {Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31848308}, issn = {2379-5077}, abstract = {To characterize the diversity and richness and explore the function and structure of swine gut microbiome and resistome in common pig-farming feedlots, we sampled and metagenomic sequenced the feces of pigs from four different industrialized feedlots located in four distant provinces across China. Surprisingly, more than half of the nonredundant genes (1,937,648, 54.3%) in the current catalogue were newly found compared with the previously published reference gene catalogue (RGC) of the pig gut microbiome. Additionally, 16 high-completeness draft genomes were obtained by analyzing the dominant species on each feedlot. Notably, seven of these species often appeared in the human body sites. Despite a smaller number of nonredundant genes, our study identified more antibiotic resistance genes than those available in the RGC. Tetracycline, aminoglycoside, and multidrug resistance genes accounted for nearly 70% of the relative abundance in the current catalogue. Slightly higher sharing ratios were shown between the industrialized feedlot pig gut microbiomes and human gut microbiomes than that between the RGC and human counterpart (14.7% versus 12.6% in genes and 94.1% versus 87.7% in functional groups, respectively). Furthermore, a remarkably high number of the antibiotic resistance proteins (n =141) were identified to be shared by the pig, human, and mouse resistome, indicating the potential for horizontal transfer of resistance genes. Of the antibiotic resistance proteins shared by pigs and humans, 50 proteins were related to tetracycline resistance, and 49 were related to aminoglycoside resistance.IMPORTANCE The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.}, }
@article {pmid31848304, year = {2019}, author = {Wang, Y and Randolph, TW and Shojaie, A and Ma, J}, title = {The Generalized Matrix Decomposition Biplot and Its Application to Microbiome Data.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31848304}, issn = {2379-5077}, support = {R01 GM114029/GM/NIGMS NIH HHS/United States ; R01 GM129512/GM/NIGMS NIH HHS/United States ; }, abstract = {Exploratory analysis of human microbiome data is often based on dimension-reduced graphical displays derived from similarities based on non-Euclidean distances, such as UniFrac or Bray-Curtis. However, a display of this type, often referred to as the principal-coordinate analysis (PCoA) plot, does not reveal which taxa are related to the observed clustering because the configuration of samples is not based on a coordinate system in which both the samples and variables can be represented. The reason is that the PCoA plot is based on the eigen-decomposition of a similarity matrix and not the singular value decomposition (SVD) of the sample-by-abundance matrix. We propose a novel biplot that is based on an extension of the SVD, called the generalized matrix decomposition biplot (GMD-biplot), which involves an arbitrary matrix of similarities and the original matrix of variable measures, such as taxon abundances. As in a traditional biplot, points represent the samples, and arrows represent the variables. The proposed GMD-biplot is illustrated by analyzing multiple real and simulated data sets which demonstrate that the GMD-biplot provides improved clustering capability and a more meaningful relationship between the arrows and points.IMPORTANCE Biplots that simultaneously display the sample clustering and the important taxa have gained popularity in the exploratory analysis of human microbiome data. Traditional biplots, assuming Euclidean distances between samples, are not appropriate for microbiome data, when non-Euclidean distances are used to characterize dissimilarities among microbial communities. Thus, incorporating information from non-Euclidean distances into a biplot becomes useful for graphical displays of microbiome data. The proposed GMD-biplot accounts for any arbitrary non-Euclidean distances and provides a robust and computationally efficient approach for graphical visualization of microbiome data. In addition, the proposed GMD-biplot displays both the samples and taxa with respect to the same coordinate system, which further allows the configuration of future samples.}, }
@article {pmid31847455, year = {2019}, author = {Parida, S and Sharma, D}, title = {The Microbiome-Estrogen Connection and Breast Cancer Risk.}, journal = {Cells}, volume = {8}, number = {12}, pages = {}, pmid = {31847455}, issn = {2073-4409}, support = {NCI NIH R01CA204555/NH/NIH HHS/United States ; }, abstract = {The microbiome is undoubtedly the second genome of the human body and has diverse roles in health and disease. However, translational progress is limited due to the vastness of the microbiome, which accounts for over 3.3 million genes, whose functions are still unclear. Numerous studies in the past decade have demonstrated how microbiome impacts various organ-specific cancers by altering the energy balance of the body, increasing adiposity, synthesizing genotoxins and small signaling molecules, and priming and regulating immune response and metabolism of indigestible dietary components, xenobiotics, and pharmaceuticals. In relation to breast cancer, one of the most prominent roles of the human microbiome is the regulation of steroid hormone metabolism since endogenous estrogens are the most important risk factor in breast cancer development especially in postmenopausal women. Intestinal microbes encode enzymes capable of deconjugating conjugated estrogen metabolites marked for excretion, pushing them back into the enterohepatic circulation in a biologically active form. In addition, the intestinal microbes also break down otherwise indigestible dietary polyphenols to synthesize estrogen-like compounds or estrogen mimics that exhibit varied estrogenic potency. The present account discusses the potential role of gastrointestinal microbiome in breast cancer development by mediating metabolism of steroid hormones and synthesis of biologically active estrogen mimics.}, }
@article {pmid31844880, year = {2019}, author = {Jiang, S and Xiao, G and Koh, AY and Kim, J and Li, Q and Zhan, X}, title = {A Bayesian zero-inflated negative binomial regression model for the integrative analysis of microbiome data.}, journal = {Biostatistics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/biostatistics/kxz050}, pmid = {31844880}, issn = {1468-4357}, abstract = {Microbiome omics approaches can reveal intriguing relationships between the human microbiome and certain disease states. Along with identification of specific bacteria taxa associated with diseases, recent scientific advancements provide mounting evidence that metabolism, genetics, and environmental factors can all modulate these microbial effects. However, the current methods for integrating microbiome data and other covariates are severely lacking. Hence, we present an integrative Bayesian zero-inflated negative binomial regression model that can both distinguish differentially abundant taxa with distinct phenotypes and quantify covariate-taxa effects. Our model demonstrates good performance using simulated data. Furthermore, we successfully integrated microbiome taxonomies and metabolomics in two real microbiome datasets to provide biologically interpretable findings. In all, we proposed a novel integrative Bayesian regression model that features bacterial differential abundance analysis and microbiome-covariate effects quantifications, which makes it suitable for general microbiome studies.}, }
@article {pmid31832327, year = {2019}, author = {Ma, ZS and Li, W}, title = {How and Why Men and Women Differ in Their Microbiomes: Medical Ecology and Network Analyses of the Microgenderome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {6}, number = {23}, pages = {1902054}, pmid = {31832327}, issn = {2198-3844}, abstract = {Microgenderome or sexual dimorphism in microbiome refers to the bidirectional interactions between microbiotas, sex hormones, and immune systems, and it is highly relevant to disease susceptibility. A critical step in exploring microgenderome is to dissect the sex differences in key community ecology properties, which has not been systematically analyzed. This study aims at filling the gap by reanalyzing the Human Microbiome Project datasets with two objectives: (i) dissecting the sex differences in community diversity and their intersubject scaling, species composition, core/periphery species, and high-salience skeletons (species interactions); (ii) offering mechanistic interpretations for (i). Conceptually, the Vellend-Hanson synthesis of community ecology that stipulates selection, drift, speciation, and dispersal as the four processes driving community dynamics is followed. Methodologically, seven approaches reflecting the state-of-the-art research in medical ecology of human microbiomes are harnessed to achieve the objectives. It is postulated that the revealed microgenderome characteristics (categorized as seven aspects of differences/similarities) exert far reaching influences on disease susceptibility, and are primarily due to the sex difference in selection effects (deterministic fitness differences in microbial species and/or species interactions with each other or with their hosts), which are, in turn, shaped/modulated by host physiology (immunity, hormones, gut-brain communications, etc.).}, }
@article {pmid31828607, year = {2019}, author = {Berkes, E and Liao, YH and Neef, D and Grandalski, M and Monsul, N}, title = {Potentiated In Vitro Probiotic Activities of Lactobacillus fermentum LfQi6 Biofilm Biomass Versus Planktonic Culture.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12602-019-09624-8}, pmid = {31828607}, issn = {1867-1314}, support = {QI2019//Quorum Innovations LLC/ ; }, abstract = {In this study, we describe enhanced in vitro probiotic activities of preformed biofilms versus planktonic cultures of Lactobacillus fermentum LfQi6 (LfQi6), a lactic acid bacterium (LAB) isolated from the human microbiome. These evaluations are used to help predict host in vivo probiotic benefits and therefore indicate that LfQi6 may provide significant probiotic benefits in the human host when administered as preformed biofilms rather than as planktonic cultures. Specifically, LfQi6 biofilms demonstrated improved in vitro performance versus LfQi6 planktonic cultures for host gastrointestinal survival and engraftment, strain-specific antimicrobial and anti-biofilm activity against clinically significant pathogens, concurrent promotion of beneficial gastrointestinal commensal biofilms, beneficial commensal enzyme activities, and host cellular-protective glutathione antioxidant activity. Evaluation of LfQi6 according to the European Food Safety Authority (EFSA 2007, 2012, 2015) Guidelines and Joint FAO/WHO Expert Consultation on Evaluation of Health and Nutritional Properties of Probiotics in Food Evaluation of Probiotics in Food (FAO/WHO, 2002) demonstrates strain safety. In summary, in vitro evaluation of Lact. fermentum LfQi6 demonstrates significant evidence for strain-specific probiotic characteristics and safety. Moreover, strain-specific as well as biofilm-phenotype-specific benefits demonstrated in vitro furthermore suggest that in vivo use of LfQi6 biofilm biomass may be of greater benefit to the human host than the use of standard planktonic cultures. This concept - potentiating probiotic benefits through the use of preformed commensal biofilms - is novel and may serve to further broaden the application of microbial biofilms to human health.}, }
@article {pmid31827811, year = {2019}, author = {Rapp, R}, title = {On mycohuman performances: fungi in current artistic research.}, journal = {Fungal biology and biotechnology}, volume = {6}, number = {}, pages = {22}, doi = {10.1186/s40694-019-0085-6}, pmid = {31827811}, issn = {2054-3085}, abstract = {This review reflects several artists and their artistic research in the field of hybrid art, bio art, or science art, working with Fungi as both subject matter and medium. The work of Saša Spačal, Tarsh Bates and Theresa Schubert is not representational in the manner of traditional fine art, but works rather through performative, multidisciplinary and research-based strategies to produce artwork through fungal material as such. My research results are based on the series &quot;Nonhuman subjectivities&quot; and &quot;Nonhuman agents&quot; that Christian de Lutz and I conceived and realized at Art Laboratory Berlin (2016-18) in various formats-exhibitions, workshops, lectures and a conference. The work of Saša Spačal and her colleagues involves creating interactive situations of symbiosis between the fungal and the human. An example of this is Myconnect, in which a biofeedback loop is related between the human participant and Oyster mushroom mycelia through a special encounter, which is mediated by non-linguistic forms of awareness and exchange-sonic, electronic and metabolic. Tarsh Bates' work with Candida albicans and Candida parapsilosis refers to a complex and intimate relation between the human and yeasts that form part of the human microbiome. Bates considers the relationship between humans and yeast as &quot;CandidaHomo Ecologies&quot; and sees both partners as equals. She explores this relationship through her work The Surface dynamics of adhesion, examines it from historical and metabolic levels through an installation that includes the live yeast growing on agar mixed with the artist's own blood. Theresa Schubert's installations and site-specific interventions treat living organisms, especially Fungi, as collaborators and co-creators. Her work Growing Geometries-Tattooing Mushrooms follows the morphological development of fungal fruiting bodies through the intervention of a tattoo. Her performative forest walks, especially the Forestal Psyche and also new actions for the &quot;Mind the Fungi&quot; project, engage the public in an intimate and multi sensory encounter with Fungi and their surrounding environment.}, }
@article {pmid31824656, year = {2019}, author = {Barton, W and O'Sullivan, O and Cotter, PD}, title = {Metabolic phenotyping of the human microbiome.}, journal = {F1000Research}, volume = {8}, number = {}, pages = {}, pmid = {31824656}, issn = {2046-1402}, mesh = {Humans ; Metabolomics ; *Microbiota ; }, abstract = {The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.}, }
@article {pmid31824493, year = {2019}, author = {Michel-Todó, L and Reche, PA and Bigey, P and Pinazo, MJ and Gascón, J and Alonso-Padilla, J}, title = {In silico Design of an Epitope-Based Vaccine Ensemble for Chagas Disease.}, journal = {Frontiers in immunology}, volume = {10}, number = {}, pages = {2698}, pmid = {31824493}, issn = {1664-3224}, abstract = {Trypanosoma cruzi infection causes Chagas disease, which affects 7 million people worldwide. Two drugs are available to treat it: benznidazole and nifurtimox. Although both are efficacious against the acute stage of the disease, this is usually asymptomatic and goes undiagnosed and untreated. Diagnosis is achieved at the chronic stage, when life-threatening heart and/or gut tissue disruptions occur in ~30% of those chronically infected. By then, the drugs' efficacy is reduced, but not their associated high toxicity. Given current deficiencies in diagnosis and treatment, a vaccine to prevent infection and/or the development of symptoms would be a breakthrough in the management of the disease. Current vaccine candidates are mostly based on the delivery of single antigens or a few different antigens. Nevertheless, due to the high biological complexity of the parasite, targeting as many antigens as possible would be desirable. In this regard, an epitope-based vaccine design could be a well-suited approach. With this aim, we have gone through publicly available databases to identify T. cruzi epitopes from several antigens. By means of a computer-aided strategy, we have prioritized a set of epitopes based on sequence conservation criteria, projected population coverage of Latin American population, and biological features of their antigens of origin. Fruit of this analysis, we provide a selection of CD8+ T cell, CD4+ T cell, and B cell epitopes that have <70% identity to human or human microbiome protein sequences and represent the basis toward the development of an epitope-based vaccine against T. cruzi.}, }
@article {pmid31824463, year = {2019}, author = {Freitag, TL and Hartikainen, A and Jouhten, H and Sahl, C and Meri, S and Anttila, VJ and Mattila, E and Arkkila, P and Jalanka, J and Satokari, R}, title = {Minor Effect of Antibiotic Pre-treatment on the Engraftment of Donor Microbiota in Fecal Transplantation in Mice.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2685}, pmid = {31824463}, issn = {1664-302X}, abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection (rCDI) and is also considered a potential treatment for a wide range of intestinal and systemic diseases. FMT corrects the microbial dysbiosis associated with rCDI, and the engraftment of donor microbiota is likely to play a key role in treatment efficacy. For disease indications other than rCDI, FMT treatment efficacy has been moderate. This may be partly due to stronger resilience of resident host microbiota in patients who do not suffer from rCDI. In rCDI, patients typically have undergone several antibiotic treatments prior to FMT, depleting the microbiota. In this study, we addressed the effect of broad-spectrum antibiotics (Ab) as a pre-treatment to FMT on the engraftment of donor microbiota in recipients. We conducted a pre-clinical study of FMT between two healthy mouse strains, Balb/c as donors and C57BL/6 as recipients, to perform FMT within the same species and to mimic interindividual FMT between human donors and patients. Microbiota composition was assessed with high-throughput 16S rDNA amplicon sequencing. The microbiota of Balb/c and C57BL/6 mice differed significantly, which allowed for the assessment of microbiota transplantation from the donor strain to the recipient. Our results showed that Ab-treatment depleted microbiota in C57BL/6 recipient mice prior to FMT. The diversity of microbiota did not recover spontaneously to baseline levels during 8 weeks after Ab-treatment, but was restored already at 2 weeks in mice receiving FMT. Interestingly, pre-treatment with antibiotics prior to FMT did not increase the overall similarity of the recipient's microbiota to that of the donor's, as compared with mice receiving FMT without Ab-treatment. Pre-treatment with Ab improved the establishment of only a few donor-derived taxa, such as Bifidobacterium, in the recipients, thus having a minor effect on the engraftment of donor microbiota in FMT. In conclusion, pre-treatment with broad-spectrum antibiotics did not improve the overall engraftment of donor microbiota, but did improve the engraftment of specific taxa. These results may inform future therapeutic studies of FMT.}, }
@article {pmid31821833, year = {2020}, author = {Golofast, B and Vales, K}, title = {The connection between microbiome and schizophrenia.}, journal = {Neuroscience and biobehavioral reviews}, volume = {108}, number = {}, pages = {712-731}, doi = {10.1016/j.neubiorev.2019.12.011}, pmid = {31821833}, issn = {1873-7528}, abstract = {There has been an accumulation of knowledge about the human microbiome, some detailed investigations of the gastrointestinal microbiota and its functions, and the highlighting of complex interactions between the gut, the gut microbiota, and the central nervous system. That assumes the involvement of the microbiome in the pathogenesis of various CNS diseases, including schizophrenia. Given this information and the fact, that the gut microbiota is sensitive to internal and environmental influences, we have speculated that among the factors that influence the formation and composition of gut microbiota during life, possible key elements in the schizophrenia development chain are hidden where gut microbiota is a linking component. This article aims to describe and understand the developmental relationships between intestinal microbiota and the risk of developing schizophrenia.}, }
@article {pmid31812808, year = {2019}, author = {Hall, CV and Lord, A and Betzel, R and Zakrzewski, M and Simms, LA and Zalesky, A and Radford-Smith, G and Cocchi, L}, title = {Co-existence of Network Architectures Supporting the Human Gut Microbiome.}, journal = {iScience}, volume = {22}, number = {}, pages = {380-391}, pmid = {31812808}, issn = {2589-0042}, abstract = {Microbial organisms of the human gut microbiome do not exist in isolation but form complex and diverse interactions to maintain health and reduce risk of disease development. The organization of the gut microbiome is assumed to be a singular assortative network, where interactions between operational taxonomic units (OTUs) can readily be clustered into segregated and distinct communities. Here, we leverage recent methodological advances in network modeling to assess whether communities in the human microbiome exhibit a single network structure or whether co-existing mesoscale network architectures are present. We found evidence for core-periphery structures in the microbiome, supported by strong, assortative community interactions. This complex architecture, coupled with previously reported functional roles of OTUs, provides a nuanced understanding of how the microbiome simultaneously promotes high microbial diversity and maintains functional redundancy.}, }
@article {pmid31812180, year = {2019}, author = {Borbet, TC and Zhang, X and Müller, A and Blaser, MJ}, title = {The role of the changing human microbiome in the asthma pandemic.}, journal = {The Journal of allergy and clinical immunology}, volume = {144}, number = {6}, pages = {1457-1466}, pmid = {31812180}, issn = {1097-6825}, support = {U01 AI122285/AI/NIAID NIH HHS/United States ; }, abstract = {Asthma and allergy incidence continue to increase globally. We have made significant strides in treating disease, but it is becoming more apparent that we need to advance our knowledge into the origins of asthmatic disease. Much recent work has indicated that microbiome composition influences immune regulation and that multiple health care factors have driven a loss in microbiome diversity in modern human populations. Evidence is growing of microbiota-driven influences on immune development, asthma susceptibility, and asthma pathogenesis. The focus of this review is to highlight the strides the field has made in characterizing the constituents of the human gastrointestinal microbiota, such as Helicobacter pylori, other members of the neonatal intestinal microbiota, and microbial peptides and metabolites that influence host immunity and immune response to allergens. As we delve further into this field of research, the goal will be to find actionable and clinical interventions to identify at-risk populations earlier to prevent disease onset. Manipulation of the host microbial community during infancy might be an especially promising approach.}, }
@article {pmid31812098, year = {2020}, author = {Neckovic, A and van Oorschot, RAH and Szkuta, B and Durdle, A}, title = {Investigation of direct and indirect transfer of microbiomes between individuals.}, journal = {Forensic science international. Genetics}, volume = {45}, number = {}, pages = {102212}, doi = {10.1016/j.fsigen.2019.102212}, pmid = {31812098}, issn = {1878-0326}, abstract = {The human microbiome encompasses the fungi, bacteria and viruses that live on, within, and immediately surrounding the body. Microbiomes have potential utility in forensic science as an evidentiary tool to link or exclude persons of interest associated with criminal activities. Research has shown the microbiome is individualised, and that personal microbial signatures can be recovered from surfaces such as phones, shoes and fabrics. Before the human microbiome may be used as an investigative tool, further research is required to investigate the utility and potential limitations surrounding microbial profiling. This includes the detectability of microbial transfer between individuals or items, the associated risks (such as contamination events) and the applicability of microbial profiling for forensic purposes. This research aimed to identify whether an individual's distinguishable microbiome could be transferred to another individual and onto substrates, and vice versa. Paper, cotton, and glass surfaces were chosen to represent a range of substrate matrices. The study involved six participants placed into three pairs; participants took part in two modes of transfer. Transfer Mode 1 involved the pair shaking hands, followed by rubbing a substrate in their right hand. Transfer Mode 2 involved individuals rubbing a substrate in their left hand, swapping substrates with their partner and then rubbing the swapped substrate in their left hand. 16S rRNA sequencing was performed on the extracted microbial DNA from participant and substrate samples. Quantitative Insights into Microbial Ecology 2 (QIIME 2) was used for sequence quality control and beta (between-sample) diversity analyses and taxonomic assignment. Principal Coordinate Analysis (PCoA) based on Jaccard distances was visualised through Emperor software to determine the phylogenetic similarity of bacterial communities between participants and among participant pairs. Statistical testing through PERMANOVA revealed significant differences in the Jaccard distances between each participant pair (P < 0.001), highlighting not only the potential distinguishability of skin microbiomes among individuals, but also the clustering effect observed between participant pairs due to the potential transfer of hand-associated microbiomes between individuals. The study demonstrated that transfer of the human skin microbiome had occurred between all participant pairs, regardless of substrate type or mode of transfer.}, }
@article {pmid31802114, year = {2019}, author = {Barrera-Vázquez, OS and Gomez-Verjan, JC}, title = {The Unexplored World of Human Virome, Mycobiome, and Archaeome in Aging.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {}, number = {}, pages = {}, doi = {10.1093/gerona/glz274}, pmid = {31802114}, issn = {1758-535X}, abstract = {In the last decades, improvements in different aspects of sanitation, medical care, and nutrition, among others, have permitted an increase in the average lifespan of human population around the world. These advances have stimulated an increased interest in the study of the aging process and age-sensitive characteristics, such as the microbial community that colonizes the human body (microbiome). The human microbiome is composed of bacteria (bacteriome), archaea (archaeome), fungi (mycobiome), and viruses (virome). To date, research has mainly been centered on the composition of the bacteriome, with other members remain poorly studied. Interestingly, changes in the composition of the microbiome have been implicated in aging and age-related diseases. Therefore, in the present perspective, we suggest expanding the scope to research to include the role and the possible associations that the other members of the microbiome could have in the aging organism. An expanded view of the microbiome would increase our knowledge of the physiology of aging and may be particularly valuable for the treatment and diagnosis of age-related diseases.}, }
@article {pmid31795231, year = {2019}, author = {Leon-Velarde, CG and Jun, JW and Skurnik, M}, title = {Yersinia Phages and Food Safety.}, journal = {Viruses}, volume = {11}, number = {12}, pages = {}, pmid = {31795231}, issn = {1999-4915}, support = {288701//Academy of Finland/International ; Decision 2016//Jane ja Aatos Erkon Säätiö/International ; }, abstract = {One of the human- and animal-pathogenic species in genus Yersinia is Yersinia enterocolitica, a food-borne zoonotic pathogen that causes enteric infections, mesenteric lymphadenitis, and sometimes sequelae such as reactive arthritis and erythema nodosum. Y. enterocolitica is able to proliferate at 4 C, making it dangerous if contaminated food products are stored under refrigeration. The most common source of Y. enterocolitica is raw pork meat. Microbiological detection of the bacteria from food products is hampered by its slow growth rate as other bacteria overgrow it. Bacteriophages can be exploited in several ways to increase food safety with regards to contamination by Y. enterocolitica. For example, Yersinia phages could be useful in keeping the contamination of food products under control, or, alternatively, the specificity of the phages could be exploited in developing rapid and sensitive diagnostic tools for the identification of the bacteria in food products. In this review, we will discuss the present state of the research on these topics.}, }
@article {pmid31790791, year = {2020}, author = {Ahmed, N and Daniel, B and Varghese, J and Evangeline, R and Jose, T}, title = {Oropharyngeal microbiome of an HIV-positive patient.}, journal = {Microbial pathogenesis}, volume = {139}, number = {}, pages = {103805}, doi = {10.1016/j.micpath.2019.103805}, pmid = {31790791}, issn = {1096-1208}, abstract = {Studies on understanding the human microbiome continue to grow rapidly; nonetheless, reports on alterations in the microbiome post HIV infection are limited. Human microbiome is an aggregate of bacteria, fungi, viruses and archaea that have co-evolved with humans. These microbes have important roles in immune modulation, vitamin synthesis, metabolism etc. The human pharyngeal microbiome, which resides in the junction between digestive and respiratory tracts, might have a key role in the prevention of respiratory tract infections, akin to the actions of the intestinal microbiome against enteric infections. The respiratory tract is constantly exposed to various environmental and endogenous microbes; however, unlike other similar mucosal surfaces, there has been limited investigation of the microbiome of the respiratory tract. HIV infection is associated with alterations in the respiratory microbiome. The aim of this study was to use next-generation sequencing to determine the composition of the oropharyngeal microbiome in a HIV-positive individual. The bacterial composition was determined by illumina sequencing using MiSeq of partial 16S rRNA genes (V3-V4). A total of 3, 57,926 reads were analyzed. Overall, the genera Proteus, Enterococcus, Bacteroides, Prevotella and Clostridium were most prevalent bacterial populations in the oropharynx of an HIV positive patient.}, }
@article {pmid31782749, year = {2019}, author = {Quagliariello, A and Di Paola, M and De Fanti, S and Gnecchi-Ruscone, GA and Martinez-Priego, L and Pérez-Villaroya, D and Sherpa, MG and Sherpa, PT and Marinelli, G and Natali, L and Di Marcello, M and Peluzzi, D and Di Cosimo, P and D'Auria, G and Pettener, D and Sazzini, M and Luiselli, D and De Filippo, C}, title = {Gut microbiota composition in Himalayan and Andean populations and its relationship with diet, lifestyle and adaptation to the high-altitude environment.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {96}, number = {}, pages = {189-208}, doi = {10.4436/JASS.97007}, pmid = {31782749}, issn = {2037-0644}, abstract = {Human populations living at high altitude evolved a number of biological adjustments to cope with a challenging environment characterised especially by reduced oxygen availability and limited nutritional resources. This condition may also affect their gut microbiota composition. Here, we explored the impact of exposure to such selective pressures on human gut microbiota by considering different ethnic groups living at variable degrees of altitude: the high-altitude Sherpa and low-altitude Tamang populations from Nepal, the high-altitude Aymara population from Bolivia, as well as a low-altitude cohort of European ancestry, used as control. We thus observed microbial profiles common to the Sherpa and Aymara, but absent in the low-altitude cohorts, which may contribute to the achievement of adaptation to high-altitude lifestyle and nutritional conditions. The collected evidences suggest that microbial signatures associated to these rural populations may enhance metabolic functions able to supply essential compounds useful for the host to cope with high altitude-related physiological changes and energy demand. Therefore, these results add another valuable piece of the puzzle to the understanding of the beneficial effects of symbiosis between microbes and their human host even from an evolutionary perspective.}, }
@article {pmid31781817, year = {2020}, author = {Bajerski, F and Bürger, A and Glasmacher, B and Keller, ERJ and Müller, K and Mühldorfer, K and Nagel, M and Rüdel, H and Müller, T and Schenkel, J and Overmann, J}, title = {Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples.}, journal = {Applied microbiology and biotechnology}, volume = {104}, number = {1}, pages = {131-144}, pmid = {31781817}, issn = {1432-0614}, support = {GDK//GDK Gemeinschaft Deutscher Kryobanken/ ; FP7-HEALTH-F4-2010-261492//Helmholtz-Gemeinschaft/ ; ExNet-0041-Phase2-3//Helmholtz-Gemeinschaft/ ; }, abstract = {The availability of bioresources is a precondition for life science research, medical applications, and diagnostics, but requires a dedicated quality management to guarantee reliable and safe storage. Anecdotal reports of bacterial isolates and sample contamination indicate that organisms may persist in liquid nitrogen (LN) storage tanks. To evaluate the safety status of cryocollections, we systematically screened organisms in the LN phase and in ice layers covering inner surfaces of storage tanks maintained in different biobanking facilities. We applied a culture-independent approach combining cell detection by epifluorescence microscopy with the amplification of group-specific marker genes and high-throughput sequencing of bacterial ribosomal genes. In the LN phase, neither cells nor bacterial 16S rRNA gene copy numbers were detectable (detection limit, 102 cells per ml, 103 gene copies per ml). In several cases, small numbers of bacteria of up to 104 cells per ml and up to 106 gene copies per ml, as well as Mycoplasma, or fungi were detected in the ice phase formed underneath the lids or accumulated at the bottom. The bacteria most likely originated from the stored materials themselves (Elizabethingia, Janthibacterium), the technical environment (Pseudomonas, Acinetobacter, Methylobacterium), or the human microbiome (Bacteroides, Streptococcus, Staphylococcus). In single cases, bacteria, Mycoplasma, fungi, and human cells were detected in the debris at the bottom of the storage tanks. In conclusion, the limited microbial load of the ice phase and in the debris of storage tanks can be effectively avoided by minimizing ice formation and by employing hermetically sealed sample containers.}, }
@article {pmid31780826, year = {2019}, author = {Tang, L}, title = {Exploring the chemical space of the human microbiome.}, journal = {Nature methods}, volume = {16}, number = {12}, pages = {1201}, doi = {10.1038/s41592-019-0671-9}, pmid = {31780826}, issn = {1548-7105}, mesh = {Humans ; Metagenome ; *Microbiota ; }, }
@article {pmid31780057, year = {2020}, author = {Garud, NR and Pollard, KS}, title = {Population Genetics in the Human Microbiome.}, journal = {Trends in genetics : TIG}, volume = {36}, number = {1}, pages = {53-67}, doi = {10.1016/j.tig.2019.10.010}, pmid = {31780057}, issn = {0168-9525}, abstract = {While the human microbiome's structure and function have been extensively studied, its within-species genetic diversity is less well understood. However, genetic mutations in the microbiome can confer biomedically relevant traits, such as the ability to extract nutrients from food, metabolize drugs, evade antibiotics, and communicate with the host immune system. The population genetic processes by which these traits evolve are complex, in part due to interacting ecological and evolutionary forces in the microbiome. Advances in metagenomic sequencing, coupled with bioinformatics tools and population genetic models, facilitate quantification of microbiome genetic variation and inferences about how this diversity arises, evolves, and correlates with traits of both microbes and hosts. In this review, we explore the population genetic forces (mutation, recombination, drift, and selection) that shape microbiome genetic diversity within and between hosts, as well as efforts towards predictive models that leverage microbiome genetics.}, }
@article {pmid31775543, year = {2019}, author = {Poon, WL and Lee, JC and Leung, KS and Alenius, H and El-Nezami, H and Karisola, P}, title = {Nanosized silver, but not titanium dioxide or zinc oxide, enhances oxidative stress and inflammatory response by inducing 5-HETE activation in THP-1 cells.}, journal = {Nanotoxicology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/17435390.2019.1687776}, pmid = {31775543}, issn = {1743-5404}, abstract = {Bioactive, oxygenated metabolites of polyunsaturated fatty acids (PUFAs) are important indicators of inflammation and oxidative stress but almost nothing is known about their interactions with nanomaterials (NMs). To investigate the effects of nano-sized materials (n-TiO2, n-ZnO, n-Ag) and their bulk-sized or ionic (b-TiO2, b-ZnO, i-Ag) counterpart, we studied the status of oxidative stress and PUFA metabolism in THP-1 cells at low-toxic concentrations (<15% cytotoxicity) 6 h or 24 h after the particle exposures by LC/MS and microarray. N-Ag had a significant and sustained impact on cellular antioxidant defense, seen as incremental synthesis and accumulation of glutathione (GSH) in the cell, and reduction of superoxide dismutase (SOD) activity. The cellular particle doses were largely dependent on exposure duration and particle dissolution, and active transporter mechanisms controlled the concentration of Zn in cytosol. Even at these sub-toxic concentrations, n-Ag was able to induce statistically significant elevation in the 5-HETE: arachidonic acid ratio at 24 h, which suggests association to oxidative stress and induction of pro-inflammatory responses. This was supported by the enhanced gene expression of chemotaxis-related genes. Overall, THP-1 cells internalized all tested particles, but only n-Ag led to low level of oxidative stress through ROS production and antioxidant balance disruption. N-Ag stimulated arachidonic acid oxidation to form 5-HETE which further magnified the inflammatory responses by enhancing the production of mitochondrial superoxide and leukocyte chemokines. Since the sustained n-Ag uptake was detected, the effects may last long and function as a trigger for the low-grade inflammation playing role in the chronic inflammatory diseases.}, }
@article {pmid31753125, year = {2019}, author = {Croitoru, DO and Piguet, V}, title = {A Mother's Touch: Emerging Roles in Development of the Cutaneous Microbiome.}, journal = {The Journal of investigative dermatology}, volume = {139}, number = {12}, pages = {2414-2416}, doi = {10.1016/j.jid.2019.06.144}, pmid = {31753125}, issn = {1523-1747}, abstract = {Skin-associated bacteria constitute a large proportion of the human microbiome and influence host immunity. The healthy cutaneous microbiome adopts site-specific composition, weeks to months postpartum. Zhu et al. (2019) expand the scope of pediatric data, tracking infant skin microflora changes by site, through childhood, and establish new associations with delivery mode and maternal microbiome.}, }
@article {pmid31752095, year = {2019}, author = {Ristori, MV and Quagliariello, A and Reddel, S and Ianiro, G and Vicari, S and Gasbarrini, A and Putignani, L}, title = {Autism, Gastrointestinal Symptoms and Modulation of Gut Microbiota by Nutritional Interventions.}, journal = {Nutrients}, volume = {11}, number = {11}, pages = {}, pmid = {31752095}, issn = {2072-6643}, abstract = {Autism spectrum disorder (ASD) is a complex behavioral syndrome that is characterized by speech and language disorders, intellectual impairment, learning and motor dysfunctions. Several genetic and environmental factors are suspected to affect the ASD phenotype including air pollution, exposure to pesticides, maternal infections, inflammatory conditions, dietary factors or consumption of antibiotics during pregnancy. Many children with ASD shows abnormalities in gastrointestinal (GI) physiology, including increased intestinal permeability, overall microbiota alterations, and gut infection. Moreover, they are &quot;picky eaters&quot; and the existence of specific sensory patterns in ASD patients could represent one of the main aspects in hampering feeding. GI disorders are associated with an altered composition of the gut microbiota. Gut microbiome is able to communicate with brain activities through microbiota-derived signaling molecules, immune mediators, gut hormones as well as vagal and spinal afferent neurons. Since the diet induces changes in the intestinal microbiota and in the production of molecules, such as the SCFA, we wanted to investigate the role that nutritional intervention can have on GI microbiota composition and thus on its influence on behavior, GI symptoms and microbiota composition and report which are the beneficial effect on ASD conditions.}, }
@article {pmid31744921, year = {2019}, author = {Estrela, AB and Nakashige, TG and Lemetre, C and Woodworth, ID and Weisman, JL and Cohen, LJ and Brady, SF}, title = {Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors.}, journal = {mBio}, volume = {10}, number = {6}, pages = {}, pmid = {31744921}, issn = {2150-7511}, support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; }, abstract = {The effect of the microbiota on its human host is driven, at least in part, by small-molecule and protein effectors it produces. Here, we report on the use of functional multigenomic screening to identify microbiota-encoded effectors. In this study, genomic DNA from 116 human-associated bacteria was cloned en masse, and the resulting multigenomic library was screened using a nuclear factor-κB reporter (NF-κB) assay. Functional multigenomics builds on the concept of functional metagenomics but takes advantage of increasing advances in cultivating and sequencing human-associated bacteria. Effector genes found to confer NF-κB-inducing activity to Escherichia coli encode proteins in four general categories: cell wall hydrolases, membrane transporters, lipopolysaccharide biosynthetic enzymes, and proteins of unknown function. The compact nature of multigenomic libraries, which results from the ability to normalize input DNA ratios, should simplify screening of libraries using diverse heterologous hosts and reporter assays, increasing the rate of discovery of novel effector genes.IMPORTANCE Human-associated bacteria are thought to encode bioactive small molecules and proteins that play an intimate role in human health and disease. Here, we report on the creation and functional screening of a multigenomic library constructed using genomic DNA from 116 bacteria found at diverse sites across the human body. Individual clones were screened for genes capable of conferring NF-κB-inducing activity to Escherichia coli NF-κB is a useful reporter for a range of cellular processes related to immunity, pathogenesis, and inflammation. Compared to the screening of metagenomic libraries, the ability to normalize input DNA ratios when constructing a multigenomic library should facilitate the more efficient examination of commensal bacteria for diverse bioactivities. Multigenomic screening takes advantage of the growing available resources in culturing and sequencing the human microbiota and generates starting points for more in-depth studies on the mechanisms by which commensal bacteria interact with their human host.}, }
@article {pmid31744351, year = {2019}, author = {Bender, JM and Li, F and Purswani, H and Capretz, T and Cerini, C and Zabih, S and Hung, L and Francis, N and Chin, S and Pannaraj, PS and Aldrovandi, G}, title = {Early exposure to antibiotics in the neonatal intensive care unit alters the taxonomic and functional infant gut microbiome.}, journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {}, number = {}, pages = {1-9}, doi = {10.1080/14767058.2019.1684466}, pmid = {31744351}, issn = {1476-4954}, abstract = {Introduction: The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study, we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time.Materials and methods: Stool samples were collected on infants from a large tertiary care neonatal intensive care unit. After DNA extraction, metagenomics libraries were generated and sequenced. Taxonomic and functional analyses were then performed. Further directed specimen sequencing for fungal species was also performed.Results: A total of 51 stool samples from 25 infants were analyzed: seven infants were on antibiotics during at least one of their collection time points. Antibiotics given at birth altered the microbiome (PERMANOVA R2 = 0.044, p = .002) but later courses did not (R2 = 0.023, p = .114). Longitudinal samples collected while off antibiotics were more similar than those collected during a transition on or off antibiotics (mean Bray-Curtis distance 0.29 vs. 0.63, Wilcoxon p = .06). Functional analysis revealed four microbial pathways that were disrupted by antibiotics given at-birth (p < .1, folate synthesis, glycerolipid metabolism, fatty acid biosynthesis, and glycolysis). No functional changes associated with current antibiotic use were identified. In a limited sample set, we saw little evidence of fungal involvement in the overall infant microbiome.Conclusion: Through this study, we have further characterized the role antibiotics have in the development of the infant microbiome. Antibiotics given at birth were associated with alterations in the microbiome and had significant impact on the functional pathways involved in folate synthesis and multiple metabolic pathways. Later courses of antibiotics led to stochastic dysbiosis and a significant decrease in Escherichia coli. Further characterization of the infant mycobiome is still needed.}, }
@article {pmid31739448, year = {2019}, author = {Mohanraj, U and Wan, X and Spruit, CM and Skurnik, M and Pajunen, MI}, title = {A Toxicity Screening Approach to Identify Bacteriophage-Encoded Anti-Microbial Proteins.}, journal = {Viruses}, volume = {11}, number = {11}, pages = {}, pmid = {31739448}, issn = {1999-4915}, support = {288701//Academy of Finland/ ; }, abstract = {The rapid emergence of antibiotic resistance among many pathogenic bacteria has created a profound need to discover new alternatives to antibiotics. Bacteriophages, the viruses of microbes, express special proteins to overtake the metabolism of the bacterial host they infect, the best known of which are involved in bacterial lysis. However, the functions of majority of bacteriophage encoded gene products are not known, i.e., they represent the hypothetical proteins of unknown function (HPUFs). In the current study we present a phage genomics-based screening approach to identify phage HPUFs with antibacterial activity with a long-term goal to use them as leads to find unknown targets to develop novel antibacterial compounds. The screening assay is based on the inhibition of bacterial growth when a toxic gene is expression-cloned into a plasmid vector. It utilizes an optimized plating assay producing a significant difference in the number of transformants after ligation of the toxic and non-toxic genes into a cloning vector. The screening assay was first tested and optimized using several known toxic and non-toxic genes. Then, it was applied to screen 94 HPUFs of bacteriophage φR1-RT, and identified four HPUFs that were toxic to Escherichia coli. This optimized assay is in principle useful in the search for bactericidal proteins of any phage, and also opens new possibilities to understanding the strategies bacteriophages use to overtake bacterial hosts.}, }
@article {pmid31739446, year = {2019}, author = {Loverdos, K and Bellos, G and Kokolatou, L and Vasileiadis, I and Giamarellos, E and Pecchiari, M and Koulouris, N and Koutsoukou, A and Rovina, N}, title = {Lung Microbiome in Asthma: Current Perspectives.}, journal = {Journal of clinical medicine}, volume = {8}, number = {11}, pages = {}, pmid = {31739446}, issn = {2077-0383}, abstract = {A growing body of evidence implicates the human microbiome as a potentially influential player actively engaged in shaping the pathogenetic processes underlying the endotypes and phenotypes of chronic respiratory diseases, particularly of the airways. In this article, we specifically review current evidence on the characteristics of lung microbiome, and specifically the bacteriome, the modes of interaction between lung microbiota and host immune system, the role of the &quot;lung-gut axis&quot;, and the functional effects thereof on asthma pathogenesis. We also attempt to explore the possibilities of therapeutic manipulation of the microbiome, aiming at the establishment of asthma prevention strategies and the optimization of asthma treatment.}, }
@article {pmid31737164, year = {2019}, author = {Kang, W and Jia, Z and Tang, D and Zhang, Z and Gao, H and He, K and Feng, Q}, title = {Fusobacterium nucleatum Facilitates Apoptosis, ROS Generation, and Inflammatory Cytokine Production by Activating AKT/MAPK and NF-κB Signaling Pathways in Human Gingival Fibroblasts.}, journal = {Oxidative medicine and cellular longevity}, volume = {2019}, number = {}, pages = {1681972}, pmid = {31737164}, issn = {1942-0994}, abstract = {Fusobacterium nucleatum (F. nucleatum) plays key roles in the initiation and progression of periodontitis. However, the pathogenic effect of F. nucleatum on human oral tissues and cells has not been fully evaluated. In this study, we aimed to analyze the pathogenic effects of F. nucleatum on human gingival fibroblasts (GFs) and clarify the potential mechanisms. RNA-sequencing analysis confirmed that F. nucleatum significantly altered the gene expression of GF as the stimulation time increased. Cell counting and EdU-labeling assays indicated that F. nucleatum inhibited GF proliferation and promoted cell apoptosis in a time- and dose-dependent manner. In addition, cell apoptosis, intracellular reactive oxygen species (ROS) generation, and proinflammatory cytokine production were dramatically elevated after F. nucleatum stimulation. Furthermore, we found that the AKT/MAPK and NF-κB signaling pathways were significantly activated by F. nucleatum infection and that a large number of genes related to cellular proliferation, apoptosis, ROS, and inflammatory cytokine production downstream of AKT/MAPK and NF-κB signaling pathways were significantly altered in F. nucleatum-stimulated GFs. These findings suggest that F. nucleatum inhibits GF proliferation and promotes cell apoptosis, ROS generation, and inflammatory cytokine production partly by activating the AKT/MAPK and NF-κB signaling pathways. Our study opens a new window for understanding the pathogenic effects of periodontal pathogens on the host oral system.}, }
@article {pmid31736896, year = {2019}, author = {Bui, TPN and Schols, HA and Jonathan, M and Stams, AJM and de Vos, WM and Plugge, CM}, title = {Mutual Metabolic Interactions in Co-cultures of the Intestinal Anaerostipes rhamnosivorans With an Acetogen, Methanogen, or Pectin-Degrader Affecting Butyrate Production.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2449}, pmid = {31736896}, issn = {1664-302X}, abstract = {The human intestinal tract harbors diverse and complex microbial communities that have a vast metabolic capacity including the breakdown of complex carbohydrates into short chain fatty acids, acetate, propionate, and butyrate. As butyrate is beneficial for gut health there is much attention on butyrogenic bacteria and their role in the colonic anaerobic food chain. However, our understanding how production of butyrate by gut microorganisms is controlled by interactions between different species and environmental nutrient availability is very limited. To address this, we set up experimental in vitro co-culture systems to study the metabolic interactions of Anaerostipes rhamnosivorans, a butyrate producer with each of its partners; Blautia hydrogenotrophica, an acetogen; Methanobrevibacter smithii, a methanogen and Bacteroides thetaiotaomicron, a versatile degrader of plant cell wall pectins; through corresponding specific cross-feeding. In all co-cultures, A. rhamnosivorans was able to benefit from its partner for enhanced butyrate formation compared to monocultures. Interspecies transfer of hydrogen or formate from A. rhamnosivorans to the acetogen B. hydrogenotrophica and in turn of acetate from the acetogen to the butyrogen were essential for butyrate formation. A. rhamnosivorans grown on glucose supported growth of M. smithii via interspecies formate/hydrogen transfer enhancing butyrate formation. In the co-culture with pectin, lactate was released by B. thetaiotaomicron which was concomitantly used by A. rhamnosivorans for the production of butyrate. Our findings indicate enhanced butyrate formation through microbe-microbe interactions between A. rhamnosivorans and an acetogen, a methanogen or a pectin-degrader. Such microbial interactions enhancing butyrate formation may be beneficial for colonic health.}, }
@article {pmid31728100, year = {2019}, author = {Migacz-Gruszka, K and Branicki, W and Obtulowicz, A and Pirowska, M and Gruszka, K and Wojas-Pelc, A}, title = {What's New in the Pathophysiology of Alopecia Areata? The Possible Contribution of Skin and Gut Microbiome in the Pathogenesis of Alopecia - Big Opportunities, Big Challenges, and Novel Perspectives.}, journal = {International journal of trichology}, volume = {11}, number = {5}, pages = {185-188}, pmid = {31728100}, issn = {0974-7753}, abstract = {The term &quot;microbiome&quot; defines the collective genome of all commensal, symbiotic, and pathogenic microbes living in the human body. The composition of microbiota in the gut and skin is influenced by many factors such as the stage of life, nutrition, lifestyle, and gender. In the past few years, several scientific papers have demonstrated an implication of microbiota in many immune-mediated diseases, for example, diabetes, ulcerative colitis, and multiple sclerosis. The alterations in the proportion of gut microbiota have emerged as potential immunomodulators with the capacity to induce physiologic as well as pathologic immune responses against the human body, causing inflammation and destruction of tissues or organs. The microbiota influences the differentiation of adaptive immune cells not only in the gut but also in the skin. Alopecia areata (AA) is a dermatologic disorder which causes hair loss in most cases resistant to treatment. There are some clinical and experimental evidences indicating that AA is the demonstration of autoimmune attack against hair follicles. The factors that may implicate such an autoimmunity in AA still remain unknown. Despite more and more evidences demonstrate that human microbiome plays a key role in human health and diseases, to the best of our knowledge, no study has been conducted to analyze an implication of microbiome in the pathogenesis of AA. Undoubtedly, there is a need to performing a study which might explain the involvement of gut and skin microbiota in the unclear pathogenesis of AA and lead to alternative treatment options for numerous patients suffering from current treatment limitations.}, }
@article {pmid31726030, year = {2019}, author = {Fehlner-Peach, H and Magnabosco, C and Raghavan, V and Scher, JU and Tett, A and Cox, LM and Gottsegen, C and Watters, A and Wiltshire-Gordon, JD and Segata, N and Bonneau, R and Littman, DR}, title = {Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {5}, pages = {680-690.e5}, pmid = {31726030}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; T32 CA009161/CA/NCI NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; /ERC_/European Research Council/International ; UL1 RR029893/RR/NCRR NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; }, mesh = {Diet ; Gastrointestinal Microbiome/*physiology ; Genetic Variation ; Genome, Bacterial/genetics ; Humans ; Intestines/microbiology ; Plants/microbiology ; Polysaccharides/*metabolism ; Prevotella/classification/*isolation &amp; purification/*metabolism ; }, abstract = {Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.}, }
@article {pmid31721508, year = {2019}, author = {Liu, YK and Xu, X and Zhou, XD}, title = {[Potential application of human microbiomes in the diagnosis and treatment of type 2 diabetes mellitus].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {37}, number = {5}, pages = {556-562}, doi = {10.7518/hxkq.2019.05.020}, pmid = {31721508}, issn = {2618-0456}, mesh = {*Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Human microbiome refers to the total microorganism genetic information of human body surface and internal, which is closely related to human health and disease. Oral and gut microbiomes are the most diverse microbial communities, which can interact and play a role in the development of the disease, and can reflect the health and disease state in real time. Type 2 diabetes mellitus is a metabolic disorder caused by both genetic and environmental factors. Recent research has shown a link between microbes and diabetes. This article reviewed the latest research on the changes of oral and gut microbiomes in type 2 diabetes mellitus patients, which expects to provide a reference for exploring the development of the disease model for prediction, diagnosis and prognosis of type 2 diabetes mellitus based on human microbiome characteristics.}, }
@article {pmid31719221, year = {2019}, author = {Chaudhari, D and Dhotre, D and Agarwal, D and Gondhali, A and Nagarkar, A and Lad, V and Patil, U and Juvekar, S and Sinkar, V and Shouche, Y}, title = {Understanding the association between the human gut, oral and skin microbiome and the Ayurvedic concept of prakriti.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719221}, issn = {0973-7138}, abstract = {Ayurveda is one of the ancient systems of medicine which is widely practised as a personalized scientific approach towards the general wellness. Ayurvedic prakriti is broadly defined as the phenotypes which are determined on the basis of physical, psychological and physiological traits irrespective of their social, ethnic, dietary and geographical stature. Prakriti is the constitution of a person, which comprises vata, pitta, and kapha and is a key determinant of how one individual is different from the other. Human microbiome is considered the 'latest discovered' human organ and microbiome research reiterates the fundamental principles of Ayurveda for creating a healthy gut environment by maintaining the individual-specific microbiome. Hence, it is important to understand the association of human microbiome with the Ayurvedic prakriti of an individual. Here, we provide a comprehensive analysis of human microbiome from the gut, oral and skin samples of healthy individuals (n=18) by 16S rRNA gene-based metagenomics using standard QIIME pipeline. In the three different prakriti samples differential abundance of Bacteroides, Desulfovibrio, Parabacteroides, Slackia, and Succinivibrio was observed in the gut microbiome. Analysis also revealed prakriti-specific presence of Mogibacterium, Propionibacterium, Pyramidobacter, Rhodococcus in the kapha prakriti individuals Planomicrobium, Hyphomicrobium, Novosphingobium in the pitta prakriti individuals and Carnobacterium, Robiginitalea, Cetobacterium, Psychrobacter in the vata prakriti individuals. Similarly, the oral and skin microbiome also revealed presence of prakriti-specific differential abundance of diverse bacterial genera. Prakriti-specific presence of bacterial taxa was recorded and only 42% microbiome in the oral samples and 52% microbiome in the skin samples were shared. Bacteria known for preventing gut inflammation by digesting the resistant starch were abundant in the pitta prakriti individuals, who are more prone to develop gut-inflammation-related disorders. In summary, human gut, oral and skin microbiome showed presence or high abundance of few bacterial taxa across three prakriti types, suggesting their specific physiological importance.}, }
@article {pmid31719220, year = {2019}, author = {Holmes, S}, title = {Successful strategies for human microbiome data generation, storage and analyses.}, journal = {Journal of biosciences}, volume = {44}, number = {5}, pages = {}, pmid = {31719220}, issn = {0973-7138}, abstract = {Current interest in the potential for clinical use of new tools for improving human health are now focused on techniques for the study of the human microbiome and its interaction with environmental and clinical covariates. This review outlines the use of statistical strategies that have been developed in past studies and can inform successful design and analyses of controlled perturbation experiments performed in the human microbiome. We carefully outline what the data are, their imperfections and how we need to transform, decontaminate and denoise them. We show how to identify the important unknown parameters and how to can leverage variability we see to produce efficient models for prediction and uncertainty quantification. We encourage a reproducible strategy that builds on best practice principles that can be adapted for effective experimental design and reproducible workflows. Nonparametric, data-driven denoising strategies already provide the best strain identification and decontamination methods. Data driven models can be combined with uncertainty quantification to provide reproducible aids to decision making in the clinical context, as long as careful, separate, registered confirmatory testing are undertaken. Here we provide guidelines for effective longitudinal studies and their analyses. Lessons learned along the way are that visualizations at every step can pinpoint problems and outliers, normalization and filtering improve power in downstream testing. We recommend collecting and binding the metadata and covariates to sample descriptors and recording complete computer scripts into an R markdown supplement that can reduce opportunities for human error and enable collaborators and readers to replicate all the steps of the study. Finally, we note that optimizing the bioinformatic and statistical workflow involves adopting a wait-and-see approach that is particularly effective in cases where the features such as 'mass spectrometry peaks' and metagenomic tables can only be partially annotated.}, }
@article {pmid31717688, year = {2019}, author = {Wojciuk, B and Salabura, A and Grygorcewicz, B and Kędzierska, K and Ciechanowski, K and Dołęgowska, B}, title = {Urobiome: In Sickness and in Health.}, journal = {Microorganisms}, volume = {7}, number = {11}, pages = {}, pmid = {31717688}, issn = {2076-2607}, abstract = {The human microbiome has been proven to contribute to the human condition, both in health and in disease. The metagenomic approach based on next-generation sequencing has challenged the dogma of urine sterility. The human urobiome consists of bacteria and eukaryotic viruses as well as bacteriophages, which potentially represent the key factor. There have been several significant findings with respect to the urobiome in the context of urological disorders. Still, the research on the urobiome in chronic kidney disease and kidney transplantation remains underrepresented, as does research on the role of the virome in the urinary microbiota. In this review, we present recent findings on the urobiome with a particular emphasis on chronic kidney disease and post-kidney transplantation status. Challenges and opportunities arising from the research on the human urobiome will also be discussed.}, }
@article {pmid31713170, year = {2019}, author = {Astudillo-de la Vega, H and Alonso-Luna, O and Ali-Pérez, J and López-Camarillo, C and Ruiz-Garcia, E}, title = {Oncobiome at the Forefront of a Novel Molecular Mechanism to Understand the Microbiome and Cancer.}, journal = {Advances in experimental medicine and biology}, volume = {1168}, number = {}, pages = {147-156}, doi = {10.1007/978-3-030-24100-1_10}, pmid = {31713170}, issn = {0065-2598}, mesh = {Bacteria/genetics ; Dysbiosis ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota/genetics/physiology ; *Neoplasms/microbiology ; }, abstract = {The microbiome comprises all the genetic material within a microbiota, that represents tenfold higher than that of our cells. The microbiota it includes a wide variety of microorganisms such as bacteria, viruses, protozoans, fungi, and archaea, and this ecosystem is personalized in any body space of every individual. Balanced microbial communities can positively contribute to training the immune system and maintaining immune homeostasis. Dysbiosis is a change in the normal microbiome composition that can initiate chronic inflammation, epithelial barrier breaches, and overgrowth of harmful bacteria. The next-generation sequencing methods have revolutionized the study of the microbiome. Bioinformatic tools to manage large volumes of new information, it became possible to assess species diversity and measure dynamic fluctuations in microbial communities. The burden of infections that are associated to human cancer is increasing but is underappreciated by the cancer research community. The rich content in microbes of normal and tumoral tissue reflect could be defining diverse physiological or pathological states. Genomic research has emerged a new focus on the interplay between the human microbiome and carcinogenesis and has been termed the 'oncobiome'. The interactions among the microbiota in all epithelium, induce changes in the host immune interactions and can be a cause of cancer. Microbes have been shown to have systemic effects on the host that influence the efficacy of anticancer drugs. Metagenomics allows to investigate the composition of microbial community. Metatranscriptome analysis applies RNA sequencing to microbial samples to determine which species are present. Cancer can be caused by changes in the microbiome. The roles of individual microbial species in cancer progression have been identified long ago for various tissue types. The identification of microbiomes of drug resistance in the treatment of cancer patients has been the subject of numerous microbiome studies. The complexity of cancer genetic alterations becomes irrelevant in certain cancers to explain the origin, the cause or the oncogenic maintenance by the oncogene addiction theory.}, }
@article {pmid31708974, year = {2019}, author = {Bianchi, M and Alisi, A and Fabrizi, M and Vallone, C and Ravà, L and Giannico, R and Vernocchi, P and Signore, F and Manco, M}, title = {Maternal Intake of n-3 Polyunsaturated Fatty Acids During Pregnancy Is Associated With Differential Methylation Profiles in Cord Blood White Cells.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1050}, pmid = {31708974}, issn = {1664-8021}, abstract = {A healthy diet during pregnancy is pivotal for the offspring health at birth and later in life. N-3 polyunsaturated fatty acids (n-3 PUFAs) are not endogenously produced in humans and are exclusively derived from the diet. They are pivotal for the fetus growth and neuronal development and seem beneficial in reducing the risk of cardiometabolic diseases and preventing later allergic disorders in the offspring by modulating the inflammatory immune response. In the present study, we investigated the association between maternal intakes of n-3PUFAs, profiled on maternal erythrocyte membranes at pregnancy term, and offspring DNA methylation on cord blood mononuclear cells in a sample of 118 mother-newborn pairs randomly drawn from the &quot;Feeding fetus' low-grade inflammation and insulin-resistance&quot; study cohort. N-3 PUFA content on erythrocyte membranes is a validated biomarker to measure objectively medium term intake of n-3 PUFAs. Based on distribution of n-3 PUFA in the whole cohort of mothers, we identified mothers with low (n-3 PUFA concentration <25th percentile), medium (n-3 PUFAs between 25th and 75th percentiles), and high n-3 PUFA content (>75th percentile). The HumanMethylation450 BeadChip (Illumina) was used for the epigenome-wide association study using the Infinium Methylation Assay. The overall DNA methylation level was not different between the three groups while there was significant difference in methylation levels at certain sites. Indeed, 8,503 sites had significantly different methylations between low and high n-3 PUFA groups, 12,716 between low and medium n-3 PUFA groups, and 18,148 between high and medium n-3 PUFA groups. We found differentially methylated genes that belong prevalently to pathways of signal transduction, metabolism, downstream signaling of G protein-coupled receptors, and gene expression. Within these pathways, we identified four differentially methylated genes, namely, MSTN, IFNA13, ATP8B3, and GABBR2, that are involved in the onset of insulin resistance and adiposity, innate immune response, phospholipid translocation across cell membranes, and mechanisms of addiction to high fat diet, alcohol, and sweet taste. In conclusion, findings of this preliminary investigation suggest that maternal intake of n-3 PUFAs during pregnancy has potential to influence the offspring DNA methylation. Validation of results in a larger cohort and investigation of biological significance and impact on the phenotype are warranted.}, }
@article {pmid31707219, year = {2019}, author = {Stubbendieck, RM and Li, H and Currie, CR}, title = {Convergent evolution of signal-structure interfaces for maintaining symbioses.}, journal = {Current opinion in microbiology}, volume = {50}, number = {}, pages = {71-78}, pmid = {31707219}, issn = {1879-0364}, support = {T15 LM007359/LM/NLM NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; U19 TW009872/TW/FIC NIH HHS/United States ; }, abstract = {Symbiotic microbes are essential to the ecological success and evolutionary diversification of multicellular organisms. The establishment and stability of bipartite symbioses are shaped by mechanisms ensuring partner fidelity between host and symbiont. In this minireview, we demonstrate how the interface of chemical signals and host structures influences fidelity between legume root nodules and rhizobia, Hawaiian bobtail squid light organs and Allivibrio fischeri, and fungus-growing ant crypts and Pseudonocardia. Subsequently, we illustrate the morphological diversity and widespread phylogenetic distribution of specialized structures used by hosts to house microbial symbionts, indicating the importance of signal-structure interfaces across the history of multicellular life. These observations, and the insights garnered from well-studied bipartite associations, demonstrate the need to concentrate on the signal-structure interface in complex and multipartite systems, including the human microbiome.}, }
@article {pmid31699101, year = {2019}, author = {Kumpitsch, C and Koskinen, K and Schöpf, V and Moissl-Eichinger, C}, title = {The microbiome of the upper respiratory tract in health and disease.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {87}, pmid = {31699101}, issn = {1741-7007}, abstract = {The human upper respiratory tract (URT) offers a variety of niches for microbial colonization. Local microbial communities are shaped by the different characteristics of the specific location within the URT, but also by the interaction with both external and intrinsic factors, such as ageing, diseases, immune responses, olfactory function, and lifestyle habits such as smoking. We summarize here the current knowledge about the URT microbiome in health and disease, discuss methodological issues, and consider the potential of the nasal microbiome to be used for medical diagnostics and as a target for therapy.}, }
@article {pmid31690595, year = {2019}, author = {Maixner, F}, title = {Molecular Reconstruction of the Diet in Human Stool Samples.}, journal = {mSystems}, volume = {4}, number = {6}, pages = {}, pmid = {31690595}, issn = {2379-5077}, abstract = {Understanding dietary effects on the gut microbial composition is one of the key questions in human microbiome research. It is highly important to have reliable dietary data on the stool samples to unambiguously link the microbiome composition to food intake. Often, however, self-reported diet surveys have low accuracy and can be misleading. Thereby, additional molecular biology-based methods could help to revise the diet composition. The article by Reese et al. [A. T. Reese, T. R. Kartzinel, B. L. Petrone, P. J. Turnbaugh, et al., mSystems 4(5):e00458-19, 2019, https://doi.org/10.1128/mSystems.00458-19] in a recent issue of mSystems describes a DNA metabarcoding strategy targeting chloroplast DNA markers in stool samples from 11 human subjects consuming both controlled and freely selected diets. The aim of this study was to evaluate the efficiency of this molecular method in detecting plant remains in the sample compared to the written dietary records. This study displays an important first step in implementing molecular dietary reconstructions in stool microbiome studies which will finally help to increase the accuracy of dietary metadata.}, }
@article {pmid31685450, year = {2019}, author = {Agorastos, A and Bozikas, VP}, title = {Gut microbiome and adaptive immunity in schizophrenia.}, journal = {Psychiatrike = Psychiatriki}, volume = {30}, number = {3}, pages = {189-192}, doi = {10.22365/jpsych.2019.303.189}, pmid = {31685450}, issn = {1105-2333}, abstract = {Over the past few years, immunopathogenesis has emerged as one of the most compelling aetiopathological models of schizophrenia (SCZ), suggesting a chronic, immune-based, low-grade inflammatory background of this devastating disorder.1,2 Mounting evidence points towards a prominent role of the adaptive immune system in SCZ, suggesting alterations in defense mechanisms, such as altered T-cell function and a shift towards B-cell immunity.3 Immune cells have the ability to infiltrate the brain and mediate a neuroimmune cross-talk through activation of microglia, production of proinflammatory cytokines and reactive oxygen species, leading to neuroinflammation, as mediator of neuroprogressive and neurodegenerative changes in SCZ.4 Antipsychotic drugs, commonly used to treat SCZ, are also known to affect the adaptive immune system, interfering with the differentiation and function of immune cells, towards their normalization in response to treatment. Adaptive immunity is principally founded on T-cell and B-cell populations, but also includes the host microbiome. The gastrointestinal microbiota is a complex ecosystem with a great organism diversity and refined genomic structure that resides in the intestinal tract and has a central position in human health and disease.5 Neuroimmune dysregulation, relying of the highly sensitive and fine-tuned equilibrium between microbiome and adaptive immunity, can tip the scales towards neuroinflammation and disruption of higher-order brain networks.4,6,7 During the last decade, the human microbiome and the microbiota-gut-brain (MGB)-axis have become a novel epicentre in mental health research as a potentially vital new determinant in the field of neuroimmunoregulation, brain development, emotions, cognition and behaviour.7 The MGB-axis represents a bidirectional, key communication pathway between the immune system and the brain, thus partly also mediating the regulation of cognitive and emotional processing. An imbalanced human microbiome might greatly influence proper neuroimmune reactions and neurodevelopment with long-lasting effects and could thus play a pivotal role in the susceptibility and aetiology of psychiatric illness. Recent research offers first evidence that patients with SCZ show marked disturbances of gut bacterial taxa composition with a decreased microbiome diversity index, party associated with specific SCZ phenotype, symptom severity and treatment response.8,9 As the elegant education of the adaptive immune compartment depends on the colonization niche, antigen type and metabolic property of different gut microbes, T-cell differentiation as well as a continuous diversification of B-cell repertoire is expressed through microbiome-related, antigen-specific receptors that define a unique clonotype.10 However, there is only sparse evidence on the precise role of the microbiome on the programming of T- and B-cells in the underlying neurobiological pathways of SCZ and even less findings on the association of molecular T- and B-cell receptor repertoire signature and microbiome clonal landscape with specific phenotypical features of the disease.11 The latest conceptual advances in immunology urge an integrative re-evaluation of previous immunological findings in SCZ through modern approaches. High-throughput, next-generation sequencing (NGS) represents a powerful singlecell transcriptomic tool to profile the whole clonal landscape of T and B cells and human microbiome. NGS thus offers a unique opportunity for in-depth characterization of cellular and molecular signatures of adaptive immune receptor repertoires and microbiome taxonomy in SCZ and investigation of their intersection as a relevant pathway of disease progression and phenotype differentiation. SCZ patients are likely to show a diverging host-microbiome immune homeostasis with disease-specific clonotypes of adaptive immune receptor repertoires associated with altered microbiome taxonomy and molecular signature differences, which, in turn, may be related to distinct symptomatic phenotypes and neurocognitive patterns. Such sophisticated immuno-bioinformatic analyses may transform our understanding of SCZ by identification of novel neuroimmune pathways, offering us clinically accessible symptomatic and diagnostic biomarkers important for personalized medicine implications.12 An increased understanding and better characterization of immuno-phenotypes in SCZ will better guide the development of novel immune-based treatments in this severe disease and pave the way for possible prevention options through implementation of antibody engineering, vaccine design, and cellular immunotherapy.}, }
@article {pmid31683170, year = {2019}, author = {Orlandi, E and Iacovelli, NA and Tombolini, V and Rancati, T and Polimeni, A and De Cecco, L and Valdagni, R and De Felice, F}, title = {Potential role of microbiome in oncogenesis, outcome prediction and therapeutic targeting for head and neck cancer.}, journal = {Oral oncology}, volume = {99}, number = {}, pages = {104453}, doi = {10.1016/j.oraloncology.2019.104453}, pmid = {31683170}, issn = {1879-0593}, abstract = {In the last decade, human microbiome research is rapidly growing involving several fields of clinical medicine and population health. Although the microbiome seems to be linked to all sorts of diseases, cancer has the biggest potential to be investigated. Following the publication of the National Institute of Health - Human Microbiome Project (NIH-HMP), the link between Head and Neck Cancer (HNC) and microbiome seems to be a fast-moving field in research area. However, robust evidence-based literature is still quite scarce. Nevertheless the relationship between oral microbiome and HNC could have important consequences for prevention and early detection of this type of tumors. The aims of the present review are: (i) to discuss current pre-clinical evidence of a role of oral microbiome in HNC; (ii) to report recent developments in understanding the human microbiome's relationship with HNC oncogenesis; (iii) to explore the issue of treatment response and treatment toxicity; (iv) to describe the role of microbiota as potentially modifiable factor suitable for targeting by therapeutics. Further studies are needed to better establish the causal relationship between oral microbiome and HNC oncogenesis. Future trials should continue to explore oral microbiome in order to build the scientific and clinical rationale of HNC preventative and ameliorate treatment outcome.}, }
@article {pmid31683111, year = {2019}, author = {Porras, AM and Brito, IL}, title = {The internationalization of human microbiome research.}, journal = {Current opinion in microbiology}, volume = {50}, number = {}, pages = {50-55}, pmid = {31683111}, issn = {1879-0364}, abstract = {The human microbiome has now been linked with myriad diseases, yet most of this research has been conducted on American and European populations that make up only 1/6th of the world's population. With growing recognition that human microbiomes differ tremendously across global populations, it is especially important to understand how these compositional differences impact health outcomes. Recent advances in infectious disease and malnutrition research have demonstrated the potential for microbiome-based strategies to address the biggest challenges in global health. This review highlights major advances toward understanding microbiome diversity across the world and its contributions to disease, and outlines key questions, challenges, and opportunities to broaden the scope of and promote inclusivity within microbiome research.}, }
@article {pmid31681437, year = {2019}, author = {Shah, N and Meisel, JS and Pop, M}, title = {Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {1022}, pmid = {31681437}, issn = {1664-8021}, abstract = {The advent of high throughput sequencing has enabled in-depth characterization of human and environmental microbiomes. Determining the taxonomic origin of microbial sequences is one of the first, and frequently only, analysis performed on microbiome samples. Substantial research has focused on the development of methods for taxonomic annotation, often making trade-offs in computational efficiency and classification accuracy. A side-effect of these efforts has been a reexamination of the bacterial taxonomy itself. Taxonomies developed prior to the genomic revolution captured complex relationships between organisms that went beyond uniform taxonomic levels such as species, genus, and family. Driven in part by the need to simplify computational workflows, the bacterial taxonomies used most commonly today have been regularized to fit within a standard seven taxonomic levels. Consequently, modern analyses of microbial communities are relatively coarse-grained. Few methods make classifications below the genus level, impacting our ability to capture biologically relevant signals. Here, we present ATLAS, a novel strategy for taxonomic annotation that uses significant outliers within database search results to group sequences in the database into partitions. These partitions capture the extent of taxonomic ambiguity within the classification of a sample. The ATLAS pipeline can be found on GitHub [https://github.com/shahnidhi/outlier_in_BLAST_hits]. We demonstrate that ATLAS provides similar annotations to phylogenetic placement methods, but with higher computational efficiency. When applied to human microbiome data, ATLAS is able to identify previously characterized taxonomic groupings, such as those in the class Clostridia and the genus Bacillus. Furthermore, the majority of partitions identified by ATLAS are at the subgenus level, replacing higher-level annotations with specific groups of species. These more precise partitions improve our detection power in determining differential abundance in microbiome association studies.}, }
@article {pmid31674689, year = {2020}, author = {Huck, O and Mulhall, H and Rubin, G and Kizelnik, Z and Iyer, R and Perpich, JD and Haque, N and Cani, PD and de Vos, WM and Amar, S}, title = {Akkermansia muciniphila reduces Porphyromonas gingivalis-induced inflammation and periodontal bone destruction.}, journal = {Journal of clinical periodontology}, volume = {47}, number = {2}, pages = {202-212}, doi = {10.1111/jcpe.13214}, pmid = {31674689}, issn = {1600-051X}, support = {RO1HL076801/HL/NHLBI NIH HHS/United States ; RO1DE014079/DE/NIDCR NIH HHS/United States ; RO1HL076801/HL/NHLBI NIH HHS/United States ; RO1DE014079/DE/NIDCR NIH HHS/United States ; }, abstract = {AIM: Akkermansia muciniphila is a beneficial gut commensal, whose anti-inflammatory properties have recently been demonstrated. This study aimed to evaluate the effect of A. muciniphila on Porphyromonas gingivalis elicited inflammation.<br><br>MATERIAL AND METHODS: In lean and obese mice, A. muciniphila was administered in P. gingivalis-induced calvarial abscess and in experimental periodontitis model (EIP). Bone destruction and inflammation were evaluated by histomorphometric analysis. In vitro, A. muciniphila was co-cultured with P. gingivalis, growth and virulence factor expression was evaluated. Bone marrow macrophages (BMMϕ) and gingival epithelial cells (TIGK) were exposed to both bacterial strains, and the expression of inflammatory mediators, as well as tight junction markers, was analysed.<br><br>RESULTS: In a model of calvarial infection, A. muciniphila decreased inflammatory cell infiltration and bone destruction. In EIP, treatment with A. muciniphila resulted in a decreased alveolar bone loss. In vitro, the addition of A. muciniphila to P. gingivalis-infected BMMϕ increased anti-inflammatory IL-10 and decreased IL-12. Additionally, A. muciniphila exposure increases the expression of junctional integrity markers such as integrin-β1, E-cadherin and ZO-1 in TIGK cells. A. muciniphila co-culture with P. gingivalis reduced gingipains mRNA expression.<br><br>DISCUSSION: This study demonstrated the protective effects of A. muciniphila administration and may open consideration to its use as an adjunctive therapeutic agent to periodontal treatment.}, }
@article {pmid31666099, year = {2019}, author = {Zhu, C and Miller, M and Lusskin, N and Mahlich, Y and Wang, Y and Zeng, Z and Bromberg, Y}, title = {Fingerprinting cities: differentiating subway microbiome functionality.}, journal = {Biology direct}, volume = {14}, number = {1}, pages = {19}, pmid = {31666099}, issn = {1745-6150}, support = {U01 GM115486/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project participants collected samples from subway surfaces in different cities and performed metagenomic sequencing. Previous studies focused on taxonomic composition of these microbiomes and no explicit functional analysis had been done till now.<br><br>RESULTS: As a part of the 2018 CAMDA challenge, we functionally profiled the available ~ 400 subway metagenomes and built predictor for city origin. In cross-validation, our model reached 81% accuracy when only the top-ranked city assignment was considered and 95% accuracy if the second city was taken into account as well. Notably, this performance was only achievable if the similarity of distribution of cities in the training and testing sets was similar. To assure that our methods are applicable without such biased assumptions we balanced our training data to account for all represented cities equally well. After balancing, the performance of our method was slightly lower (76/94%, respectively, for one or two top ranked cities), but still consistently high. Here we attained an added benefit of independence of training set city representation. In testing, our unbalanced model thus reached (an over-estimated) performance of 90/97%, while our balanced model was at a more reliable 63/90% accuracy. While, by definition of our model, we were not able to predict the microbiome origins previously unseen, our balanced model correctly judged them to be NOT-from-training-cities over 80% of the time. Our function-based outlook on microbiomes also allowed us to note similarities between both regionally close and far-away cities. Curiously, we identified the depletion in mycobacterial functions as a signature of cities in New Zealand, while photosynthesis related functions fingerprinted New York, Porto and Tokyo.<br><br>CONCLUSIONS: We demonstrated the power of our high-speed function annotation method, mi-faser, by analysing ~ 400 shotgun metagenomes in 2 days, with the results recapitulating functional signals of different city subway microbiomes. We also showed the importance of balanced data in avoiding over-estimated performance. Our results revealed similarities between both geographically close (Ofa and Ilorin) and distant (Boston and Porto, Lisbon and New York) city subway microbiomes. The photosynthesis related functional signatures of NYC were previously unseen in taxonomy studies, highlighting the strength of functional analysis.}, }
@article {pmid31664160, year = {2020}, author = {Daisley, BA and Pitek, AP and Chmiel, JA and Al, KF and Chernyshova, AM and Faragalla, KM and Burton, JP and Thompson, GJ and Reid, G}, title = {Novel probiotic approach to counter Paenibacillus larvae infection in honey bees.}, journal = {The ISME journal}, volume = {14}, number = {2}, pages = {476-491}, pmid = {31664160}, issn = {1751-7370}, abstract = {American foulbrood (AFB) is a highly virulent disease afflicting honey bees (Apis mellifera). The causative organism, Paenibacillus larvae, attacks honey bee brood and renders entire hives dysfunctional during active disease states, but more commonly resides in hives asymptomatically as inactive spores that elude even vigilant beekeepers. The mechanism of this pathogenic transition is not fully understood, and no cure exists for AFB. Here, we evaluated how hive supplementation with probiotic lactobacilli (delivered through a nutrient patty; BioPatty) affected colony resistance towards a naturally occurring AFB outbreak. Results demonstrated a significantly lower pathogen load and proteolytic activity of honey bee larvae from BioPatty-treated hives. Interestingly, a distinctive shift in the microbiota composition of adult nurse bees occurred irrespective of treatment group during the monitoring period, but only vehicle-supplemented nurse bees exhibited higher P. larvae loads. In vitro experiments utilizing laboratory-reared honey bee larvae showed Lactobacillus plantarum Lp39, Lactobacillus rhamnosus GR-1, and Lactobacillus kunkeei BR-1 (contained in the BioPatty) could reduce pathogen load, upregulate expression of key immune genes, and improve survival during P. larvae infection. These findings suggest the usage of a lactobacilli-containing hive supplement, which is practical and affordable for beekeepers, may be effective for reducing enzootic pathogen-related hive losses.}, }
@article {pmid31662819, year = {2019}, author = {Royston, KJ and Adedokun, B and Olopade, OI}, title = {Race, the microbiome and colorectal cancer.}, journal = {World journal of gastrointestinal oncology}, volume = {11}, number = {10}, pages = {773-787}, pmid = {31662819}, issn = {1948-5204}, abstract = {In the past decade, more cancer researchers have begun to understand the significance of cancer prevention, which has prompted a shift in the increasing body of scientific literature. An area of fascination and great potential is the human microbiome. Recent studies suggest that the gut microbiota has significant roles in an individual's ability to avoid cancer, with considerable focus on the gut microbiome and colorectal cancer. That in mind, racial disparities with regard to colorectal cancer treatment and prevention are generally understudied despite higher incidence and mortality rates among Non-Hispanic Blacks compared to other racial and ethnic groups in the United States. A comprehension of ethnic differences with relation to colorectal cancer, dietary habits and the microbiome is a meritorious area of investigation. This review highlights literature that identifies and bridges the gap in understanding the role of the human microbiome in racial disparities across colorectal cancer. Herein, we explore the differences in the gut microbiota, common short chain fatty acids produced in abundance by microbes, and their association with racial differences in cancer acquisition.}, }
@article {pmid31654515, year = {2019}, author = {Musso, P and Chiappini, E and Bernardini, R}, title = {Human microbiome and allergic diseases in children: pathogenetic role and therapeutic options.}, journal = {Current pediatric reviews}, volume = {}, number = {}, pages = {}, doi = {10.2174/1573396315666191025110849}, pmid = {31654515}, issn = {1875-6336}, abstract = {The recent and extensive study of the microbiome has provided an enormous amount of data concerning the type and possible functions of microorganisms present in the gut, airways, genital tract, and skin. These data showed interpersonal differences in the composition of the microbiome and these differences suggest a link between the microbiome, the immune modulation, and the pathogenesis of allergic diseases. This research is particularly relevant in paediatrics, since allergic diseases are constantly increasing and there is evidence in the paediatric age that shows that the composition of the microbiome in the foetal and neonatal period plays a key role in the development of the immune system: vaginal delivery, breastfeeding, childhood spent in rural environments and/or in contact with animals result in a greater biodiversity of the microbiome with the presence of protective species that reduce the activation of Th2 lymphocytes, involved in allergic reactions. Further studies are necessary to better understand the microbiota role in the pathogenesis of atopy in order to understand if specific probiotics and prebiotics, administered orally or topically, can affect the microbiota composition and modulate immune system functions, producing a therapeutic effect in the treatment of allergic diseases. This narrative review analysed the available literature regarding the correlation between the microbiome and the development of allergic diseases and with special focus on paediatric studies. The skin, gut or lung dysbiosis can be a cofactor in the pathogenesis of allergies and the remodulation of the microbiome becomes an important therapeutic challenge.}, }
@article {pmid31650413, year = {2019}, author = {Klimko, AI and Cherdyntseva, TA and Brioukhanov, AL and Netrusov, AI}, title = {In Vitro Evaluation of Probiotic Potential of Selected Lactic Acid Bacteria Strains.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, doi = {10.1007/s12602-019-09599-6}, pmid = {31650413}, issn = {1867-1314}, abstract = {Research of human microbiome demonstrates that in order to develop next generation of probiotic agents, it is necessary to choose bacterial strains featured by special properties, such as the ability of the cells to attach to intestinal walls, resistance to bile and acids, bacteriocin synthesis, antioxidative and antipathogenic activity, and survivability in intestines. Thirty-three strains of lactic acid bacteria of Lactobacillus and Lactococcus genera from the Lomonosov Moscow State University Collection of Microorganisms (CM MSU) have been tested for important probiotic properties which assist these bacteria to settle effectively in intestines: cell adhesion, ability to form biofilms, agglutination with lectin (concanavalin A), and antimicrobial activity. The results of experiments clearly demonstrate that all these properties can be classified as strain characteristics and differ even within the same species. Besides the cultures of Lactobacillus with good agglutination ability with concanavalin A (Lact. caucasicus CM MSU 155, Lact. brevis CM MSU 521), we also discovered strains with high adhesion properties (Lact. acidophilus CM MSU 146-89% affinity for hexadecane; Lact. paracasei CM MSU 527-85%; Lact. plantarum CM MSU 508-78%; Lact. caucasicus CM MSU 155-70%; and Lact. delbrueckii CM MSU 571-57%), biofilm formation ability with a hydrophobic carrier (Lact. plantarum CM MSU 588-OD590 of crystal violet extracts = 1.336; Lact. brevis CM MSU 521-OD590 = 1.207; and Lact. brevis CM MSU 535-OD590 = 1.151), and with high antimicrobial activity specially to Staphylococcus aureus. Lact. brevis CM MSU 521 possesses the best property combination, which makes it potentially applicable as a very good lactic acid probiotic strain.}, }
@article {pmid31649646, year = {2019}, author = {Engevik, MA and Morra, CN and Röth, D and Engevik, K and Spinler, JK and Devaraj, S and Crawford, SE and Estes, MK and Kalkum, M and Versalovic, J}, title = {Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2305}, pmid = {31649646}, issn = {1664-302X}, abstract = {Microbial metabolites, including B complex vitamins contribute to diverse aspects of human health. Folate, or vitamin B9, refers to a broad category of biomolecules that include pterin, para-aminobenzoic acid (pABA), and glutamate subunits. Folates are required for DNA synthesis and epigenetic regulation. In addition to dietary nutrients, the gut microbiota has been recognized as a source of B complex vitamins, including folate. This study evaluated the predicted folate synthesis capabilities in the genomes of human commensal microbes identified in the Human Microbiome Project and folate production by representative strains of six human intestinal bacterial phyla. Bacterial folate synthesis genes were ubiquitous across 512 gastrointestinal reference genomes with 13% of the genomes containing all genes required for complete de novo folate synthesis. An additional 39% of the genomes had the genetic capacity to synthesize folates in the presence of pABA, an upstream intermediate that can be obtained through diet or from other intestinal microbes. Bacterial folate synthesis was assessed during exponential and stationary phase growth through the evaluation of expression of select folate synthesis genes, quantification of total folate production, and analysis of folate polyglutamylation. Increased expression of key folate synthesis genes was apparent in exponential phase, and increased folate polyglutamylation occurred during late stationary phase. Of the folate producers, we focused on the commensal Lactobacillus reuteri to examine host-microbe interactions in relation to folate and examined folate receptors in the physiologically relevant human enteroid model. RNAseq data revealed segment-specific folate receptor distribution. Treatment of human colonoid monolayers with conditioned media (CM) from wild-type L. reuteri did not influence the expression of key folate transporters proton-coupled folate transporter (PCFT) or reduced folate carrier (RFC). However, CM from L. reuteri containing a site-specific inactivation of the folC gene, which prevents the bacteria from synthesizing a polyglutamate tail on folate, significantly upregulated RFC expression. No effects were observed using L. reuteri with a site inactivation of folC2, which results in no folate production. This work sheds light on the contributions of microbial folate to overall folate status and mammalian host metabolism.}, }
@article {pmid31649168, year = {2019}, author = {Sonnenburg, JL and Sonnenburg, ED}, title = {Vulnerability of the industrialized microbiota.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6464}, pages = {}, doi = {10.1126/science.aaw9255}, pmid = {31649168}, issn = {1095-9203}, support = {R01 DK085025/DK/NIDDK NIH HHS/United States ; }, abstract = {The human body is an ecosystem that is home to a complex array of microbes known as the microbiome or microbiota. This ecosystem plays an important role in human health, but as a result of recent lifestyle changes occurring around the planet, whole populations are seeing a major shift in their gut microbiota. Measures meant to kill or limit exposure to pathogenic microbes, such as antibiotics and sanitation, combined with other factors such as processed food, have had unintended consequences for the human microbial ecosystem, including changes that may be difficult to reverse. Microbiota alteration and the accompanying loss of certain functional attributes might result in the microbial communities of people living in industrialized societies being suboptimal for human health. As macroecologists, conservationists, and climate scientists race to document, understand, predict, and delay global changes in our wider environment, microbiota scientists may benefit by using analogous approaches to study and protect our intimate microbial ecosystems.}, }
@article {pmid31647664, year = {2019}, author = {Hellweger, FL and Vick, C and Rückbeil, F and Bucci, V}, title = {Fresh Ideas Bloom in Gut Healthcare to Cross-Fertilize Lake Management.}, journal = {Environmental science &amp; technology}, volume = {53}, number = {24}, pages = {14099-14112}, doi = {10.1021/acs.est.9b04218}, pmid = {31647664}, issn = {1520-5851}, abstract = {Harmful bacteria may be the most significant threat to human gut and lake ecosystem health, and they are often managed using similar tools, like poisoning with antibiotics or algicides. Out-of-the-box thinking in human microbiome engineering is leading to novel methods, like engineering bacteria to kill pathogens, &quot;persuade&quot; them not to produce toxins, or &quot;mop up&quot; their toxins. The bacterial agent can be given a competitive edge via an exclusive nutrient, and they can be engineered to commit suicide once their work is done. Viruses can kill pathogens with specific DNA sequences or knock out their antibiotic resistance genes using CRISPR technology. Some of these ideas may work for lakes. We critically review novel methods for managing harmful bacteria in the gut from the perspective of managing toxic cyanobacteria in lakes, and discuss practical aspects such as modifying bacteria using genetic engineering or directed evolution, mass culturing and controlling the agents. A key knowledge gap is in the ecology of strains, like toxigenic vs nontoxigenic Microcystis, including allelopathic and Black Queen interactions. Some of the &quot;gut methods&quot; may have future potential for lakes, but there presently is no substitute for established management approaches, including reducing N and P nutrient inputs, and mitigating climate change.}, }
@article {pmid31639026, year = {2019}, author = {Greathouse, KL and Sinha, R and Vogtmann, E}, title = {DNA extraction for human microbiome studies: the issue of standardization.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {212}, pmid = {31639026}, issn = {1474-760X}, mesh = {DNA/*isolation &amp; purification/standards ; Feces/chemistry ; Genomics/*standards ; Humans ; *Microbiota ; }, abstract = {Among the laboratory and bioinformatic processing steps for human microbiome studies, a lack of consistency in DNA extraction methodologies is hindering the ability to compare results between studies and sometimes leading to errant conclusions. The purpose of this article is to highlight the issues related to DNA extraction methods and to suggest minimum standard requirements that should be followed to ensure consistency and reproducibility.}, }
@article {pmid31636011, year = {2019}, author = {Altay, O and Nielsen, J and Uhlen, M and Boren, J and Mardinoglu, A}, title = {Systems biology perspective for studying the gut microbiota in human physiology and liver diseases.}, journal = {EBioMedicine}, volume = {49}, number = {}, pages = {364-373}, pmid = {31636011}, issn = {2352-3964}, abstract = {The advancement in high-throughput sequencing technologies and systems biology approaches have revolutionized our understanding of biological systems and opened a new path to investigate unacknowledged biological phenomena. In parallel, the field of human microbiome research has greatly evolved and the relative contribution of the gut microbiome to health and disease have been systematically explored. This review provides an overview of the network-based and translational systems biology-based studies focusing on the function and composition of gut microbiota. We also discussed the association between the gut microbiome and the overall human physiology, as well as hepatic diseases and other metabolic disorders.}, }
@article {pmid31635533, year = {2019}, author = {Renson, A and Herd, P and Dowd, JB}, title = {Sick Individuals and Sick (Microbial) Populations: Challenges in Epidemiology and the Microbiome.}, journal = {Annual review of public health}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-publhealth-040119-094423}, pmid = {31635533}, issn = {1545-2093}, abstract = {The human microbiome represents a new frontier in understanding the biology of human health. While epidemiology in this area is still in its infancy, its scope will likely expand dramatically over the coming years. To rise to the challenge, we argue that epidemiology should capitalize on its population perspective as a critical complement to molecular microbiome research, allowing for the illumination of contextual mechanisms that may vary more across populations rather than among individuals. We first briefly review current research on social context and the gut microbiome, focusing specifically on socioeconomic status (SES) and race/ethnicity. Next, we reflect on the current state of microbiome epidemiology through the lens of one specific area, the association of the gut microbiome and metabolic disorders. We identify key methodological shortcomings of current epidemiological research in this area, including extensive selection bias, the use of noncompositionally robust measures, and a lack of attention to social factors as confounders or effect modifiers. Expected final online publication date for the Annual Review of Public Health, Volume 41 is April 1, 2020. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, }
@article {pmid31633390, year = {2019}, author = {Baker, JL and He, X and Shi, W}, title = {Precision Reengineering of the Oral Microbiome for Caries Management.}, journal = {Advances in dental research}, volume = {30}, number = {2}, pages = {34-39}, pmid = {31633390}, issn = {1544-0737}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; R01 DE020102/DE/NIDCR NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE026186/DE/NIDCR NIH HHS/United States ; }, mesh = {Biofilms ; *Dental Caries ; *Dental Plaque ; Humans ; *Microbiota ; Streptococcus mutans ; }, abstract = {Technological advancements have revolutionized our understanding of the complexity and importance of the human microbiome. This progress has also emphasized the need for precision therapeutics, as it has underscored the dilemmas, such as dysbiosis and increasing antibiotic resistance, associated with current, broad-spectrum treatment modalities. Dental caries remains the most common chronic disease worldwide, accompanied by a tremendous financial and social burden, despite widespread and efficacious fluoride and hygienic regimens. Over the past several decades, various precision approaches to combat dental caries, including vaccines, probiotics, and antimicrobial compounds, have been pursued. Despite the distinct overall conceptual strengths of each approach, for various reasons, there are currently no approved precision antibiotic therapeutics to prevent dental caries. Specifically targeted antimicrobial peptides (STAMPs) are synthetic molecules that combine the antibiotic moiety of a traditional antimicrobial peptide with a targeting domain to provide specificity against a particular organism. Conjoining the killing domain from the antimicrobial, novispirin G10, and a targeting domain derived from the Streptococcus mutans pheromone, CSP, the STAMP C16G2 was designed to provide targeted killing of S. mutans, widely considered the keystone species in dental caries pathogenesis. C16G2 was able to selectively eliminate S. mutans from complex ecosystems while leaving closely related, yet health-associated, oral species unharmed. This remodeling of the dental plaque community is expected to have significant advantages compared to conventional broad-spectrum mouthwashes, as the intact, surviving community is apt to prevent reinfection by pathogens. Following successful phase I clinical trials that evaluated the safety and basic microbiology of C16G2 treatments, the phase II trials of several C16G2 formulations are currently in progress. C16G2 represents an exciting advance in precision therapeutics, and the STAMP platform provides vast opportunities for both the development of additional therapeutics and the overall study of microbial ecology.}, }
@article {pmid31629686, year = {2019}, author = {Cao, L and Gurevich, A and Alexander, KL and Naman, CB and Leão, T and Glukhov, E and Luzzatto-Knaan, T and Vargas, F and Quinn, R and Bouslimani, A and Nothias, LF and Singh, NK and Sanders, JG and Benitez, RAS and Thompson, LR and Hamid, MN and Morton, JT and Mikheenko, A and Shlemov, A and Korobeynikov, A and Friedberg, I and Knight, R and Venkateswaran, K and Gerwick, WH and Gerwick, L and Dorrestein, PC and Pevzner, PA and Mohimani, H}, title = {MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.}, journal = {Cell systems}, volume = {9}, number = {6}, pages = {600-608.e4}, pmid = {31629686}, issn = {2405-4720}, support = {R01 GM118815/GM/NIGMS NIH HHS/United States ; R01 GM107550/GM/NIGMS NIH HHS/United States ; P41 GM103484/GM/NIGMS NIH HHS/United States ; R01 GM097509/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; T32 CA009523/CA/NCI NIH HHS/United States ; }, abstract = {Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an important class of natural products that contain antibiotics and a variety of other bioactive compounds. The existing methods for discovery of RiPPs by combining genome mining and computational mass spectrometry are limited to discovering specific classes of RiPPs from small datasets, and these methods fail to handle unknown post-translational modifications. Here, we present MetaMiner, a software tool for addressing these challenges that is compatible with large-scale screening platforms for natural product discovery. After searching millions of spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure against just eight genomic and metagenomic datasets, MetaMiner discovered 31 known and seven unknown RiPPs from diverse microbial communities, including human microbiome and lichen microbiome, and microorganisms isolated from the International Space Station.}, }
@article {pmid31623122, year = {2019}, author = {Dobrange, E and Peshev, D and Loedolff, B and Van den Ende, W}, title = {Fructans as Immunomodulatory and Antiviral Agents: The Case of Echinacea.}, journal = {Biomolecules}, volume = {9}, number = {10}, pages = {}, pmid = {31623122}, issn = {2218-273X}, abstract = {Throughout history, medicinal purposes of plants have been studied, documented, and acknowledged as an integral part of human healthcare systems. The development of modern medicine still relies largely on this historical knowledge of the use and preparation of plants and their extracts. Further research into the human microbiome highlights the interaction between immunomodulatory responses and plant-derived, prebiotic compounds. One such group of compounds includes the inulin-type fructans (ITFs), which may also act as signaling molecules and antioxidants. These multifunctional compounds occur in a small proportion of plants, many of which have recognized medicinal properties. Echinacea is a well-known medicinal plant and products derived from it are sold globally for its cold- and flu-preventative and general health-promoting properties. Despite the well-documented phytochemical profile of Echinacea plants and products, little research has looked into the possible role of ITFs in these products. This review aims to highlight the occurrence of ITFs in Echinacea derived formulations and the potential role they play in immunomodulation.}, }
@article {pmid31622559, year = {2020}, author = {Van Treuren, W and Dodd, D}, title = {Microbial Contribution to the Human Metabolome: Implications for Health and Disease.}, journal = {Annual review of pathology}, volume = {15}, number = {}, pages = {345-369}, doi = {10.1146/annurev-pathol-020117-043559}, pmid = {31622559}, issn = {1553-4014}, support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; }, abstract = {The human gastrointestinal tract is home to an incredibly dense population of microbes. These microbes employ unique strategies to capture energy in this largely anaerobic environment. In the process of breaking down dietary- and host-derived substrates, the gut microbiota produce a broad range of metabolic products that accumulate to high levels in the gut. Increasingly, studies are revealing that these chemicals impact host biology, either by acting on cells within the gastrointestinal tract or entering circulation and exerting their effects at distal sites within the body. Given the high level of functional diversity in the gut microbiome and the varied diets that we consume, the repertoire of microbiota-derived molecules within our bodies varies dramatically across individuals. Thus, the microbes in our gut and the metabolic end products they produce represent a phenotypic lever that we can potentially control to develop new therapeutics for personalized medicine. Here, we review current understanding of how microbes in the gastrointestinal tract contribute to the molecules within our gut and those that circulate within our bodies. We also highlight examples of how these molecules affect host physiology and discuss potential strategies for controlling their production to promote human health and to treat disease.}, }
@article {pmid31617360, year = {2019}, author = {Lam, KL and Cheung, PC}, title = {Carbohydrate-Based Prebiotics in Targeted Modulation of Gut Microbiome.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {45}, pages = {12335-12340}, doi = {10.1021/acs.jafc.9b04811}, pmid = {31617360}, issn = {1520-5118}, mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Carbohydrates/chemistry/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestines/microbiology ; Prebiotics/*analysis ; }, abstract = {The Human Microbiome Project has prompted unprecedented advancement in microbiome science. Personalized microbiome modulation with precision (PMMP) is one of the emerging yet challenging fields in microbiome research. Carbohydrate-based prebiotics (CBPs) have been shown to modulate the gut microbiome to various extents according to different structural characteristics, such as degree of polymerization, branching, glycosidic linkage, monosaccharide profile, and chemical modification. Subsequently, a targeted modulation of the microbiome might be achieved by using CBPs with a specific structure. A multidimensional database can be established based on the structure-microbiome and structure-microbial-marker relationships. Such relationships could facilitate the development of synbiotics and PMMP.}, }
@article {pmid31617205, year = {2020}, author = {Sharma, A and Das, P and Buschmann, M and Gilbert, JA}, title = {The Future of Microbiome-Based Therapeutics in Clinical Applications.}, journal = {Clinical pharmacology and therapeutics}, volume = {107}, number = {1}, pages = {123-128}, doi = {10.1002/cpt.1677}, pmid = {31617205}, issn = {1532-6535}, abstract = {The microbiome, a collection of microorganisms, their genomes, and the surrounding environmental conditions, is akin to a human organ, and knowledge is emerging on its role in human health and diseases. The influence of the microbiome in drug response has only been investigated in detail for the last 10 years. The human microbiome is a complex and highly dynamic system, which varies dramatically between individuals, yet there exists a common core microbiome that is heritable and can be transmitted to progeny. Here, we review the role of the human microbiome, which is now widely accepted as a major factor that drives the interpersonal variation in therapeutic response. We describe examples in which the microbiome modifies drug action. Despite its complexity, the microbiome can be readily altered, with the potential to increase the benefits and reduce the toxicity and side effects associated with pharmaceutical drugs. The potential of new microbiome-based strategies, such as fecal microbiota transplant, probiotics, and phage therapy, as promising medical therapeutics are outlined. We also suggest a combination reductionist and system-level approaches that could be applied to further investigate the role of microbiota in drug metabolism modulation of drug response. Finally, we emphasize the importance of combining microbiome and pharmacology studies as a novel means to treat disease and reduce side effects.}, }
@article {pmid31616466, year = {2019}, author = {Srivastava, D and Baksi, KD and Kuntal, BK and Mande, SS}, title = {&quot;EviMass&quot;: A Literature Evidence-Based Miner for Human Microbial Associations.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {849}, pmid = {31616466}, issn = {1664-8021}, abstract = {The importance of understanding microbe-microbe as well as microbe-disease associations is one of the key thrust areas in human microbiome research. High-throughput metagenomic and transcriptomic projects have fueled discovery of a number of new microbial associations. Consequently, a plethora of information is being added routinely to biomedical literature, thereby contributing toward enhancing our knowledge on microbial associations. In this communication, we present a tool called &quot;EviMass&quot; (Evidence based mining of human Microbial Associations), which can assist biologists to validate their predicted hypotheses from new microbiome studies. Users can interactively query the processed back-end database for microbe-microbe and disease-microbe associations. The EviMass tool can also be used to upload microbial association networks generated from a human &quot;disease-control&quot; microbiome study and validate the associations from biomedical literature. Additionally, a list of differentially abundant microbes for the corresponding disease can be queried in the tool for reported evidences. The results are presented as graphical plots, tabulated summary, and other evidence statistics. EviMass is a comprehensive platform and is expected to enable microbiome researchers not only in mining microbial associations, but also enriching a new research hypothesis. The tool is available free for academic use at https://web.rniapps.net/evimass.}, }
@article {pmid31608855, year = {2019}, author = {Lilley, ECH and Morris, AT and Silberg, JL}, title = {The Mid-Atlantic Twin Registry of Virginia Commonwealth University.}, journal = {Twin research and human genetics : the official journal of the International Society for Twin Studies}, volume = {22}, number = {6}, pages = {753-756}, doi = {10.1017/thg.2019.87}, pmid = {31608855}, issn = {1832-4274}, abstract = {The Mid-Atlantic Twin Registry (MATR) is a population-based registry of more than 60,000 twins primarily born or living in Virginia, North Carolina and South Carolina. Researchers may utilize the MATR for administration of research services, including study recruitment, data or sample (e.g., DNA) collection, archival dataset creation, as well as data collection through mailed, phone or online surveys. In addition, the MATR houses the MATR Repository, with over 1700 DNA samples primarily from whole blood available for researchers interested in DNA genotyping. For over 40 years MATR twins have participated in research studies with investigators from a range of scientific disciplines and institutions. These studies, which have resulted in numerous publications, explored diverse topics, including substance use, smoking behaviors, developmental psychopathology, bullying, children's health, cardiovascular disease, cancer, the human microbiome, epigenetics of aging, children of twins and sleep homeostasis. Researchers interested in utilizing twins are encouraged to contact the MATR to discuss potential research opportunities.}, }
@article {pmid31608406, year = {2019}, author = {Farmakiotis, D}, title = {The human microbiome and checkpoint inhibition: potential benefits from antibiotic stewardship.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciz1003}, pmid = {31608406}, issn = {1537-6591}, }
@article {pmid31608279, year = {2019}, author = {Kang, W and Jia, Z and Tang, D and Zhao, X and Shi, J and Jia, Q and He, K and Feng, Q}, title = {Time-Course Transcriptome Analysis for Drug Repositioning in Fusobacterium nucleatum-Infected Human Gingival Fibroblasts.}, journal = {Frontiers in cell and developmental biology}, volume = {7}, number = {}, pages = {204}, pmid = {31608279}, issn = {2296-634X}, abstract = {Fusobacterium nucleatum (F. nucleatum) is a crucial periodontal pathogen and human gingival fibroblasts (GFs) are the first line of defense against oral pathogens. However, the research on potential molecular mechanisms of host defense and effective treatment of F. nucleatum infection in GFs remains scarce. In this study, we undertook a time-series experiment and performed an RNA-seq analysis to explore gene expression profiles during the process of F. nucleatum infection in GFs. Differentially expressed genes (DEGs) could be divided into three coexpression clusters. Functional analysis revealed that the immune-related signaling pathways were more overrepresented at the early stage, while metabolic pathways were mainly enriched at the late stage. We computationally identified several U.S. Food and Drug Administration (FDA)-approved drugs that could protect the F. nucleatum infected GFs via a coexpression-based drug repositioning approach. Biologically, we confirmed that six drugs (etravirine, zalcitabine, wortmannin, calcium D-pantothenate, ellipticine, and tanespimycin) could significantly decrease F. nucleatum-induced reactive oxygen species (ROS) generation and block the Protein Kinase B (PKB/AKT)/mitogen-activated protein kinase signaling pathways. Our study provides more detailed molecular mechanisms of the process by which F. nucleatum infects GFs and illustrates the value of the cogena-based drug repositioning method and the potential therapeutic application of these tested drugs in the treatment of F. nucleatum infection.}, }
@article {pmid31607556, year = {2019}, author = {Tett, A and Huang, KD and Asnicar, F and Fehlner-Peach, H and Pasolli, E and Karcher, N and Armanini, F and Manghi, P and Bonham, K and Zolfo, M and De Filippis, F and Magnabosco, C and Bonneau, R and Lusingu, J and Amuasi, J and Reinhard, K and Rattei, T and Boulund, F and Engstrand, L and Zink, A and Collado, MC and Littman, DR and Eibach, D and Ercolini, D and Rota-Stabelli, O and Huttenhower, C and Maixner, F and Segata, N}, title = {The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {5}, pages = {666-679.e7}, pmid = {31607556}, issn = {1934-6069}, support = {TL1 TR001447/TR/NCATS NIH HHS/United States ; /ERC_/European Research Council/International ; /HHMI/Howard Hughes Medical Institute/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 DK103358/DK/NIDDK NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Diet ; Ethiopia ; Feces/microbiology ; Fossils/*microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Bacterial/*genetics ; Ghana ; Humans ; Prevotella/*classification/*genetics/isolation &amp; purification ; Tanzania ; }, abstract = {Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In a cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes and explored the genetic and population structure of P. copri. P. copri encompasses four distinct clades (>10% inter-clade genetic divergence) that we propose constitute the P. copri complex, and all clades were confirmed by isolate sequencing. These clades are nearly ubiquitous and co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity in the complex with notable differences in carbohydrate metabolism, suggesting that multi-generational dietary modifications may be driving reduced prevalence in Westernized populations. Analysis of ancient metagenomes highlighted patterns of P. copri presence consistent with modern non-Westernized populations and a clade delineation time pre-dating human migratory waves out of Africa. These findings reveal that P. copri exhibits a high diversity that is underrepresented in Western-lifestyle populations.}, }
@article {pmid31603985, year = {2020}, author = {McCrory, C and Fiorito, G and McLoughlin, S and Polidoro, S and Cheallaigh, CN and Bourke, N and Karisola, P and Alenius, H and Vineis, P and Layte, R and Kenny, RA}, title = {Epigenetic Clocks and Allostatic Load Reveal Potential Sex-Specific Drivers of Biological Aging.}, journal = {The journals of gerontology. Series A, Biological sciences and medical sciences}, volume = {75}, number = {3}, pages = {495-503}, doi = {10.1093/gerona/glz241}, pmid = {31603985}, issn = {1758-535X}, abstract = {Allostatic load (AL) and epigenetic clocks both attempt to characterize the accelerated aging of biological systems, but at present it is unclear whether these measures are complementary or distinct. This study examines the cross-sectional association of AL with epigenetic age acceleration (EAA) in a subsample of 490 community-dwelling older adults participating in The Irish Longitudinal study on Aging (TILDA). A battery of 14 biomarkers representing the activity of four different physiological systems: immunological, cardiovascular, metabolic, renal, was used to construct the AL score. DNA methylation age was computed according to the algorithms described by Horvath, Hannum, and Levine allowing for estimation of whether an individual is experiencing accelerated or decelerated aging. Horvath, Hannum, and Levine EAA correlated 0.05, 0.03, and 0.21 with AL, respectively. Disaggregation by sex revealed that AL was more strongly associated with EAA in men compared with women as assessed using Horvath's clock. Metabolic dysregulation was a strong driver of EAA in men as assessed using Horvath and Levine's clock, while metabolic and cardiovascular dysregulation were associated with EAA in women using Levine's clock. Results indicate that AL and the epigenetic clocks are measuring different age-related variance and implicate sex-specific drivers of biological aging.}, }
@article {pmid31601287, year = {2019}, author = {Stinson, LF}, title = {Establishment of the early-life microbiome: a DOHaD perspective.}, journal = {Journal of developmental origins of health and disease}, volume = {}, number = {}, pages = {1-10}, doi = {10.1017/S2040174419000588}, pmid = {31601287}, issn = {2040-1752}, abstract = {The human microbiome plays a number of critical roles in host physiology. Evidence from longitudinal cohort studies and animal models strongly supports the theory that maldevelopment of the microbiome in early life can programme later-life disease. The early-life microbiome develops in a clear stepwise manner over the first 3 years of life. During this highly dynamic time, insults such as antibiotic use and formula feeding can adversely affect the composition and temporal development of the microbiome. Such experiences predispose infants for the development of chronic health conditions later in life. This review highlights key factors that disrupt the early-life microbiome and highlights major non-communicable diseases which are underpinned by early-life dysbiosis.}, }
@article {pmid31600503, year = {2019}, author = {Shkoporov, AN and Clooney, AG and Sutton, TDS and Ryan, FJ and Daly, KM and Nolan, JA and McDonnell, SA and Khokhlova, EV and Draper, LA and Forde, A and Guerin, E and Velayudhan, V and Ross, RP and Hill, C}, title = {The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {4}, pages = {527-541.e5}, doi = {10.1016/j.chom.2019.09.009}, pmid = {31600503}, issn = {1934-6069}, mesh = {Bacteroides/isolation &amp; purification/*virology ; Faecalibacterium/isolation &amp; purification/*virology ; Gastrointestinal Microbiome/*genetics ; Humans ; Longitudinal Studies ; Metagenome/genetics ; Microviridae/classification/*genetics/isolation &amp; purification ; Prevotella/isolation &amp; purification/*virology ; Viral Load ; }, abstract = {The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.}, }
@article {pmid31600337, year = {2019}, author = {Andreev, VP and Liu, G and Zee, J and Henn, L and Flores, GE and Merion, RM}, title = {Clustering of the structures by using &quot;snakes-&amp;-dragons&quot; approach, or correlation matrix as a signal.}, journal = {PloS one}, volume = {14}, number = {10}, pages = {e0223267}, pmid = {31600337}, issn = {1932-6203}, abstract = {Biological, ecological, social, and technological systems are complex structures with multiple interacting parts, often represented by networks. Correlation matrices describing interdependency of the variables in such structures provide key information for comparison and classification of such systems. Classification based on correlation matrices could supplement or improve classification based on variable values, since the former reveals similarities in system structures, while the latter relies on the similarities in system states. Importantly, this approach of clustering correlation matrices is different from clustering elements of the correlation matrices, because our goal is to compare and cluster multiple networks-not the nodes within the networks. A novel approach for clustering correlation matrices, named &quot;snakes-&amp;-dragons,&quot; is introduced and illustrated by examples from neuroscience, human microbiome, and macroeconomics.}, }
@article {pmid31597320, year = {2019}, author = {Holster, S and Hooiveld, GJ and Repsilber, D and Vos, WM and Brummer, RJ and König, J}, title = {Allogenic Faecal Microbiota Transfer Induces Immune-Related Gene Sets in the Colon Mucosa of Patients with Irritable Bowel Syndrome.}, journal = {Biomolecules}, volume = {9}, number = {10}, pages = {}, pmid = {31597320}, issn = {2218-273X}, support = {Spinoza 2018//Nederlands Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; ESPEN Research Fellowship 2017//European Society for Clinical Nutrition and Metabolism/ ; 20110225//Knowledge Foundation/ ; }, abstract = {Faecal microbiota transfer (FMT) consists of the introduction of new microbial communities into the intestine of a patient, with the aim of restoring a disturbed gut microbiota. Even though it is used as a potential treatment for various diseases, it is unknown how the host mucosa responds to FMT. This study aims to investigate the colonic mucosa gene expression response to allogenic (from a donor) or autologous (own) FMT in patients with irritable bowel syndrome (IBS). In a recently conducted randomised, double-blinded, controlled clinical study, 17 IBS patients were treated with FMT by colonoscopy. RNA was isolated from colonic biopsies collected by sigmoidoscopy at baseline, as well as two weeks and eight weeks after FMT. In patients treated with allogenic FMT, predominantly immune response-related gene sets were induced, with the strongest response two weeks after the FMT. In patients treated with autologous FMT, predominantly metabolism-related gene sets were affected. Furthermore, several microbiota genera showed correlations with immune-related gene sets, with different correlations found after allogenic compared to autologous FMT. This study shows that the microbe-host response is influenced by FMT on the mucosal gene expression level, and that there are clear differences in response to allogenic compared to autologous FMT.}, }
@article {pmid31594829, year = {2019}, author = {Zhao, H and Fu, S and Yu, Y and Zhang, Z and Li, P and Ma, Q and Jia, W and Ning, K and Qu, S and Liu, Q}, title = {MetaMed: Linking Microbiota Functions with Medicine Therapeutics.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31594829}, issn = {2379-5077}, abstract = {Understanding how the human microbiome affects human health has consequences for treating disease and minimizing unwanted side effects in clinical research. Here, we present MetaMed (http://metamed.rwebox.com/index), a novel and integrative system-wide correlation mapping system to link bacterial functions and medicine therapeutics, providing novel hypotheses for deep investigation of microbe therapeutic effects on human health. Furthermore, comprehensive relationships between microbes living in the environment and drugs were discovered, providing a rich source for discovering microbiota metabolites with great potential for pharmaceutical applications.}, }
@article {pmid31592582, year = {2019}, author = {Li, W and Ma, ZS}, title = {Diversity scaling of human vaginal microbial communities.}, journal = {Zoological research}, volume = {40}, number = {6}, pages = {587-594}, pmid = {31592582}, issn = {2095-8137}, mesh = {Bacteria/*classification ; Female ; Humans ; Microbiota ; Postpartum Period ; Vagina/*microbiology ; }, abstract = {The composition and diversity of the human vaginal microbial community have been investigated intensively due to the diversity-stability relationship (DSR)-based hypothesis for bacterial vaginosis (BV) etiology, which was first proposed in the 1990s and has received renewed interest in recent years. Nevertheless, diversity changes (scaling) across individuals in a cohort or population have not yet been addressed, which is significant both theoretically and practically. Theoretically, biodiversity scaling is the core of biogeography, and practically, inter-subject heterogeneity is critical for understanding the etiology and epidemiology of human microbiome-associated diseases such as BV. Here we applied the diversity-area relationship (DAR), a recent extension to the classic species-area relationship (SAR), to study diversity scaling of the vaginal microbiome by reanalyzing reported data collected from 1 107 postpartum women. The model used here characterized the power-law (or its extension) relationships between accrued diversity and areas (numbers of individuals), upon which four biogeographic profiles were thus defined. Specifically, we established the DAR profile (relationship between diversity scaling parameter and so-termed diversity order (q)), similarly pair-wise diversity overlap (PDO) profile, maximal accrual diversity (MAD) profile, and ratio of individual-level to population-level diversity (RIP) profile. These four profiles offer valuable tools to assess and predict diversity scaling (changes) in the human vaginal microbiome across individuals, as well as to understand the dynamics of vaginal microbiomes in healthy women.}, }
@article {pmid31590679, year = {2019}, author = {Amato, KR and Mallott, EK and McDonald, D and Dominy, NJ and Goldberg, T and Lambert, JE and Swedell, L and Metcalf, JL and Gomez, A and Britton, GAO and Stumpf, RM and Leigh, SR and Knight, R}, title = {Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {201}, pmid = {31590679}, issn = {1474-760X}, mesh = {Animals ; Cercopithecidae/classification/genetics/microbiology ; Diet ; Ecosystem ; *Gastrointestinal Microbiome ; Hominidae/classification/genetics ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates.<br><br>RESULTS: Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates.<br><br>CONCLUSIONS: Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.}, }
@article {pmid31588499, year = {2020}, author = {Bradley, PH and Pollard, KS}, title = {phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.}, journal = {Bioinformatics (Oxford, England)}, volume = {36}, number = {4}, pages = {1289-1290}, doi = {10.1093/bioinformatics/btz722}, pmid = {31588499}, issn = {1367-4811}, abstract = {SUMMARY: Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in community composition. These methods help to identify functionally important genes because they test for associations beyond those expected when related microbes occupy similar environments. We present phylogenize, a pipeline with web, QIIME 2 and R interfaces that allows researchers to perform phylogenetic regression on 16S amplicon and shotgun sequencing data and to visualize results. phylogenize applies broadly to both host-associated and environmental microbiomes. Using Human Microbiome Project and Earth Microbiome Project data, we show that phylogenize draws similar conclusions from 16S versus shotgun sequencing and reveals both known and candidate pathways associated with host colonization.<br><br>phylogenize is available at https://phylogenize.org and https://bitbucket.org/pbradz/phylogenize.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid31583780, year = {2019}, author = {Hooks, KB and O'Malley, MA}, title = {Contrasting Strategies: Human Eukaryotic Versus Bacterial Microbiome Research.}, journal = {The Journal of eukaryotic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jeu.12766}, pmid = {31583780}, issn = {1550-7408}, support = {ANR-10-IDEX-03-02//Agence Nationale de la Recherche/ ; FL170100160//Australian Research Council/ ; }, abstract = {Most discussions of human microbiome research have focused on bacterial investigations and findings. Our target is to understand how human eukaryotic microbiome research is developing, its potential distinctiveness, and how problems can be addressed. We start with an overview of the entire eukaryotic microbiome literature (578 papers), show tendencies in the human-based microbiome literature, and then compare the eukaryotic field to more developed human bacterial microbiome research. We are particularly concerned with problems of interpretation that are already apparent in human bacterial microbiome research (e.g. disease causality, probiotic interventions, evolutionary claims). We show where each field converges and diverges, and what this might mean for progress in human eukaryotic microbiome research. Our analysis then makes constructive suggestions for the future of the field.}, }
@article {pmid31582523, year = {2019}, author = {Sugimoto, Y and Camacho, FR and Wang, S and Chankhamjon, P and Odabas, A and Biswas, A and Jeffrey, PD and Donia, MS}, title = {A metagenomic strategy for harnessing the chemical repertoire of the human microbiome.}, journal = {Science (New York, N.Y.)}, volume = {366}, number = {6471}, pages = {}, doi = {10.1126/science.aax9176}, pmid = {31582523}, issn = {1095-9203}, support = {DP2 AI124441/AI/NIAID NIH HHS/United States ; }, abstract = {Extensive progress has been made in determining the effects of the microbiome on human physiology and disease, but the underlying molecules and mechanisms governing these effects remain largely unexplored. Here, we combine a new computational algorithm with synthetic biology to access biologically active small molecules encoded directly in human microbiome-derived metagenomic sequencing data. We discover that members of a clinically used class of molecules are widely encoded in the human microbiome and that they exert potent antibacterial activities against neighboring microbes, implying a possible role in niche competition and host defense. Our approach paves the way toward a systematic unveiling of the chemical repertoire encoded by the human microbiome and provides a generalizable platform for discovering molecular mediators of microbiome-host and microbiome-microbiome interactions.}, }
@article {pmid31575764, year = {2019}, author = {Chmiel, JA and Daisley, BA and Burton, JP and Reid, G}, title = {Deleterious Effects of Neonicotinoid Pesticides on Drosophila melanogaster Immune Pathways.}, journal = {mBio}, volume = {10}, number = {5}, pages = {}, pmid = {31575764}, issn = {2150-7511}, abstract = {Neonicotinoid insecticides are common agrochemicals that are used to kill pest insects and improve crop yield. However, sublethal exposure can exert unintentional toxicity to honey bees and other beneficial pollinators by dysregulating innate immunity. Generation of hydrogen peroxide (H2O2) by the dual oxidase (Duox) pathway is a critical component of the innate immune response, which functions to impede infection and maintain homeostatic regulation of the gut microbiota. Despite the importance of this pathway in gut immunity, the consequences of neonicotinoid exposure on Duox signaling have yet to be studied. Here, we use a Drosophila melanogaster model to investigate the hypothesis that imidacloprid (a common neonicotinoid) can affect the Duox pathway. The results demonstrated that exposure to sublethal imidacloprid reduced H2O2 production by inhibiting transcription of the Duox gene. Furthermore, the reduction in Duox expression was found to be a result of imidacloprid interacting with the midgut portion of the immune deficiency pathway. This impairment led to a loss of microbial regulation, as exemplified by a compositional shift and increased total abundance of Lactobacillus and Acetobacter spp. (dominant microbiota members) found in the gut. In addition, we demonstrated that certain probiotic lactobacilli could ameliorate Duox pathway impairment caused by imidacloprid, but this effect was not directly dependent on the Duox pathway itself. This study is the first to demonstrate the deleterious effects that neonicotinoids can have on Duox-mediated generation of H2O2 and highlights a novel coordination between two important innate immune pathways present in insects.IMPORTANCE Sublethal exposure to certain pesticides (e.g., neonicotinoid insecticides) is suspected to contribute to honey bee (Apis mellifera) population decline in North America. Neonicotinoids are known to interfere with immune pathways in the gut of insects, but the underlying mechanisms remain elusive. We used a Drosophila melanogaster model to understand how imidacloprid (a common neonicotinoid) interferes with two innate immune pathways-Duox and Imd. We found that imidacloprid dysregulates these pathways to reduce hydrogen peroxide production, ultimately leading to a dysbiotic shift in the gut microbiota. Intriguingly, we found that presupplementation with probiotic bacteria could mitigate the harmful effects of imidacloprid. Thus, these observations uncover a novel mechanism of pesticide-induced immunosuppression that exploits the interconnectedness of two important insect immune pathways.}, }
@article {pmid31572693, year = {2019}, author = {Reid, G}, title = {The Need to Focus on Therapy Instead of Associations.}, journal = {Frontiers in cellular and infection microbiology}, volume = {9}, number = {}, pages = {327}, pmid = {31572693}, issn = {2235-2988}, abstract = {Molecular analyses of the vaginal microbiota have uncovered a vast array of organisms in this niche, but not so far changed what has been known for a long time: lactobacilli are dominant in health, and the diagnosis and treatment of symptomatic bacterial vaginosis is sub-optimal, and has not changed for over 40 years. While the lowering cost of DNA sequencing has attracted more researchers to the field, and bioinformatics, and statistical tools have made it possible to produce large datasets, it is functional and actionable studies that are more urgently needed, not more microbial abundance, and health or disease-associative data. The triggers of dysbiosis remain to be identified, but ultimately treatment will require disrupting biofilms of primarily anaerobic bacteria and replacing them with the host's own lactobacilli, or health-promoting organisms. The options of using probiotic strains to displace the biofilms and for prebiotics to encourage resurgence of the indigenous lactobacilli hold great promise, but more researchers need to develop, and test these concepts in humans. The enormity of the problem of vaginal dysbiosis cannot be understated. It should not take another 40 years to offer better management options.}, }
@article {pmid31563878, year = {2019}, author = {Cammarota, G and Ianiro, G and Kelly, CR and Mullish, BH and Allegretti, JR and Kassam, Z and Putignani, L and Fischer, M and Keller, JJ and Costello, SP and Sokol, H and Kump, P and Satokari, R and Kahn, SA and Kao, D and Arkkila, P and Kuijper, EJ and Vehreschild, MJG and Pintus, C and Lopetuso, L and Masucci, L and Scaldaferri, F and Terveer, EM and Nieuwdorp, M and López-Sanromán, A and Kupcinskas, J and Hart, A and Tilg, H and Gasbarrini, A}, title = {International consensus conference on stool banking for faecal microbiota transplantation in clinical practice.}, journal = {Gut}, volume = {68}, number = {12}, pages = {2111-2121}, pmid = {31563878}, issn = {1468-3288}, mesh = {Clostridium Infections/microbiology/*therapy ; Clostridium difficile/*isolation &amp; purification ; *Consensus ; Donor Selection ; Fecal Microbiota Transplantation/*methods ; *Gastrointestinal Microbiome ; Humans ; Specimen Handling/methods ; }, abstract = {Although faecal microbiota transplantation (FMT) has a well-established role in the treatment of recurrent Clostridioides difficile infection (CDI), its widespread dissemination is limited by several obstacles, including lack of dedicated centres, difficulties with donor recruitment and complexities related to regulation and safety monitoring. Given the considerable burden of CDI on global healthcare systems, FMT should be widely available to most centres.Stool banks may guarantee reliable, timely and equitable access to FMT for patients and a traceable workflow that ensures safety and quality of procedures. In this consensus project, FMT experts from Europe, North America and Australia gathered and released statements on the following issues related to the stool banking: general principles, objectives and organisation of the stool bank; selection and screening of donors; collection, preparation and storage of faeces; services and clients; registries, monitoring of outcomes and ethical issues; and the evolving role of FMT in clinical practice,Consensus on each statement was achieved through a Delphi process and then in a plenary face-to-face meeting. For each key issue, the best available evidence was assessed, with the aim of providing guidance for the development of stool banks in order to promote accessibility to FMT in clinical practice.}, }
@article {pmid31562947, year = {2019}, author = {Hynönen, U and Zoetendal, EG and Virtala, AK and Shetty, S and Hasan, S and Jakava-Viljanen, M and de Vos, WM and Palva, A}, title = {Molecular ecology of the yet uncultured bacterial Ct85-cluster in the mammalian gut.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102104}, doi = {10.1016/j.anaerobe.2019.102104}, pmid = {31562947}, issn = {1095-8274}, abstract = {In our previous studies on irritable bowel syndrome (IBS) -associated microbiota by molecular methods, we demonstrated that a particular 16S rRNA gene amplicon was more abundant in the feces of healthy subjects or mixed type IBS (IBS-M) -sufferers than in the feces of individuals with diarrhea-type IBS (IBS-D). In the current study, we demonstrated that this, so called Ct85-amplicon, consists of a cluster of very heterogeneous 16S rRNA gene sequences, and defined six 16S rRNA gene types, a to f, within this cluster, each representing a novel species-, genus- or family level taxon. We then designed specific PCR primers for these sequence types, mapped the distribution of the Ct85-cluster sequences and that of the newly defined sequence types in several animal species and compared the sequence types present in the feces of healthy individuals and IBS sufferers using two IBS study cohorts, Finnish and Dutch. Various Ct85-cluster sequence types were detected in the fecal samples of several companion and production animal species with remarkably differing prevalences and abundances. The Ct85 sequence type composition of swine closely resembled that of humans. One of the five types (d) shared between humans and swine was not present in any other animals tested, while one sequence type (b) was found only in human samples. In both IBS study cohorts, one type (e) was more prevalent in healthy individuals than in the IBS-M group. By revealing various sequence types in the widespread Ct85-cluster and their distribution, the results improve our understanding of these uncultured bacteria, which is essential for future efforts to cultivate representatives of the Ct85-cluster and reveal their roles in IBS.}, }
@article {pmid31555247, year = {2019}, author = {Ghose, C and Ly, M and Schwanemann, LK and Shin, JH and Atab, K and Barr, JJ and Little, M and Schooley, RT and Chopyk, J and Pride, DT}, title = {The Virome of Cerebrospinal Fluid: Viruses Where We Once Thought There Were None.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2061}, pmid = {31555247}, issn = {1664-302X}, abstract = {Traditionally, medicine has held that some human body sites are sterile and that the introduction of microbes to these sites results in infections. This paradigm shifted significantly with the discovery of the human microbiome and acceptance of these commensal microbes living across the body. However, the central nervous system (CNS) is still believed by many to be sterile in healthy people. Using culture-independent methods, we examined the virome of cerebrospinal fluid (CSF) from a cohort of mostly healthy human subjects. We identified a community of DNA viruses, most of which were identified as bacteriophages. Compared to other human specimen types, CSF viromes were not ecologically distinct. There was a high alpha diversity cluster that included feces, saliva, and urine, and a low alpha diversity cluster that included CSF, body fluids, plasma, and breast milk. The high diversity cluster included specimens known to have many bacteria, while other specimens traditionally assumed to be sterile formed the low diversity cluster. There was an abundance of viruses shared among CSF, breast milk, plasma, and body fluids, while each generally shared less with urine, feces, and saliva. These shared viruses ranged across different virus families, indicating that similarities between these viromes represent more than just a single shared virus family. By identifying a virome in the CSF of mostly healthy individuals, it is now less likely that any human body site is devoid of microbes, which further highlights the need to decipher the role that viral communities may play in human health.}, }
@article {pmid31555238, year = {2019}, author = {Pires, ES and Hardoim, CCP and Miranda, KR and Secco, DA and Lobo, LA and de Carvalho, DP and Han, J and Borchers, CH and Ferreira, RBR and Salles, JF and Domingues, RMCP and Antunes, LCM}, title = {The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {2003}, pmid = {31555238}, issn = {1664-302X}, abstract = {During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.}, }
@article {pmid31546582, year = {2019}, author = {Dizzell, S and Nazli, A and Reid, G and Kaushic, C}, title = {Protective Effect of Probiotic Bacteria and Estrogen in Preventing HIV-1-Mediated Impairment of Epithelial Barrier Integrity in Female Genital Tract.}, journal = {Cells}, volume = {8}, number = {10}, pages = {}, pmid = {31546582}, issn = {2073-4409}, support = {FRN 126019//CIHR/Canada ; FRN 138657//CIHR/Canada ; }, abstract = {Approximately 40% of global HIV-1 transmission occurs in the female genital tract (FGT) through heterosexual transmission. Epithelial cells lining the FGT provide the first barrier to HIV-1 entry. Previous studies have suggested that certain hormonal contraceptives or a dysbiosis of the vaginal microbiota can enhance HIV-1 acquisition in the FGT. We examined the effects of lactobacilli and female sex hormones on the barrier functions and innate immune responses of primary endometrial genital epithelial cells (GECs). Two probiotic strains, Lactobacillus reuteri RC-14 and L. rhamnosus GR-1, were tested, as were sex hormones estrogen (E2), progesterone (P4), and the hormonal contraceptive medroxyprogesterone acetate (MPA). Our results demonstrate that probiotic lactobacilli enhance barrier function without affecting cytokines. Treatment of GECs with MPA resulted in reduced barrier function. In contrast, E2 treatment enhanced barrier function and reduced production of proinflammatory cytokines. Comparison of hormones plus lactobacilli as a pre-treatment prior to HIV exposure revealed a dominant effect of lactobacilli in preventing loss of barrier function by GECs. In summary, the combination of E2 and lactobacilli had the best protective effect against HIV-1 seen by enhancement of barrier function and reduction in proinflammatory cytokines. These studies provide insights into how probiotic lactobacilli in the female genital microenvironment can alter HIV-1-mediated barrier disruption and how the combination of E2 and lactobacilli may decrease susceptibility to primary HIV infection.}, }
@article {pmid31545899, year = {2019}, author = {Chu, J and Vila-Farres, X and Brady, SF}, title = {Bioactive Synthetic-Bioinformatic Natural Product Cyclic Peptides Inspired by Nonribosomal Peptide Synthetase Gene Clusters from the Human Microbiome.}, journal = {Journal of the American Chemical Society}, volume = {141}, number = {40}, pages = {15737-15741}, pmid = {31545899}, issn = {1520-5126}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; U19 AI142731/AI/NIAID NIH HHS/United States ; }, abstract = {Bioinformatic analysis of sequenced bacterial genomes has uncovered an increasing number of natural product biosynthetic gene clusters (BGCs) to which no known bacterial metabolite can be ascribed. One emerging method we have investigated for studying these BGCs is the synthetic-Bioinformatic Natural Product (syn-BNP) approach. The syn-BNP approach replaces transcription, translation, and in vivo enzymatic biosynthesis of natural products with bioinformatic algorithms to predict the output of a BGC and in vitro chemical synthesis to produce the predicted structure. Here we report on expanding the syn-BNP approach to the design and synthesis of cyclic peptides inspired by nonribosomal peptide synthetase BGCs associated with the human microbiota. While no syn-BNPs we tested inhibited the growth of bacteria or yeast, five were found to be active in the human cell-based MTT metabolic activity assay. Interestingly, active peptides were mostly inspired by BGCs found in the genomes of opportunistic pathogens that are often more commonly associated with environments outside the human microbiome. The cyclic syn-BNP studies presented here provide further evidence of its potential for identifying bioactive small molecules directly from the instructions encoded in the primary sequences of natural product BGCs.}, }
@article {pmid31545522, year = {2019}, author = {Bosch, TCG}, title = {Multidisciplinary Approaches to Exploring Human-Microbiome Interactions.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {10}, pages = {1-2}, doi = {10.1002/bies.201900130}, pmid = {31545522}, issn = {1521-1878}, }
@article {pmid31537666, year = {2019}, author = {Yerushalmy, O and Coppenhagen-Glazer, S and Nir-Paz, R and Tuomala, H and Skurnik, M and Kiljunen, S and Hazan, R}, title = {Complete Genome Sequences of Two Klebsiella pneumoniae Phages Isolated as Part of an International Effort.}, journal = {Microbiology resource announcements}, volume = {8}, number = {38}, pages = {}, pmid = {31537666}, issn = {2576-098X}, abstract = {We report the genomic sequences of phages KpCHEMY26 and KpGranit, isolated in Israel during a worldwide effort against a multidrug- and phage-resistant strain of Klebsiella pneumoniae from a patient in Finland. These results demonstrate the importance of an efficient worldwide network for collaborating in personalized therapy for infectious diseases.}, }
@article {pmid31533707, year = {2019}, author = {Willmann, M and Vehreschild, MJGT and Biehl, LM and Vogel, W and Dörfel, D and Hamprecht, A and Seifert, H and Autenrieth, IB and Peter, S}, title = {Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study.}, journal = {BMC biology}, volume = {17}, number = {1}, pages = {76}, pmid = {31533707}, issn = {1741-7007}, mesh = {Anti-Bacterial Agents/*adverse effects/therapeutic use ; Ciprofloxacin/*adverse effects/therapeutic use ; Cohort Studies ; *Drug Resistance, Microbial/drug effects/genetics ; Gastrointestinal Microbiome/*drug effects ; Genes, Bacterial/drug effects ; Germany ; Humans ; Longitudinal Studies ; Metagenomics/methods ; Plasmids/*drug effects ; Trimethoprim, Sulfamethoxazole Drug Combination/*adverse effects/therapeutic use ; }, abstract = {BACKGROUND: The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome.<br><br>RESULTS: Using shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance.<br><br>CONCLUSIONS: Our study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT02058888 . Registered February 10 2014.}, }
@article {pmid31532533, year = {2019}, author = {Bhuta, R and Nieder, M and Jubelirer, T and Ladas, EJ}, title = {The Gut Microbiome and Pediatric Cancer: Current Research and Gaps in Knowledge.}, journal = {Journal of the National Cancer Institute. Monographs}, volume = {2019}, number = {54}, pages = {169-173}, doi = {10.1093/jncimonographs/lgz026}, pmid = {31532533}, issn = {1745-6614}, abstract = {The human microbiome consists of trillions of microbial cells that interact with one another and the human host to play a clinically significant role in health and disease. Gut microbial changes have been identified in cancer pathogenesis, at disease diagnosis, during therapy, and even long after completion of treatment. Alterations in the gut microbiome have been linked to treatment-related toxicity and potential long-term morbidity and mortality in children with cancer. Such alterations are plausible given immune modulation due to disease as well as exposure to cytotoxic chemotherapy, infections, and antibiotics. The following review presents our current scientific understanding on the role of the gut microbiome in pediatric cancer, identifies gaps in knowledge, and suggests future research goals.}, }
@article {pmid31530872, year = {2019}, author = {Köberl, M and Erschen, S and Etemadi, M and White, RA and El-Arabi, TF and Berg, G}, title = {Deciphering the microbiome shift during fermentation of medicinal plants.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {13461}, pmid = {31530872}, issn = {2045-2322}, abstract = {The importance of the human-microbiome relationship for positive health outcomes has become more apparent over the last decade. Influencing the gut microbiome via modification of diet represents a possibility of maintaining a healthy gut flora. Fermented food and lactic acid bacteria (LAB) display a preventive way to inhibit microbial dysbioses and diseases, but their ecology on plants is poorly understood. We characterized the microbiome of medicinal plants (Matricaria chamomilla L. and Calendula officinalis L.) using 16S rRNA gene profiling from leaves that were fermented over a six-week time course. The unfermented samples were characterized by a distinct phyllosphere microbiome, while the endosphere revealed a high similarity. During fermentation, significant microbial shifts were observed, whereby LAB were enhanced in all approaches but never numerically dominated. Among the LAB, Enterococcaceae were identified as the most dominant family in both plants. M. chamomilla community had higher relative abundances of Lactobacillaceae and Carnobacteriaceae, while C. officinalis showed a higher presence of Leuconostocaceae and Streptococcaceae. The natural leaf microbiome and the indigenous LAB communities of field-grown Asteraceae medicinal plants are plant-specific and habitat-specific and are subjected to significant shifts during fermentation. Leaf surfaces as well as leaf endospheres were identified as sources for biopreservative LAB.}, }
@article {pmid31524305, year = {2019}, author = {Amato, KR and Jeyakumar, T and Poinar, H and Gros, P}, title = {Shifting Climates, Foods, and Diseases: The Human Microbiome through Evolution.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {41}, number = {10}, pages = {e1900034}, doi = {10.1002/bies.201900034}, pmid = {31524305}, issn = {1521-1878}, abstract = {Human evolution has been punctuated by climate anomalies, structuring environments, deadly infections, and altering landscapes. How well humans adapted to these new circumstances had direct effects on fitness and survival. Here, how the gut microbiome could have contributed to human evolutionary success through contributions to host nutritional buffering and infectious disease resistance is reviewed. How changes in human genetics, diet, disease exposure, and social environments almost certainly altered microbial community composition is also explored. Emerging research points to the microbiome as a key player in host responses to environmental change. Therefore, the reciprocal interactions between humans and their microbes are likely to have shaped human patterns of local adaptation throughout our shared evolutionary history. Recent alterations in human lifestyle, however, are altering human microbiomes in unprecedented ways. The consequences of interrupted host-microbe relationships for human adaptive potential in the future are unknown.}, }
@article {pmid31522775, year = {2019}, author = {Requena, T and Velasco, M}, title = {The human microbiome in sickness and in health.}, journal = {Revista clinica espanola}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.rce.2019.07.004}, pmid = {31522775}, issn = {1578-1860}, abstract = {The study of the human microbiome has led to an exceptional increase in the current understanding of the importance of microbiota for health throughout all stages of life. Human microbial colonization occurs in the skin, genitourinary system and, mainly, in the oral cavity and intestinal tract. In these locations, the human microbiota establishes a symbiotic relationship with the host and helps maintain the physiological homeostasis. Lifestyle, age, diet and use of antibiotics are the main regulators of the composition and functionality of human microbiota. Recent studies have indicated the reduction in microbial diversity as one of the contributors to the development of diseases. In addition to phylogenetic diversity studies, further metagenomic studies are needed at the functional level of the human microbiome to improve our understanding of its involvement in human health.}, }
@article {pmid31520544, year = {2020}, author = {Polkowska-Pruszyńska, B and Gerkowicz, A and Krasowska, D}, title = {The gut microbiome alterations in allergic and inflammatory skin diseases - an update.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {34}, number = {3}, pages = {455-464}, doi = {10.1111/jdv.15951}, pmid = {31520544}, issn = {1468-3083}, abstract = {The human microbiome is a wide range of microorganisms residing in and on our body. The homeostasis between host immune system and the microbial environment allows mutual benefits and protection. Physiological bacterial colonization is essential for the establishment of organism immunity. The human microbiota ecosystem can be divided into several compartments, out of which intestinal flora strongly affects our health and plays a crucial role in the pathophysiology of many diseases. The gastrointestinal tract, being a major guardian of the immune system, maintains the homeostasis with the commensal microorganisms by tolerating the typical flora antigens. The dysbiosis may trigger an inflammatory response followed by tissue damage or autoimmune processes. The gut microbiome alterations are linked to the pathogenesis of the allergic, cardiovascular, gastrointestinal, metabolic, neurodevelopmental, psychiatric and neurodegenerative diseases and cancer. Moreover, there is increasing evidence connecting the skin condition with the gastrointestinal microbiome, which has been described as the skin-gut axis. The aim of this study was to review the literature regarding the role of the gut microbiome alterations in the pathogenesis of selected allergic and inflammatory skin diseases.}, }
@article {pmid31519129, year = {2019}, author = {Ndika, J and Seemab, U and Poon, WL and Fortino, V and El-Nezami, H and Karisola, P and Alenius, H}, title = {Silver, titanium dioxide, and zinc oxide nanoparticles trigger miRNA/isomiR expression changes in THP-1 cells that are proportional to their health hazard potential.}, journal = {Nanotoxicology}, volume = {13}, number = {10}, pages = {1380-1395}, doi = {10.1080/17435390.2019.1661040}, pmid = {31519129}, issn = {1743-5404}, abstract = {After over a decade of nanosafety research, it is indisputable that the vast majority of nano-sized particles induce a plethora of adverse cellular responses - the severity of which is linked to the material's physicochemical properties. Differentiated THP-1 cells were previously exposed for 6 h and 24 h to silver, titanium dioxide, and zinc oxide nanoparticles at the maximum molar concentration at which no more than 15% cellular cytotoxicity was observed. All three nanoparticles differed in extent of induction of biological pathways corresponding to immune response signaling and metal ion homeostasis. In this study, we integrated gene and miRNA expression profiles from the same cells to propose miRNA biomarkers of adverse exposure to metal-based nanoparticles. We employed RNA sequencing together with a quantitative strategy that also enables analysis of the overlooked repertoire of length and sequence miRNA variants called isomiRs. Whilst only modest changes in expression were observed within the first 6 h of exposure, the miRNA/isomiR (miR) profiles of each nanoparticle were unique. Via canonical correlation and pathway enrichment analyses, we identified a co-regulated miR-mRNA cluster, predicted to be highly relevant for cellular response to metal ion homeostasis. These miRs were annotated to be canonical or variant isoforms of hsa-miR-142-5p, -342-3p, -5100, -6087, -6894-3p, and -7704. Hsa-miR-5100 was differentially expressed in response to each nanoparticle in both the 6 h and 24 h exposures. Taken together, this co-regulated miR-mRNA cluster could represent potential biomarkers of sub-toxic metal-based nanoparticle exposure.}, }
@article {pmid31502535, year = {2019}, author = {Forsberg, KJ and Bhatt, IV and Schmidtke, DT and Javanmardi, K and Dillard, KE and Stoddard, BL and Finkelstein, IJ and Kaiser, BK and Malik, HS}, title = {Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31502535}, issn = {2050-084X}, support = {R01 GM105691/GM/NIGMS NIH HHS/United States ; F31 GM125201/GM/NIGMS NIH HHS/United States ; R01 GM124131/GM/NIGMS NIH HHS/United States ; F-1808//Welch Foundation/International ; }, mesh = {Bacterial Proteins/genetics/isolation &amp; purification/*metabolism ; CRISPR-Associated Protein 9/*antagonists &amp; inhibitors ; Enzyme Inhibitors/isolation &amp; purification/*metabolism ; Feces/microbiology/virology ; Humans ; Metagenomics ; *Microbiota ; Mouth/microbiology/virology ; Viral Proteins/genetics/isolation &amp; purification/*metabolism ; }, abstract = {CRISPR-Cas systems protect bacteria and archaea from phages and other mobile genetic elements, which use small anti-CRISPR (Acr) proteins to overcome CRISPR-Cas immunity. Because Acrs are challenging to identify, their natural diversity and impact on microbial ecosystems are underappreciated. To overcome this discovery bottleneck, we developed a high-throughput functional selection to isolate ten DNA fragments from human oral and fecal metagenomes that inhibit Streptococcus pyogenes Cas9 (SpyCas9) in Escherichia coli. The most potent Acr from this set, AcrIIA11, was recovered from a Lachnospiraceae phage. We found that AcrIIA11 inhibits SpyCas9 in bacteria and in human cells. AcrIIA11 homologs are distributed across diverse bacteria; many distantly-related homologs inhibit both SpyCas9 and a divergent Cas9 from Treponema denticola. We find that AcrIIA11 antagonizes SpyCas9 using a different mechanism than other previously characterized Type II-A Acrs. Our study highlights the power of functional selection to uncover widespread Cas9 inhibitors within diverse microbiomes.}, }
@article {pmid31502171, year = {2020}, author = {Kumar, M and Singh, P and Murugesan, S and Vetizou, M and McCulloch, J and Badger, JH and Trinchieri, G and Al Khodor, S}, title = {Microbiome as an Immunological Modifier.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2055}, number = {}, pages = {595-638}, doi = {10.1007/978-1-4939-9773-2_27}, pmid = {31502171}, issn = {1940-6029}, abstract = {Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.}, }
@article {pmid31495055, year = {2019}, author = {Boto, L and Pineda, M and Pineda, R}, title = {Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it.}, journal = {The FEBS journal}, volume = {286}, number = {20}, pages = {3959-3967}, doi = {10.1111/febs.15054}, pmid = {31495055}, issn = {1742-4658}, support = {CGL2016-75262-P//Dirección General de Investigación Científica y Técnica/ ; }, abstract = {Horizontal gene transfer (HGT) is widespread among prokaryotes driving their evolution. In this paper, we review the potential impact in humans of the HGT between prokaryotes living in close association with humans in two scenarios: horizontal transfer in human microbiomes and transfer between microbes living in human managed environments. Although our vision is focused on the possible impact of these transfers in the propagation of antibiotic resistance genes or pathogenicity determinants, we also discuss possible human physiological adaptations via gene transfer between resident and occasional bacteria in the human microbiome.}, }
@article {pmid31493521, year = {2019}, author = {Fielding, RA and Reeves, AR and Jasuja, R and Liu, C and Barrett, BB and Lustgarten, MS}, title = {Muscle strength is increased in mice that are colonized with microbiota from high-functioning older adults.}, journal = {Experimental gerontology}, volume = {127}, number = {}, pages = {110722}, pmid = {31493521}, issn = {1873-6815}, support = {K01 AG050700/AG/NIA NIH HHS/United States ; }, abstract = {Evidence in support of a gut-muscle axis has been reported in rodents, but studies in older adult humans are limited. Accordingly, the primary goals of the present study were to compare gut microbiome composition in older adults that differed in terms of the percentage of whole body lean mass and physical functioning (high-functioning, HF, n = 18; low-functioning, LF, n = 11), and to evaluate the causative role of the gut microbiome on these variables by transferring fecal samples from older adults into germ-free mice. Family-level Prevotellaceae, genus-level Prevotella and Barnesiella, and the bacterial species Barnesiella intestinihominis were higher in HF older adults at the initial study visit, at a 1-month follow-up visit, in HF human fecal donors, and in HF-colonized mice, when compared with their LF counterparts. Grip strength was significantly increased by 6.4% in HF-, when compared with LF-colonized mice. In contrast, despite significant differences for the percentage of whole body lean mass and physical functioning when comparing the human fecal donors, the percentage of whole body lean mass and treadmill endurance capacity were not different when comparing human microbiome-containing mice. In sum, these data suggest a role for gut bacteria on the maintenance of muscle strength, but argue against a role for gut bacteria on the maintenance of the percentage of whole body lean mass or endurance capacity, findings that collectively add to elucidation of the gut-muscle axis in older adults.}, }
@article {pmid31493090, year = {2019}, author = {Wheeler, KM and Liss, MA}, title = {The Microbiome and Prostate Cancer Risk.}, journal = {Current urology reports}, volume = {20}, number = {10}, pages = {66}, pmid = {31493090}, issn = {1534-6285}, mesh = {Animals ; Gastrointestinal Microbiome/physiology ; Humans ; Male ; Mice ; Microbiota/*physiology ; Prostate/*microbiology/virology ; Prostatic Neoplasms/etiology/*microbiology/*therapy/virology ; Urine/microbiology/virology ; Urogenital System/microbiology ; }, abstract = {PURPOSE OF THE REVIEW: There is an abundance of evidence that the human microbiome plays an important and nuanced role in controlling human metabolism, immunity, and cancer. Herein we aim to review the most current research looking at prostate cancer and its link with the gut and genitourinary microbiome. There is now a host of evidence for a unique genitourinary (GU) microbiome. The prostate microbiota, to include viral, bacterial, fungal, and parasitic contributions, as assessed from formalin-fixed tissue is described nicely in the study by Banerjee et al. Further hierarchical analysis by this group found a unique microbiome signature for higher Gleason score cancers and validation PCR studies noted a marked number of viral genomic insertions into host DNA. Shretha et al. also recently established unique GU microbiomes in patients with prostate cancer or benign prostate pathology based on urine samples. The gut microbiome likely also has an indirect but significant role in prostate cancer development and treatment. Liss et al. and Golombos et al. found significant associations between specific gut microbiota and prostate cancer. Interestingly, the balance of inflammatory and anti-inflammatory bacterial lipopolysaccharides, production of bile salts, and metabolism of dietary fiber to short chain fatty acids all likely play important roles in creating systemic pro- or anti-carcinogenic states. In terms of prostate cancer treatment effects, Sfanos et al. noted a unique microbial signature in patients undergoing oral androgen deprivation therapy (ADT) as compared with prostate cancer patients not on ADT. Patients undergoing ADT also had enrichment of bacterial metabolic pathways promoting androgen synthesis. Together, these studies have identified a unique GU microbiome and linked both the GU microbiome and unique gut microbial signatures with prostate cancer and prostate cancer treatments. Whether this information can be used in cancer prevention, treatment, or diagnosis are areas of ongoing and active research.}, }
@article {pmid31492655, year = {2019}, author = {Soto-Perez, P and Bisanz, JE and Berry, JD and Lam, KN and Bondy-Denomy, J and Turnbaugh, PJ}, title = {CRISPR-Cas System of a Prevalent Human Gut Bacterium Reveals Hyper-targeting against Phages in a Human Virome Catalog.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {3}, pages = {325-335.e5}, pmid = {31492655}, issn = {1934-6069}, support = {DP5 OD021344/OD/NIH HHS/United States ; R01 HL122593/HL/NHLBI NIH HHS/United States ; }, mesh = {Actinobacteria/virology ; Bacteria/genetics/*virology ; Bacteriophages/*genetics ; Base Sequence ; *CRISPR-Cas Systems ; DNA, Bacterial/analysis ; DNA, Viral/analysis ; Databases, Genetic ; Gastrointestinal Tract/*microbiology ; Genome, Bacterial ; Genome, Viral ; Humans ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {Bacteriophages are abundant within the human gastrointestinal tract, yet their interactions with gut bacteria remain poorly understood, particularly with respect to CRISPR-Cas immunity. Here, we show that the type I-C CRISPR-Cas system in the prevalent gut Actinobacterium Eggerthella lenta is transcribed and sufficient for specific targeting of foreign and chromosomal DNA. Comparative analyses of E. lenta CRISPR-Cas systems across (meta)genomes revealed 2 distinct clades according to cas sequence similarity and spacer content. We assembled a human virome database (HuVirDB), encompassing 1,831 samples enriched for viral DNA, to identify protospacers. This revealed matches for a majority of spacers, a marked increase over other databases, and uncovered &quot;hyper-targeted&quot; phage sequences containing multiple protospacers targeted by several E. lenta strains. Finally, we determined the positional mismatch tolerance of observed spacer-protospacer pairs. This work emphasizes the utility of merging computational and experimental approaches for determining the function and targets of CRISPR-Cas systems.}, }
@article {pmid31492538, year = {2020}, author = {Wang, S and Ryan, CA and Boyaval, P and Dempsey, EM and Ross, RP and Stanton, C}, title = {Maternal Vertical Transmission Affecting Early-life Microbiota Development.}, journal = {Trends in microbiology}, volume = {28}, number = {1}, pages = {28-45}, doi = {10.1016/j.tim.2019.07.010}, pmid = {31492538}, issn = {1878-4380}, abstract = {The association of the human microbiome with health outcomes has attracted much interest toward its therapeutic manipulation. The likelihood of modulating the human microbiome in early life is high and offers great potential to exert profound effects on human development since the early microbiota shows more flexibility compared to that of adults. The human microbiota, being similar to human genetics, can be transmitted from mother to infant, providing insights into early microbiota acquisition, subsequent development, and potential opportunities for intervention. Here, we review adaptations of the maternal microbiota during pregnancy, birth, and infancy, the acquisition and succession of early-life microbiota, and highlight recent efforts to elucidate mother-to-infant microbiota transmission. We further discuss how the mother-to-infant microbial transmission is shaped; and finally we address potential directions for future studies to promote our understanding within this field.}, }
@article {pmid31489307, year = {2019}, author = {Cammarota, G and Putignani, L and Gasbarrini, A}, title = {Gut microbiome beats two to zero host genome.}, journal = {Hepatobiliary surgery and nutrition}, volume = {8}, number = {4}, pages = {378-380}, pmid = {31489307}, issn = {2304-3881}, }
@article {pmid31488215, year = {2019}, author = {Badal, VD and Wright, D and Katsis, Y and Kim, HC and Swafford, AD and Knight, R and Hsu, CN}, title = {Challenges in the construction of knowledge bases for human microbiome-disease associations.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {129}, pmid = {31488215}, issn = {2049-2618}, abstract = {The last few years have seen tremendous growth in human microbiome research, with a particular focus on the links to both mental and physical health and disease. Medical and experimental settings provide initial sources of information about these links, but individual studies produce disconnected pieces of knowledge bounded in context by the perspective of expert researchers reading full-text publications. Building a knowledge base (KB) consolidating these disconnected pieces is an essential first step to democratize and accelerate the process of accessing the collective discoveries of human disease connections to the human microbiome. In this article, we survey the existing tools and development efforts that have been produced to capture portions of the information needed to construct a KB of all known human microbiome-disease associations and highlight the need for additional innovations in natural language processing (NLP), text mining, taxonomic representations, and field-wide vocabulary standardization in human microbiome research. Addressing these challenges will enable the construction of KBs that help identify new insights amenable to experimental validation and potentially clinical decision support.}, }
@article {pmid31481604, year = {2019}, author = {Basu Thakur, P and Long, AR and Nelson, BJ and Kumar, R and Rosenberg, AF and Gray, MJ}, title = {Complex Responses to Hydrogen Peroxide and Hypochlorous Acid by the Probiotic Bacterium Lactobacillus reuteri.}, journal = {mSystems}, volume = {4}, number = {5}, pages = {}, pmid = {31481604}, issn = {2379-5077}, abstract = {Inflammatory diseases of the gut are associated with increased intestinal oxygen concentrations and high levels of inflammatory oxidants, including hydrogen peroxide (H2O2) and hypochlorous acid (HOCl), which are antimicrobial compounds produced by the innate immune system. This contributes to dysbiotic changes in the gut microbiome, including increased populations of proinflammatory enterobacteria (Escherichia coli and related species) and decreased levels of health-associated anaerobic Firmicutes and Bacteroidetes The pathways for H2O2 and HOCl resistance in E. coli have been well studied, but little is known about how commensal and probiotic bacteria respond to inflammatory oxidants. In this work, we have characterized the transcriptomic response of the anti-inflammatory, gut-colonizing Gram-positive probiotic Lactobacillus reuteri to both H2O2 and HOCl. L. reuteri mounts distinct but overlapping responses to each of these stressors, and both gene expression and survival were strongly affected by the presence or absence of oxygen. Oxidative stress response in L. reuteri required several factors not found in enterobacteria, including the small heat shock protein Lo18, polyphosphate kinase 2, and RsiR, an L. reuteri-specific regulator of anti-inflammatory mechanisms.IMPORTANCE Reactive oxidants, including hydrogen peroxide and hypochlorous acid, are antimicrobial compounds produced by the immune system during inflammation. Little is known, however, about how many important types of bacteria present in the human microbiome respond to these oxidants, especially commensal and other health-associated species. We have now mapped the stress response to both H2O2 and HOCl in the intestinal lactic acid bacterium Lactobacillus reuteri.}, }
@article {pmid31478123, year = {2019}, author = {Abid, MB and Koh, CJ}, title = {Probiotics in health and disease: fooling Mother Nature?.}, journal = {Infection}, volume = {47}, number = {6}, pages = {911-917}, pmid = {31478123}, issn = {1439-0973}, mesh = {Gastrointestinal Microbiome ; Humans ; Observational Studies as Topic ; Probiotics/*therapeutic use ; Randomized Controlled Trials as Topic ; *Terminology as Topic ; }, abstract = {Probiotics are ubiquitous, consumption by the general public is common, and the dogma remains that they are beneficial for general and gut health. However, evolving evidence suggests a potentially &quot;harmful&quot; impact of many commercially available probiotics. There is also significant variability in formulations that leads to a lack of a universally acceptable definition of probiotics. In this perspective, we review the flaws with definition, relevant observational and randomized studies that showed both positive and negative impacts on health and disease, unbiased interpretation of key trials, emerging evidence from microbiome and immuno-oncological studies, and impact on systemic immunity. We propose that caution be exercised prior to endorsements of their illness-directed consumption and rampant general usage. As a deeper understanding of the human microbiome accrues and our ability to manipulate this complex ecosystem improves, the probiotic of tomorrow might be the precision tool that deals with diseases on a broad front. Gut microbiome, akin to fingerprints, is indigenous to an individual and 'one size fits all' prescription strategy should be discouraged until a more universally acceptable 'favorable taxa' or a 'personalized probiotic,' to complement an individual's native microbiota, gets fashioned.}, }
@article {pmid31475212, year = {2019}, author = {Godoy-Vitorino, F}, title = {Human microbial ecology and the rising new medicine.}, journal = {Annals of translational medicine}, volume = {7}, number = {14}, pages = {342}, pmid = {31475212}, issn = {2305-5839}, abstract = {The first life forms on earth were Prokaryotic, and the evolution of all Eukaryotic life occurred with the help of bacteria. Animal-associated microbiota also includes members of the archaea, fungi, protists, and viruses. The genomes of this host-associated microbial life are called the microbiome. Across the mammalian tree, microbiomes guarantee the development of immunity, physiology, and resistance to pathogens. In humans, all surfaces and cavities are colonized by a microbiome, maintained by a careful balance between the host response and its colonizers-thus humans are considered now supraorganisms. These microbiomes supply essential ecosystem services that benefit health through homeostasis, and the loss of the indigenous microbiota leads to dysbiosis, which can have significant consequences to disease. This educational review aims to describe the importance of human microbial ecology, explain the ecological terms applied to the study of the human microbiome, developments within the cutting-edge microbiome field, and implications to diagnostic and treatment.}, }
@article {pmid31474424, year = {2019}, author = {Derrien, M and Alvarez, AS and de Vos, WM}, title = {The Gut Microbiota in the First Decade of Life.}, journal = {Trends in microbiology}, volume = {27}, number = {12}, pages = {997-1010}, doi = {10.1016/j.tim.2019.08.001}, pmid = {31474424}, issn = {1878-4380}, abstract = {Appreciation of the importance of the gut microbiome is growing, and it is becoming increasingly relevant to identify preventive or therapeutic solutions targeting it. The composition and function of the gut microbiota are relatively well described for infants (less than 3 years) and adults, but have been largely overlooked in pre-school (3-6 years) and primary school-age (6-12 years) children, as well as teenagers (12-18 years). Early reports suggested that the infant microbiota would attain an adult-like structure at the age of 3 years, but recent studies have suggested that microbiota development may take longer. This development time is of key importance because there is evidence to suggest that deviations in this development may have consequences in later life. In this review, we provide an overview of current knowledge concerning the gut microbiota, its evolution, variation, and response to dietary challenges during the first decade of life with a focus on healthy pre-school and primary school-age children (up to 12 years) from various populations around the globe. This knowledge should facilitate the identification of diet-based approaches targeting individuals of this age group, to promote the development of a healthy microbiota in later life.}, }
@article {pmid31473416, year = {2019}, author = {Yan, ZZ and Chen, QL and Zhang, YJ and He, JZ and Hu, HW}, title = {Antibiotic resistance in urban green spaces mirrors the pattern of industrial distribution.}, journal = {Environment international}, volume = {132}, number = {}, pages = {105106}, doi = {10.1016/j.envint.2019.105106}, pmid = {31473416}, issn = {1873-6750}, mesh = {Australia ; Cities ; Drug Resistance, Microbial/*genetics ; Environmental Monitoring ; *Genes, Bacterial ; Industry ; *Parks, Recreational ; *Poaceae ; Real-Time Polymerase Chain Reaction ; Soil/*chemistry ; Soil Microbiology ; }, abstract = {Urban green spaces are closely related to the activities and health of urban residents. Turf grass and soil are two major interfaces between the environmental and human microbiome, which represent potential pathways for the spread of antibiotic resistance genes (ARGs) from environmental to human microbiome through skin-surface contact. However, the information regarding the prevalence of ARGs in urban green spaces and drivers in shaping their distribution patterns remain unclear. Here, we profiled a wide spectrum of ARGs in grass phyllosphere and soils from 40 urban parks across Greater Melbourne, Australia, using high throughput quantitative PCR. A total of 217 and 218 unique ARGs and MGEs were detected in grass phyllosphere and soils, respectively, conferring resistance to almost all major classes of antibiotics commonly used in human and animals. The plant microbiome contained a core resistome, which occupied >84% of the total abundance of ARGs. In contrast, no core resistome was identified in the soil microbiome. The difference between plant and soil resistome composition was attributed to the difference in bacterial community structure and intensity of environmental and anthropogenic influence. Most importantly, the abundance of ARGs in urban green spaces was significantly positively related to industrial factors including total number of business, number of manufacturing, and number of electricity, gas, water and waste services in the region. Structural equation models further revealed that industrial distribution was a major factor shaping the ARG profiles in urban green spaces after accounting for multiple drivers. These findings have important implications for mitigation of the potential risks posed by ARGs to urban residents.}, }
@article {pmid31464810, year = {2019}, author = {Putignani, L and Gasbarrini, A and Dallapiccola, B}, title = {Potential of multiomics technology in precision medicine.}, journal = {Current opinion in gastroenterology}, volume = {35}, number = {6}, pages = {491-498}, pmid = {31464810}, issn = {1531-7056}, abstract = {PURPOSE OF REVIEW: The 'precision medicine' refers to the generation of identification and classification criteria for advanced taxonomy of patients, exploiting advanced models to infer optimized clinical decisions for each disease phenotype.<br><br>RECENT FINDINGS: The current article reviews new advances in the past 18 months on the microbiomics science intended as new discipline contributing to advanced 'precision medicine'. Recently published data highlight the importance of multidimensional data in the description of deep disease phenotypes, including microbiome and immune profiling, and support the efficacy of the systems medicine to better stratify patients, hence optimizing diagnostics, clinical management and response to treatments.<br><br>SUMMARY: The articles referenced in this review help inform the reader on new decision-support systems that can be based on multiomics patients' data including microbiome and immune profiling. These harmonized and integrated data can be elaborated by artificial intelligence to generate optimized diagnostic pipelines and clinical interventions.}, }
@article {pmid31457107, year = {2018}, author = {Herd, P and Palloni, A and Rey, F and Dowd, JB}, title = {Social and population health science approaches to understand the human microbiome.}, journal = {Nature human behaviour}, volume = {2}, number = {11}, pages = {808-815}, pmid = {31457107}, issn = {2397-3374}, support = {P30 AG017266/AG/NIA NIH HHS/United States ; R01 AG041868/AG/NIA NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; UL1 TR000427/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Interdisciplinary Communication ; Interdisciplinary Research/organization &amp; administration/trends ; *Microbiota ; Public Health/methods/trends ; Social Medicine/*methods ; }, abstract = {The microbiome is now considered our 'second genome' with potentially comparable importance to the genome in determining human health. There is, however, a relatively limited understanding of the broader environmental factors, particularly social conditions, that shape variation in human microbial communities. Fulfilling the promise of microbiome research - particularly the microbiome's potential for modification - will require collaboration between biologists and social and population scientists. For life scientists, the plasticity and adaptiveness of the microbiome calls for an agenda to understand the sensitivity of the microbiome to broader social environments already known to be powerful predictors of morbidity and mortality. For social and population scientists, attention to the microbiome may help answer nagging questions about the underlying biological mechanisms that link social conditions to health. We outline key substantive and methodological advances that can be made if collaborations between social and population health scientists and life scientists are strategically pursued.}, }
@article {pmid31456069, year = {2019}, author = {Chen, J and Douglass, J and Prasath, V and Neace, M and Atrchian, S and Manjili, MH and Shokouhi, S and Habibi, M}, title = {The microbiome and breast cancer: a review.}, journal = {Breast cancer research and treatment}, volume = {178}, number = {3}, pages = {493-496}, doi = {10.1007/s10549-019-05407-5}, pmid = {31456069}, issn = {1573-7217}, abstract = {The human microbiome plays an integral role in physiology, with most microbes considered benign or beneficial. However, some microbes are known to be detrimental to human health, including organisms linked to cancers and other diseases characterized by aberrant inflammation. Dysbiosis, a state of microbial imbalance with harmful bacteria species outcompeting benign bacteria, can lead to maladies including cancer. The microbial composition varies across body sites, with the gut, urogenital, and skin microbiomes particularly well characterized. However, the microbiome associated with normal breast tissue and breast diseases is poorly understood. Collectively, studies have shown that breast tissue has a distinct microbiome with particular species enriched in the breast tissue itself, as well as the nipple aspirate and gut bacteria of women with breast cancer. More importantly, the breast and associated microbiomes may modulate therapeutic response and serve as potential biomarkers for diagnosing and staging breast cancer.}, }
@article {pmid31455640, year = {2019}, author = {Creekmore, BC and Gray, JH and Walton, WG and Biernat, KA and Little, MS and Xu, Y and Liu, J and Gharaibeh, RZ and Redinbo, MR}, title = {Mouse Gut Microbiome-Encoded β-Glucuronidases Identified Using Metagenome Analysis Guided by Protein Structure.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31455640}, issn = {2379-5077}, abstract = {Gut microbial β-glucuronidase (GUS) enzymes play important roles in drug efficacy and toxicity, intestinal carcinogenesis, and mammalian-microbial symbiosis. Recently, the first catalog of human gut GUS proteins was provided for the Human Microbiome Project stool sample database and revealed 279 unique GUS enzymes organized into six categories based on active-site structural features. Because mice represent a model biomedical research organism, here we provide an analogous catalog of mouse intestinal microbial GUS proteins-a mouse gut GUSome. Using metagenome analysis guided by protein structure, we examined 2.5 million unique proteins from a comprehensive mouse gut metagenome created from several mouse strains, providers, housing conditions, and diets. We identified 444 unique GUS proteins and organized them into six categories based on active-site features, similarly to the human GUSome analysis. GUS enzymes were encoded by the major gut microbial phyla, including Firmicutes (60%) and Bacteroidetes (21%), and there were nearly 20% for which taxonomy could not be assigned. No differences in gut microbial gus gene composition were observed for mice based on sex. However, mice exhibited gus differences based on active-site features associated with provider, location, strain, and diet. Furthermore, diet yielded the largest differences in gus composition. Biochemical analysis of two low-fat-associated GUS enzymes revealed that they are variable with respect to their efficacy of processing both sulfated and nonsulfated heparan nonasaccharides containing terminal glucuronides.IMPORTANCE Mice are commonly employed as model organisms of mammalian disease; as such, our understanding of the compositions of their gut microbiomes is critical to appreciating how the mouse and human gastrointestinal tracts mirror one another. GUS enzymes, with importance in normal physiology and disease, are an attractive set of proteins to use for such analyses. Here we show that while the specific GUS enzymes differ at the sequence level, a core GUSome functionality appears conserved between mouse and human gastrointestinal bacteria. Mouse strain, provider, housing location, and diet exhibit distinct GUSomes and gus gene compositions, but sex seems not to affect the GUSome. These data provide a basis for understanding the gut microbial GUS enzymes present in commonly used laboratory mice. Further, they demonstrate the utility of metagenome analysis guided by protein structure to provide specific sets of functionally related proteins from whole-genome metagenome sequencing data.}, }
@article {pmid31455639, year = {2019}, author = {Cao, L and Shcherbin, E and Mohimani, H}, title = {A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota.}, journal = {mSystems}, volume = {4}, number = {4}, pages = {}, pmid = {31455639}, issn = {2379-5077}, support = {DP2 GM137413/GM/NIGMS NIH HHS/United States ; }, abstract = {The human microbiome consists of thousands of different microbial species, and tens of thousands of bioactive small molecules are associated with them. These associated molecules include the biosynthetic products of microbiota and the products of microbial transformation of host molecules, dietary components, and pharmaceuticals. The existing methods for characterization of these small molecules are currently time consuming and expensive, and they are limited to the cultivable bacteria. Here, we propose a method for detecting microbiota-associated small molecules based on the patterns of cooccurrence of molecular and microbial features across multiple microbiomes. We further map each molecule to the clade in a phylogenetic tree that is responsible for its production/transformation. We applied our proposed method to the tandem mass spectrometry and metagenomics data sets collected by the American Gut Project and to microbiome isolates from cystic fibrosis patients and discovered the genes in the human microbiome responsible for the production of corynomycolenic acid, which serves as a ligand for human T cells and induces a specific immune response against infection. Moreover, our method correctly associated pseudomonas quinolone signals, tyrvalin, and phevalin with their known biosynthetic gene clusters.IMPORTANCE Experimental advances have enabled the acquisition of tandem mass spectrometry and metagenomics sequencing data from tens of thousands of environmental/host-oriented microbial communities. Each of these communities contains hundreds of microbial features (corresponding to microbial species) and thousands of molecular features (corresponding to microbial natural products). However, with the current technology, it is very difficult to identify the microbial species responsible for the production/biotransformation of each molecular feature. Here, we develop association networks, a new approach for identifying the microbial producer/biotransformer of natural products through cooccurrence analysis of metagenomics and mass spectrometry data collected on multiple microbiomes.}, }
@article {pmid31448542, year = {2020}, author = {Brüssow, H}, title = {Problems with the concept of gut microbiota dysbiosis.}, journal = {Microbial biotechnology}, volume = {13}, number = {2}, pages = {423-434}, pmid = {31448542}, issn = {1751-7915}, abstract = {The human microbiome research is with the notable exception of fecal transplantation still mostly in a descriptive phase. Part of the difficulty for translating research into medical interventions is due to the large compositional complexity of the microbiome resulting in datasets that need sophisticated statistical methods for their analysis and do not lend to industrial applications. Another part of the difficulty might be due to logical flaws in terminology particularly concerning 'dysbiosis' that avoids circular conclusions and is based on sound ecological and evolutionary reasoning. Many case-control studies are underpowered necessitating more meta-analyses that sort out consistent from spurious dysbiosis-disease associations. We also need for the microbiome a transition from statistical associations to causal relationships with diseases that fulfil a set of modified Koch's postulates for commensals. Disturbingly, the most sophisticated statistical analyses explain only a small percentage of the variance in the microbiome. Microbe-microbe interactions irrelevant to the host and stochastic processes might play a greater role than anticipated. To satisfy the concept of Karl Popper about conjectures and refutations in the scientific process, we should also conduct more experiments that try to refute the role of the commensal gut microbiota for human health and disease.}, }
@article {pmid31443276, year = {2019}, author = {Satokari, R}, title = {Modulation of Gut Microbiota for Health by Current and Next-Generation Probiotics.}, journal = {Nutrients}, volume = {11}, number = {8}, pages = {}, pmid = {31443276}, issn = {2072-6643}, support = {304490, 323156//Academy of Finland/International ; Senior Fellow Grant//Sigrid Juséliuksen Säätiö/International ; }, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Prebiotics ; *Probiotics ; *Synbiotics ; }, abstract = {The human gut microbiota is a complex ecosystem and has an essential role in maintaining intestinal and systemic health. Microbiota dysbiosis is associated with a number of intestinal and systemic conditions and its modulation for human health is of great interest. Gut microbiota is a source of novel health-promoting bacteria, often termed as next-generation probiotics in order to distinguish them from traditional probiotics. The previous lessons learned with traditional probiotics can help the development of next-generation probiotics that target specific health issues and needs.}, }
@article {pmid31442396, year = {2019}, author = {Mittelman, K and Burstein, D}, title = {Tiny Hidden Genes within Our Microbiome.}, journal = {Cell}, volume = {178}, number = {5}, pages = {1034-1035}, doi = {10.1016/j.cell.2019.07.039}, pmid = {31442396}, issn = {1097-4172}, abstract = {Exploration of tiny protein-coding sequences within the human microbiome reveals thousands of conserved gene families that have been overlooked by traditional analyses. These small proteins may play key roles in the crosstalk among bacteria within the microbiome and in interactions with their human hosts.}, }
@article {pmid31440433, year = {2019}, author = {Mu, X and Zhao, C and Yang, J and Wei, X and Zhang, J and Liang, C and Gai, Z and Zhang, C and Zhu, D and Wang, Y and Zhang, L}, title = {Group B Streptococcus colonization induces Prevotella and Megasphaera abundance-featured vaginal microbiome compositional change in non-pregnant women.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e7474}, pmid = {31440433}, issn = {2167-8359}, abstract = {Background: Previous studies have indicated that variations in the vaginal microbiome result in symptomatic conditions. Group B Streptococcus (GBS) is a significant neonatal pathogen and maternal vaginal colonization has been recognized as an important risk factor for neonatal disease. Therefore, it is important to discover the relationship between the composition of the vaginal microbiome and GBS colonization. This study explores the potential relationship between the composition of the vaginal microbiome and GBS colonization in non-pregnant Chinese women.<br><br>Methods: A total of 22 GBS-positive, non-pregnant women and 44 matched GBS-negative women were recruited for the current study. The composition of the vaginal microbiome was profiled by sequencing the 16S rRNA genes. The microbiome diversity and variation were then evaluated.<br><br>Results: The vaginal microbiome of the 66 subjects enrolled in the current study were compared and the results showed that GBS-positive women exhibited significant vaginal microbial differences compared with the GBS-negative women based on the analysis of similarities (r = 0.306, p < 0.01). The relative abundance of the bacterial genus Lactobacillus (p < 0.01) was significantly lower in the GBS-positive group, while the abundances of the bacterial genera Prevotella (p < 0.01), Megasphaera (p < 0.01), and Streptococcus (p < 0.01) were significantly higher in the GBS-positive group.<br><br>Discussion: The current study addressed significant variations across the communities of the vaginal microbiome in GBS-positive and GBS-negative women in a Chinese cohort, which paves the way for a larger cohort-based clinical validation study and the development of therapeutic probiotics in the future.}, }
@article {pmid31440325, year = {2019}, author = {Guo, J and Lv, Q and Ariff, A and Zhang, X and Peacock, CS and Song, Y and Wen, X and Saiganesh, A and Melton, PE and Dykes, GA and Moses, EK and LE Souëf, PN and Lu, F and Zhang, G}, title = {Western oropharyngeal and gut microbial profiles are associated with allergic conditions in Chinese immigrant children.}, journal = {The World Allergy Organization journal}, volume = {12}, number = {8}, pages = {100051}, pmid = {31440325}, issn = {1939-4551}, abstract = {Background: The allergy epidemic resulting from western environment/lifestyles is potentially due to modifications of the human microbiome. Therefore, it is of interest to study immigrants living in a western environment as well as their counterparts in the country of origin to understand differences in their microbiomes and health status.<br><br>Methods: We investigated 58 Australian Chinese (AC) children from Perth, Western Australia as well as 63 Chinese-born Chinese (CC) children from a city in China. Oropharyngeal (OP) and fecal samples were collected. To assess the microbiomes, 16s ribosomal RNA (rRNA) sequencing for variable regions V3 and V4 was used. Skin prick tests (SPT) were performed to measure the children's atopic status. Information on food allergy and wheezing were acquired from a questionnaire.<br><br>Results: AC children had more allergic conditions than CC children. The alpha diversity (mean species diversity) of both OP and gut microbiome was lower in AC children compared to CC children for richness estimate (Chao1), while diversity evenness (Shannon index) was higher. The beta diversity (community similarity) displayed a distinct separation of the OP and gut microbiota between AC and CC children. An apparent difference in microbial abundance was observed for many bacteria. In AC children, we sought to establish consistent trends in bacterial relative abundance that are either higher or lower in AC versus CC children and higher or lower in children with allergy versus those without allergy. The majority of OP taxa showed a consistent trend while the majority of fecal taxa showed a contrasting trend.<br><br>Conclusion: Distinct differences in microbiome compositions were found in both oropharyngeal and fecal samples of AC and CC children. The association of the OP microbiome with allergic condition is different from that of the gut microbiome in AC children. The microbiome profiles are changed by the western environment/lifestyle and are associated with allergies in Chinese immigrant children in Australia.}, }
@article {pmid31437194, year = {2019}, author = {Pendegraft, AH and Guo, B and Yi, N}, title = {Bayesian hierarchical negative binomial models for multivariable analyses with applications to human microbiome count data.}, journal = {PloS one}, volume = {14}, number = {8}, pages = {e0220961}, pmid = {31437194}, issn = {1932-6203}, mesh = {Bayes Theorem ; DNA, Bacterial/*genetics ; Databases, Factual ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Internet ; Microbial Consortia/*genetics ; Microbiota/*genetics ; Multivariate Analysis ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA ; }, abstract = {The analyses of large volumes of metagenomic data extracted from aggregate populations of microscopic organisms residing on and in the human body are advancing contemporary understandings of the integrated participation of microbes in human health and disease. Next generation sequencing technology facilitates said analyses in terms of diversity, community composition, and differential abundance by filtering and binning microbial 16S rRNA genes extracted from human tissues into operational taxonomic units. However, current statistical tools restrict study designs to investigations of limited numbers of host characteristics mediated by limited numbers of samples potentially yielding a loss of relevant information. This paper presents a Bayesian hierarchical negative binomial model as an efficient technique capable of compensating for multivariable sets including tens or hundreds of host characteristics as covariates further expanding analyses of human microbiome count data. Simulation studies reveal that the Bayesian hierarchical negative binomial model provides a desirable strategy by often outperforming three competing negative binomial model in terms of type I error while simultaneously maintaining consistent power. An application of the Bayesian hierarchical negative binomial model using subsets of the open data published by the American Gut Project demonstrates an ability to identify operational taxonomic units significantly differentiable among persons diagnosed by a medical professional with either inflammatory bowel disease or irritable bowel syndrome that are consistent with contemporary gastrointestinal literature.}, }
@article {pmid31433970, year = {2019}, author = {Spencer, SP and Fragiadakis, GK and Sonnenburg, JL}, title = {Pursuing Human-Relevant Gut Microbiota-Immune Interactions.}, journal = {Immunity}, volume = {51}, number = {2}, pages = {225-239}, doi = {10.1016/j.immuni.2019.08.002}, pmid = {31433970}, issn = {1097-4180}, support = {R01 DK085025/DK/NIDDK NIH HHS/United States ; T32 DK007056/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Gastrointestinal Microbiome/*immunology ; Homeostasis ; *Host-Pathogen Interactions ; Humans ; *Immune System ; Immunity ; Patient-Centered Care ; }, abstract = {The gut microbiota is a complex and plastic network of diverse organisms intricately connected with human physiology. Recent advances in profiling approaches of both the microbiota and the immune system now enable a deeper exploration of immunity-microbiota connections. An important next step is to elucidate a human-relevant &quot;map&quot; of microbial-immune wiring while focusing on animal studies to probe a prioritized subset of interactions. Here, we provide an overview of this field's current status and discuss two approaches for establishing priorities for detailed investigation: (1) longitudinal intervention studies in humans probing the dynamics of both the microbiota and the immune system and (2) the study of traditional populations to assess lost features of human microbial identity whose absence may be contributing to the rise of immunological disorders. These human-centered approaches offer a judicious path forward to understand the impact of the microbiota in immune development and function.}, }
@article {pmid31425594, year = {2019}, author = {Mougeot, JC and Stevens, CB and Morton, DS and Brennan, MT and Mougeot, FB}, title = {Oral Microbiome and Cancer Therapy-Induced Oral Mucositis.}, journal = {Journal of the National Cancer Institute. Monographs}, volume = {2019}, number = {53}, pages = {}, doi = {10.1093/jncimonographs/lgz002}, pmid = {31425594}, issn = {1745-6614}, abstract = {Characterization of the role of oral microbiome in cancer therapy-induced oral mucositis (CTOM) is critical in preventing the clinically deleterious effects on patients' health that are associated with CTOM. Funding initiatives related to the National Institutes of Health human microbiome project have resulted in groundbreaking advancements in biology and medicine during the last decade. These advancements have shown that a human being is in fact a superorganism made of human cells and associated symbiotic or commensal microbiota. In this review, we describe the state of science as it relates to fundamental knowledge on oral microbiome and its role in CTOM. We also discuss how state-of-the-art technologies and systems biology tools may be used to help tackle the difficult challenges ahead to develop effective treatments or preventive therapies for oral mucositis. We make a clear distinction between disease processes pertaining to the oral microbiome, which includes opportunistic pathogens that may be defined as pathobionts, and those infectious disease processes initiated by exogenous pathogens. We also explored the extent to which knowledge from the gastrointestinal tract in disease and intestinal mucositis could help us better understand CTOM pathobiology. Finally, we propose a model in which the oral microbiome participates in the current five-step CTOM pathobiology model. With the advent of more sophisticated metagenomics technologies and methods of analysis, much hope lies ahead to implement an effective holistic approach to treat cancer patients affected by CTOM.}, }
@article {pmid31417531, year = {2019}, author = {Conteville, LC and Oliveira-Ferreira, J and Vicente, ACP}, title = {Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter-Gatherer Group.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1743}, pmid = {31417531}, issn = {1664-302X}, abstract = {Human groups that still maintain traditional modes of subsistence (hunter-gatherers and rural agriculturalists) represent human groups non-impacted by urban-industrialized lifestyles, and therefore their gut microbiome provides the basis for understanding the human microbiome evolution and its association with human health and disease. The Yanomami is the largest semi-nomadic hunter-gatherer group of the Americas, exploring different niches of the Amazon rainforest in Brazil and Venezuela. Here, based on shotgun metagenomic data, we characterized the gut microbiome of the Yanomami from Brazil and compared taxonomically and functionally with the Yanomami from Venezuela, with other traditional groups from the Amazon and an urban-industrialized group. Taxonomic biomarkers were identified to each South American traditional group studied, including each Yanomami group. Broader levels of functional categories poorly discriminated the traditional and urban-industrialized groups, but the stratification of these categories revealed clear segregation of these groups. The Yanomami/Brazil gut microbiome presented unique functional features, such as a higher abundance of gene families involved in regulation/cell signaling, motility/chemotaxis, and virulence, contrasting with the gut microbiomes from the Yanomami/Venezuela and the other groups. Our study revealed biomarkers, and taxonomic and functional features that distinguished the gut microbiome of Yanomami/Brazil and Yanomami/Venezuela individuals, despite their shared lifestyle, culture, and genetic background. These differences may be a reflection of the environmental and seasonal diversity of the niches they explore. Overall, their microbiome profiles are shared with South American and African traditional groups, probably due to their lifestyle. The unique features identified within the Yanomami highlight the bias imposed by underrepresented sampling, and factors such as variations over space and time (seasonality) that impact, mainly, the hunter-gatherers.}, }
@article {pmid31417492, year = {2019}, author = {Sudo, N}, title = {Biogenic Amines: Signals Between Commensal Microbiota and Gut Physiology.}, journal = {Frontiers in endocrinology}, volume = {10}, number = {}, pages = {504}, pmid = {31417492}, issn = {1664-2392}, abstract = {There is increasing interest in the interactions among the gut microbiota, gut, and brain, which is often referred to as the &quot;microbiota-gut-brain&quot; axis. Biogenic amines including dopamine, norepinephrine, serotonin, and histamines are all generated by commensal gut microorganisms and are suggested to play roles as signaling molecules mediating the function of the &quot;microbiota-gut-brain&quot; axis. In addition, such amines generated in the gut have attracted attention in terms of possible clues into the etiologies of depression, anxiety, and even psychosis. This review covers the latest research related to the potential role of microbe-derived amines such as catecholamine, serotonin, histamine, as well as other trace amines, in modulating not only gut physiology but also brain function of the host. Further attention in this field can offer not only insight into expanding the fundamental roles and impacts of the human microbiome, but also further offer new therapeutic strategies for psychological disorders based on regulating the balance of resident bacteria.}, }
@article {pmid31417479, year = {2019}, author = {Lacorte, E and Gervasi, G and Bacigalupo, I and Vanacore, N and Raucci, U and Parisi, P}, title = {A Systematic Review of the Microbiome in Children With Neurodevelopmental Disorders.}, journal = {Frontiers in neurology}, volume = {10}, number = {}, pages = {727}, pmid = {31417479}, issn = {1664-2295}, abstract = {Background and Purpose: A relationship between gut microbiome and central nervous system (CNS), have been suggested. The human microbiome may have an influence on brain's development, thus implying that dysbiosis may contribute in the etiology and progression of some neurological/neuropsychiatric disorders. The objective of this systematic review was to identify evidence on the characterization and potential distinctive traits of the microbiome of children with neurodevelopmental disorders, as compared to healthy children. Methods: The review was performed following the methodology described in the Cochrane handbook for systematic reviews, and was reported based on the PRISMA statement for reporting systematic reviews and meta-analyses. All literature published up to April 2019 was retrieved searching the databases PubMed, ISI Web of Science and the Cochrane Database of Systematic Reviews. Only observational studies, published in English and reporting data on the characterization of the microbiome in humans aged 0-18 years with a neurodevelopmental disorder were included. Neurodevelopmental disorders were categorized according to the definition included in the Diagnostic and Statistical Manual of Mental Disorders, version 5 (DSM-5). Results: Bibliographic searches yielded 9,237 records. One study was identified through other data sources. A total of 16 studies were selected based on their relevance and pertinence to the topic of the review, and were then applied the predefined inclusion and exclusion criteria. A total of 10 case-control studies met the inclusion criteria, and were thus included in the qualitative analysis and applied the NOS score. Two studies reported data on the gut microbiome of children with ADHD, while 8 reported data on either the gut (n = 6) or the oral microbiome (n = 2) of children with ASD. Conclusions: All the 10 studies included in this review showed a high heterogeneity in terms of sample size, gender, clinical issues, and type of controls. This high heterogeneity, along with the small sample size of the included studies, strongly limited the external validity of results. The quality assessment performed using the NOS score showed an overall low to moderate methodological quality of the included studies. To better clarify the potential role of microbiome in patients with neurodevelopmental disorders, further high-quality observational (specifically cohort) studies are needed.}, }
@article {pmid31415755, year = {2019}, author = {Tierney, BT and Yang, Z and Luber, JM and Beaudin, M and Wibowo, MC and Baek, C and Mehlenbacher, E and Patel, CJ and Kostic, AD}, title = {The Landscape of Genetic Content in the Gut and Oral Human Microbiome.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {2}, pages = {283-295.e8}, pmid = {31415755}, issn = {1934-6069}, support = {R00 ES023504/ES/NIEHS NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; R21 ES025052/ES/NIEHS NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; K99 ES023504/ES/NIEHS NIH HHS/United States ; }, mesh = {Bacteria/classification/genetics ; Biodiversity ; Cluster Analysis ; DNA Fingerprinting ; Databases, Factual ; Gastrointestinal Tract/microbiology ; Genetic Heterogeneity ; Host Microbial Interactions ; Humans ; Metagenome/*genetics ; Metagenomics ; Microbiota/*genetics/*physiology ; Mouth/microbiology ; Multigene Family ; Phenotype ; }, abstract = {Despite substantial interest in the species diversity of the human microbiome and its role in disease, the scale of its genetic diversity, which is fundamental to deciphering human-microbe interactions, has not been quantified. Here, we conducted a cross-study meta-analysis of metagenomes from two human body niches, the mouth and gut, covering 3,655 samples from 13 studies. We found staggering genetic heterogeneity in the dataset, identifying a total of 45,666,334 non-redundant genes (23,961,508 oral and 22,254,436 gut) at the 95% identity level. Fifty percent of all genes were &quot;singletons,&quot; or unique to a single metagenomic sample. Singletons were enriched for different functions (compared with non-singletons) and arose from sub-population-specific microbial strains. Overall, these results provide potential bases for the unexplained heterogeneity observed in microbiome-derived human phenotypes. One the basis of these data, we built a resource, which can be accessed at https://microbial-genes.bio.}, }
@article {pmid31410749, year = {2019}, author = {Zhang, F and Wang, M and Yang, J and Xu, Q and Liang, C and Chen, B and Zhang, J and Yang, Y and Wang, H and Shang, Y and Wang, Y and Mu, X and Zhu, D and Zhang, C and Yao, M and Zhang, L}, title = {Response of gut microbiota in type 2 diabetes to hypoglycemic agents.}, journal = {Endocrine}, volume = {66}, number = {3}, pages = {485-493}, doi = {10.1007/s12020-019-02041-5}, pmid = {31410749}, issn = {1559-0100}, abstract = {PURPOSE: Accumulated evidence has indicated that the gut microbiome affected the pharmacology of anti-diabetic agents, and their metabolic products induced by the agents transformed the structure of gastrointestinal microbiota in return. However, the studies around heredity, ethnicity, or living condition, referring to human microbiome were mostly represented by an occidental pattern partial and rare studies that focused on the effect of several first-line hypoglycemic agents on the gut flora in a single medical center. Therefore, we aimed to explore the interaction between gut microbiome and type 2 diabetes (T2D) or hypoglycemics in Chinese population.<br><br>METHODS: A total of 130 T2D patients with a specific hypoglycemic treatment and 50 healthy volunteers were enrolled in this study. Gut microbiome compositons were analyzed by 16S ribosomal RNA gene-based sequencing protocol.<br><br>RESULTS: Hypoglycemic agents contributed to the alteration of specific species in gut bacteria rather than its total diversity. Metformin increased the abundance of Spirochaete, Turicibacter, and Fusobacterium. Insulin also increased Fusobacterium, and α-glucosidase inhibitors (α-GIs) contributed to the plentitude of Bifidobacterium and Lactobacillus. Both metformin and insulin improved taurine and hypotaurine metabolism, and α-GI promoted several amino acid pathways. Although the community of gut microbiota with metformin and insulin showed similarity, significant differences were available in each diabetic group with hypoglycemia.<br><br>CONCLUSIONS: Gut microbiota is significantly associated with anti-diabetic agents. The gut microbiome and metabolism have shown respective characteristics in different T2D groups, which were also significantly different from the healthy group. This study provides some new insights for identification and exploration of the pathogenesis of T2D.}, }
@article {pmid31409863, year = {2019}, author = {Pereira, EM and de Mattos, CS and Dos Santos, OC and Ferreira, DC and de Oliveira, TLR and Laport, MS and de Oliveira Ferreira, E and Dos Santos, KRN}, title = {Staphylococcus hominis subspecies can be identified by SDS-PAGE or MALDI-TOF MS profiles.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {11736}, pmid = {31409863}, issn = {2045-2322}, abstract = {Staphylococcus hominis is part of the normal human microbiome. Two subspecies, S. hominis hominis (Shh) and S. hominis novobiosepticus (Shn), have clinical significance. Forty-nine S. hominis isolates were analyzed by the MicroScan automated system, SDS-PAGE and MALDI-TOF methods, followed by partial sequencing of the 16S rDNA gene. The trehalose fermentation test, disk diffusion and broth microdilution tests were used to identify (novobiocin test) and access the susceptibility to oxacillin and vancomycin of isolates. The SCCmec elements and genomic diversity were evaluated by PCR and PFGE methods, respectively. Profiles of 28 (57%; 8 Shh and 20 Shn) isolates corroborated with the results found in all the applied methods of identification. The remaining 21 (43%) isolates were phenotypically identified as Shh by MicroScan; however, they were identified as Shn by SDS-PAGE and mass spectral, and confirmed by 16S rDNA sequencing. Among 41 isolates identified as Shn by the molecular and mass spectrometry methods, 19 (41%) were novobiocin-sensitive, and the trehalose test indicated 11 positive isolates, which are considered atypical phenotypic results for this subspecies. In addition, 92.7% of the isolates identified as Shn by these methods carried mecA gene, while only 12.5% of the Shh isolates were positive. Together, the results highlighted the SDS-PAGE and MALDI-TOF MS methods as promising tools for discriminating S. hominis subspecies.}, }
@article {pmid31402904, year = {2019}, author = {Gargiullo, L and Del Chierico, F and D'Argenio, P and Putignani, L}, title = {Gut Microbiota Modulation for Multidrug-Resistant Organism Decolonization: Present and Future Perspectives.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1704}, pmid = {31402904}, issn = {1664-302X}, abstract = {The emergence of antimicrobial resistance (AMR) is of great concern to global public health. Treatment of multi-drug resistant (MDR) infections is a major clinical challenge: the increase in antibiotic resistance leads to a greater risk of therapeutic failure, relapses, longer hospitalizations, and worse clinical outcomes. Currently, there are no validated treatments for many MDR or pandrug-resistant (PDR) infections, and preventing the spread of these pathogens through hospital infection control procedures and antimicrobial stewardship programs is often the only tool available to healthcare providers. Therefore, new solutions to control the colonization of MDR pathogens are urgently needed. In this narrative review, we discuss current knowledge of microbiota-mediated mechanisms of AMR and strategies for MDR colonization control. We focus particularly on fecal microbiota transplantation for MDR intestinal decolonization and report updated literature on its current clinical use.}, }
@article {pmid31402586, year = {2019}, author = {Mora, D and Filardi, R and Arioli, S and Boeren, S and Aalvink, S and de Vos, WM}, title = {Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3.}, journal = {Microbial biotechnology}, volume = {12}, number = {6}, pages = {1371-1386}, pmid = {31402586}, issn = {1751-7915}, abstract = {The growing commercial interest in multi-strain formulations marketed as probiotics has not been accompanied by an equal increase in the evaluation of quality levels of these biotechnological products. The multi-strain product VSL#3 was used as a model to setup a microbiological characterization that could be extended to other formulations with high complexity. Shotgun metagenomics by deep Illumina sequencing was applied to DNA isolated from the commercial VSL#3 product to confirm strains identity safety and composition. Single-cell analysis was used to evaluate the cell viability, and β-galactosidase and urease activity have been used as marker to monitor the reproducibility of the production process. Similarly, these lots were characterized in detail by a metaproteomics approach for which a robust protein extraction protocol was combined with advanced mass spectrometry. The results identified over 1600 protein groups belonging to all strains present in the VSL#3 formulation. Of interest, only 3.2 % proteins showed significant differences mainly related to small variations in strain abundance. The protocols developed in this study addressed several quality criteria that are relevant for marketed multi-strain products and these represent the first efforts to define the quality of complex probiotic formulations such as VSL#3.}, }
@article {pmid31402174, year = {2019}, author = {Sberro, H and Fremin, BJ and Zlitni, S and Edfors, F and Greenfield, N and Snyder, MP and Pavlopoulos, GA and Kyrpides, NC and Bhatt, AS}, title = {Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes.}, journal = {Cell}, volume = {178}, number = {5}, pages = {1245-1259.e14}, pmid = {31402174}, issn = {1097-4172}, support = {K08 CA184420/CA/NCI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; S10 OD023452/OD/NIH HHS/United States ; }, abstract = {Small proteins are traditionally overlooked due to computational and experimental difficulties in detecting them. To systematically identify small proteins, we carried out a comparative genomics study on 1,773 human-associated metagenomes from four different body sites. We describe >4,000 conserved protein families, the majority of which are novel; ∼30% of these protein families are predicted to be secreted or transmembrane. Over 90% of the small protein families have no known domain and almost half are not represented in reference genomes. We identify putative housekeeping, mammalian-specific, defense-related, and protein families that are likely to be horizontally transferred. We provide evidence of transcription and translation for a subset of these families. Our study suggests that small proteins are highly abundant and those of the human microbiome, in particular, may perform diverse functions that have not been previously reported.}, }
@article {pmid31396188, year = {2019}, author = {Hietala, V and Horsma-Heikkinen, J and Carron, A and Skurnik, M and Kiljunen, S}, title = {The Removal of Endo- and Enterotoxins From Bacteriophage Preparations.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1674}, pmid = {31396188}, issn = {1664-302X}, abstract = {The production of phages for therapeutic purposes demands fast, efficient and scalable purification procedures. Phage lysates have a wide range of impurities, of which endotoxins of gram-negative bacteria and protein toxins produced by many pathogenic bacterial species are harmful to humans. The highest allowed endotoxin concentration for parenterally applied medicines is 5 EU/kg/h. The aim of this study was to evaluate the feasibility of different purification methods in endotoxin and protein toxin removal in the production of phage preparations for clinical use. In the purification assays, we utilized three phages: Escherichia phage vB_EcoM_fHoEco02, Acinetobacter phage vB_ApiM_fHyAci03, and Staphylococcus phage vB_SauM_fRuSau02. The purification methods tested in the study were precipitation with polyethylene glycol, ultracentrifugation, ultrafiltration, anion exchange chromatography, octanol extraction, two different endotoxin removal columns, and different combinations thereof. The efficiency of the applied purification protocols was evaluated by measuring phage titer and either endotoxins or staphylococcal enterotoxins A and C (SEA and SEC, respectively) from samples taken from different purification steps. The most efficient procedure in endotoxin removal was the combination of ultrafiltration and EndoTrap HD affinity column, which was able to reduce the endotoxin-to-phage ratio of vB_EcoM_fHoEco02 lysate from 3.5 × 104 Endotoxin Units (EU)/109 plaque forming units (PFU) to 0.09 EU/109 PFU. The combination of ultrafiltration and anion exchange chromatography resulted in ratio 96 EU/109 PFU, and the addition of octanol extraction step into this procedure still reduced this ratio threefold. The other methods tested either resulted to less efficient endotoxin removal or required the use of harmful chemicals that should be avoided when producing phage preparations for medical use. Ultrafiltration with 100,000 MWCO efficiently removed enterotoxins from vB_SauM_fRuSau02 lysate (from 1.3 to 0.06 ng SEA/109 PFU), and anion exchange chromatography reduced the enterotoxin concentration below 0.25 ng/ml, the detection limit of the assay.}, }
@article {pmid31388693, year = {2020}, author = {Stoyancheva, G}, title = {Study of helveticin gene in Lactobacillus crispatus strains and evaluation of its use as a phylogenetic marker.}, journal = {Archives of microbiology}, volume = {202}, number = {1}, pages = {205-208}, doi = {10.1007/s00203-019-01711-2}, pmid = {31388693}, issn = {1432-072X}, mesh = {*Genetic Markers/genetics ; Humans ; Lactobacillus/*genetics ; Lactobacillus crispatus/*classification/*genetics ; *Microbiota ; *Phylogeny ; Probiotics/classification ; }, abstract = {Lactobacilli are a part of the human microbiome in healthy humans. Studies of their physiological and genetic characteristics are the basis for their use in probiotic preparations. This report is a brief description of the helveticin gene found in two Lactobacillus crispatus strains, which are a part of the human microbiome. Our analysis showed that the two variants of the gene are not solely characteristic of strains isolated from humans. In the phylogenetic analysis, we found that the studied sequence (this gene) showed a significant difference between the species of the genus Lactobacillus and could be used as a phylogenetic marker.}, }
@article {pmid31387651, year = {2019}, author = {Roura, E and Depoortere, I and Navarro, M}, title = {Review: Chemosensing of nutrients and non-nutrients in the human and porcine gastrointestinal tract.}, journal = {Animal : an international journal of animal bioscience}, volume = {13}, number = {11}, pages = {2714-2726}, doi = {10.1017/S1751731119001794}, pmid = {31387651}, issn = {1751-732X}, mesh = {Animals ; Appetite ; Carbohydrate Metabolism ; Cholecystokinin/metabolism ; Enteroendocrine Cells/metabolism ; *Food Preferences ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/physiology ; Ghrelin/metabolism ; Glucagon-Like Peptide 1/metabolism ; Humans ; Intestinal Mucosa/metabolism ; Nutrients ; Peptide YY/metabolism ; Swine/microbiology/*physiology ; Taste ; }, abstract = {The gastrointestinal tract (GIT) is an interface between the external and internal milieus that requires continuous monitoring for nutrients or pathogens and toxic chemicals. The study of the physiological/molecular mechanisms, mediating the responses to the monitoring of the GIT contents, has been referred to as chemosensory science. While most of the progress in this area of research has been obtained in laboratory rodents and humans, significant steps forward have also been reported in pigs. The objective of this review was to update the current knowledge on nutrient chemosensing in pigs in light of recent advances in humans and laboratory rodents. A second objective relates to informing the existence of nutrient sensors with their functionality, particularly linked to the gut peptides relevant to the onset/offset of appetite. Several cell types of the intestinal epithelium such as Paneth, goblet, tuft and enteroendocrine cells (EECs) contain subsets of chemosensory receptors also found on the tongue as part of the taste system. In particular, EECs show specific co-expression patterns between nutrient sensors and/or transceptors (transport proteins with sensing functions) and anorexigenic hormones such as cholecystokinin (CCK), peptide tyrosine tyrosine (PYY) or glucagon-like peptide-1 (GLP-1), amongst others. In addition, the administration of bitter compounds has an inhibitory effect on GIT motility and on appetite through GLP-1-, CCK-, ghrelin- and PYY-labelled EECs in the human small intestine and colon. Furthermore, the mammalian chemosensory system is the target of some bacterial metabolites. Recent studies on the human microbiome have discovered that commensal bacteria have developed strategies to stimulate chemosensory receptors and trigger host cellular functions. Finally, the study of gene polymorphisms related to nutrient sensors explains differences in food choices, food intake and appetite between individuals.}, }
@article {pmid31383276, year = {2019}, author = {Chu, DM and Valentine, GC and Seferovic, MD and Aagaard, KM}, title = {The Development of the Human Microbiome: Why Moms Matter.}, journal = {Gastroenterology clinics of North America}, volume = {48}, number = {3}, pages = {357-375}, doi = {10.1016/j.gtc.2019.04.004}, pmid = {31383276}, issn = {1558-1942}, support = {R01 DK089201/DK/NIDDK NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; }, mesh = {Female ; Fetus/*microbiology ; Humans ; Infant, Newborn ; Maternal Nutritional Physiological Phenomena ; *Microbiota ; Pregnancy ; Uterus/microbiology ; }, abstract = {The human body is cohabitated with trillions of commensal bacteria that are essential for our health. However, certain bacteria can also cause diseases in the human host. Before the microbiome can be attributed to disease risk and pathogenesis, normal acquisition and development of the microbiome must be understood. Here, we explore the evidence surrounding in utero microbial exposures and the significant of this exposure in the proper development of the fetal and neonatal microbiome. We further explore the development of the fetal and neonatal microbiome and its relationship to preterm birth, feeding practices, and mode of delivery, and maternal diet.}, }
@article {pmid31379797, year = {2019}, author = {Lo Presti, A and Zorzi, F and Del Chierico, F and Altomare, A and Cocca, S and Avola, A and De Biasio, F and Russo, A and Cella, E and Reddel, S and Calabrese, E and Biancone, L and Monteleone, G and Cicala, M and Angeletti, S and Ciccozzi, M and Putignani, L and Guarino, MPL}, title = {Fecal and Mucosal Microbiota Profiling in Irritable Bowel Syndrome and Inflammatory Bowel Disease.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1655}, pmid = {31379797}, issn = {1664-302X}, abstract = {An imbalance in the bacterial species resulting in the loss of intestinal homeostasis has been described in inflammatory bowel diseases (IBD) and irritable bowel syndrome (IBS). In this prospective study, we investigated whether IBD and IBS patients exhibit specific changes in richness and distribution of fecal and mucosal-associated microbiota. Additionally, we assessed potential 16S rRNA gene amplicons biomarkers for IBD, IBS, and controls (CTRLs) by comparison of taxonomic composition. The relative abundance of bacteria, at phylum and genus/species levels, and the bacterial diversity were determined through 16S rRNA sequence-based fecal and mucosal microbiota analysis. Linear discriminant analysis effect size (LEfSe) was used for biomarker discovery associated to IBD and IBS as compared to CTRLs. In fecal and mucosal samples, the microbiota richness was characterized by a microbial diversity reduction, going from CTRLs to IBS to IBD. β-diversity analysis showed a clear separation between IBD and CTRLs and between IBD and IBS with no significant separation between IBS and CTRLs. β-diversity showed a clear separation between mucosa and stool samples in all the groups. In IBD, there was no difference between inflamed and not inflamed mucosa. Based upon the LEfSe data, the Anaerostipes and Ruminococcaceae were identified as the most differentially abundant bacterial taxa in CTRLs. Erysipelotrichi was identified as potential biomarker for IBS, while Gammaproteobacteria, Enterococcus, and Enterococcaceae for IBD. This study provides an overview of the alterations of microbiota and may aid in identifying potential 16S rRNA gene amplicons mucosal biomarkers for IBD and IBS.}, }
@article {pmid31378678, year = {2019}, author = {Colosimo, DA and Kohn, JA and Luo, PM and Piscotta, FJ and Han, SM and Pickard, AJ and Rao, A and Cross, JR and Cohen, LJ and Brady, SF}, title = {Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {2}, pages = {273-282.e7}, pmid = {31378678}, issn = {1934-6069}, support = {R01 AT009562/AT/NCCIH NIH HHS/United States ; }, mesh = {Angiogenic Proteins/agonists ; Animals ; Bacteria/*metabolism ; Cadaverine/metabolism/pharmacology ; Fatty Acids/metabolism/pharmacology ; Fermentation ; Germ-Free Life ; Histamine Agonists ; Host Microbial Interactions/*immunology/*physiology ; Humans ; Immune System ; Ligands ; Mice ; Mice, Inbred C57BL ; Microbiota/*immunology/*physiology ; Models, Animal ; Propionates/metabolism/pharmacology ; Receptors, G-Protein-Coupled/*agonists/metabolism ; Receptors, Histamine/drug effects ; Receptors, Neurotransmitter/agonists ; }, abstract = {Despite evidence linking the human microbiome to health and disease, how the microbiota affects human physiology remains largely unknown. Microbiota-encoded metabolites are expected to play an integral role in human health. Therefore, assigning function to these metabolites is critical to understanding these complex interactions and developing microbiota-inspired therapies. Here, we use large-scale functional screening of molecules produced by individual members of a simplified human microbiota to identify bacterial metabolites that agonize G-protein-coupled receptors (GPCRs). Multiple metabolites, including phenylpropanoic acid, cadaverine, 9-10-methylenehexadecanoic acid, and 12-methyltetradecanoic acid, were found to interact with GPCRs associated with diverse functions within the nervous and immune systems, among others. Collectively, these metabolite-receptor pairs indicate that diverse aspects of human health are potentially modulated by structurally simple metabolites arising from primary bacterial metabolism.}, }
@article {pmid31370220, year = {2019}, author = {Vitetta, L and Llewellyn, H and Oldfield, D}, title = {Gut Dysbiosis and the Intestinal Microbiome: Streptococcus thermophilus a Key Probiotic for Reducing Uremia.}, journal = {Microorganisms}, volume = {7}, number = {8}, pages = {}, pmid = {31370220}, issn = {2076-2607}, abstract = {In the intestines, probiotics can produce antagonistic effects such as antibiotic-like compounds, bactericidal proteins such as bacteriocins, and encourage the production of metabolic end products that may assist in preventing infections from various pathobionts (capable of pathogenic activity) microbes. Metabolites produced by intestinal bacteria and the adoptions of molecular methods to cross-examine and describe the human microbiome have refreshed interest in the discipline of nephology. As such, the adjunctive administration of probiotics for the treatment of chronic kidney disease (CKD) posits that certain probiotic bacteria can reduce the intestinal burden of uremic toxins. Uremic toxins eventuate from the over manifestation of glucotoxicity and lipotoxicity, increased activity of the hexosamine and polyol biochemical and synthetic pathways. The accumulation of advanced glycation end products that have been regularly associated with a dysbiotic colonic microbiome drives the overproduction of uremic toxins in the colon and the consequent local pro-inflammatory processes. Intestinal dysbiosis associated with significant shifts in abundance and diversity of intestinal bacteria with a resultant and maintained uremia promoting an uncontrolled mucosal pro-inflammatory state. In this narrative review we further address the efficacy of probiotics and highlighted in part the probiotic bacterium Streptococcus thermophilus as an important modulator of uremic toxins in the gut of patients diagnosed with chronic kidney disease. In conjunction with prudent nutritional practices it may be possible to prevent the progression of CKD and significantly downregulate mucosal pro-inflammatory activity with the administration of probiotics that contain S. thermophilus.}, }
@article {pmid31367386, year = {2019}, author = {Fall, NS and Lo, CI and Fournier, PE and Sokhna, C and Raoult, D and Fenollar, F and Lagier, JC}, title = {Arcanobacterium ihumii sp. nov., Varibaculum vaginae sp. nov. and Tessaracoccus timonensis sp. nov., isolated from vaginal swabs from healthy Senegalese women.}, journal = {New microbes and new infections}, volume = {31}, number = {}, pages = {100585}, pmid = {31367386}, issn = {2052-2975}, abstract = {Culturomics studies the microbial variety of the human microbiome by combining diversified culture conditions, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene identification. This study identifies three putative new bacterial species: Arcanobacterium ihumii sp. nov. strain Marseille-P5647T, Varibaculum vaginae sp. nov. strain Marseille-P5644T and Tessaracoccus timonensis sp. nov. strain Marseille-P5995T, which we describe according to the concept of taxonogenomics.}, }
@article {pmid31354638, year = {2019}, author = {Yin, G and Xia, Y}, title = {Assessing the Hybrid Effects of Neutral and Niche Processes on Gut Microbiome Influenced by HIV Infection.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1467}, pmid = {31354638}, issn = {1664-302X}, abstract = {That both stochastic neutral and deterministic niche forces are in effect in shaping the community assembly and diversity maintenance is becoming an increasingly important consensus. However, assessing the effects of disease on the balance between the two forces in the human microbiome has not been explored to the best of our knowledge. In this article, we applied a hybrid model to address this issue by analyzing the potential effect of HIV infection on the human gut microbiome and adopted a further step of multimodality testing to improve the interpretation of their model. Our study revealed that although niche process is the dominant force in shaping human gut microbial communities, niche process- and neutral process-driven taxa could coexist in the same microbiome, confirming the notion of their joint responsibility. However, we failed to detect the effect of HIV infection in changing the balance. This suggests that the rule governing community assembly and diversity maintenance may be changed by the disturbance from HIV infection-caused dysbiosis. Although we admit that the general question of disease effect on community assembly and diversity maintenance may still be an open question, our study presents the first piece of evidence to reject the significant influence of diseases.}, }
@article {pmid31339096, year = {2019}, author = {Pietilä, JP and Meri, T and Siikamäki, H and Tyyni, E and Kerttula, AM and Pakarinen, L and Jokiranta, TS and Kantele, A}, title = {Dientamoeba fragilis - the most common intestinal protozoan in the Helsinki Metropolitan Area, Finland, 2007 to 2017.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {24}, number = {29}, pages = {}, pmid = {31339096}, issn = {1560-7917}, abstract = {BackgroundDespite the global distribution of the intestinal protozoan Dientamoeba fragilis, its clinical picture remains unclear. This results from underdiagnosis: microscopic screening methods either lack sensitivity (wet preparation) or fail to reveal Dientamoeba (formalin-fixed sample).AimIn a retrospective study setting, we characterised the clinical picture of dientamoebiasis and compared it with giardiasis. In addition, we evaluated an improved approach to formalin-fixed samples for suitability in Dientamoeba diagnostics.MethodsThis study comprised four parts: (i) a descriptive part scrutinising rates of Dientamoeba findings; (ii) a methodological part analysing an approach to detect Dientamoeba-like structures in formalin samples; (iii) a clinical part comparing demographics and symptoms between patients with dientamoebiasis (n = 352) and giardiasis (n = 272), and (iv) a therapeutic part (n = 89 patients) investigating correlation between faecal eradication and clinical improvement.ResultsThe rate of Dientamoeba findings increased 20-fold after introducing criteria for Dientamoeba-like structures in formalin-fixed samples (88.9% sensitivity and 83.3% specificity). A further increase was seen after implementing faecal PCR. Compared with patients with giardiasis, the symptoms in the Dientamoeba group lasted longer and more often included abdominal pain, cramping, faecal urgency and loose rather than watery stools. Resolved symptoms correlated with successful faecal eradication (p < 0.001).ConclusionsPreviously underdiagnosed, Dientamoeba has become the most frequently recorded pathogenic enteroparasite in Finland. This presumably results from improved diagnostics with either PCR or detection of Dientamoeba-like structures in formalin-fixed samples, an approach applicable also in resource-poor settings. Symptoms of dientamoebiasis differ slightly from those of giardiasis; patients with distressing symptoms require treatment.}, }
@article {pmid31338330, year = {2019}, author = {Dong, Z and Chen, B and Pan, H and Wang, D and Liu, M and Yang, Y and Zou, M and Yang, J and Xiao, K and Zhao, R and Zheng, X and Zhang, L and Zhang, Y}, title = {Detection of Microbial 16S rRNA Gene in the Serum of Patients With Gastric Cancer.}, journal = {Frontiers in oncology}, volume = {9}, number = {}, pages = {608}, pmid = {31338330}, issn = {2234-943X}, abstract = {Aberrance in the blood bacterial microbiome has been identified and validated in several non-infectious diseases, including cancer. The occurrence and progression of gastric cancer has been found to be associated with alterations in the microbiome composition. However, the composition of the blood microbiome in patients with gastric cancer is not well-characterized. To test this hypothesis, we conducted a case-control study to investigate the microbiota compositions in the serum of patients with gastric cancer. The serum microbiome was investigated in patients with gastric cancer, atypical hyperplasia, chronic gastritis, and in healthy controls using 16S rRNA gene sequencing targeting the V1-V2 region. Our results revealed that the structure of the serum microbiome in gastric cancer was significantly different from all other groups, and alpha diversity decreased from the healthy control to patients with gastric cancer. The serum microbiome correlated significantly with tumor-node-metastasis (TNM) stage, lymphatic metastasis, tumor diameter, and invasion depth in gastric cancer. Three genera or species, namely, Acinetobacter, Bacteroides, Haemophilus parainfluenzae, were enriched in patients with gastric cancer, whereas Sphingomonas, Comamonas, and Pseudomonas stutzeri were enriched in the healthy control. Furthermore, the structure of serum microbiota differed between gastric cancer lymphatic metastasis and non-lymphatic metastasis. As a pilot investigation to characterizing the serum microbiome in gastric cancer, our study provided a foundation for improving our understanding of the role of microbiota in the pathogenesis of gastric cancer.}, }
@article {pmid31337891, year = {2019}, author = {Kumar, M and Ji, B and Zengler, K and Nielsen, J}, title = {Modelling approaches for studying the microbiome.}, journal = {Nature microbiology}, volume = {4}, number = {8}, pages = {1253-1267}, doi = {10.1038/s41564-019-0491-9}, pmid = {31337891}, issn = {2058-5276}, mesh = {Bacteria/metabolism ; Disease ; Health ; Humans ; Metabolomics ; Metagenome ; Microbial Interactions ; *Microbiota/genetics/physiology ; *Models, Theoretical ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Advances in metagenome sequencing of the human microbiome have provided a plethora of new insights and revealed a close association of this complex ecosystem with a range of human diseases. However, there is little knowledge about how the different members of the microbial community interact with each other and with the host, and we lack basic mechanistic understanding of these interactions related to health and disease. Mathematical modelling has been demonstrated to be highly advantageous for gaining insights into the dynamics and interactions of complex systems and in recent years, several modelling approaches have been proposed to enhance our understanding of the microbiome. Here, we review the latest developments and current approaches, and highlight how different modelling strategies have been applied to unravel the highly dynamic nature of the human microbiome. Furthermore, we discuss present limitations of different modelling strategies and provide a perspective of how modelling can advance understanding and offer new treatment routes to impact human health.}, }
@article {pmid31337077, year = {2019}, author = {Scribano, D and Marzano, V and Levi Mortera, S and Sarshar, M and Vernocchi, P and Zagaglia, C and Putignani, L and Palamara, AT and Ambrosi, C}, title = {Insights into the Periplasmic Proteins of Acinetobacter baumannii AB5075 and the Impact of Imipenem Exposure: A Proteomic Approach.}, journal = {International journal of molecular sciences}, volume = {20}, number = {14}, pages = {}, pmid = {31337077}, issn = {1422-0067}, mesh = {Acinetobacter Infections/microbiology ; Acinetobacter baumannii/*drug effects/*metabolism ; Amino Acids/metabolism ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Dose-Response Relationship, Drug ; Drug Resistance, Bacterial ; Gene Expression Regulation, Bacterial/drug effects ; Imipenem/*pharmacology ; Lipid Metabolism/drug effects ; Microbial Sensitivity Tests ; Oxidative Stress ; Periplasmic Proteins/genetics/*metabolism ; Phenotype ; Proteome ; Proteomics/methods ; }, abstract = {Carbapenem-resistant Acinetobacter baumannii strains cause life-threatening infections due to the lack of therapeutic options. Although the main mechanisms underlying antibiotic-resistance have been extensively studied, the general response to maintain bacterial viability under antibiotic exposure deserves to be fully investigated. Since the periplasmic space contains several proteins with crucial cellular functions, besides carbapenemases, we decided to study the periplasmic proteome of the multidrug-resistant (MDR) A. baumannii AB5075 strain, grown in the absence and presence of imipenem (IMP). Through the proteomic approach, 65 unique periplasmic proteins common in both growth conditions were identified: eight proteins involved in protein fate, response to oxidative stress, energy metabolism, antibiotic-resistance, were differentially expressed. Among them, ABUW_1746 and ABUW_2363 gene products presented the tetratricopeptide repeat motif, mediating protein-protein interactions. The expression switch of these proteins might determine specific protein interactions to better adapt to changing environmental conditions. ABUW_2868, encoding a heat shock protein likely involved in protection against oxidative stress, was upregulated in IMP-exposed bacteria. Accordingly, the addition of periplasmic proteins from A. baumannii cultured with IMP increased bacterial viability in an antioxidant activity assay. Overall, this study provides the first insights about the composition of the periplasmic proteins of a MDR A. baumannii strain, its biological response to IMP and suggests possible new targets to develop alternative antibiotic drugs.}, }
@article {pmid31337018, year = {2019}, author = {Wakabayashi, R and Nakahama, Y and Nguyen, V and Espinoza, JL}, title = {The Host-Microbe Interplay in Human Papillomavirus-Induced Carcinogenesis.}, journal = {Microorganisms}, volume = {7}, number = {7}, pages = {}, pmid = {31337018}, issn = {2076-2607}, abstract = {Every year nearly half a million new cases of cervix cancer are diagnosed worldwide, making this malignancy the fourth commonest cancer in women. In 2018, more than 270,000 women died of cervix cancer globally with 85% of them being from developing countries. The majority of these cancers are caused by the infection with carcinogenic strains of human papillomavirus (HPV), which is also causally implicated in the development of other malignancies, including cancer of the anus, penis cancer and head and neck cancer. HPV is by far the most common sexually transmitted infection worldwide, however, most infected people do not develop cancer and do not even have a persistent infection. The development of highly effective HPV vaccines against most common high-risk HPV strains is a great medical achievement of the 21st century that could prevent up to 90% of cervix cancers. In this article, we review the current understanding of the balanced virus-host interaction that can lead to either virus elimination or the establishment of persistent infection and ultimately malignant transformation. We also highlight the influence of certain factors inherent to the host, including the immune status, genetic variants and the coexistence of other microbe infections and microbiome composition in the dynamic of HPV infection induced carcinogenesis.}, }
@article {pmid31336807, year = {2019}, author = {Hamidi, B and Wallace, K and Alekseyenko, AV}, title = {MODIMA, a Method for Multivariate Omnibus Distance Mediation Analysis, Allows for Integration of Multivariate Exposure-Mediator-Response Relationships.}, journal = {Genes}, volume = {10}, number = {7}, pages = {}, pmid = {31336807}, issn = {2073-4425}, support = {R01 LM012517/LM/NLM NIH HHS/United States ; R21 TR002513/TR/NCATS NIH HHS/United States ; UL1 TR001450/TR/NCATS NIH HHS/United States ; U54 CA210962/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Computational Biology/*methods ; Computer Simulation ; Datasets as Topic ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Models, Statistical ; Multivariate Analysis ; }, abstract = {Many important exposure-response relationships, such as diet and weight, can be influenced by intermediates, such as the gut microbiome. Understanding the role of these intermediates, the mediators, is important in refining cause-effect theories and discovering additional medical interventions (e.g., probiotics, prebiotics). Mediation analysis has been at the heart of behavioral health research, rapidly gaining popularity with the biomedical sciences in the last decade. A specific analytic challenge is being able to incorporate an entire 'omics assay as a mediator. To address this challenge, we propose a hypothesis testing framework for multivariate omnibus distance mediation analysis (MODIMA). We use the power of energy statistics, such as partial distance correlation, to allow for analysis of multivariate exposure-mediator-response triples. Our simulation results demonstrate the favorable statistical properties of our approach relative to the available alternatives. Finally, we demonstrate the application of the proposed methods in two previously published microbiome datasets. Our framework adds a new tool to the toolbox of approaches to the integration of 'omics big data.}, }
@article {pmid31328778, year = {2019}, author = {Pebenito, AM and Liu, M and Nazzal, L and Blaser, MJ}, title = {Development of a Humanized Murine Model for the Study of Oxalobacter formigenes Intestinal Colonization.}, journal = {The Journal of infectious diseases}, volume = {220}, number = {11}, pages = {1848-1858}, pmid = {31328778}, issn = {1537-6613}, abstract = {BACKGROUND: Oxalobacter formigenes are bacteria that colonize the human gut and degrade oxalate, a component of most kidney stones. Findings of clinical and epidemiological studies suggest that O. formigenes colonization reduces the risk for kidney stones. We sought to develop murine models to allow investigating O. formigenes in the context of its native human microbiome.<br><br>METHODS: For humanization, we transplanted pooled feces from healthy, noncolonized human donors supplemented with a human O. formigenes strain into recipient mice. We transplanted microbiota into mice that were treated with broad-spectrum antibiotics to suppress their native microbiome, were germ free, or received humanization without pretreatment or received sham gavage (controls).<br><br>RESULTS: All humanized mice were stably colonized with O. formigenes through 8 weeks after gavage, whereas mice receiving sham gavage remained uncolonized (P < .001). Humanization significantly changed the murine intestinal microbial community structure (P < .001), with humanized germ-free and antibiotic-treated groups overlapping in β-diversity. Both germ-free and antibiotic-treated mice had significantly increased numbers of human species compared with sham-gavaged mice (P < .001).<br><br>CONCLUSIONS: Transplanting mice with human feces and O. formigenes introduced new microbial populations resembling the human microbiome, with stable O. formigenes colonization; such models can define optimal O. formigenes strains to facilitate clinical trials.}, }
@article {pmid31327398, year = {2019}, author = {O'Gorman, DB and Pena-Diaz, AM and Drosdowech, D and Faber, KJ and Athwal, GS and Burton, JP and Al, K and Huang, T and Qiu, B}, title = {Response to Long et al regarding: &quot;Cutibacterium acnes and the shoulder microbiome&quot;.}, journal = {Journal of shoulder and elbow surgery}, volume = {28}, number = {8}, pages = {e277-e278}, doi = {10.1016/j.jse.2019.04.047}, pmid = {31327398}, issn = {1532-6500}, }
@article {pmid31323792, year = {2019}, author = {Santiago-Rodriguez, TM and Hollister, EB}, title = {Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut.}, journal = {Viruses}, volume = {11}, number = {7}, pages = {}, pmid = {31323792}, issn = {1999-4915}, abstract = {The virome is comprised of endogenous retroviruses, eukaryotic viruses, and bacteriophages and is increasingly being recognized as an essential part of the human microbiome. The human virome is associated with Type-1 diabetes (T1D), Type-2 diabetes (T2D), Inflammatory Bowel Disease (IBD), Human Immunodeficiency Virus (HIV) infection, and cancer. Increasing evidence also supports trans-kingdom interactions of viruses with bacteria, small eukaryotes and host in disease progression. The present review focuses on virus ecology and biology and how this translates mostly to human gut virome research. Current challenges in the field and how the development of bioinformatic tools and controls are aiding to overcome some of these challenges are also discussed. Finally, the present review also focuses on how human gut virome research could result in translational and clinical studies that may facilitate the development of therapeutic approaches.}, }
@article {pmid31322866, year = {2019}, author = {Huddleston, JP and Thoden, JB and Dopkins, BJ and Narindoshvili, T and Fose, BJ and Holden, HM and Raushel, FM}, title = {Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12.}, journal = {Biochemistry}, volume = {58}, number = {31}, pages = {3340-3353}, pmid = {31322866}, issn = {1520-4995}, support = {R01 GM115921/GM/NIGMS NIH HHS/United States ; R01 GM122825/GM/NIGMS NIH HHS/United States ; }, abstract = {The ydj gene cluster is found in 80% of sequenced Escherichia coli genomes and other closely related species in the human microbiome. On the basis of the annotations of the enzymes located in this cluster, it is expected that together they catalyze the catabolism of an unknown carbohydrate. The focus of this investigation is on YdjI, which is in the ydj gene cluster of E. coli K-12. It is predicted to be a class II aldolase of unknown function. Here we describe a structural and functional characterization of this enzyme. YdjI catalyzes the hydrogen/deuterium exchange of the pro-S hydrogen at C3 of dihydroxyacetone phosphate (DHAP). In the presence of DHAP, YdjI catalyzes an aldol condensation with a variety of aldo sugars. YdjI shows a strong preference for higher-order (seven-, eight-, and nine-carbon) monosaccharides with specific hydroxyl stereochemistries and a negatively charged terminus (carboxylate or phosphate). The best substrate is l-arabinuronic acid with an apparent kcat of 3.0 s-1. The product, l-glycero-l-galacto-octuluronate-1-phosphate, has a kcat/Km value of 2.1 × 103 M-1 s-1 in the retro-aldol reaction with YdjI. This is the first recorded synthesis of l-glycero-l-galacto-octuluronate-1-phosphate and six similar carbohydrates. The crystal structure of YdjI, determined to a nominal resolution of 1.75 Å (Protein Data Bank entry 6OFU), reveals unusual positions for two arginine residues located near the active site. Computational docking was utilized to distinguish preferable binding orientations for l-glycero-l-galacto-octuluronate-1-phosphate. These results indicate a possible alternative binding orientation for l-glycero-l-galacto-octuluronate-1-phosphate compared to that observed in other class II aldolases, which utilize shorter carbohydrate molecules.}, }
@article {pmid31321880, year = {2019}, author = {Peters, DL and Wang, W and Zhang, X and Ning, Z and Mayne, J and Figeys, D}, title = {Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome.}, journal = {Proteomics}, volume = {19}, number = {16}, pages = {e1800363}, doi = {10.1002/pmic.201800363}, pmid = {31321880}, issn = {1615-9861}, support = {GPH-129340//CIHR/Canada ; MOP-114872//CIHR/Canada ; }, abstract = {The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signaling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases are reviewed.}, }
@article {pmid31319564, year = {2019}, author = {Ticinesi, A and Nouvenne, A and Cerundolo, N and Catania, P and Prati, B and Tana, C and Meschi, T}, title = {Gut Microbiota, Muscle Mass and Function in Aging: A Focus on Physical Frailty and Sarcopenia.}, journal = {Nutrients}, volume = {11}, number = {7}, pages = {}, pmid = {31319564}, issn = {2072-6643}, mesh = {Aged ; Animals ; *Frailty ; Gastrointestinal Microbiome/*physiology ; Humans ; Muscle, Skeletal/*physiology ; Sarcopenia/*physiopathology ; }, abstract = {Human gut microbiota is able to influence the host physiology by regulating multiple processes, including nutrient absorption, inflammation, oxidative stress, immune function, and anabolic balance. Aging is associated with reduced microbiota biodiversity, increased inter-individual variability, and over-representation of pathobionts, and these phenomena may have great relevance for skeletal muscle mass and function. For this reason, the presence of a gut-muscle axis regulating the onset and progression of age-related physical frailty and sarcopenia has been recently hypothesized. In this narrative review, we summarize the studies supporting a possible association between gut microbiota-related parameters with measures of muscle mass, muscle function, and physical performance in animal models and humans. Reduced muscle mass has been associated with distinct microbiota composition and reduced fermentative capacity in mice, and the administration of probiotics or butyrate to mouse models of muscle wasting has been associated with improved muscle mass. However, no studies have targeted the human microbiome associated with sarcopenia. Limited evidence from human studies shows an association between microbiota composition, involving key taxa such as Faecalibacterium and Bifidobacterium, and grip strength. Similarly, few studies conducted on patients with parkinsonism showed a trend towards a different microbiota composition in those with reduced gait speed. No studies have assessed the association of fecal microbiota with other measures of physical performance. However, several studies, mainly with a cross-sectional design, suggest an association between microbiota composition and frailty, mostly assessed according to the deficit accumulation model. Namely, frailty was associated with reduced microbiota biodiversity, and lower representation of butyrate-producing bacteria. Therefore, we conclude that the causal link between microbiota and physical fitness is still uncertain due to the lack of targeted studies and the influence of a large number of covariates, including diet, exercise, multimorbidity, and polypharmacy, on both microbiota composition and physical function in older age. However, the relationship between gut microbiota and physical function remains a very promising area of research for the future.}, }
@article {pmid31316375, year = {2019}, author = {Novotný, M and Klimova, B and Valis, M}, title = {Microbiome and Cognitive Impairment: Can Any Diets Influence Learning Processes in a Positive Way?.}, journal = {Frontiers in aging neuroscience}, volume = {11}, number = {}, pages = {170}, pmid = {31316375}, issn = {1663-4365}, abstract = {The aim of this review is to summarize the effect of human intestinal microbiome on cognitive impairments and to focus primarily on the impact of diet and eating habits on learning processes. Better understanding of the microbiome could revolutionize the possibilities of therapy for many diseases. The authors performed a literature review of available studies on the research topic describing the influence of human microbiome and diet on cognitive impairment or learning processes found in the world's acknowledged databases Web of Science, PubMed, Springer, and Scopus. The digestive tube is populated by billions of living microorganisms including viruses, bacteria, protozoa, helminths, and microscopic fungi. In adulthood, under physiological conditions, the intestinal microbiome appears to be relatively steady. However, it is not true that it would not be influenced, both in the positive sense of the word and in the negative one. The basic pillars that maintain a steady microbiome are genetics, lifestyle, diet and eating habits, geography, and age. It is reported that the gastrointestinal tract and the brain communicate with each other through several pathways and one can speak about gut-brain axis. New evidence is published every year about the association of intestinal dysbiosis and neurological/psychiatric diseases. On the other hand, specific diets and eating habits can have a positive effect on a balanced microbiota composition and thus contribute to the enhancement of cognitive functions, which are important for any learning process.}, }
@article {pmid31315786, year = {2019}, author = {Zhou, H and Suo, J and Zhu, J}, title = {[Therapeutic Relevance of Human Microbiota and Lung Cancer].}, journal = {Zhongguo fei ai za zhi = Chinese journal of lung cancer}, volume = {22}, number = {7}, pages = {464-469}, pmid = {31315786}, issn = {1999-6187}, mesh = {Carcinogenesis ; Humans ; Lung Neoplasms/*microbiology/pathology/*therapy ; *Microbiota ; }, abstract = {The human microbiome is closely related to human health status. Disruption of the symbiotic balance of the human microbiome is commonly found in systematic diseases such as diabetes, obesity, and chronic gastric diseases. The human microbiome confers benefits or disease susceptibility to the human body through multiple pathways, associated with approximately 20% of malignancies. The incidence and mortality of lung cancer (LC) in men in China are the highest among all malignancies, which is a serious threat to human health. Emerging evidence has suggested that the human microbiota may be closely related to lung cancer at multiple levels, e.g., by affecting metabolic, inflammatory, or immune pathways. At the same time, the human microbiota affects the efficacy of lung cancer on chemoradiotherapy, gene therapy, immunotherapy and other treatments. Immunotherapy is a promising method for the treatment of malignancies such as lung cancer, but the efficacy of immune checkpoint inhibitors in patients is heterogeneous. Preclinical studies based on lung cancer cell lines suggest that the intestinal microbiota can modulate responses to anti--PD-1 therapy through interactions with the host immune system. But for lung cancer patients, whether the intestinal flora can still regulate immunotherapy remains controversial. In this mini-review, we summarize current research findings describing therapeutic relevance of human microbiota and lung cancer. A better knowledge of the interplay between the human microbiome and lung cancer may promote the development of innovative strategies for prevention and personalized treatment in lung cancer.}, }
@article {pmid31312608, year = {2019}, author = {Gallon, P and Parekh, M and Ferrari, S and Fasolo, A and Ponzin, D and Borroni, D}, title = {Metagenomics in ophthalmology: Hypothesis or real prospective?.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {23}, number = {}, pages = {e00355}, pmid = {31312608}, issn = {2215-017X}, abstract = {Metagenomic analysis was originally associated with the studies of genetic material from environmental samples. But, with the advent of the Human Microbiome Project, it has now been applied in clinical practices. The ocular surface (OS) is the most exposed part of the eye, colonized by several microbial communities (both, OS and environmental) that contribute to the maintenance of the physiological state. Limited knowledge has been acquired on these microbes due to the limitations of conventional diagnostic methods. Emerging fields of research are focusing on Next Generation Sequencing (NGS) technologies to obtain reliable information on the OS microbiome. Currently only pre-specified pathogens can be detected by conventional culture-based techniques or Polymerase Chain Reaction (PCR), but there are conditions to state whether metagenomics could revolutionize the diagnosis of ocular diseases. The aim of this review is to provide an updated overview of the studies involving NGS technology for OS microbiome.}, }
@article {pmid31307469, year = {2019}, author = {Huang, C and Shi, G}, title = {Smoking and microbiome in oral, airway, gut and some systemic diseases.}, journal = {Journal of translational medicine}, volume = {17}, number = {1}, pages = {225}, pmid = {31307469}, issn = {1479-5876}, abstract = {The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn's disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.}, }
@article {pmid31301004, year = {2019}, author = {Li, JKM and Chiu, PKF and Ng, CF}, title = {The impact of microbiome in urological diseases: a systematic review.}, journal = {International urology and nephrology}, volume = {51}, number = {10}, pages = {1677-1697}, pmid = {31301004}, issn = {1573-2584}, mesh = {Humans ; *Microbiota ; Urologic Diseases/*microbiology ; }, abstract = {OBJECTIVE: The term microbiome is used to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space, in which there were increasing evidences to suggest that they might have potential roles in various medical conditions. While the study of microbiome in the urinary system is not as robust as the systems included in the Human Microbiome Project, there are still evidences in the literature showing that microbiome may have a role in urological diseases. Therefore, we would like to perform a systematic review on the topic and summarize the available evidence on the impact of microbiome on urological diseases.<br><br>METHODOLOGY: This review was performed according to the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement. After screening 589 abstracts and including additional studies (such as references from review papers), 76 studies were included for review and discussion.<br><br>RESULTS: Studies had suggested that there were correlations of microbiome of different body cavities (e.g., fecal, urinary and seminal fluid) with urological diseases. Also, different diseases would have different microbiome profile in different body cavities. Unfortunately, the studies on the association of microbiome and urological diseases were still either weak or inconsistent.<br><br>CONCLUSION: Studies suggested that there might be some relationship between microbiome and various urological diseases. However, further large-scale studies with control of confounding factors should be performed under a standardized methodology in order to have better understanding of the relationship. Also, more standardized reporting protocol for microbiome studies should be considered for better communications in future studies.}, }
@article {pmid31297102, year = {2019}, author = {Zhang, Z and Yang, J and Feng, Q and Chen, B and Li, M and Liang, C and Li, M and Li, Z and Xu, Q and Zhang, L and Chen, W}, title = {Compositional and Functional Analysis of the Microbiome in Tissue and Saliva of Oral Squamous Cell Carcinoma.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1439}, pmid = {31297102}, issn = {1664-302X}, abstract = {Oral squamous cell carcinoma (OSCC) is affected by the interaction between oral pathogen and holobionts, or the combination of the host and its microbial communities. Studies have indicated the structure and feature of the microbiome in OSCC tissue and saliva, the relationships between microbiota and OSCC sites, stages remain unclear. In the present study, OSCC tissue (T), saliva (S) and mouthwash (W) samples were collected from the same subjects and carried out the microbiome study by 16S sequencing. The results showed the T group was significantly different from the S and W groups with the character of lower richness and diversity. Proteobacteria were most enriched in the T group at the phylum level, while Firmicutes were predominant in groups S and W. At the genus level, the predominant taxa of group T were Acinetobacter and Fusobacterium, and for group S and W, the predominant taxa were Streptococcus and Prevotella. The genera related to late stage tumors were Acinetobacter and Fusobacterium, suggesting microbiota may be implicated in OSCC developing. Both compositional and functional analyses indicated that microbes in tumor tissue were potential indicator for the initiation and development of OSCC.}, }
@article {pmid31295421, year = {2019}, author = {Lam, KN and Alexander, M and Turnbaugh, PJ}, title = {Precision Medicine Goes Microscopic: Engineering the Microbiome to Improve Drug Outcomes.}, journal = {Cell host &amp; microbe}, volume = {26}, number = {1}, pages = {22-34}, pmid = {31295421}, issn = {1934-6069}, support = {R01 HL122593/HL/NHLBI NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; T32 AI060537/AI/NIAID NIH HHS/United States ; }, mesh = {Drug Therapy/*methods ; Drug-Related Side Effects and Adverse Reactions ; Humans ; *Microbiota ; Precision Medicine/*methods/trends ; Treatment Outcome ; }, abstract = {Despite the recognition, nearly a century ago, that the human microbiome plays a clinically relevant role in drug disposition, mechanistic insights, and translational applications are still limited. Here, we highlight the recent re-emergence of &quot;pharmacomicrobiomics,&quot; which seeks to understand how inter-individual variations in the microbiome shape drug efficacy and side effect profiles. Multiple bacterial species, genes, and enzymes have already been implicated in the direct biotransformation of drugs, both from targeted case studies and from systematic computational and experimental analyses. Indirect mechanisms are also at play; for example, microbial interactions with the host immune system can have broad effects on immunomodulatory drugs. Finally, we discuss multiple emerging strategies for the precise manipulation of complex microbial communities to improve treatment outcomes. In the coming years, we anticipate a shift toward a more comprehensive view of precision medicine that encompasses our human and microbial genomes and their combined metabolic activities.}, }
@article {pmid31292231, year = {2019}, author = {Mike, LA}, title = {mSphere of Influence: Systematically Decoding Microbial Chemical Communication.}, journal = {mSphere}, volume = {4}, number = {4}, pages = {}, pmid = {31292231}, issn = {2379-5042}, mesh = {Bacteria/genetics/*metabolism/pathogenicity ; *Bacterial Physiological Phenomena ; Biosynthetic Pathways/*genetics ; Humans ; *Microbiota ; Multigene Family ; Secondary Metabolism ; }, abstract = {Laura A. Mike works in the field of bacterial pathogenesis. In this mSphere of Influence article, she reflects on how &quot;Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters&quot; by P. Cimermancic et al. (Cell 158:412-421, 2014, https://doi.org/10.1016/j.cell.2014.06.034) and &quot;A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics&quot; by M. S. Donia et al. (Cell 158:1402-1414, 2014, https://doi.org/10.1016/j.cell.2014.08.032) made an impact on her by systematically identifying microbiome-associated biosynthetic gene clusters predicted to synthesize secondary metabolites, which may facilitate interspecies interactions.}, }
@article {pmid31288283, year = {2019}, author = {Wree, A and Geisler, LJ and Tacke, F}, title = {[Microbiome &amp; NASH - partners in crime driving progression of fatty liver disease].}, journal = {Zeitschrift fur Gastroenterologie}, volume = {57}, number = {7}, pages = {871-882}, doi = {10.1055/a-0755-2595}, pmid = {31288283}, issn = {1439-7803}, mesh = {Disease Progression ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Liver Cirrhosis ; *Microbiota ; Non-alcoholic Fatty Liver Disease/*microbiology/pathology ; }, abstract = {Along with the increasing prevalence of obesity, metabolic syndrome and type 2 diabetes, non-alcoholic fatty liver disease (NAFLD) is rapidly increasing and poses a major challenge for gastroenterologists. Many studies have demonstrated that the microbiome is closely associated with the progression of nutrition-related diseases, especially of fatty liver disease. Changes in the quantity and quality of the intestinal flora, commonly referred to as dysbiosis, result in altered food metabolism, increased permeability of the intestinal barrier (&quot;leaky gut&quot;) and consecutive inflammatory processes in the liver. This favors both the progression of obesity and metabolic disorders as well as NAFLD towards non-alcoholic steatohepatitis (NASH), hepatic fibrosis, cirrhosis and hepatocellular carcinoma (HCC). Important molecular mechanisms include microbial metabolites, microbial and endogenous signaling substances (so-called PAMPs/DAMPs) as well as bile acids. Essential cellular mechanisms include immune cells in the gut and liver, especially macrophages and Kupffer cells, as well as intestinal epithelial cells and hepatocytes as central regulators of metabolism. In this review article, we briefly summarize the relevant species of the human microbiome, describe the microbial analytics, explain the most important molecular relationships between microbiome and NAFLD/NASH, and finally the opportunities and challenges of microbiome-modulating therapy for the treatment of fatty liver disease.}, }
@article {pmid31284576, year = {2019}, author = {Jackson, BR and Chow, N and Forsberg, K and Litvintseva, AP and Lockhart, SR and Welsh, R and Vallabhaneni, S and Chiller, T}, title = {On the Origins of a Species: What Might Explain the Rise of Candida auris?.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {}, pmid = {31284576}, issn = {2309-608X}, abstract = {Candida auris is an emerging multidrug-resistant yeast first described in 2009 that has since caused healthcare-associated outbreaks of severe human infections around the world. In some hospitals, it has become a leading cause of invasive candidiasis. C. auris is markedly different from most other pathogenic Candida species in its genetics, antifungal resistance, and ability to spread between patients. The reasons why this fungus began spreading widely in the last decade remain a mystery. We examine available data on C. auris and related species, including genomic epidemiology, phenotypic characteristics, and sites of detection, to put forth hypotheses on its possible origins. C. auris has not been detected in the natural environment; related species have been detected in in plants, insects, and aquatic environments, as well as from human body sites. It can tolerate hypersaline environments and higher temperatures than most Candida species. We explore hypotheses about the pre-emergence niche of C. auris, whether in the environmental or human microbiome, and speculate on factors that might have led to its spread, including the possible roles of healthcare, antifungal use, and environmental changes, including human activities that might have expanded its presence in the environment or caused increased human contact.}, }
@article {pmid31282802, year = {2018}, author = {Amsterdam, D and Ostrov, BE}, title = {The Impact of the Microbiome on Immunosenescence.}, journal = {Immunological investigations}, volume = {47}, number = {8}, pages = {801-811}, doi = {10.1080/08820139.2018.1537570}, pmid = {31282802}, issn = {1532-4311}, mesh = {Adaptive Immunity ; Aging/*immunology ; Animals ; Humans ; Immunity, Innate ; Microbiota/*immunology ; }, abstract = {Human microbiome investigations now provide evidence that changes in the microbiome over time and their interaction with the immune, endocrine, and nervous systems are associated with a wide array of disorders. Human immunological studies typically absent a microbiome consideration in their investigations. An area of recent exploration is the role of the microbiome as a critical partner in the development and function of the human immune system in aging. It is well known that immunologic maturation is influenced by a lifetime of interactions of the host with its companion microbiome. It is generally not well recognized that intestinal microbes play an essential role in the development and expansion of gut mucosal and systemic immune function. Gut microbial communities of elderly people have different composition and behavior compared to healthy younger adults. Comorbidities associated with microbial pathogens and an aberrant immune system tend to increase with aging. This review underscores the impact of the human-microbiome interface on the development and function of the immune system and on immunosenescence. These changes have important implications regarding health and health system utilization in the elderly population.}, }
@article {pmid31279340, year = {2019}, author = {Velsko, IM and Fellows Yates, JA and Aron, F and Hagan, RW and Frantz, LAF and Loe, L and Martinez, JBR and Chaves, E and Gosden, C and Larson, G and Warinner, C}, title = {Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {102}, pmid = {31279340}, issn = {2049-2618}, abstract = {BACKGROUND: Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates.<br><br>RESULTS: Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins.<br><br>CONCLUSIONS: Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.}, }
@article {pmid31278975, year = {2019}, author = {Soligo, M and Albini, M and Bertoli, FL and Marzano, V and Protto, V and Bracci-Laudiero, L and Minnone, G and De Benedetti, F and Chiaretti, A and Mantuano, E and Manni, L}, title = {Different responses of PC12 cells to different pro-nerve growth factor protein variants.}, journal = {Neurochemistry international}, volume = {129}, number = {}, pages = {104498}, doi = {10.1016/j.neuint.2019.104498}, pmid = {31278975}, issn = {1872-9754}, abstract = {The present work aimed to explore the innovative hypothesis that different transcript/protein variants of a pro-neurotrophin may generate different biological outcomes in a cellular system. Nerve growth factor (NGF) is important in the development and progression of neurodegenerative and cancer conditions. Mature NGF (mNGF) originates from a precursor, proNGF, produced in mouse in two major variants, proNGF-A and proNGF-B. Different receptors bind mNGF and proNGF, generating neurotrophic or neurotoxic outcomes. It is known that dysregulation in the proNGF/mNGF ratio and in NGF-receptors expression affects brain homeostasis. To date, however, the specific roles of the two major proNGF variants remain unexplored. Here we attempted a first characterization of the possible differential effects of proNGF-A and proNGF-B on viability, differentiation and endogenous ngf gene expression in the PC12 cell line. We also investigated the differential involvement of NGF receptors in the actions of proNGF. We found that native mouse mNGF, proNGF-A and proNGF-B elicited different effects on PC12 cell survival and differentiation. Only mNGF and proNGF-A promoted neurotrophic responses when all NGF receptors are exposed at the cell surface. Tropomyosine receptor kinase A (TrkA) blockade inhibited cell differentiation, regardless of which NGF was added to culture media. Only proNGF-A exerted a pro-survival effect when TrkA was inhibited. Conversely, proNGF-B exerted differentiative effects when the p75 neurotrophin receptor (p75NTR) was antagonized. Stimulation with NGF variants differentially regulated the autocrine production of distinct proNgf mRNA. Overall, our findings suggest that mNGF and proNGF-A may elicit similar neurotrophic effects, not necessarily linked to activation of the same NGF-receptor, while the action of proNGF-B may be determined by the NGF-receptors balance. Thus, the proposed involvement of proNGF/NGF on the development and progression of neurodegenerative and tumor conditions may depend on the NGF-receptors balance, on specific NGF trancript expression and on the proNGF protein variant ratio.}, }
@article {pmid31277695, year = {2019}, author = {Ilves, M and Kinaret, PAS and Ndika, J and Karisola, P and Marwah, V and Fortino, V and Fedutik, Y and Correia, M and Ehrlich, N and Loeschner, K and Besinis, A and Vassallo, J and Handy, RD and Wolff, H and Savolainen, K and Greco, D and Alenius, H}, title = {Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation.}, journal = {Particle and fibre toxicology}, volume = {16}, number = {1}, pages = {28}, pmid = {31277695}, issn = {1743-8977}, mesh = {Animals ; Copper/chemistry/*toxicity ; Female ; Gene Expression Profiling ; Genome-Wide Association Study ; Mice, Inbred BALB C ; Nanoparticles/chemistry/*toxicity ; Neutrophil Infiltration/*drug effects ; Ovalbumin/immunology ; Pneumonia/*chemically induced/genetics/immunology/pathology ; Polyethylene Glycols/*chemistry ; Surface Properties ; Transcriptome/*drug effects ; }, abstract = {BACKGROUND: Copper oxide (CuO) nanomaterials are used in a wide range of industrial and commercial applications. These materials can be hazardous, especially if they are inhaled. As a result, the pulmonary effects of CuO nanomaterials have been studied in healthy subjects but limited knowledge exists today about their effects on lungs with allergic airway inflammation (AAI). The objective of this study was to investigate how pristine CuO modulates allergic lung inflammation and whether surface modifications can influence its reactivity. CuO and its carboxylated (CuO COOH), methylaminated (CuO NH3) and PEGylated (CuO PEG) derivatives were administered here on four consecutive days via oropharyngeal aspiration in a mouse model of AAI. Standard genome-wide gene expression profiling as well as conventional histopathological and immunological methods were used to investigate the modulatory effects of the nanomaterials on both healthy and compromised immune system.<br><br>RESULTS: Our data demonstrates that although CuO materials did not considerably influence hallmarks of allergic airway inflammation, the materials exacerbated the existing lung inflammation by eliciting dramatic pulmonary neutrophilia. Transcriptomic analysis showed that CuO, CuO COOH and CuO NH3 commonly enriched neutrophil-related biological processes, especially in healthy mice. In sharp contrast, CuO PEG had a significantly lower potential in triggering changes in lungs of healthy and allergic mice revealing that surface PEGylation suppresses the effects triggered by the pristine material.<br><br>CONCLUSIONS: CuO as well as its functionalized forms worsen allergic airway inflammation by causing neutrophilia in the lungs, however, our results also show that surface PEGylation can be a promising approach for inhibiting the effects of pristine CuO. Our study provides information for health and safety assessment of modified CuO materials, and it can be useful in the development of nanomedical applications.}, }
@article {pmid31275260, year = {2019}, author = {Rodionov, DA and Arzamasov, AA and Khoroshkin, MS and Iablokov, SN and Leyn, SA and Peterson, SN and Novichkov, PS and Osterman, AL}, title = {Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1316}, pmid = {31275260}, issn = {1664-302X}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; R01 GM108527/GM/NIGMS NIH HHS/United States ; }, abstract = {The human gut microbiome harbors a diverse array of metabolic pathways contributing to its development and homeostasis via a complex web of diet-dependent metabolic interactions within the microbial community and host. Genomics-based reconstruction and predictive modeling of these interactions would provide a framework for diagnostics and treatment of dysbiosis-related syndromes via rational selection of therapeutic prebiotics and dietary nutrients. Of particular interest are micronutrients, such as B-group vitamins, precursors of indispensable metabolic cofactors, that are produced de novo by some gut bacteria (prototrophs) but must be provided exogenously in the diet for many other bacterial species (auxotrophs) as well as for the mammalian host. Cross-feeding of B vitamins between prototrophic and auxotrophic species is expected to strongly contribute to the homeostasis of microbial communities in the distal gut given the efficient absorption of dietary vitamins in the upper gastrointestinal tract. To confidently estimate the balance of microbiome micronutrient biosynthetic capabilities and requirements using available genomic data, we have performed a subsystems-based reconstruction of biogenesis, salvage and uptake for eight B vitamins (B1, B2, B3, B5, B6, B7, B9, and B12) and queuosine (essential factor in tRNA modification) over a reference set of 2,228 bacterial genomes representing 690 cultured species of the human gastrointestinal microbiota. This allowed us to classify the studied organisms with respect to their pathway variants and infer their prototrophic vs. auxotrophic phenotypes. In addition to canonical vitamin pathways, several conserved partial pathways were identified pointing to alternative routes of syntrophic metabolism and expanding a microbial vitamin &quot;menu&quot; by several pathway intermediates (vitamers) such as thiazole, quinolinate, dethiobiotin, pantoate. A cross-species comparison was applied to assess the extent of conservation of vitamin phenotypes at distinct taxonomic levels (from strains to families). The obtained reference collection combined with 16S rRNA gene-based phylogenetic profiles was used to deduce phenotype profiles of the human gut microbiota across in two large cohorts. This analysis provided the first estimate of B-vitamin requirements, production and sharing capabilities in the human gut microbiome establishing predictive phenotype profiling as a new approach to classification of microbiome samples. Future expansion of our reference genomic collection of metabolic phenotypes will allow further improvement in coverage and accuracy of predictive phenotype profiling of the human microbiome.}, }
@article {pmid31264406, year = {2019}, author = {Claassens, NJ and Finger-Bou, M and Scholten, B and Muis, F and de Groot, JJ and de Gier, JW and de Vos, WM and van der Oost, J}, title = {Bicistronic Design-Based Continuous and High-Level Membrane Protein Production in Escherichia coli.}, journal = {ACS synthetic biology}, volume = {8}, number = {7}, pages = {1685-1690}, pmid = {31264406}, issn = {2161-5063}, abstract = {Escherichia coli has been widely used as a platform microorganism for both membrane protein production and cell factory engineering. The current methods to produce membrane proteins in this organism require the induction of target gene expression and often result in unstable, low yields. Here, we present a method combining a constitutive promoter with a library of bicistronic design (BCD) elements, which enables inducer-free, tuned translation initiation for optimal protein production. Our system mediates stable, constitutive production of bacterial membrane proteins at yields that outperform those obtained with E. coli Lemo21(DE3), the current gold standard for bacterial membrane protein production. We envisage that the continuous, fine-tunable, and high-level production of membrane proteins by our method will greatly facilitate their study and their utilization in engineering cell factories.}, }
@article {pmid31263750, year = {2019}, author = {Katsnelson, A}, title = {Standards Seekers Put the Human Microbiome in Their Sights.}, journal = {ACS central science}, volume = {5}, number = {6}, pages = {929-932}, doi = {10.1021/acscentsci.9b00557}, pmid = {31263750}, issn = {2374-7943}, }
@article {pmid31263284, year = {2019}, author = {Depommier, C and Everard, A and Druart, C and Plovier, H and Van Hul, M and Vieira-Silva, S and Falony, G and Raes, J and Maiter, D and Delzenne, NM and de Barsy, M and Loumaye, A and Hermans, MP and Thissen, JP and de Vos, WM and Cani, PD}, title = {Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study.}, journal = {Nature medicine}, volume = {25}, number = {7}, pages = {1096-1103}, pmid = {31263284}, issn = {1546-170X}, support = {336452//European Research Council/International ; }, mesh = {Adult ; Aged ; *Dietary Supplements ; Double-Blind Method ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; Insulin Resistance ; Middle Aged ; Obesity/*diet therapy/metabolism/microbiology ; Overweight/*diet therapy/metabolism/microbiology ; Pilot Projects ; *Verrucomicrobia ; }, abstract = {Metabolic syndrome is characterized by a constellation of comorbidities that predispose individuals to an increased risk of developing cardiovascular pathologies as well as type 2 diabetes mellitus1. The gut microbiota is a new key contributor involved in the onset of obesity-related disorders2. In humans, studies have provided evidence for a negative correlation between Akkermansia muciniphila abundance and overweight, obesity, untreated type 2 diabetes mellitus or hypertension3-8. Since the administration of A. muciniphila has never been investigated in humans, we conducted a randomized, double-blind, placebo-controlled pilot study in overweight/obese insulin-resistant volunteers; 40 were enrolled and 32 completed the trial. The primary end points were safety, tolerability and metabolic parameters (that is, insulin resistance, circulating lipids, visceral adiposity and body mass). Secondary outcomes were gut barrier function (that is, plasma lipopolysaccharides) and gut microbiota composition. In this single-center study, we demonstrated that daily oral supplementation of 1010 A. muciniphila bacteria either live or pasteurized for three months was safe and well tolerated. Compared to placebo, pasteurized A. muciniphila improved insulin sensitivity (+28.62 ± 7.02%, P = 0.002), and reduced insulinemia (-34.08 ± 7.12%, P = 0.006) and plasma total cholesterol (-8.68 ± 2.38%, P = 0.02). Pasteurized A. muciniphila supplementation slightly decreased body weight (-2.27 ± 0.92 kg, P = 0.091) compared to the placebo group, and fat mass (-1.37 ± 0.82 kg, P = 0.092) and hip circumference (-2.63 ± 1.14 cm, P = 0.091) compared to baseline. After three months of supplementation, A. muciniphila reduced the levels of the relevant blood markers for liver dysfunction and inflammation while the overall gut microbiome structure was unaffected. In conclusion, this proof-of-concept study (clinical trial no. NCT02637115) shows that the intervention was safe and well tolerated and that supplementation with A. muciniphila improves several metabolic parameters.}, }
@article {pmid31262073, year = {2019}, author = {Tavakoli, A and Flanagan, JL}, title = {The Case for a More Holistic Approach to Dry Eye Disease: Is It Time to Move beyond Antibiotics?.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {8}, number = {3}, pages = {}, pmid = {31262073}, issn = {2079-6382}, abstract = {Dry eye disease (DED) is one of the most frequent presentations to optometrists with over 16 million US adults (6.8% of adult population) diagnosed as having this disorder. The majority of associated marketed products offer relief from symptomatology but do not address aetiology. DED harbours many distinguishing features of a chronic inflammatory disorder. The recent explosion in human microbiome research has sparked interest in the ocular microbiome and its role in the preservation and extension of ocular surface health and in the contribution of the gut microbiome to chronic systemic inflammation and associated &quot;Western life-style&quot; diseases. With a significant lack of success for many patients using currently available DED treatments, in this era of the microbiome, we are interested in exploring potential novel therapies that aim to reconstitute healthy bacterial communities both locally and distally (in the gut) as a treatment for DED. Although this direction of investigation is in its infancy, burgeoning interest makes such a review timely. This paper considers a number of studies into the use functional foods and associated products to ameliorate dry eye.}, }
@article {pmid31261078, year = {2019}, author = {Valentine, G and Prince, A and Aagaard, KM}, title = {The Neonatal Microbiome and Metagenomics: What Do We Know and What Is the Future?.}, journal = {NeoReviews}, volume = {20}, number = {5}, pages = {e258-e271}, doi = {10.1542/neo.20-5-e258}, pmid = {31261078}, issn = {1526-9906}, abstract = {The human microbiota includes the trillions of microorganisms living in the human body whereas the human microbiome includes the genes and gene products of this microbiota. Bacteria were historically largely considered to be pathogens that inevitably led to human disease. However, because of advances in both cultivation-based methods and the advent of metagenomics, bacteria are now recognized to be largely beneficial commensal organisms and thus, key to normal and healthy human development. This relatively new area of medical research has elucidated insights into diseases such as inflammatory bowel disease and obesity, as well as metabolic and atopic disorders. However, much remains unknown about the complexity of microbe-microbe and microbe-host interactions. Future efforts aimed at answering key questions pertaining to the early establishment of the microbiome, alongside what defines its dysbiosis, will likely lead to long-term health and mitigation of disease. Here, we review the relevant literature pertaining to modulations in the perinatal and neonatal microbiome, the impact of environmental and maternal factors in shaping the neonatal microbiome, and future questions and directions in the exciting emerging arena of metagenomic medicine.}, }
@article {pmid31253623, year = {2019}, author = {Korpela, K and Dikareva, E and Hanski, E and Kolho, KL and de Vos, WM and Salonen, A}, title = {Cohort profile: Finnish Health and Early Life Microbiota (HELMi) longitudinal birth cohort.}, journal = {BMJ open}, volume = {9}, number = {6}, pages = {e028500}, pmid = {31253623}, issn = {2044-6055}, abstract = {PURPOSE: HELMi (Health and Early Life Microbiota) is a longitudinal, prospective general population birth cohort, set up to identify environmental, lifestyle and genetic factors that modify the intestinal microbiota development in the first years of life and their relation to child health and well-being.<br><br>PARTICIPANTS: The HELMi cohort consists of 1055 healthy term infants born in 2016-2018 mainly at the capital region of Finland and their parents. The intestinal microbiota development of the infants is characterised based on nine, strategically selected, faecal samples and connected to extensive online questionnaire-collected metadata at weekly to monthly intervals focusing on the diet, other exposures and family's lifestyle as well as the health and growth of the child. Motor and cognitive developmental screening takes place at 18 months. Infant's DNA sample, mother's breast milk sample and both parent's spot faecal samples have been collected.<br><br>FINDINGS TO DATE: The mean age of the mothers was 32.8 (SD 4.1) and fathers/coparents 34.8 (5.3) years at the time of enrolment. Seventeen percentage (n=180) of the infants were born by caesarean section. Just under half (49%) were firstborns; 50.7% were males. At 3 months of age, 86% of the babies were exclusively breastfed and 2% exclusively formula-fed.<br><br>FUTURE PLANS: The current follow-up from pregnancy to first 24 months will be completed in March 2020, totalling to over 10 000 biological samples and over 50 000 questionnaire entries. The results are expected to identify environmental and host factors that affect early gut microbiota development and health, and hence give indications of how to prevent or reverse microbiota perturbations in infancy. This prospective cohort will be followed up further to identify how the early microbiota relates to later health outcomes, especially weight gain, infections and allergic and other chronic diseases.<br><br>TRIAL REGISTRATION NUMBER: NCT03996304; Pre-results.}, }
@article {pmid31253198, year = {2019}, author = {Lokugamage, AU and Pathberiya, SDC}, title = {The microbiome seeding debate - let's frame it around women-centred care.}, journal = {Reproductive health}, volume = {16}, number = {1}, pages = {91}, pmid = {31253198}, issn = {1742-4755}, mesh = {Cesarean Section/*standards ; Female ; Humans ; Infant, Newborn ; *Microbiota ; Patient-Centered Care/*standards ; Pregnancy ; Vagina/*microbiology ; }, abstract = {In a global culture that is increasingly interested in ecological interventions, probiotics, 'friendly bacteria', microbiome preservation/restoration and long-term health, there is growing awareness of the idea of seeding the vaginal microbiome in the new born after caesarean section. It is postulated as a way of restoring helpful missing microbes and preventing long term non-communicable diseases of babies delivered by caesarean section. Currently, there is a deluge of evidence being published on the human microbiome, which can be challenging to digest and absorb by scientists, clinicians and patients. The specific evidence base around this technique is at its early stages. This commentary discusses what advice is currently available from a feminist and a person-centred care perspective.<br><br>ABSTRAKT: Det er en voksende interesse internasjonalt for økologiske intervensjoner, probiotika, 'snille bakterier', bevaring/gjenoppretting av. mikrobiomet og helse i et langtidsperspektiv. I denne sammenhengen er det en økende interesse for tanken om å så det vaginale mikrobiomet (vaginal seeding) på den nyfødte etter et keisersnitt. Dette er postulert som en måte å gjenopprette manglende normalflora/mikrobiom og forebygge langvarige ikke-smittsomme sykdommer hos barn født med keisersnitt. For tiden publiseres det mye forskning om menneskets mikrobiom, noe som kan være utfordrende å fordøye og ta til seg for forskere, klinikere og pasienter. Forskningen på denne spesifikke metoden er i sin begynnelse. Denne kommentaren drøfter hvilke råd som for øyeblikket er tilgjengelige, fra et feministisk og personsentrert omsorgsperspektiv. POPULARISERT SAMMENDRAG På NORSK: Det menneskelige mikrobiomet er summen av alle bakteriene som dekker den menneskelige kroppen og det hjelper kroppen i å fungere optimalt. Når mikrobiomet forstyrres, vil kroppen kunne få betennelsesreaksjoner og allergier. I fødsel finnes de «gode» bakteriene i kvinnens vagina. (det vaginale mikrobiomet) som man tror vil være fordelaktig for babyens evne til å utvikle et sunt immunsystem. Babyer som er født med keisersnitt vil ikke bli eksponert for disse «gode» bakteriene og det kan påvirke barnets immunforsvar negativt og potensielt øke sjansen for allergier og betennelsesreaksjoner i kroppen på lang sikt. Vaginal seeding (et forsøk på å gjenopprette balansen og noen av de gode bakterier i spedbarnet gjennom å tilføre mors vaginale bakterier via en kompress som strykes over spedbarnets ansikt) Vaginal seeding er en metode som noen forskere sier muligens delvis gjenoppretter de manglende «gode» bakteriene etter et keisersnitt. Forskningen er på et tidlig stadium. Det har vært avisartikler og en film om emnet og mødre har funnet ut om vaginal seeding som en måte å gjenopprette denne delen av babyens mikrobiom. Foreldre ønsker å diskutere vaginal seeding, men på nåværende tidspunkt er helsevesenet avventende og helsepersonell er ikke godt nok informert. Denne artikkelen vil se på den pågående diskusjonen. RéSUMé: Dans une culture mondiale qui s'intéresse de plus en plus aux interventions écologiques, aux probiotiques, aux «bactéries amicales», à la préservation / restauration du microbiome et à la santé à long terme, on commence à prendre conscience de l'idée d'ensemencer le microbiome vaginal chez le nouveau-né après une césarienne. Il est postulé comme un moyen de restaurer les microbes manquants et d'aider à prévenir les maladies non transmissibles à long terme des bébés mis au monde par césarienne. Il existe actuellement un déluge de preuves sur le microbiome humain, qui peuvent être difficiles à digérer et à absorber par les scientifiques, les cliniciens et les patients. La base de preuves spécifique autour de cette technique en est à ses débuts. Ce commentaire discute des conseils actuellement disponibles dans une perspective de soins féministe et centrée sur la personne. RéSUMé SIMPLIFIé: Le microbiome humain est constitué de tous les microbes qui recouvrent le corps humain et qui aident le corps à bien fonctionner. Lorsque le microbiome est perturbé, le corps devient plus inflammatoire et est sujet aux allergies. Lors de l'accouchement, le vagin d'une mère (le microbiome vaginal) contient des &quot;bactéries amicales&quot; qui pourraient être bénéfiques pour l'enfant et aider le bébé à développer un système immunitaire en bonne santé. Les bébés nés par césarienne ne sont généralement pas exposés à ces «bactéries bénéfiques», ce qui pourrait affecter négativement le système immunitaire du bébé et potentiellement augmenter le risque d'allergies et d'inflammation à long terme. Selon certains scientifiques, l'ensemencement vaginal pourrait partiellement restaurer les «bactéries amies» manquantes après la césarienne. La recherche en est à ses débuts. Il y a eu des articles de journaux et un film à ce sujet, et les mères ont découvert l'existence d'un ensemencement vaginal (où une compresse placée dans le vagin de la mère pourrait être appliquée sur l'enfant après la césarienne) afin de restaurer une partie du microbiome du bébé. Les parents souhaitent discuter de l'ensemencement vaginal, mais à l'heure actuelle, les organisations médicales sont prudentes et les praticiens ne sont pas suffisamment informés. Cet article examine le débat en cours.<br><br>RESUMO: Numa cultura global que está cada vez mais interessada em intervenções ecológicas, probióticos, &quot;bactérias amigáveis&quot;, preservação/restauração do microbioma e saúde a longo prazo, há uma crescente consciência sobre a ideia de semear o microbioma vaginal no recém-nascido após uma cirurgia cesariana. Isso está sendo postulado como uma forma de restaurar micróbios úteis que lhe faltariam e prevenir doenças não transmissíveis em longo prazo para bebês que nasceram pela via cirúrgica. Atualmente, há um aumento massivo de evidências sendo publicadas sobre o microbioma humano cuja absorção e digestão pode ser desafiadora para cientistas, clínicos e pacientes. A base específica da evidência que cerca essa técnica ainda está em estágios preliminares. Este comentário discute o aconselhamento atualmente disponível numa perspectiva feminista e centrada na pessoa. SíNTESE SIMPLIFICADA: O microbioma humano está composto por todos os micróbios que cobrem o corpo humano e que ajudam o corpo a funcionar bem. Quando o microbioma é perturbado, o corpo tem mais inflamações e maior propensão a desenvolver alergias. Ao nascimento, há &quot;bactérias amigáveis&quot; na vagina materna (o microbioma vaginal) que podem ser benéficas à criança e ajudar o bebê a desenvolver um sistema imunológico saudável. Bebês que nascem por cesariana usualmente não são expostos a essas &quot;bactérias amigáveis&quot; e isso poderá afetar negativamente o sistema imunológico do bebê, aumentando potencialmente a probabilidade de alegrias e inflamações no longo prazo. A semeadura de bactéria vaginais é um método que alguns cientistas afirmam que poderá restaurar parcialmente as &quot;bactérias amigáveis&quot; faltantes depois de uma cesariana. Essa pesquisa está em fase preliminar. Houve alguns artigos em jornais e um filme sobre isso, e as mães descobriram a possibilidade da semeadura vaginal (quando é feito um swab da vagina materna que é esfregado no bebê após a cesárea) para restaurar parte do microbioma do bebê. Pais desejam discutir a semeadura vaginal, mas, no momento, as organizações médicas têm sido cautelosas e os profissionais não estão adequadamente informados. Este artigo aborda o debate em andamento.<br><br>RESUMEN: En una cultura global que está cada vez más interesada en las intervenciones ecológicas, los probióticos, las &quot;bacterias amigables&quot;, la conservación/restauración de microbiomas y la salud a largo plazo, hay una creciente conciencia de la idea de sembrar el microbioma vaginal en el recién nacido después de la cesárea. Se postula como una forma de restaurar los microbios útiles faltantes y prevenir las enfermedades no transmisibles a largo plazo de los bebés nacidos por cesárea. Actualmente, se está publicando una gran cantidad de pruebas sobre el microbioma humano, que pueden ser difíciles de digerir y absorber por parte de científicos, clínicos y pacientes. La base de la evidencia específica en torno a esta técnica se encuentra en sus primeras etapas. Este artículo analiza qué consejos están disponibles actualmente desde una perspectiva feminista y de atención centrada en la persona.<br><br>RESUMEN EN LENGUAJE SENCILLO: El microbioma humano está hecho de todos las bacterias que cubren el cuerpo humano y que ayudan al cuerpo a funcionar bien. Cuando se altera el microbioma, el cuerpo se inflama más y es propenso a las alergias. En el parto, hay &quot;bacterias amigables&quot; en la vagina de la madre (el microbioma vaginal) que podrían ser beneficiosas para el niño y ayudar al bebé a desarrollar un sistema inmunológico saludable. Los bebés que nacen por cesárea generalmente no se exponen a estas &quot;bacterias amigables&quot; y esto podría afectar negativamente el sistema inmunológico del bebé, lo que podría aumentar la probabilidad de alergias e inflamación a largo plazo. La siembra vaginal es un método que algunos científicos dicen que podría restaurar parcialmente las &quot;bacterias amigables&quot; que faltan después de la cesárea. La investigación se encuentra en sus primeras etapas. Han habido artículos periodísticos y una película sobre esto, y las madres se han enterado de la siembra vaginal (donde se puede frotar el niño con una torunda de la vagina de la madre después de la cesárea) para restaurar la parte del microbioma del bebé. Los padres quieren hablar sobre la siembra vaginal, pero en la actualidad las organizaciones médicas son cautelosas y los profesionales no están informados adecuadamente. Este artículo analiza el debate en curso.}, }
@article {pmid31246421, year = {2019}, author = {Gumkowski, JD and Martinie, RJ and Corrigan, PS and Pan, J and Bauerle, MR and Almarei, M and Booker, SJ and Silakov, A and Krebs, C and Boal, AK}, title = {Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme.}, journal = {Biochemistry}, volume = {58}, number = {29}, pages = {3169-3184}, pmid = {31246421}, issn = {1520-4995}, support = {R00 GM100011/GM/NIGMS NIH HHS/United States ; R35 GM119707/GM/NIGMS NIH HHS/United States ; }, abstract = {Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly. The cfr gene has been identified as a mobile genetic element in diverse bacteria and in the genome of select Bacillales and Clostridiales species. Despite the importance of Cfr, few representatives have been purified and characterized in vitro. Here we show that Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays. C. difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif. The C-terminal domain can be truncated with minimal impact on C. difficile Cfr activity, but the rate of turnover is decreased upon disruption of the Fe2+-binding site by Zn2+ substitution or ligand mutation. These findings indicate an important purpose for the observed C-terminal iron in the native fusion protein. Bioinformatic analysis of the C. difficile Cfr Cys-rich domain shows that it is widespread (∼1400 homologues) as a stand-alone gene in pathogenic or commensal Bacilli and Clostridia, with >10% encoded adjacent to a predicted radical SAM RNA methylase. Although the domain is not essential for in vitro C. difficile Cfr activity, the genomic co-occurrence and high abundance in the human microbiome suggest a possible functional role for a specialized rubredoxin in certain radical SAM RNA methylases that are relevant to human health.}, }
@article {pmid31231350, year = {2019}, author = {Savijoki, K and Nyman, TA and Kainulainen, V and Miettinen, I and Siljamäki, P and Fallarero, A and Sandholm, J and Satokari, R and Varmanen, P}, title = {Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1272}, pmid = {31231350}, issn = {1664-302X}, abstract = {Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins) of GG cells grown with glucose and fructose in planktonic and biofilm cultures were identified and compared, which indicated carbohydrate source-dependent variations, especially during biofilm growth. The most distinctive differences under these conditions were detected with several surface adhesins (e.g., MBF, SpaC pilus protein and penicillin-binding proteins), enzymes (glycoside hydrolases, PrsA, PrtP, PrtR, and HtrA) and moonlighting proteins (glycolytic, transcription/translation and stress-associated proteins, r-proteins, tRNA synthetases, Clp family proteins, PepC, PepN, and PepA). The abundance of several known adhesins and candidate moonlighters, including enzymes acting on casein-derived peptides (ClpP, PepC, and PepN), increased in the biofilm cells grown on fructose, from which the surface-associated aminopeptidase activity mediated by PepC and PepN was further confirmed by an enzymatic assay. The mucus binding factor (MBF) was found most abundant in fructose grown biofilm cells whereas SpaC adhesin was identified specifically from planktonic cells growing on fructose. An additional indirect ELISA indicated both growth mode- and carbohydrate-dependent differences in abundance of SpaC, whereas the overall adherence of GG assessed with porcine mucus indicated that the carbon source and the growth mode affected mucus adhesion. The adherence of GG cells to mucus was almost completely inhibited by anti-SpaC antibodies regardless of growth mode and/or carbohydrate source, indicating the key role of the SpaCBA pilus in adherence under the tested conditions. Altogether, our results suggest that carbon source and growth mode coordinate mechanisms shaping the proteinaceous composition of GG cell surface, which potentially contributes to resistance, nutrient acquisition and cell-cell interactions under different conditions. In conclusion, the present study shows that different growth regimes and conditions can have a profound impact on the adherent and antigenic features of GG, thereby providing new information on how to gain additional benefits from this probiotic.}, }
@article {pmid31231319, year = {2019}, author = {Stinson, LF and Boyce, MC and Payne, MS and Keelan, JA}, title = {The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {1124}, pmid = {31231319}, issn = {1664-302X}, abstract = {The human microbiome includes trillions of bacteria, many of which play a vital role in host physiology. Numerous studies have now detected bacterial DNA in first-pass meconium and amniotic fluid samples, suggesting that the human microbiome may commence in utero. However, these data have remained contentious due to underlying contamination issues. Here, we have used a previously described method for reducing contamination in microbiome workflows to determine if there is a fetal bacterial microbiome beyond the level of background contamination. We recruited 50 women undergoing non-emergency cesarean section deliveries with no evidence of intra-uterine infection and collected first-pass meconium and amniotic fluid samples. Full-length 16S rRNA gene sequencing was performed using PacBio SMRT cell technology, to allow high resolution profiling of the fetal gut and amniotic fluid bacterial microbiomes. Levels of inflammatory cytokines were measured in amniotic fluid, and levels of immunomodulatory short chain fatty acids (SCFAs) were quantified in meconium. All meconium samples and most amniotic fluid samples (36/43) contained bacterial DNA. The meconium microbiome was dominated by reads that mapped to Pelomonas puraquae. Aside from this species, the meconium microbiome was remarkably heterogeneous between patients. The amniotic fluid microbiome was more diverse and contained mainly reads that mapped to typical skin commensals, including Propionibacterium acnes and Staphylococcus spp. All meconium samples contained acetate and propionate, at ratios similar to those previously reported in infants. P. puraquae reads were inversely correlated with meconium propionate levels. Amniotic fluid cytokine levels were associated with the amniotic fluid microbiome. Our results demonstrate that bacterial DNA and SCFAs are present in utero, and have the potential to influence the developing fetal immune system.}, }
@article {pmid31220972, year = {2019}, author = {Koontz, JM and Dancy, BCR and Horton, CL and Stallings, JD and DiVito, VT and Lewis, JA}, title = {The Role of the Human Microbiome in Chemical Toxicity.}, journal = {International journal of toxicology}, volume = {38}, number = {4}, pages = {251-264}, doi = {10.1177/1091581819849833}, pmid = {31220972}, issn = {1092-874X}, mesh = {Animals ; Hazardous Substances/*toxicity ; Humans ; Microbiota/*drug effects ; }, abstract = {There is overwhelming evidence that the microbiome must be considered when evaluating the toxicity of chemicals. Disruption of the normal microbial flora is a known effect of toxic exposure, and these disruptions may lead to human health effects. In addition, the biotransformation of numerous compounds has been shown to be dependent on microbial enzymes, with the potential for different host health outcomes resulting from variations in the microbiome. Evidence suggests that such metabolism of environmental chemicals by enzymes from the host's microbiota can affect the toxicity of that chemical to the host. Chemical-microbial interactions can be categorized into two classes: Microbiome Modulation of Toxicity (MMT) and Toxicant Modulation of the Microbiome (TMM). MMT refers to transformation of a chemical by microbial enzymes or metabolites to modify the chemical in a way that makes it more or less toxic. TMM is a change in the microbiota that results from a chemical exposure. These changes span a large magnitude of effects and may vary from microbial gene regulation, to inhibition of a specific enzyme, to the death of the microbes. Certain microbiomes or microbiota may become associated with different health outcomes, such as resistance or susceptibility to exposure to certain toxic chemicals, the ability to recover following a chemical-induced injury, the presence of disease-associated phenotypes, and the effectiveness of immune responses. Future work in toxicology will require an understanding of how the microbiome interacts with toxicants to fully elucidate how a compound will affect a diverse, real-world population.}, }
@article {pmid31220751, year = {2019}, author = {Zhang, YJ and Hu, HW and Chen, QL and Singh, BK and Yan, H and Chen, D and He, JZ}, title = {Transfer of antibiotic resistance from manure-amended soils to vegetable microbiomes.}, journal = {Environment international}, volume = {130}, number = {}, pages = {104912}, doi = {10.1016/j.envint.2019.104912}, pmid = {31220751}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics/isolation &amp; purification ; *Drug Resistance, Microbial/genetics ; High-Throughput Nucleotide Sequencing ; Lettuce/*microbiology ; Manure/*analysis ; *Microbiota ; Real-Time Polymerase Chain Reaction ; Soil/chemistry ; *Soil Microbiology ; Victoria ; }, abstract = {The increasing antimicrobial resistance in manure-amended soil can potentially enter food chain, representing an important vehicle for antibiotic resistance genes (ARGs) transmission into human microbiome. However, the pathways for transmission of ARGs from soil to plant remain unclear. Here, we explored the impacts of poultry and cattle manure application on the patterns of resistome in soil and lettuce microbiome including rhizosphere, root endosphere, leaf endosphere and phyllosphere, to identify the potential transmission routes of ARGs in the soil-plant system. After 90 days of cultivation, a total of 144 ARGs were detected in all samples using high-throughput quantitative PCR. Rhizosphere soil samples harbored the most diverse ARGs compared with other components of lettuce. Cattle manure application increased the abundance of ARGs in root endophyte, while poultry manure application increased ARGs in rhizosphere, root endophyte and phyllosphere, suggesting that poultry manure may have a stronger impact on lettuce resistomes. The ARG profiles were significantly correlated with the bacterial community, and the enrichment of soil and plant resistomes was strongly affected by the bacterial taxa including Solibacteres, Chloroflexi, Acidobacteria, Gemm-1 and Gemmatimonadetes, as revealed by the network analyses. Moreover, the overlaps of ARGs between lettuce tissues and soil were identified, which indicated that plant and environmental resistomes are interconnected. Our findings provide insights into the transmission routes of ARGs from manured soil to vegetables, and highlight the potential risks of plant resistome migration to the human food chain.}, }
@article {pmid31218869, year = {2019}, author = {Shen, X and Yao, YF and Li, JY and Li, Y}, title = {[Human mycobiome and diseases].}, journal = {Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology}, volume = {37}, number = {3}, pages = {314-319}, doi = {10.7518/hxkq.2019.03.017}, pmid = {31218869}, issn = {2618-0456}, mesh = {Bacteria ; *Disease ; Female ; Fungi ; Humans ; *Microbiota ; Mouth ; *Mycobiome ; }, abstract = {The proportion of mycobiome is less than 1% of human microbiome. However, fungal community plays a key role in human health and diseases. With high-throughput sequencing applications, the structure and composition of mycobiome in the mouth, lung, gut, vagina, and skin have been analyzed, and the role of microbiome in diseases has been investigated. Mycobiome also influences the composition of bacteriome and includes key species that maintain the structure and function of microbial communities. Fungi also influence host immune responses. In this review, we summarized the mycobiome com-position at various sites and different diseases and the interactions between fungi-bacteria and fungi-host.}, }
@article {pmid31202124, year = {2019}, author = {Picardo, SL and Coburn, B and Hansen, AR}, title = {The microbiome and cancer for clinicians.}, journal = {Critical reviews in oncology/hematology}, volume = {141}, number = {}, pages = {1-12}, doi = {10.1016/j.critrevonc.2019.06.004}, pmid = {31202124}, issn = {1879-0461}, mesh = {Carcinogenesis ; Female ; Gastrointestinal Microbiome/immunology/physiology ; Humans ; Immunity/physiology ; Immunologic Factors/therapeutic use ; Immunotherapy ; Male ; Microbiota/immunology/*physiology ; Neoplasms/immunology/*microbiology/*therapy ; }, abstract = {The human microbiome is an emerging target in cancer development and therapeutics. It may be directly oncogenic, through promotion of mucosal inflammation or systemic dysregulation, or may alter anti-cancer immunity/therapy. Microorganisms within, adjacent to and distant from tumors may affect cancer progression, and interactions and differences between these populations can influence the course of disease. Here we review the microbiome as it pertains to cancer for clinicians. The microbiota of cancers including colorectal, pancreas, breast and prostate are discussed. We examine &quot;omics&quot; technologies, microbiota associated with tumor tissue and tumor-site fluids such as feces and urine, as well as indirect effects of the gut microbiome. We describe roles of the microbiome in immunotherapy, and how it can be modulated to improve cancer therapeutics. While research is still at an early stage, there is potential to exploit the microbiome, as modulation may increase efficacy of treatments, reduce toxicities and prevent carcinogenesis.}, }
@article {pmid31201356, year = {2019}, author = {Szafrański, SP and Kilian, M and Yang, I and Bei der Wieden, G and Winkel, A and Hegermann, J and Stiesch, M}, title = {Diversity patterns of bacteriophages infecting Aggregatibacter and Haemophilus species across clades and niches.}, journal = {The ISME journal}, volume = {13}, number = {10}, pages = {2500-2522}, pmid = {31201356}, issn = {1751-7370}, mesh = {Aggregatibacter/classification/*virology ; Bacteriophages/classification/genetics/isolation &amp; purification/*physiology ; Base Composition ; Biodiversity ; Genome, Viral ; Genomics ; Haemophilus/classification/*virology ; Host Specificity ; Humans ; Lysogeny ; Metagenome ; Phylogeny ; Prophages/classification/genetics/isolation &amp; purification/physiology ; }, abstract = {Aggregatibacter and Haemophilus species are relevant human commensals and opportunistic pathogens. Consequently, their bacteriophages may have significant impact on human microbial ecology and pathologies. Our aim was to reveal the prevalence and diversity of bacteriophages infecting Aggregatibacter and Haemophilus species that colonize the human body. Genome mining with comparative genomics, screening of clinical isolates, and profiling of metagenomes allowed characterization of 346 phages grouped in 52 clusters and 18 superclusters. Less than 10% of the identified phage clusters were represented by previously characterized phages. Prophage diversity patterns varied significantly for different phage types, host clades, and environmental niches. A more diverse phage community lysogenizes Haemophilus influenzae and Haemophilus parainfluenzae strains than Aggregatibacter actinomycetemcomitans and &quot;Haemophilus ducreyi&quot;. Co-infections occurred more often in &quot;H. ducreyi&quot;. Phages from Aggregatibacter actinomycetemcomitans preferably lysogenized strains of specific serotype. Prophage patterns shared by subspecies clades of different bacterial species suggest similar ecoevolutionary drivers. Changes in frequencies of DNA uptake signal sequences and guanine-cytosine content reflect phage-host long-term coevolution. Aggregatibacter and Haemophilus phages were prevalent at multiple oral sites. Together, these findings should help exploring the ecoevolutionary forces shaping virus-host interactions in the human microbiome. Putative lytic phages, especially phiKZ-like, may provide new therapeutic options.}, }
@article {pmid31194675, year = {2019}, author = {Bernstein, DB and Dewhirst, FE and Segrè, D}, title = {Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {31194675}, issn = {2050-084X}, support = {T32GM008764/GM/NIGMS NIH HHS/United States ; T32 GM008764/GM/NIGMS NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R01 GM121950/GM/NIGMS NIH HHS/United States ; DE-SC0012627//Biological and Environmental Research/International ; RGP0020/2016//Human Frontier Science Program/International ; NSFOCE-BSF 1635070//National Science Foundation/International ; HR0011-15-C-0091//Defense Advanced Research Projects Agency/International ; R37DE016937/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; R01GM121950/GM/NIGMS NIH HHS/United States ; R01DE024468/DE/NIDCR NIH HHS/United States ; 1457695//National Science Foundation/International ; }, mesh = {Computational Biology ; Humans ; *Metabolic Networks and Pathways ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Mouth/*microbiology ; }, abstract = {The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several Saccharibacteria (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.}, }
@article {pmid31188557, year = {2019}, author = {Kooter, I and Ilves, M and Gröllers-Mulderij, M and Duistermaat, E and Tromp, PC and Kuper, F and Kinaret, P and Savolainen, K and Greco, D and Karisola, P and Ndika, J and Alenius, H}, title = {Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model.}, journal = {ACS nano}, volume = {13}, number = {6}, pages = {6932-6946}, pmid = {31188557}, issn = {1936-086X}, abstract = {More than 5% of any population suffers from asthma, and there are indications that these individuals are more sensitive to nanoparticle aerosols than the healthy population. We used an air-liquid interface model of inhalation exposure to investigate global transcriptomic responses in reconstituted three-dimensional airway epithelia of healthy and asthmatic subjects exposed to pristine (nCuO) and carboxylated (nCuOCOOH) copper oxide nanoparticle aerosols. A dose-dependent increase in cytotoxicity (highest in asthmatic donor cells) and pro-inflammatory signaling within 24 h confirmed the reliability and sensitivity of the system to detect acute inhalation toxicity. Gene expression changes between nanoparticle-exposed versus air-exposed cells were investigated. Hierarchical clustering based on the expression profiles of all differentially expressed genes (DEGs), cell-death-associated DEGs (567 genes), or a subset of 48 highly overlapping DEGs categorized all samples according to &quot;exposure severity&quot;, wherein nanoparticle surface chemistry and asthma are incorporated into the dose-response axis. For example, asthmatics exposed to low and medium dose nCuO clustered with healthy donor cells exposed to medium and high dose nCuO, respectively. Of note, a set of genes with high relevance to mucociliary clearance were observed to distinctly differentiate asthmatic and healthy donor cells. These genes also responded differently to nCuO and nCuOCOOH nanoparticles. Additionally, because response to transition-metal nanoparticles was a highly enriched Gene Ontology term (FDR 8 × 10-13) from the subset of 48 highly overlapping DEGs, these genes may represent biomarkers to a potentially large variety of metal/metal oxide nanoparticles.}, }
@article {pmid31186074, year = {2019}, author = {Nichols, RG and Peters, JM and Patterson, AD}, title = {Interplay Between the Host, the Human Microbiome, and Drug Metabolism.}, journal = {Human genomics}, volume = {13}, number = {1}, pages = {27}, pmid = {31186074}, issn = {1479-7364}, support = {ES022186/ES/NIEHS NIH HHS/United States ; ES028288/ES/NIEHS NIH HHS/United States ; ES026684/ES/NIEHS NIH HHS/United States ; Tobacco CURE//Pennsylvania Department of Health/International ; PEN04607//National Institute of Food and Agriculture/International ; PEN04607//National Institute of Food and Agriculture/International ; CA124533/CA/NCI NIH HHS/United States ; }, abstract = {The human microbiome is composed of four major areas including intestinal, skin, vaginal, and oral microbiomes, with each area containing unique species and unique functionalities. The human microbiome may be modulated with prebiotics, probiotics, and postbiotics to potentially aid in the treatment of diseases like irritable bowel syndrome, bacterial vaginosis, atopic dermatitis, gingivitis, obesity, or cancer. There is also potential for many of the inhabitants of the human microbiome to directly modulate host gene expression and modulate host detoxifying enzyme activity like cytochrome P450s (CYPs), dehydrogenases, and carboxylesterases. Therefore, the microbiome may be important to consider during drug discovery, risk assessment, and dosing regimens for various diseases given that the human microbiome has been shown to impact host detoxification processes.}, }
@article {pmid31183114, year = {2019}, author = {Zhao, L and Xu, J and Shang, X and Li, X and Li, Q and Li, S}, title = {Synaptic memory devices from CoO/Nb:SrTiO3 junction.}, journal = {Royal Society open science}, volume = {6}, number = {4}, pages = {181098}, pmid = {31183114}, issn = {2054-5703}, abstract = {Non-volatile memristors are promising for future hardware-based neurocomputation application because they are capable of emulating biological synaptic functions. Various material strategies have been studied to pursue better device performance, such as lower energy cost, better biological plausibility, etc. In this work, we show a novel design for non-volatile memristor based on CoO/Nb:SrTiO3 heterojunction. We found the memristor intrinsically exhibited resistivity switching behaviours, which can be ascribed to the migration of oxygen vacancies and charge trapping and detrapping at the heterojunction interface. The carrier trapping/detrapping level can be finely adjusted by regulating voltage amplitudes. Gradual conductance modulation can therefore be realized by using proper voltage pulse stimulations. And the spike-timing-dependent plasticity, an important Hebbian learning rule, has been implemented in the device. Our results indicate the possibility of achieving artificial synapses with CoO/Nb:SrTiO3 heterojunction. Compared with filamentary type of the synaptic device, our device has the potential to reduce energy consumption, realize large-scale neuromorphic system and work more reliably, since no structural distortion occurs.}, }
@article {pmid31180804, year = {2019}, author = {Mark Welch, JL and Dewhirst, FE and Borisy, GG}, title = {Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.}, journal = {Annual review of microbiology}, volume = {73}, number = {}, pages = {335-358}, doi = {10.1146/annurev-micro-090817-062503}, pmid = {31180804}, issn = {1545-3251}, support = {R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; }, abstract = {Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.}, }
@article {pmid31169619, year = {2019}, author = {Wijeyesekera, A and Wagner, J and De Goffau, M and Thurston, S and Rodrigues Sabino, A and Zaher, S and White, D and Ridout, J and Peters, MJ and Ramnarayan, P and Branco, RG and Torok, ME and Valla, F and Meyer, R and Klein, N and Frost, G and Parkhill, J and Holmes, E and Pathan, N}, title = {Multi-Compartment Profiling of Bacterial and Host Metabolites Identifies Intestinal Dysbiosis and Its Functional Consequences in the Critically Ill Child.}, journal = {Critical care medicine}, volume = {47}, number = {9}, pages = {e727-e734}, pmid = {31169619}, issn = {1530-0293}, support = {082372/WT_/Wellcome Trust/United Kingdom ; MR/N029399/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {OBJECTIVES: Adverse physiology and antibiotic exposure devastate the intestinal microbiome in critical illness. Time and cost implications limit the immediate clinical potential of microbial sequencing to identify or treat intestinal dysbiosis. Here, we examined whether metabolic profiling is a feasible method of monitoring intestinal dysbiosis in critically ill children.<br><br>DESIGN: Prospective multicenter cohort study.<br><br>SETTING: Three U.K.-based PICUs.<br><br>PATIENTS: Mechanically ventilated critically ill (n = 60) and age-matched healthy children (n = 55).<br><br>INTERVENTIONS: Collection of urine and fecal samples in children admitted to the PICU. A single fecal and urine sample was collected in healthy controls.<br><br>MEASUREMENTS AND MAIN RESULTS: Untargeted and targeted metabolic profiling using 1H-nuclear magnetic resonance spectroscopy and liquid chromatography-mass spectrometry or urine and fecal samples. This was integrated with analysis of fecal bacterial 16S ribosomal RNA profiles and clinical disease severity indicators. We observed separation of global urinary and fecal metabolic profiles in critically ill compared with healthy children. Urinary excretion of mammalian-microbial co-metabolites hippurate, 4-cresol sulphate, and formate were reduced in critical illness compared with healthy children. Reduced fecal excretion of short-chain fatty acids (including butyrate, propionate, and acetate) were observed in the patient cohort, demonstrating that these metabolites also distinguished between critical illness and health. Dysregulation of intestinal bile metabolism was evidenced by increased primary and reduced secondary fecal bile acid excretion. Fecal butyrate correlated with days free of intensive care at 30 days (r = 0.38; p = 0.03), while urinary formate correlated inversely with vasopressor requirement (r = -0.2; p = 0.037).<br><br>CONCLUSIONS: Disruption to the functional activity of the intestinal microbiome may result in worsening organ failure in the critically ill child. Profiling of bacterial metabolites in fecal and urine samples may support identification and treatment of intestinal dysbiosis in critical illness.}, }
@article {pmid31169073, year = {2019}, author = {Hsu, T and Gemmell, MR and Franzosa, EA and Berry, S and Mukhopadhya, I and Hansen, R and Michaud, M and Nielsen, H and Miller, WG and Nielsen, H and Bajaj-Elliott, M and Huttenhower, C and Garrett, WS and Hold, GL}, title = {Comparative genomics and genome biology of Campylobacter showae.}, journal = {Emerging microbes &amp; infections}, volume = {8}, number = {1}, pages = {827-840}, pmid = {31169073}, issn = {2222-1751}, mesh = {Bacterial Proteins/genetics ; Campylobacter/classification/*genetics/isolation &amp; purification/pathogenicity ; Campylobacter Infections/*microbiology ; Crohn Disease/microbiology ; Gastroenteritis/microbiology ; *Genome, Bacterial ; Genomics ; Humans ; Phenotype ; Phylogeny ; Virulence ; Virulence Factors/genetics ; }, abstract = {Campylobacter showae a bacterium historically linked to gingivitis and periodontitis, has recently been associated with inflammatory bowel disease and colorectal cancer. Our aim was to generate genome sequences for new clinical C. showae strains and identify functional properties explaining their pathogenic potential. Eight C. showae genomes were assessed, four strains isolated from inflamed gut tissues from paediatric Crohn's disease patients, three strains from colonic adenomas, and one from a gastroenteritis patient stool. Genome assemblies were analyzed alongside the only 3 deposited C. showae genomes. The pangenome from these 11 strains consisted of 4686 unique protein families, and the core genome size was estimated at 1050 ± 15 genes with each new genome contributing an additional 206 ± 16 genes. Functional assays indicated that colonic strains segregated into 2 groups: adherent/invasive vs. non-adherent/non-invasive strains. The former possessed Type IV secretion machinery and S-layer proteins, while the latter contained Cas genes and other CRISPR associated proteins. Comparison of gene profiles with strains in Human Microbiome Project metagenomes showed that gut-derived isolates share genes specific to tongue dorsum and supragingival plaque counterparts. Our findings indicate that C. showae strains are phenotypically and genetically diverse and suggest that secretion systems may play an important role in virulence potential.}, }
@article {pmid31168910, year = {2020}, author = {Vress, D and Lim, B}, title = {Understanding the human microbiome: new icing on an old cake.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {127}, number = {2}, pages = {138}, doi = {10.1111/1471-0528.15816}, pmid = {31168910}, issn = {1471-0528}, mesh = {Bacterial Infections ; Female ; Gastrointestinal Tract/immunology/*microbiology ; Humans ; *Microbiota/physiology ; Urogenital System/immunology/*microbiology ; }, }
@article {pmid31167634, year = {2019}, author = {LaPierre, N and Mangul, S and Alser, M and Mandric, I and Wu, NC and Koslicki, D and Eskin, E}, title = {MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.}, journal = {BMC genomics}, volume = {20}, number = {Suppl 5}, pages = {423}, pmid = {31167634}, issn = {1471-2164}, support = {R01 ES021801/ES/NIEHS NIH HHS/United States ; R01 MH101782/MH/NIMH NIH HHS/United States ; K25 HL080079/HL/NHLBI NIH HHS/United States ; P01 HL028481/HL/NHLBI NIH HHS/United States ; U01 DA024417/DA/NIDA NIH HHS/United States ; T32 EB016640/EB/NIBIB NIH HHS/United States ; R01 ES022282/ES/NIEHS NIH HHS/United States ; P01 HL030568/HL/NHLBI NIH HHS/United States ; R01 GM083198/GM/NIGMS NIH HHS/United States ; }, mesh = {Algorithms ; Computational Biology/*methods ; Fungi/classification/*genetics ; *Genetic Markers ; Genome, Fungal ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/*methods ; *Microbiota ; Sequence Analysis, DNA/*methods ; Viruses/classification/*genetics ; }, abstract = {BACKGROUND: High throughput sequencing has spurred the development of metagenomics, which involves the direct analysis of microbial communities in various environments such as soil, ocean water, and the human body. Many existing methods based on marker genes or k-mers have limited sensitivity or are too computationally demanding for many users. Additionally, most work in metagenomics has focused on bacteria and archaea, neglecting to study other key microbes such as viruses and eukaryotes.<br><br>RESULTS: Here we present a method, MiCoP (Microbiome Community Profiling), that uses fast-mapping of reads to build a comprehensive reference database of full genomes from viruses and eukaryotes to achieve maximum read usage and enable the analysis of the virome and eukaryome in each sample. We demonstrate that mapping of metagenomic reads is feasible for the smaller viral and eukaryotic reference databases. We show that our method is accurate on simulated and mock community data and identifies many more viral and fungal species than previously-reported results on real data from the Human Microbiome Project.<br><br>CONCLUSIONS: MiCoP is a mapping-based method that proves more effective than existing methods at abundance profiling of viruses and eukaryotes in metagenomic samples. MiCoP can be used to detect the full diversity of these communities. The code, data, and documentation are publicly available on GitHub at: https://github.com/smangul1/MiCoP .}, }
@article {pmid31164901, year = {2019}, author = {Tang, ZZ and Chen, G and Hong, Q and Huang, S and Smith, HM and Shah, RD and Scholz, M and Ferguson, JF}, title = {Multi-Omic Analysis of the Microbiome and Metabolome in Healthy Subjects Reveals Microbiome-Dependent Relationships Between Diet and Metabolites.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {454}, pmid = {31164901}, issn = {1664-8021}, support = {15SDG24890015//American Heart Association-American Stroke Association/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; U01 HL108636/HL/NHLBI NIH HHS/United States ; }, abstract = {The human microbiome has been associated with health status, and risk of disease development. While the etiology of microbiome-mediated disease remains to be fully elucidated, one mechanism may be through microbial metabolism. Metabolites produced by commensal organisms, including in response to host diet, may affect host metabolic processes, with potentially protective or pathogenic consequences. We conducted multi-omic phenotyping of healthy subjects (N = 136), in order to investigate the interaction between diet, the microbiome, and the metabolome in a cross-sectional sample. We analyzed the nutrient composition of self-reported diet (3-day food records and food frequency questionnaires). We profiled the gut and oral microbiome (16S rRNA) from stool and saliva, and applied metabolomic profiling to plasma and stool samples in a subset of individuals (N = 75). We analyzed these multi-omic data to investigate the relationship between diet, the microbiome, and the gut and circulating metabolome. On a global level, we observed significant relationships, particularly between long-term diet, the gut microbiome and the metabolome. Intake of plant-derived nutrients as well as consumption of artificial sweeteners were associated with significant differences in circulating metabolites, particularly bile acids, which were dependent on gut enterotype, indicating that microbiome composition mediates the effect of diet on host physiology. Our analysis identifies dietary compounds and phytochemicals that may modulate bacterial abundance within the gut and interact with microbiome composition to alter host metabolism.}, }
@article {pmid31164869, year = {2019}, author = {Belforte, FS and Fernandez, N and Tonín Monzón, F and Rosso, AD and Quesada, S and Cimolai, MC and Millán, A and Cerrone, GE and Frechtel, GD and Burcelin, R and Coluccio Leskow, F and Penas-Steinhardt, A}, title = {Getting to Know the Gut Microbial Diversity of Metropolitan Buenos Aires Inhabitants.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {965}, pmid = {31164869}, issn = {1664-302X}, support = {T37 MD001452/MD/NIMHD NIH HHS/United States ; }, abstract = {In recent years, the field of immunology has been revolutionized by the growing understanding of the fundamental role of microbiota in the immune system function. The immune system has evolved to maintain a symbiotic relationship with these microbes. The aim of our study was to know in depth the uncharacterized metagenome of the Buenos Aires (BA) city population and its metropolitan area, being the second most populated agglomeration in the southern hemisphere. For this purpose, we evaluated 30 individuals (age: 35.23 ± 8.26 years and BMI: 23.91 ± 3.4 kg/m2), from the general population of BA. The hypervariable regions V3-V4 of the bacterial 16S gene was sequenced by MiSeq-Illumina system, obtaining 47526 ± 4718 sequences/sample. The dominant phyla were Bacteroidetes, Firmicutes, Proteobacteria, Verrucomicrobia, and Actinobacteria. Additionally, we compared the microbiota of BA with other westernized populations (Santiago de Chile, Rosario-Argentina, United States-Human-microbiome-project, Bologna-Italy) and the Hadza population of hunter-gatherers. The unweighted UniFrac clustered together all westernized populations, leaving the hunter-gatherer population from Hadza out. In particular, Santiago de Chile's population turns out to be the closest to BA's, principally due to the presence of Verrucomicrobiales of the genus Akkermansia. These microorganisms have been proposed as a hallmark of a healthy gut. Finally, westernized populations showed more abundant metabolism related KEEG pathways than hunter-gatherers, including carbohydrate metabolism (amino sugar and nucleotide sugar metabolism), amino acid metabolism (alanine, aspartate and glutamate metabolism), lipid metabolism, biosynthesis of secondary metabolites, and sulfur metabolism. These findings contribute to promote research and comparison of the microbiome in different human populations, in order to develop more efficient therapeutic strategies for the restoration of a healthy dialogue between host and environment.}, }
@article {pmid31163166, year = {2019}, author = {Granato, ET and Meiller-Legrand, TA and Foster, KR}, title = {The Evolution and Ecology of Bacterial Warfare.}, journal = {Current biology : CB}, volume = {29}, number = {11}, pages = {R521-R537}, doi = {10.1016/j.cub.2019.04.024}, pmid = {31163166}, issn = {1879-0445}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 209397/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Bacteria have evolved a wide range of mechanisms to harm and kill their competitors, including chemical, mechanical and biological weapons. Here we review the incredible diversity of bacterial weapon systems, which comprise antibiotics, toxic proteins, mechanical weapons that stab and pierce, viruses, and more. The evolution of bacterial weapons is shaped by many factors, including cell density and nutrient abundance, and how strains are arranged in space. Bacteria also employ a diverse range of combat behaviours, including pre-emptive attacks, suicidal attacks, and reciprocation (tit-for-tat). However, why bacteria carry so many weapons, and why they are so often used, remains poorly understood. By comparison with animals, we argue that the way that bacteria live - often in dense and genetically diverse communities - is likely to be key to their aggression as it encourages them to dig in and fight alongside their clonemates. The intensity of bacterial aggression is such that it can strongly affect communities, via complex coevolutionary and eco-evolutionary dynamics, which influence species over space and time. Bacterial warfare is a fascinating topic for ecology and evolution, as well as one of increasing relevance. Understanding how bacteria win wars is important for the goal of manipulating the human microbiome and other important microbial systems.}, }
@article {pmid31158845, year = {2019}, author = {Zimmermann, M and Zimmermann-Kogadeeva, M and Wegmann, R and Goodman, AL}, title = {Mapping human microbiome drug metabolism by gut bacteria and their genes.}, journal = {Nature}, volume = {570}, number = {7762}, pages = {462-467}, pmid = {31158845}, issn = {1476-4687}, support = {DP2 GM105456/GM/NIGMS NIH HHS/United States ; R01 DK114793/DK/NIDDK NIH HHS/United States ; R35 GM118159/GM/NIGMS NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/classification/enzymology/*genetics/*metabolism ; Bacteroides thetaiotaomicron/enzymology/genetics/metabolism ; Diltiazem/metabolism ; Female ; Gastrointestinal Microbiome/*genetics/physiology ; Genome, Bacterial/genetics ; Germ-Free Life ; Humans ; Male ; Mice ; Pharmaceutical Preparations/administration &amp; dosage/*metabolism ; Substrate Specificity ; }, abstract = {Individuals vary widely in their responses to medicinal drugs, which can be dangerous and expensive owing to treatment delays and adverse effects. Although increasing evidence implicates the gut microbiome in this variability, the molecular mechanisms involved remain largely unknown. Here we show, by measuring the ability of 76 human gut bacteria from diverse clades to metabolize 271 orally administered drugs, that many drugs are chemically modified by microorganisms. We combined high-throughput genetic analyses with mass spectrometry to systematically identify microbial gene products that metabolize drugs. These microbiome-encoded enzymes can directly and substantially affect intestinal and systemic drug metabolism in mice, and can explain the drug-metabolizing activities of human gut bacteria and communities on the basis of their genomic contents. These causal links between the gene content and metabolic activities of the microbiota connect interpersonal variability in microbiomes to interpersonal differences in drug metabolism, which has implications for medical therapy and drug development across multiple disease indications.}, }
@article {pmid31154251, year = {2019}, author = {Williams, DW and Gibson, G}, title = {Classification of individuals and the potential to detect sexual contact using the microbiome of the pubic region.}, journal = {Forensic science international. Genetics}, volume = {41}, number = {}, pages = {177-187}, doi = {10.1016/j.fsigen.2019.05.004}, pmid = {31154251}, issn = {1878-0326}, mesh = {Adult ; Aged ; Female ; *Genitalia ; Hair/*microbiology ; Humans ; Male ; *Microbiota ; Middle Aged ; Principal Component Analysis ; RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; *Sexual Behavior ; Young Adult ; }, abstract = {In the absence of traditional DNA evidence, detection of sexual contact during intercourse is an important need for forensic analysis that might be addressed by studies of the pubic microbiome. Since 16S sequencing of various other body parts has shown that the microbiome may be individualizing, we reasoned that transfer of the assailant's microbiome to a victim might be detectable. Microbiome profiles were generated from pubic hairs and swabs taken from the pubic mound region of 12 couples and 19 singles, and evaluated for similarity over an average of four collection times with varying degrees of self-reported sexual activity. A model constructed using a Random Forest classifier was able to predict samples belonging to the same individual collected up to 6 months apart, demonstrating the stability of the pubic mound microbiome over this time frame. Couples were found to be significantly more similar to one another than to unrelated members of the opposite sex, in proportion to shared sexual activity. Further analyses using the Deblur method to assign operational taxonomic units (OTUs) establish that at least 10% of the victim's pubic microbiome must be derived from the attacker in order to detect transfer, but that single transfer events will not generally be discovered. Nevertheless, Bayesian SourceTracker software is shown to have potential to establish that sexual contact occurred when the assailant is known, or to exonerate suspects as contributors to a mixed microbiome. Our results establish limited potential of the pubic hair/pubic area microbiome as a tool for forensic associations.}, }
@article {pmid31142868, year = {2019}, author = {}, title = {After the Integrative Human Microbiome Project, what's next for the microbiome community?.}, journal = {Nature}, volume = {569}, number = {7758}, pages = {599}, doi = {10.1038/d41586-019-01674-w}, pmid = {31142868}, issn = {1476-4687}, mesh = {Female ; Humans ; Infant, Newborn ; *Microbiota ; Pregnancy ; *Premature Birth ; Vagina ; }, }
@article {pmid31142863, year = {2019}, author = {Proctor, L}, title = {Priorities for the next 10 years of human microbiome research.}, journal = {Nature}, volume = {569}, number = {7758}, pages = {623-625}, doi = {10.1038/d41586-019-01654-0}, pmid = {31142863}, issn = {1476-4687}, mesh = {Biomedical Research/economics/*trends ; Female ; Holistic Health ; Host Microbial Interactions/immunology/*physiology ; Humans ; Infant ; Infant, Newborn ; Microbiota/*physiology ; National Institutes of Health (U.S.)/economics ; Species Specificity ; Time Factors ; Tissue Distribution ; United States ; }, }
@article {pmid31142855, year = {2019}, author = {Lloyd-Price, J and Arze, C and Ananthakrishnan, AN and Schirmer, M and Avila-Pacheco, J and Poon, TW and Andrews, E and Ajami, NJ and Bonham, KS and Brislawn, CJ and Casero, D and Courtney, H and Gonzalez, A and Graeber, TG and Hall, AB and Lake, K and Landers, CJ and Mallick, H and Plichta, DR and Prasad, M and Rahnavard, G and Sauk, J and Shungin, D and Vázquez-Baeza, Y and White, RA and ,  and Braun, J and Denson, LA and Jansson, JK and Knight, R and Kugathasan, S and McGovern, DPB and Petrosino, JF and Stappenbeck, TS and Winter, HS and Clish, CB and Franzosa, EA and Vlamakis, H and Xavier, RJ and Huttenhower, C}, title = {Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.}, journal = {Nature}, volume = {569}, number = {7758}, pages = {655-662}, pmid = {31142855}, issn = {1476-4687}, support = {U54 DK102557/DK/NIDDK NIH HHS/United States ; U01 DK062413/DK/NIDDK NIH HHS/United States ; U01 DK097430/DK/NIDDK NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HG005969/HG/NHGRI NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Fungi/pathogenicity ; Gastrointestinal Microbiome/*genetics/immunology ; Health ; Humans ; Inflammatory Bowel Diseases/immunology/*microbiology/therapy/virology ; Phylogeny ; Species Specificity ; Transcriptome ; Viruses/pathogenicity ; }, abstract = {Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database (http://ibdmdb.org), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases.}, }
@article {pmid31142853, year = {2019}, author = {, }, title = {The Integrative Human Microbiome Project.}, journal = {Nature}, volume = {569}, number = {7758}, pages = {641-648}, pmid = {31142853}, issn = {1476-4687}, support = {R01 HD092415/HD/NICHD NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; U54 DE023786/DE/NIDCR NIH HHS/United States ; UH2 AI083263/AI/NIAID NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; }, mesh = {Diet ; Female ; Gastrointestinal Microbiome/physiology ; Host Microbial Interactions/physiology ; Humans ; Infant, Newborn ; *Infant, Premature ; Infections/complications/microbiology ; Inflammatory Bowel Diseases/*microbiology ; *Microbiota/physiology ; National Institutes of Health (U.S.)/*organization &amp; administration ; Prediabetic State/complications/*microbiology ; Pregnancy ; Research/*organization &amp; administration ; Time Factors ; United States ; Vagina/microbiology ; }, abstract = {The NIH Human Microbiome Project (HMP) has been carried out over ten years and two phases to provide resources, methods, and discoveries that link interactions between humans and their microbiomes to health-related outcomes. The recently completed second phase, the Integrative Human Microbiome Project, comprised studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and stressors that affect individuals with prediabetes. The associated research begins to elucidate mechanisms of host-microbiome interactions under these conditions, provides unique data resources (at the HMP Data Coordination Center), and represents a paradigm for future multi-omic studies of the human microbiome.}, }
@article {pmid31142849, year = {2019}, author = {Fettweis, JM and Serrano, MG and Brooks, JP and Edwards, DJ and Girerd, PH and Parikh, HI and Huang, B and Arodz, TJ and Edupuganti, L and Glascock, AL and Xu, J and Jimenez, NR and Vivadelli, SC and Fong, SS and Sheth, NU and Jean, S and Lee, V and Bokhari, YA and Lara, AM and Mistry, SD and Duckworth, RA and Bradley, SP and Koparde, VN and Orenda, XV and Milton, SH and Rozycki, SK and Matveyev, AV and Wright, ML and Huzurbazar, SV and Jackson, EM and Smirnova, E and Korlach, J and Tsai, YC and Dickinson, MR and Brooks, JL and Drake, JI and Chaffin, DO and Sexton, AL and Gravett, MG and Rubens, CE and Wijesooriya, NR and Hendricks-Muñoz, KD and Jefferson, KK and Strauss, JF and Buck, GA}, title = {The vaginal microbiome and preterm birth.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {1012-1021}, pmid = {31142849}, issn = {1546-170X}, support = {R01 HD092415/HD/NICHD NIH HHS/United States ; UH3 AI083263/AI/NIAID NIH HHS/United States ; U54 DE023786/DE/NIDCR NIH HHS/United States ; R21 HD092965/HD/NICHD NIH HHS/United States ; UH2 AI083263/AI/NIAID NIH HHS/United States ; R25 GM090084/GM/NIGMS NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; }, mesh = {Adult ; African Americans ; Biodiversity ; Cohort Studies ; Cytokines/metabolism ; Female ; Host Microbial Interactions/immunology ; Humans ; Infant, Newborn ; Inflammation Mediators/metabolism ; Longitudinal Studies ; Metagenomics ; *Microbiota/genetics/immunology ; Premature Birth/etiology/immunology/*microbiology ; Risk Factors ; United States ; Vagina/immunology/*microbiology ; Young Adult ; }, abstract = {The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes 'omics' data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth.}, }
@article {pmid31140702, year = {2019}, author = {Varoni, EM and Bavarian, R and Robledo-Sierra, J and Porat Ben-Amy, D and Wade, WG and Paster, B and Kerr, R and Peterson, DE and Frandsen Lau, E}, title = {World Workshop on Oral Medicine VII: Targeting the microbiome for oral medicine specialists-Part 1. A methodological guide.}, journal = {Oral diseases}, volume = {25 Suppl 1}, number = {}, pages = {12-27}, doi = {10.1111/odi.13063}, pmid = {31140702}, issn = {1601-0825}, support = {Steering guidance regarding additional text for ac//World Workshop on Oral Medicine VII/ ; }, mesh = {Congresses as Topic ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Microbiota ; *Mouth Diseases ; *Oral Medicine ; Specialization ; }, abstract = {Advances in high-throughput sequencing technologies have allowed for a rapid increase in knowledge about the human microbiome in both healthy and diseased states, which is expected to increase our understanding of multifactorial diseases. The World Workshop on Oral Medicine VII chose the microbiome as one of its topics of focus. Part 1 of this review provides updated knowledge in the field of microbiome research, describes the advantages and disadvantages of currently available sequencing technologies, and proposes a seven-step &quot;recipe&quot; for designing and performing studies that is supported by contemporary evidence. Part 2 of this review in a companion paper discusses the results of high-throughput sequencing studies published to date on the microbiota associated with oral mucosal diseases. The goal of this collective enterprise is to encourage more oral medicine specialists to become engaged in multidisciplinary collaborations to investigate the role of the microbiome in relation to oral diseases, which could potentially lead to enhanced diagnosis, risk assessment and treatment of these patients.}, }
@article {pmid31133693, year = {2019}, author = {Gilbert, JA and Lynch, SV}, title = {Community ecology as a framework for human microbiome research.}, journal = {Nature medicine}, volume = {25}, number = {6}, pages = {884-889}, doi = {10.1038/s41591-019-0464-9}, pmid = {31133693}, issn = {1546-170X}, support = {P01 AI089473/AI/NIAID NIH HHS/United States ; }, mesh = {Biodiversity ; Computational Biology ; Ecosystem ; Host Microbial Interactions ; Humans ; *Microbiota ; Models, Biological ; Research ; }, abstract = {The field of human microbiome research has revealed the intimate co-association of humans with diverse communities of microbes in various habitats in the human body, and the necessity of these microbes for the maintenance of human health. Microbial heterogeneity between humans and across spatial and temporal gradients requires multidimensional datasets and a unifying set of theories and statistical tools to analyze the human microbiome and fully realize the potential of this field. Here we consider the utility of community ecology as a framework for the interrogation and interpretation of the human microbiome.}, }
@article {pmid31123962, year = {2019}, author = {Pulkkinen, E and Wicklund, A and Oduor, JMO and Skurnik, M and Kiljunen, S}, title = {Characterization of vB_ApiM_fHyAci03, a novel lytic bacteriophage that infects clinical Acinetobacter strains.}, journal = {Archives of virology}, volume = {164}, number = {8}, pages = {2197-2199}, pmid = {31123962}, issn = {1432-8798}, support = {TYH2018228//Special state subsidy for health science research/ ; TYH2015411//Special state subsidy for health science research/ ; }, mesh = {Acinetobacter/*virology ; Bacteriophages/*genetics ; DNA, Viral/genetics ; Genome, Viral/genetics ; Host Specificity/genetics ; Myoviridae/genetics ; Phylogeny ; }, abstract = {We present here the isolation and characterization of Acinetobacter pittii phage vB_ApiM_fHyAci03 (fHyAci03), which belongs to the family Myoviridae. The fHyAci03 genome was found to be 165,975 bp in length and predicted to contain 255 genes. While the whole genome was 92.4% identical to Acinetobacter baumannii phage KARL-1, phylogenetic analysis based on phage long distal tail fiber amino acid sequences assigned fHyAci03 and KARL-1 to different subclusters, reflecting their different host species. Together with phylogenetic analysis, genome comparisons indicated that fHyAci03 is a novel member of the subfamily Tevenvirinae. Host range experiments revealed that fHyAci03 could infect two clinical strains of Acinetobacter nosocomialis and six clinical strains of A. pittii. Thus, fHyAci03 is a novel lytic phage that infects clinical Acinetobacter strains and represents a potential new candidate to be used in phage therapy.}, }
@article {pmid31123296, year = {2019}, author = {Virtanen, S and Rantsi, T and Virtanen, A and Kervinen, K and Nieminen, P and Kalliala, I and Salonen, A}, title = {Vaginal Microbiota Composition Correlates Between Pap Smear Microscopy and Next Generation Sequencing and Associates to Socioeconomic Status.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {7750}, pmid = {31123296}, issn = {2045-2322}, support = {TYH2014310/1179003//Helsingin ja Uudenmaan Sairaanhoitopiiri (Helsinki University Central Hospital)/ ; TYH2014310/1179003//Helsingin ja Uudenmaan Sairaanhoitopiiri (Helsinki University Central Hospital)/ ; TYH2014310/1179003//Helsingin ja Uudenmaan Sairaanhoitopiiri (Helsinki University Central Hospital)/ ; }, abstract = {Recent research on vaginal microbiota relies on high throughput sequencing while microscopic methods have a long history in clinical use. We investigated the correspondence between microscopic findings of Pap smears and the vaginal microbiota composition determined by next generation sequencing among 50 asymptomatic women. Both methods produced coherent results regarding the distinction between Lactobacillus-dominant versus mixed microbiota, reassuring gynaecologists for the use of Pap smear or wet mount microscopy for rapid evaluation of vaginal bacteria as part of diagnosis. Cytologic findings identified women with bacterial vaginosis and revealed that cytolysis of vaginal epithelial cells is associated to Lactobacillus crispatus-dominated microbiota. Education and socio-economic status were associated to the vaginal microbiota variation. Our results highlight the importance of including socio-economic status as a co-factor in future vaginal microbiota studies.}, }
@article {pmid31122279, year = {2019}, author = {Ross, AA and Rodrigues Hoffmann, A and Neufeld, JD}, title = {The skin microbiome of vertebrates.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {79}, pmid = {31122279}, issn = {2049-2618}, abstract = {The skin constitutes the primary physical barrier between vertebrates and their external environment. Characterization of skin microorganisms is essential for understanding how a host evolves in association with its microbial symbionts, modeling immune system development, diagnosing illnesses, and exploring the origins of potential zoonoses that affect humans. Although many studies have characterized the human microbiome with culture-independent techniques, far less is known about the skin microbiome of other mammals, amphibians, birds, fish, and reptiles. The aim of this review is to summarize studies that have leveraged high-throughput sequencing to better understand the skin microorganisms that associate with members of classes within the subphylum Vertebrata. Specifically, links will be explored between the skin microbiome and vertebrate characteristics, including geographic location, biological sex, animal interactions, diet, captivity, maternal transfer, and disease. Recent literature on parallel patterns between host evolutionary history and their skin microbial communities, or phylosymbiosis, will also be analyzed. These factors must be considered when designing future microbiome studies to ensure that the conclusions drawn from basic research translate into useful applications, such as probiotics and successful conservation strategies for endangered and threatened animals.}, }
@article {pmid31121812, year = {2019}, author = {Biesiekierski, JR and Jalanka, J and Staudacher, HM}, title = {Can Gut Microbiota Composition Predict Response to Dietary Treatments?.}, journal = {Nutrients}, volume = {11}, number = {5}, pages = {}, pmid = {31121812}, issn = {2072-6643}, mesh = {Animals ; Bacteria/classification/isolation &amp; purification ; Blood Glucose/analysis ; Diet ; Gastrointestinal Microbiome/*physiology ; Humans ; Irritable Bowel Syndrome/*diet therapy/*microbiology ; Mice ; Obesity/*diet therapy/*microbiology ; Treatment Outcome ; Weight Loss ; }, abstract = {Dietary intervention is a challenge in clinical practice because of inter-individual variability in clinical response. Gut microbiota is mechanistically relevant for a number of disease states and consequently has been incorporated as a key variable in personalised nutrition models within the research context. This paper aims to review the evidence related to the predictive capacity of baseline microbiota for clinical response to dietary intervention in two specific health conditions, namely, obesity and irritable bowel syndrome (IBS). Clinical trials and larger predictive modelling studies were identified and critically evaluated. The findings reveal inconsistent evidence to support baseline microbiota as an accurate predictor of weight loss or glycaemic response in obesity, or as a predictor of symptom improvement in irritable bowel syndrome, in dietary intervention trials. Despite advancement in quantification methodologies, research in this area remains challenging and larger scale studies are needed until personalised nutrition is realistically achievable and can be translated to clinical practice.}, }
@article {pmid31117024, year = {2019}, author = {Amato, KR}, title = {Missing Links: the Role of Primates in Understanding the Human Microbiome.}, journal = {mSystems}, volume = {4}, number = {3}, pages = {}, pmid = {31117024}, issn = {2379-5077}, abstract = {The gut microbiome can influence host energy balances and metabolic programming. While this information is valuable in a disease context, it also has important implications for understanding host energetics from an ecological and evolutionary perspective. Here I argue that gut microbial influences on host life history-the timing of events that make up an organism's life-are an overlooked but robust area of study given that variation in life history is linked directly to host energetic budgets and allocation patterns. Additionally, while cultural influences on life history complicate the exploration of these links in humans, nonhuman primates represent an alternative system in which more robust associations can be made. By integrating human and nonhuman primate microbiome research within the context of life history theory, we will be able to more effectively pinpoint microbial contributions to host phenotypes. This information will improve our understanding of host-microbe interactions in health and disease and will transform the fields of ecology and evolution more generally.}, }
@article {pmid31113222, year = {2019}, author = {Lew, KN and Starkweather, A and Cong, X and Judge, M}, title = {A Mechanistic Model of Gut-Brain Axis Perturbation and High-Fat Diet Pathways to Gut Microbiome Homeostatic Disruption, Systemic Inflammation, and Type 2 Diabetes.}, journal = {Biological research for nursing}, volume = {21}, number = {4}, pages = {384-399}, doi = {10.1177/1099800419849109}, pmid = {31113222}, issn = {1552-4175}, mesh = {Animals ; Diabetes Mellitus, Type 2/*metabolism ; Diet, High-Fat ; Dietary Fats/*metabolism ; *Gastrointestinal Microbiome ; Humans ; Inflammation/*metabolism ; Insulin Resistance ; Lipopolysaccharides/metabolism ; Obesity/*metabolism ; }, abstract = {Type 2 diabetes (T2D) is a highly prevalent metabolic disease, affecting nearly 10% of the American population. Although the etiopathogenesis of T2D remains poorly understood, advances in DNA sequencing technologies have allowed for sophisticated interrogation of the human microbiome, providing insight into the role of the gut microbiome in the development and progression of T2D. An emerging body of research reveals that gut-brain axis (GBA) perturbations and a high-fat diet (HFD), along with other modifiable and nonmodifiable risk factors, contribute to gut microbiome homeostatic imbalance. Homeostatic imbalance or disruption increases gut wall permeability and facilitates translocation of endotoxins (lipopolysaccharides) into the circulation with resultant systemic inflammation. Chronic, low-grade systemic inflammation ensues with pro-inflammatory pathways activated, contributing to obesity, insulin resistance (IR), pancreatic β-cell decline, and, thereby, T2D. While GBA perturbations and HFD are implicated in provoking these conditions, prior mechanistic models have tended to examine HFD and GBA pathways exclusively without considering their shared pathways to T2D. Addressing this gap, this article proposes a mechanistic model informed by animal and human studies to advance scientific understanding of (1) modifiable and nonmodifiable risk factors for gut microbiome homeostatic disruption, (2) HFD and GBA pathways contributing to homeostatic disruption, and (3) shared GBA and HFD pro-inflammatory pathways to obesity, IR, β-cell decline, and T2D. The proposed mechanistic model, based on the extant literature, proposes a framework for studying the complex relationships of the gut microbiome to T2D to advance study in this promising area of research.}, }
@article {pmid31107866, year = {2019}, author = {Mainali, K and Bewick, S and Vecchio-Pagan, B and Karig, D and Fagan, WF}, title = {Detecting interaction networks in the human microbiome with conditional Granger causality.}, journal = {PLoS computational biology}, volume = {15}, number = {5}, pages = {e1007037}, pmid = {31107866}, issn = {1553-7358}, mesh = {Causality ; Computational Biology ; Gastrointestinal Microbiome ; Hand/microbiology ; Humans ; *Microbial Interactions ; *Microbiota ; *Models, Biological ; Species Specificity ; Tongue/microbiology ; }, abstract = {Human microbiome research is rife with studies attempting to deduce microbial correlation networks from sequencing data. Standard correlation and/or network analyses may be misleading when taken as an indication of taxon interactions because &quot;correlation is neither necessary nor sufficient to establish causation&quot;; environmental filtering can lead to correlation between non-interacting taxa. Unfortunately, microbial ecologists have generally used correlation as a proxy for causality although there is a general consensus about what constitutes a causal relationship: causes both precede and predict effects. We apply one of the first causal models for detecting interactions in human microbiome samples. Specifically, we analyze a long duration, high resolution time series of the human microbiome to decipher the networks of correlation and causation of human-associated microbial genera. We show that correlation is not a good proxy for biological interaction; we observed a weak negative relationship between correlation and causality. Strong interspecific interactions are disproportionately positive, whereas almost all strong intraspecific interactions are negative. Interestingly, intraspecific interactions also appear to act at a short timescale causing vast majority of the effects within 1-3 days. We report how different taxa are involved in causal relationships with others, and show that strong interspecific interactions are rarely conserved across two body sites whereas strong intraspecific interactions are much more conserved, ranging from 33% between the gut and right-hand to 70% between the two hands. Therefore, in the absence of guiding assumptions about ecological interactions, Granger causality and related techniques may be particularly helpful for understanding the driving factors governing microbiome composition and structure.}, }
@article {pmid31102759, year = {2019}, author = {Levi Mortera, S and Soggiu, A and Vernocchi, P and Del Chierico, F and Piras, C and Carsetti, R and Marzano, V and Britti, D and Urbani, A and Roncada, P and Putignani, L}, title = {Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach.}, journal = {Journal of proteomics}, volume = {203}, number = {}, pages = {103378}, doi = {10.1016/j.jprot.2019.103378}, pmid = {31102759}, issn = {1876-7737}, abstract = {Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.}, }
@article {pmid31093759, year = {2019}, author = {Oduor, JMO and Kiljunen, S and Kadija, E and Mureithi, MW and Nyachieo, A and Skurnik, M}, title = {Genomic characterization of four novel Staphylococcus myoviruses.}, journal = {Archives of virology}, volume = {164}, number = {8}, pages = {2171-2173}, doi = {10.1007/s00705-019-04267-0}, pmid = {31093759}, issn = {1432-8798}, support = {28.06.2017 (Decision letter date)//International Society for Infectious Diseases/European Society of Clinical Microbiology and Infectious Diseases (ISID/ESCMID) Fellowships/ ; TM-17- 10301//EDUFI FELLOWSHIP (Finland)/ ; TM-18- 10752//EDUFI FELLOWSHIP (Finland)/ ; 14.10.2016 (Decision letter date)//Jane ja Aatos Erkon Säätiö (FI)/ ; }, mesh = {DNA, Viral/genetics ; Genome, Viral/genetics ; Genomics/methods ; Myoviridae/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; Staphylococcus/*genetics ; Staphylococcus Phages/genetics ; }, abstract = {We report here the annotation of the complete genomes of four novel lytic Staphylococcus phages; Stab20, Stab21, Stab22 and Stab23. These phages have double-stranded DNA genomes ranging between 153,338 and 155,962 bp in size with terminal repeats of 10,814-12,304 bp. The genome analysis suggests that they represent new phage species within the genus Kayvirus in the subfamily Twortvirinae of the family Herelleviridae.}, }
@article {pmid31092590, year = {2019}, author = {Scott, AJ and Alexander, JL and Merrifield, CA and Cunningham, D and Jobin, C and Brown, R and Alverdy, J and O'Keefe, SJ and Gaskins, HR and Teare, J and Yu, J and Hughes, DJ and Verstraelen, H and Burton, J and O'Toole, PW and Rosenberg, DW and Marchesi, JR and Kinross, JM}, title = {International Cancer Microbiome Consortium consensus statement on the role of the human microbiome in carcinogenesis.}, journal = {Gut}, volume = {68}, number = {9}, pages = {1624-1632}, pmid = {31092590}, issn = {1468-3288}, support = {R01 CA135379/CA/NCI NIH HHS/United States ; R01 CA204403/CA/NCI NIH HHS/United States ; C42378/A25637/CRUK_/Cancer Research UK/United Kingdom ; /DH_/Department of Health/United Kingdom ; }, mesh = {Animals ; Biomedical Research/methods/trends ; *Carcinogenesis/genetics/immunology ; Colorectal Neoplasms/genetics/immunology/microbiology ; DNA Damage ; Dysbiosis/complications/immunology/microbiology ; Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology ; *Microbiota ; Neoplasms/genetics/immunology/*microbiology ; }, abstract = {OBJECTIVE: In this consensus statement, an international panel of experts deliver their opinions on key questions regarding the contribution of the human microbiome to carcinogenesis.<br><br>DESIGN: International experts in oncology and/or microbiome research were approached by personal communication to form a panel. A structured, iterative, methodology based around a 1-day roundtable discussion was employed to derive expert consensus on key questions in microbiome-oncology research.<br><br>RESULTS: Some 18 experts convened for the roundtable discussion and five key questions were identified regarding: (1) the relevance of dysbiosis/an altered gut microbiome to carcinogenesis; (2) potential mechanisms of microbiota-induced carcinogenesis; (3) conceptual frameworks describing how the human microbiome may drive carcinogenesis; (4) causation versus association; and (5) future directions for research in the field.The panel considered that, despite mechanistic and supporting evidence from animal and human studies, there is currently no direct evidence that the human commensal microbiome is a key determinant in the aetiopathogenesis of cancer. The panel cited the lack of large longitudinal, cohort studies as a principal deciding factor and agreed that this should be a future research priority. However, while acknowledging gaps in the evidence, expert opinion was that the microbiome, alongside environmental factors and an epigenetically/genetically vulnerable host, represents one apex of a tripartite, multidirectional interactome that drives carcinogenesis.<br><br>CONCLUSION: Data from longitudinal cohort studies are needed to confirm the role of the human microbiome as a key driver in the aetiopathogenesis of cancer.}, }
@article {pmid31091091, year = {2019}, author = {Bui, TPN and Troise, AD and Fogliano, V and de Vos, WM}, title = {Anaerobic Degradation of N-ε-Carboxymethyllysine, a Major Glycation End-Product, by Human Intestinal Bacteria.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {23}, pages = {6594-6602}, pmid = {31091091}, issn = {1520-5118}, mesh = {Adult ; Anaerobiosis ; Bacteria/classification/genetics/isolation &amp; purification/*metabolism ; Colon/*microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Glycation End Products, Advanced/chemistry/*metabolism ; Glycosylation ; Humans ; Infant ; Lysine/*analogs &amp; derivatives/chemistry/metabolism ; }, abstract = {Modifications of lysine contribute to the amount of dietary advanced glycation end-products reaching the colon. However, little is known about the ability of intestinal bacteria to metabolize dietary N-ε-carboxymethyllysine (CML). Successive transfers of fecal microbiota in growth media containing CML were used to identify and isolate species able to metabolize CML under anaerobic conditions. From our study, only donors exposed to processed foods degraded CML, and anaerobic bacteria enrichments from two of them used 77 and 100% of CML. Oscillibacter and Cloacibacillus evryensis increased in the two donors after the second transfer, highlighting that the bacteria from these taxa could be candidates for anaerobic CML degradation. A tentative identification of CML metabolites produced by a pure culture of Cloacibacillus evryensis was performed by mass spectrometry: carboxymethylated biogenic amines and carboxylic acids were identified as CML degradation products. The study confirmed the ability of intestinal bacteria to metabolize CML under anoxic conditions.}, }
@article {pmid31090586, year = {2019}, author = {Chernikova, D and Yuan, I and Shaker, M}, title = {Prevention of allergy with diverse and healthy microbiota: an update.}, journal = {Current opinion in pediatrics}, volume = {31}, number = {3}, pages = {418-425}, doi = {10.1097/MOP.0000000000000766}, pmid = {31090586}, issn = {1531-698X}, mesh = {*Asthma/microbiology ; Cesarean Section ; Child ; *Dermatitis, Atopic/microbiology ; Female ; *Food Hypersensitivity/microbiology ; Humans ; Infant ; *Microbiota ; Pregnancy ; }, abstract = {PURPOSE OF REVIEW: Microbiota consist of symbiotic microscopic neighbors that interact on and within our bodies in diverse and incompletely understood ways throughout our lifetime. Though various associations with allergic disease have been described, clear effective therapeutic interventions to prevent allergy have been elusive.<br><br>RECENT FINDINGS: The human microbiome is influenced by multiple factors, including: mode of infant delivery (vaginal vs. cesarean section), breastfeeding, diet, presence of siblings and pets, exposure to antibiotics and other medications (particularly antacids), lifestyle, and developmental context. Microbial species promoting atopic responses and tolerance have been described. Specific microbiota likely act through distinct metabolic pathways to promote the health of their human hosts, optimally directing the developing immune system away from pro-allergic, Th2-dominated responses to more T-regulatory-influenced behaviors.<br><br>SUMMARY: Evidence suggests that specific healthy infant microbiome signatures may influence development of some components of the allergic march of childhood by decreasing atopic dermatitis, asthma, and food allergy. Further understanding of factors that influence healthy microbiota may lead to specific strategies tailored for early intervention and disease prevention.}, }
@article {pmid31076500, year = {2019}, author = {Ahmed, B and Cox, MJ and Cuthbertson, L}, title = {Growing up with your airway microbiota: a risky business.}, journal = {Thorax}, volume = {74}, number = {6}, pages = {525-526}, doi = {10.1136/thoraxjnl-2019-213162}, pmid = {31076500}, issn = {1468-3296}, mesh = {Humans ; *Microbiota ; Respiratory System ; *Respiratory Tract Infections ; }, }
@article {pmid31076212, year = {2019}, author = {Beghini, F and Renson, A and Zolnik, CP and Geistlinger, L and Usyk, M and Moody, TU and Thorpe, L and Dowd, JB and Burk, R and Segata, N and Jones, HE and Waldron, L}, title = {Tobacco exposure associated with oral microbiota oxygen utilization in the New York City Health and Nutrition Examination Study.}, journal = {Annals of epidemiology}, volume = {34}, number = {}, pages = {18-25.e3}, pmid = {31076212}, issn = {1873-2585}, support = {R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Biomarkers/blood ; Cotinine/*blood ; Female ; Humans ; Male ; *Microbiota ; Mouth/*microbiology ; New York City/epidemiology ; RNA, Ribosomal, 16S/genetics ; Saliva/*chemistry ; Tobacco Smoke Pollution/*analysis ; Tobacco Smoking/*blood ; }, abstract = {PURPOSE: The effect of tobacco exposure on the oral microbiome has not been established.<br><br>METHODS: We performed amplicon sequencing of the 16S ribosomal RNA gene V4 variable region to estimate bacterial community characteristics in 259 oral rinse samples, selected based on self-reported smoking and serum cotinine levels, from the 2013-2014 New York City Health and Nutrition Examination Study. We identified differentially abundant operational taxonomic units (OTUs) by primary and secondhand tobacco exposure, and used &quot;microbe set enrichment analysis&quot; to assess shifts in microbial oxygen utilization.<br><br>RESULTS: Cigarette smoking was associated with depletion of aerobic OTUs (Enrichment Score test statistic ES = -0.75, P = .002) with a minority (29%) of aerobic OTUs enriched in current smokers compared with never smokers. Consistent shifts in the microbiota were observed for current cigarette smokers as for nonsmokers with secondhand exposure as measured by serum cotinine levels. Differential abundance findings were similar in crude and adjusted analyses.<br><br>CONCLUSIONS: Results support a plausible link between tobacco exposure and shifts in the oral microbiome at the population level through three lines of evidence: (1) a shift in microbiota oxygen utilization associated with primary tobacco smoke exposure; (2) consistency of abundance fold changes associated with current smoking and shifts along the gradient of secondhand smoke exposure among nonsmokers; and (3) consistency after adjusting for a priori hypothesized confounders.}, }
@article {pmid31070803, year = {2019}, author = {Rodricks, J and Huang, Y and Mantus, E and Shubat, P}, title = {Do Interactions Between Environmental Chemicals and the Human Microbiome Need to Be Considered in Risk Assessments?.}, journal = {Risk analysis : an official publication of the Society for Risk Analysis}, volume = {39}, number = {11}, pages = {2353-2358}, pmid = {31070803}, issn = {1539-6924}, support = {R01 AI129958/AI/NIAID NIH HHS/United States ; R03 HL138310/HL/NHLBI NIH HHS/United States ; }, abstract = {One of the most dynamic and fruitful areas of current health-related research concerns the various roles of the human microbiome in disease. Evidence is accumulating that interactions between substances in the environment and the microbiome can affect risks of disease, in both beneficial and adverse ways. Although most of the research has concerned the roles of diet and certain pharmaceutical agents, there is increasing interest in the possible roles of environmental chemicals. Chemical risk assessment has, to date, not included consideration of the influence of the microbiome. We suggest that failure to consider the possible roles of the microbiome could lead to significant error in risk assessment results. Our purpose in this commentary is to summarize some of the evidence supporting our hypothesis and to urge the risk assessment community to begin considering and influencing how results from microbiome-related research could be incorporated into chemical risk assessments. An additional emphasis in our commentary concerns the distinct possibility that research on chemical-microbiome interactions will also reduce some of the significant uncertainties that accompany current risk assessments. Of particular interest is evidence suggesting that the microbiome has an influence on variability in disease risk across populations and (of particular interest to chemical risk) in animal and human responses to chemical exposure. The possible explanatory power of the microbiome regarding sources of variability could reduce what might be the most significant source of uncertainty in chemical risk assessment.}, }
@article {pmid31064829, year = {2019}, author = {Zhu, L and Zou, Q and Cao, X and Cronan, JE}, title = {Enterococcus faecalis Encodes an Atypical Auxiliary Acyl Carrier Protein Required for Efficient Regulation of Fatty Acid Synthesis by Exogenous Fatty Acids.}, journal = {mBio}, volume = {10}, number = {3}, pages = {}, pmid = {31064829}, issn = {2150-7511}, support = {R01 AI015650/AI/NIAID NIH HHS/United States ; R37 AI015650/AI/NIAID NIH HHS/United States ; }, mesh = {Acyl Carrier Protein/genetics/*metabolism ; Bacterial Proteins/genetics/*metabolism ; Biosynthetic Pathways ; Enterococcus faecalis/genetics/*metabolism ; Fatty Acids/*metabolism ; *Gene Expression Regulation, Bacterial ; Lipid Metabolism ; Operon ; }, abstract = {Acyl carrier proteins (ACPs) play essential roles in the synthesis of fatty acids and transfer of long fatty acyl chains into complex lipids. The Enterococcus faecalis genome contains two annotated acp genes, called acpA and acpB AcpA is encoded within the fatty acid synthesis (fab) operon and appears essential. In contrast, AcpB is an atypical ACP, having only 30% residue identity with AcpA, and is not essential. Deletion of acpB has no effect on E. faecalis growth or de novo fatty acid synthesis in media lacking fatty acids. However, unlike the wild-type strain, where growth with oleic acid resulted in almost complete blockage of de novo fatty acid synthesis, the ΔacpB strain largely continued de novo fatty acid synthesis under these conditions. Blockage in the wild-type strain is due to repression of fab operon transcription, leading to levels of fatty acid synthetic proteins (including AcpA) that are insufficient to support de novo synthesis. Transcription of the fab operon is regulated by FabT, a repressor protein that binds DNA only when it is bound to an acyl-ACP ligand. Since AcpA is encoded in the fab operon, its synthesis is blocked when the operon is repressed and acpA thus cannot provide a stable supply of ACP for synthesis of the acyl-ACP ligand required for DNA binding by FabT. In contrast to AcpA, acpB transcription is unaffected by growth with exogenous fatty acids and thus provides a stable supply of ACP for conversion to the acyl-ACP ligand required for repression by FabT. Indeed, ΔacpB and ΔfabT strains have essentially the same de novo fatty acid synthesis phenotype in oleic acid-grown cultures, which argues that neither strain can form the FabT-acyl-ACP repression complex. Finally, acylated derivatives of both AcpB and AcpA were substrates for the E. faecalis enoyl-ACP reductases and for E. faecalis PlsX (acyl-ACP; phosphate acyltransferase).IMPORTANCE AcpB homologs are encoded by many, but not all, lactic acid bacteria (Lactobacillales), including many members of the human microbiome. The mechanisms regulating fatty acid synthesis by exogenous fatty acids play a key role in resistance of these bacteria to those antimicrobials targeted at fatty acid synthesis enzymes. Defective regulation can increase resistance to such inhibitors and also reduce pathogenesis.}, }
@article {pmid31059117, year = {2019}, author = {Jagodzinski, A and Zielinska, E and Laczmanski, L and Hirnle, L}, title = {The early years of life. Are they influenced by our microbiome?.}, journal = {Ginekologia polska}, volume = {90}, number = {4}, pages = {228-232}, doi = {10.5603/GP.2019.0041}, pmid = {31059117}, issn = {2543-6767}, mesh = {Child ; *Child Development ; Child, Preschool ; Gastrointestinal Microbiome ; Humans ; Hypersensitivity ; Infant ; Infant, Newborn ; *Microbiota ; Milk, Human ; Parturition ; }, abstract = {Human microbiome contains the genetic pool of bacteria and other microbes such as Achaea, fungi and viruses inhabiting the human body. It holds an immense potential to affect both physiological and pathological processes. The microbiome's composition can be defined in detail by analyzing ribosomal 16S rRNA and metagenomic tests. Recent increases in cesar- ean sections, the use of antibiotics during pregnancy, the increasing amount of prematurely born children and changes in infant nutrition have an impact on the microbiome forming process. A correlation between the bowel microbiome's com- position and the occurrence of certain diseases, especially inflammatory bowel diseases (IBD), asthma and type 1 diabetes has been demonstrated. The influence on the development of cognitive functions and behaviour has also been displayed. This correlation justifies attempts to restore the beneficial the composition of the microbiome through the use of probiotics, vaginal microflora transfer in case of cesarean section and encouraging breastfeeding. Development of multiple studies on the topic of the human microbiome and its impact on the human body is necessary in order to reach final conclusions. The aim of this article is to summarize recent findings regarding the development of the human microbiome from the first days of life and the influence of changes in its composition on human health.}, }
@article {pmid31057522, year = {2019}, author = {Fiedorová, K and Radvanský, M and Němcová, E and Grombiříková, H and Bosák, J and Černochová, M and Lexa, M and Šmajs, D and Freiberger, T}, title = {The Impact of DNA Extraction Methods on Stool Bacterial and Fungal Microbiota Community Recovery.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {821}, pmid = {31057522}, issn = {1664-302X}, abstract = {Our understanding of human gut microbiota in health and disease depends on accurate and reproducible microbial data acquisition. The critical step in this process is to apply an appropriate methodology to extract microbial DNA, since biases introduced during the DNA extraction process may result in inaccurate microbial representation. In this study, we attempted to find a DNA extraction protocol which could be effectively used to analyze both the bacterial and fungal community. We evaluated the effect of five DNA extraction methods (QIAamp DNA Stool Mini Kit, PureLinkTM Microbiome DNA Purification Kit, ZR Fecal DNA MiniPrepTM Kit, NucleoSpin® DNA Stool Kit, and IHMS protocol Q) on bacterial and fungal gut microbiome recovery using (i) a defined system of germ-free mice feces spiked with bacterial or fungal strains, and (ii) non-spiked human feces. In our experimental setup, we confirmed that the examined methods significantly differed in efficiency and quality, which affected the identified stool microbiome composition. In addition, our results indicated that fungal DNA extraction might be prone to be affected by reagent/kit contamination, and thus an appropriate blank control should be included in mycobiome research. Overall, standardized IHMS protocol Q, recommended by the International Human Microbiome Consortium, performed the best when considering all the parameters analyzed, and thus could be applied not only in bacterial, but also in fungal microbiome research.}, }
@article {pmid31055031, year = {2019}, author = {Seferovic, MD and Pace, RM and Carroll, M and Belfort, B and Major, AM and Chu, DM and Racusin, DA and Castro, ECC and Muldrew, KL and Versalovic, J and Aagaard, KM}, title = {Visualization of microbes by 16S in situ hybridization in term and preterm placentas without intraamniotic infection.}, journal = {American journal of obstetrics and gynecology}, volume = {221}, number = {2}, pages = {146.e1-146.e23}, doi = {10.1016/j.ajog.2019.04.036}, pmid = {31055031}, issn = {1097-6868}, mesh = {Adult ; DNA Barcoding, Taxonomic ; Female ; Humans ; In Situ Hybridization ; Metagenomics ; Microbiota ; Placenta/*microbiology ; Pregnancy ; Premature Birth ; RNA, Bacterial/analysis ; *RNA, Ribosomal, 16S ; Sequence Analysis, RNA ; Term Birth ; }, abstract = {BACKGROUND: Numerous reports have documented bacteria in the placental membranes and basal plate decidua in the absence of immunopathology using histologic techniques. Similarly, independent metagenomic characterizations have identified an altered taxonomic makeup in association with spontaneous preterm birth. Here we sought to corroborate these findings by localizing presumptive intact bacteria using molecular histology within the placental microanatomy.<br><br>OBJECTIVE: Here we examined for microbes in term and preterm gestations using a signal-amplified 16S universal in situ hybridization probe set for bacterial rRNA, alongside traditional histologic methods of Warthin-Starry and Gram stains, as well as clinical culture methodologies. We further sought to differentiate accompanying 16S gene sequencing taxonomic profiles from germ-free (gnotobiotic) mouse and extraction and amplicon contamination controls.<br><br>STUDY DESIGN: Placentas were collected from a total of 53 subjects, composed of term labored (n = 4) and unlabored cesarean deliveries (n = 22) and preterm vaginal (n = 18) and cesarean deliveries (n = 8); a placenta from a single subject with clinical and histologic evident choriomanionitis was employed as a positive control (n = 1). The preterm cohort included spontaneous preterm birth with (n = 6) and without (n = 10) preterm premature rupture of membranes, as well as medically indicated preterm births (n = 10). Placental microbes were visualized using an in situ hybridization probe set designed against highly conserved regions of the bacterial 16S ribosome, which produces an amplified stable signal using branched DNA probes. Extracted bacterial nucleic acids from these same samples were subjected to 16S rRNA metagenomic sequencing (Illumina, V4) for course taxonomic analysis, alongside environmental and kit contaminant controls. A subset of unlabored, cesarean-delivered term pregnancies were also assessed with clinical culture for readily cultivatable pathogenic microbes.<br><br>RESULTS: Molecular in situ hybridization of bacterial rRNA enabled visualization and localization of low-abundance microbes after systematic high-power scanning. Despite the absence of clinical or histologic chorioamnionitis in 52 of 53 subjects, instances of 16S rRNA signal were confidently observed in 13 of 16 spontaneous preterm birth placentas, which was not significantly different from term unlabored cesarean specimens (18 of 22; P > .05). 16S rRNA signal was largely localized to the villous parenchyma and/or syncytiotrophoblast, and less commonly the chorion and the maternal intervillous space. In all term and unlabored cesarean deliveries, visualization of evident placental microbes by in situ hybridization occurred in the absence of clinical or histologic detection using conventional clinical cultivation, hematoxylin-eosin, and Gram staining. In 1 subject, appreciable villous bacteria localized to an infarction, where 16S microbial detection was confirmed by Warthin-Starry stain. In all instances, parallel sample principle coordinate analysis using Bray-Cutis distances of 16S rRNA gene sequencing data demonstrated consistent taxonomic distinction from all negative or potential contamination controls (P = .024, PERMANOVA). Classification from contaminant filtered data identified a distinct taxonomic makeup among term and preterm cohorts when compared with contaminant controls (false discovery rate <0.05).<br><br>CONCLUSION: Presumptively intact placental microbes are visualized as low-abundance, low-biomass and sparse populations within the placenta regardless of gestational age and mode of delivery. Their taxonomic makeup is distinct from contamination controls. These findings further support several previously published findings, including our own, which have used metagenomics to characterize low-abundance and low-biomass microbial communities in the placenta.}, }
@article {pmid31047664, year = {2019}, author = {Chetwynd, AJ and Ogilvie, LA and Nzakizwanayo, J and Pazdirek, F and Hoch, J and Dedi, C and Gilbert, D and Abdul-Sada, A and Jones, BV and Hill, EM}, title = {The potential of nanoflow liquid chromatography-nano electrospray ionisation-mass spectrometry for global profiling the faecal metabolome.}, journal = {Journal of chromatography. A}, volume = {1600}, number = {}, pages = {127-136}, doi = {10.1016/j.chroma.2019.04.028}, pmid = {31047664}, issn = {1873-3778}, support = {G0901553//Medical Research Council/United Kingdom ; }, mesh = {Bile Acids and Salts/analysis ; *Chromatography, Liquid ; Eicosanoids/analysis ; Feces/*chemistry ; Female ; Healthy Volunteers ; Humans ; Male ; *Metabolome ; Metabolomics ; Phospholipids/analysis ; Pilot Projects ; *Spectrometry, Mass, Electrospray Ionization ; }, abstract = {Faeces are comprised of a wide array of metabolites arising from the circulatory system as well as the human microbiome. A global metabolite analysis (metabolomics) of faecal extracts offers the potential to uncover new compounds which may be indicative of the onset of bowel diseases such as colorectal cancer (CRC). To date, faecal metabolomics is still in its infancy and the compounds of low abundance present in faecal extracts poorly characterised. In this study, extracts of faeces from healthy subjects were profiled using a sensitive nanoflow-nanospray LC-MS platform which resulted in highly repeatable peak retention times (<2% CV) and intensities (<15% CV). Analysis of the extracts revealed wide coverage of the faecal metabolome including detection of low abundant signalling compounds such as sex steroids and eicosanoids, alongside highly abundant pharmaceuticals and tetrapyrrole metabolites. A small pilot study investigating differences in metabolomics profiles of faecal samples obtained from 7 CRC, 25 adenomatous polyp and 26 healthy groups revealed that secondary bile acids, conjugated androgens, eicosanoids, phospholipids and an unidentified haem metabolite were potential classes of metabolites that discriminated between the CRC and control sample groups. However, much larger follow up studies are needed to confirm which components of the faecal metabolome are associated with actual CRC disease rather than dietary influences. This study reveals the potential of nanospray-nanoflow LC-MS profiling of faecal samples from large scale cohort studies for uncovering the role of the faecal metabolome in colorectal disease formation.}, }
@article {pmid31046835, year = {2019}, author = {Sharma, A and Richardson, M and Cralle, L and Stamper, CE and Maestre, JP and Stearns-Yoder, KA and Postolache, TT and Bates, KL and Kinney, KA and Brenner, LA and Lowry, CA and Gilbert, JA and Hoisington, AJ}, title = {Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {70}, pmid = {31046835}, issn = {2049-2618}, abstract = {BACKGROUND: The microbiome of the built environment has important implications for human health and wellbeing; however, bidirectional exchange of microbes between occupants and surfaces can be confounded by lifestyle, architecture, and external environmental exposures. Here, we present a longitudinal study of United States Air Force Academy cadets (n = 34), which have substantial homogeneity in lifestyle, diet, and age, all factors that influence the human microbiome. We characterized bacterial communities associated with (1) skin and gut samples from roommate pairs, (2) four built environment sample locations inside the pairs' dormitory rooms, (3) four built environment sample locations within shared spaces in the dormitory, and (4) room-matched outdoor samples from the window ledge of their rooms.<br><br>RESULTS: We analyzed 2,170 samples, which generated 21,866 unique amplicon sequence variants. Linear convergence of microbial composition and structure was observed between an occupants' skin and the dormitory surfaces that were only used by that occupant (i.e., desk). Conversely, bacterial community beta diversity (weighted Unifrac) convergence between the skin of both roommates and the shared dormitory floor between the two cadet's beds was not seen across the entire study population. The sampling period included two semester breaks in which the occupants vacated their rooms; upon their return, the beta diversity similarity between their skin and the surfaces had significantly decreased compared to before the break (p < 0.05). There was no apparent convergence between the gut and building microbiota, with the exception of communal bathroom door-handles, which suggests that neither co-occupancy, diet, or lifestyle homogenization had a significant impact on gut microbiome similarity between these cadets over the observed time frame. As a result, predictive classifier models were able to identify an individual more accurately based on the gut microbiota (74%) compared to skin (51%).<br><br>CONCLUSIONS: To the best of our knowledge, this is the first study to show an increase in skin microbial similarity of two individuals who start living together for the first time and who are not genetically related or romantically involved. Cohabitation was significantly associated with increased skin microbiota similarity but did not significantly influence the gut microbiota. Following a departure from the occupied space of several weeks, the skin microbiota, but not the gut microbiota, showed a significant reduction in similarity relative to the building. Overall, longitudinal observation of these dynamics enables us to dissect the influence of occupation, diet, and lifestyle factors on occupant and built environment microbial ecology.}, }
@article {pmid31042284, year = {2019}, author = {Vangay, P and Hillmann, BM and Knights, D}, title = {Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks.}, journal = {GigaScience}, volume = {8}, number = {5}, pages = {}, pmid = {31042284}, issn = {2047-217X}, support = {R01 AI121383/NIAID NIH HHS/National Institute of Allergy and Infectious Diseases Extramural Activities/United States ; }, mesh = {Algorithms ; *Databases, Genetic ; Humans ; Machine Learning ; Microbiota/*genetics ; *Software ; }, abstract = {The use of machine learning in high-dimensional biological applications, such as the human microbiome, has grown exponentially in recent years, but algorithm developers often lack the domain expertise required for interpretation and curation of the heterogeneous microbiome datasets. We present Microbiome Learning Repo (ML Repo, available at https://knights-lab.github.io/MLRepo/), a public, web-based repository of 33 curated classification and regression tasks from 15 published human microbiome datasets. We highlight the use of ML Repo in several use cases to demonstrate its wide application, and we expect it to be an important resource for algorithm developers.}, }
@article {pmid31028005, year = {2019}, author = {Zhao, S and Lieberman, TD and Poyet, M and Kauffman, KM and Gibbons, SM and Groussin, M and Xavier, RJ and Alm, EJ}, title = {Adaptive Evolution within Gut Microbiomes of Healthy People.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {5}, pages = {656-667.e8}, pmid = {31028005}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {*Adaptation, Biological ; Adult ; Bacteroides fragilis/*genetics/*growth &amp; development ; Female ; *Gastrointestinal Microbiome ; Genetics, Population ; Healthy Volunteers ; Humans ; Male ; Metagenomics ; *Microbiota ; Mutation ; Selection, Genetic ; Young Adult ; }, abstract = {Natural selection shapes bacterial evolution in all environments. However, the extent to which commensal bacteria diversify and adapt within the human gut remains unclear. Here, we combine culture-based population genomics and metagenomics to investigate the within-microbiome evolution of Bacteroides fragilis. We find that intra-individual B. fragilis populations contain substantial de novo nucleotide and mobile element diversity, preserving years of within-person history. This history reveals multiple signatures of within-person adaptation, including parallel evolution in sixteen genes. Many of these genes are implicated in cell-envelope biosynthesis and polysaccharide utilization. Tracking evolutionary trajectories using near-daily metagenomic sampling, we find evidence for years-long coexistence in one subject despite adaptive dynamics. We used public metagenomes to investigate one adaptive mutation common in our cohort and found that it emerges frequently in Western, but not Chinese, microbiomes. Collectively, these results demonstrate that B. fragilis adapts within individual microbiomes, pointing to factors that promote long-term gut colonization.}, }
@article {pmid31024514, year = {2019}, author = {Raju, SC and Lagström, S and Ellonen, P and de Vos, WM and Eriksson, JG and Weiderpass, E and Rounge, TB}, title = {Gender-Specific Associations Between Saliva Microbiota and Body Size.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {767}, pmid = {31024514}, issn = {1664-302X}, abstract = {Objective: The human intestinal microbiota likely play an important role in the development of overweight and obesity. However, the associations between saliva microbiota and body mass index (BMI) have been sparsely studied. The aim of this study was to identify the associations between saliva microbiota and body size in Finnish children.<br><br>Methods: The saliva microbiota of 900 Finnish children, aged 11-14 years with measured height and weight, was characterized using 16S rRNA (V3-V4) sequencing.<br><br>Results: The core saliva microbiota consisted of 14 genera that were present in more than 95% of the Finnish children. The saliva microbiota profiles were gender-specific with higher alpha-diversity in boys than girls and significant differences between the genders in community composition and abundances. Alpha-diversity differed between normal weight and overweight girls and between normal weight and obese boys. The composition was dissimilar between normal weight and obese girls, but not in boys. The relative abundance profiles differed according to body size. Decrease in commensal saliva bacteria were observed in all the body sizes when compared to normal weight children. Notably, the relative abundance of bacteria related to, Veillonella, Prevotella, Selenomonas, and Streptococcus was reduced in obese children.<br><br>Conclusion: Saliva microbiota diversity and composition were significantly associated with body size and gender in Finnish children. Body size-specific saliva microbiota profiles open new avenues for studying the potential roles of microbiota in weight development and management.}, }
@article {pmid31021803, year = {2019}, author = {Wassan, JT and Wang, H and Browne, F and Zheng, H}, title = {Phy-PMRFI: Phylogeny-Aware Prediction of Metagenomic Functions Using Random Forest Feature Importance.}, journal = {IEEE transactions on nanobioscience}, volume = {18}, number = {3}, pages = {273-282}, doi = {10.1109/TNB.2019.2912824}, pmid = {31021803}, issn = {1558-2639}, mesh = {Algorithms ; Databases, Genetic ; *Decision Trees ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome/*genetics ; *Metagenomics/classification/methods ; Microbiota/genetics ; Pharynx/microbiology ; Phylogeny ; *Support Vector Machine ; }, abstract = {High-throughput sequencing techniques have accelerated functional metagenomics studies through the generation of large volumes of omics data. The integration of these data using computational approaches is potentially useful for predicting metagenomic functions. Machine learning (ML) models can be trained using microbial features which are then used to classify microbial data into different functional classes. For example, ML analyses over the human microbiome data has been linked to the prediction of important biological states. For analysing omics data, integrating abundance count of taxonomical features with their biological relationships is important. These relationships can potentially be uncovered from the phylogenetic tree of microbial taxa. In this paper, we propose a novel integrative framework Phy-PMRFI. This framework is driven by the phylogeny-based modeling of omics data to predict metagenomic functions using important features selected by a random forest importance (RFI) strategy. The proposed framework integrates the underlying phylogenetic tree information with abundance measures of microbial species (features) by creating a novel phylogeny and abundance aware matrix structure (PAAM). Phy-PMRFI progresses by ranking the microbial features using an RFI measure. This is then used as input for microbiome classification. The resultant feature set enhances the performance of the state-of-art methods such as support vector machines. Our proposed integrative framework also outperforms the state-of-the-art pipeline of phylogenetic isometric log-ratio transform (PhILR) and MetaPhyl. Prediction accuracy of 90 % is obtained with Phy-PMRFI over human throat microbiome in comparison to other approaches of PhILR with 53% and MetaPhyl with 71% accuracy.}, }
@article {pmid31009573, year = {2019}, author = {Zhang, X and Figeys, D}, title = {Perspective and Guidelines for Metaproteomics in Microbiome Studies.}, journal = {Journal of proteome research}, volume = {18}, number = {6}, pages = {2370-2380}, doi = {10.1021/acs.jproteome.9b00054}, pmid = {31009573}, issn = {1535-3907}, support = {MOP-114872//CIHR/Canada ; }, abstract = {The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.}, }
@article {pmid31009405, year = {2019}, author = {Holster, S and Lindqvist, CM and Repsilber, D and Salonen, A and de Vos, WM and König, J and Brummer, RJ}, title = {The Effect of Allogenic Versus Autologous Fecal Microbiota Transfer on Symptoms, Visceral Perception and Fecal and Mucosal Microbiota in Irritable Bowel Syndrome: A Randomized Controlled Study.}, journal = {Clinical and translational gastroenterology}, volume = {10}, number = {4}, pages = {e00034}, pmid = {31009405}, issn = {2155-384X}, abstract = {OBJECTIVES: Fecal microbiota transfer (FMT) is suggested as a potential treatment for patients with irritable bowel syndrome (IBS). We aimed to study the effect of allogenic and autologous FMT on IBS symptoms, visceral sensitivity, and compositional changes in fecal and mucosa-adherent microbiota.<br><br>METHODS: Seventeen patients with IBS were randomized either to receive fecal material from a healthy donor (allogenic) or to receive their own fecal material (autologous). The fecal material was administered into the cecum by whole colonoscopy after bowel cleansing.<br><br>RESULTS: No significant differences were found between the allogenic and the autologous FMT regarding symptom scores. However, symptom scores of patients receiving allogenic fecal material significantly decreased after FMT compared with baseline (P = 0.02), which was not the case in the autologous group (P = 0.16). Visceral sensitivity was not affected except for a small beneficial effect on urge scores in the autologous group (P < 0.05). While both fecal and mucosa-adherent microbiota of some patients shifted to their respective donor's fecal microbiota, some patients showed no relevant microbial changes after allogenic FMT. Large compositional shifts in fecal and mucosa-adherent microbiota also occurred in the autologous group.<br><br>CONCLUSIONS: This study showed that a single FMT by colonoscopy may have beneficial effects in IBS; however, the allogenic fecal material was not superior to the autologous fecal material. This suggests that bowel cleansing prior to the colonoscopy and/or processing of the fecal material as part of the FMT routine contribute to symptoms and gut microbiota composition changes in IBS.}, }
@article {pmid31005411, year = {2019}, author = {Hollister, EB and Oezguen, N and Chumpitazi, BP and Luna, RA and Weidler, EM and Rubio-Gonzales, M and Dahdouli, M and Cope, JL and Mistretta, TA and Raza, S and Metcalf, GA and Muzny, DM and Gibbs, RA and Petrosino, JF and Heitkemper, M and Savidge, TC and Shulman, RJ and Versalovic, J}, title = {Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {21}, number = {3}, pages = {449-461}, pmid = {31005411}, issn = {1943-7811}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; K23 DK101688/DK/NIDDK NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; R03 DK117219/DK/NIDDK NIH HHS/United States ; R01 NR005337/NR/NINR NIH HHS/United States ; }, abstract = {Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role of recurrent abdominal pain in IBS, we evaluated the relationships of pediatric IBS and abdominal pain with intestinal microbes and fecal metabolites using a comprehensive clinical characterization and multiomics strategy. Using rigorous clinical phenotyping, we identified preadolescent children (aged 7 to 12 years) with Rome III IBS (n = 23) and healthy controls (n = 22) and characterized their fecal microbial communities using whole-genome shotgun metagenomics and global unbiased fecal metabolomic profiling. Correlation-based approaches and machine learning algorithms identified associations between microbes, metabolites, and abdominal pain. IBS cases differed from controls with respect to key bacterial taxa (eg, Flavonifractor plautii and Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions (eg, carbohydrate metabolism and amino acid metabolism), and higher-order metabolites (eg, secondary bile acids, sterols, and steroid-like compounds). Significant associations between abdominal pain frequency and severity and intestinal microbial features were identified. A random forest classifier built on metagenomic and metabolic markers successfully distinguished IBS cases from controls (area under the curve, 0.93). Leveraging multiple lines of evidence, intestinal microbes, genes/pathways, and metabolites were associated with IBS, and these features were capable of distinguishing children with IBS from healthy children. These multi-omics features, and their links to childhood IBS coupled with nutritional interventions, may lead to new microbiome-guided diagnostic and therapeutic strategies.}, }
@article {pmid31003081, year = {2019}, author = {Díez López, C and Vidaki, A and Ralf, A and Montiel González, D and Radjabzadeh, D and Kraaij, R and Uitterlinden, AG and Haas, C and Lao, O and Kayser, M}, title = {Novel taxonomy-independent deep learning microbiome approach allows for accurate classification of different forensically relevant human epithelial materials.}, journal = {Forensic science international. Genetics}, volume = {41}, number = {}, pages = {72-82}, doi = {10.1016/j.fsigen.2019.03.015}, pmid = {31003081}, issn = {1878-0326}, mesh = {*Deep Learning ; Female ; Forensic Genetics/methods ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Saliva/microbiology ; *Sequence Analysis, RNA ; Skin/microbiology ; Vagina/microbiology ; }, abstract = {Correct identification of different human epithelial materials such as from skin, saliva and vaginal origin is relevant in forensic casework as it provides crucial information for crime reconstruction. However, the overlap in human cell type composition between these three epithelial materials provides challenges for their differentiation and identification when using previously proposed human cell biomarkers, while their microbiota composition largely differs. By using validated 16S rRNA gene massively parallel sequencing data from the Human Microbiome Project of 1636 skin, oral and vaginal samples, 50 taxonomy-independent deep learning networks were trained to classify these three tissues. Validation testing was performed in de-novo generated high-throughput 16S rRNA gene sequencing data using the Ion Torrent™ Personal Genome Machine from 110 test samples: 56 hand skin, 31 saliva and 23 vaginal secretion specimens. Body-site classification accuracy of these test samples was very high as indicated by AUC values of 0.99 for skin, 0.99 for oral, and 1 for vaginal secretion. Misclassifications were limited to 3 (5%) skin samples. Additional forensic validation testing was performed in mock casework samples by de-novo high-throughput sequencing of 19 freshly-prepared samples and 22 samples aged for 1 up to 7.6 years. All of the 19 fresh and 20 (91%) of the 22 aged mock casework samples were correctly tissue-type classified. Moreover, comparing the microbiome results with outcomes from previous human mRNA-based tissue identification testing in the same 16 aged mock casework samples reveals that our microbiome approach performs better in 12 (75%), similarly in 2 (12.5%), and less good in 2 (12.5%) of the samples. Our results demonstrate that this new microbiome approach allows for accurate tissue-type classification of three human epithelial materials of skin, oral and vaginal origin, which is highly relevant for future forensic investigations.}, }
@article {pmid30994455, year = {2019}, author = {Inkpen, SA}, title = {Health, ecology and the microbiome.}, journal = {eLife}, volume = {8}, number = {}, pages = {}, pmid = {30994455}, issn = {2050-084X}, abstract = {Advances in microbiomics have changed the way in which many researchers think about health and disease. These changes have also raised a number of philosophical questions around these topics, such as the types of living systems to which these concepts can be applied. Here, I discuss the human microbiome from two perspectives: the first treats the microbiome as part of a larger system that includes the human; the second treats the microbiome as an independent ecosystem that provides services to humans. Drawing on the philosophy of medicine and ecology, I explore two questions: i) how can we make sense of disease and dysfunction in these two perspectives? ii) are these two perspectives complimentary or do they compete with each other?}, }
@article {pmid30994187, year = {2019}, author = {Wang, T and Yang, C and Zhao, H}, title = {Prediction analysis for microbiome sequencing data.}, journal = {Biometrics}, volume = {75}, number = {3}, pages = {875-884}, doi = {10.1111/biom.13061}, pmid = {30994187}, issn = {1541-0420}, mesh = {Algorithms ; Bacteria/genetics ; Humans ; Likelihood Functions ; Microbiota/*genetics ; Monte Carlo Method ; Regression Analysis ; *Sequence Analysis ; }, abstract = {One goal of human microbiome studies is to relate host traits with human microbiome compositions. The analysis of microbial community sequencing data presents great statistical challenges, especially when the samples have different library sizes and the data are overdispersed with many zeros. To address these challenges, we introduce a new statistical framework, called predictive analysis in metagenomics via inverse regression (PAMIR), to analyze microbiome sequencing data. Within this framework, an inverse regression model is developed for overdispersed microbiota counts given the trait, and then a prediction rule is constructed by taking advantage of the dimension-reduction structure in the model. An efficient Monte Carlo expectation-maximization algorithm is proposed for maximum likelihood estimation. The method is further generalized to accommodate other types of covariates. We demonstrate the advantages of PAMIR through simulations and two real data examples.}, }
@article {pmid30993039, year = {2019}, author = {Garretto, A and Hatzopoulos, T and Putonti, C}, title = {virMine: automated detection of viral sequences from complex metagenomic samples.}, journal = {PeerJ}, volume = {7}, number = {}, pages = {e6695}, pmid = {30993039}, issn = {2167-8359}, abstract = {Metagenomics has enabled sequencing of viral communities from a myriad of different environments. Viral metagenomic studies routinely uncover sequences with no recognizable homology to known coding regions or genomes. Nevertheless, complete viral genomes have been constructed directly from complex community metagenomes, often through tedious manual curation. To address this, we developed the software tool virMine to identify viral genomes from raw reads representative of viral or mixed (viral and bacterial) communities. virMine automates sequence read quality control, assembly, and annotation. Researchers can easily refine their search for a specific study system and/or feature(s) of interest. In contrast to other viral genome detection tools that often rely on the recognition of viral signature sequences, virMine is not restricted by the insufficient representation of viral diversity in public data repositories. Rather, viral genomes are identified through an iterative approach, first omitting non-viral sequences. Thus, both relatives of previously characterized viruses and novel species can be detected, including both eukaryotic viruses and bacteriophages. Here we present virMine and its analysis of synthetic communities as well as metagenomic data sets from three distinctly different environments: the gut microbiota, the urinary microbiota, and freshwater viromes. Several new viral genomes were identified and annotated, thus contributing to our understanding of viral genetic diversity in these three environments.}, }
@article {pmid30992349, year = {2019}, author = {Aleti, G and Baker, JL and Tang, X and Alvarez, R and Dinis, M and Tran, NC and Melnik, AV and Zhong, C and Ernst, M and Dorrestein, PC and Edlund, A}, title = {Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease.}, journal = {mBio}, volume = {10}, number = {2}, pages = {}, pmid = {30992349}, issn = {2150-7511}, support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; K99 DE024543/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; }, mesh = {Bacteria/genetics/isolation &amp; purification ; Biosynthetic Pathways/*genetics ; Child ; Child, Preschool ; Computational Biology ; Dental Caries/microbiology ; Dysbiosis ; Humans ; Mass Spectrometry ; Metagenome ; *Microbial Interactions ; Microbiota/*genetics ; Mouth/*microbiology ; *Multigene Family ; Periodontitis/microbiology ; Saliva/microbiology ; }, abstract = {Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world's most common chronic diseases.IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world's most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.}, }
@article {pmid30981803, year = {2019}, author = {Parida, S and Sharma, D}, title = {The power of small changes: Comprehensive analyses of microbial dysbiosis in breast cancer.}, journal = {Biochimica et biophysica acta. Reviews on cancer}, volume = {1871}, number = {2}, pages = {392-405}, doi = {10.1016/j.bbcan.2019.04.001}, pmid = {30981803}, issn = {1879-2561}, support = {R01 CA204555/NCI NIH HHS/National Cancer Institute/United States ; }, mesh = {Animals ; Breast Neoplasms/*microbiology ; *Dysbiosis ; Female ; Humans ; }, abstract = {Disparate occurrence of breast cancer remains an intriguing question since only a subset of women with known risk factors develop cancer. Recent studies suggest an active role of local and distant microbiota in breast cancer initiation, progression, and overall prognosis. A dysbiotic microbiota predisposes the body to develop cancer by inducing genetic instability, initiating DNA damage and proliferation of the damaged progeny, eliciting favorable immune response, metabolic dysregulation and altered response to therapy. In this review, we present our analyses of the existing datasets and discuss the local dysbiosis observed in breast cancer patients and different aspects of breast carcinogenesis that can be potentially influenced by local breast microbiota. Striking differences between microbial community compositions in breast of cancer patients compared to healthy individuals were noted. Differences in microbiome were also apparent between benign and malignant disease and between nipple aspirate fluid of healthy individuals and breast survivors. We also discuss the identification of distinct bacterial, fungal, viral as well as parasite signatures for breast cancer. These microbes are capable of producing numerous secondary metabolites that can act as signaling mediators effecting breast cancer progression. We review how microbes potentially alter response to therapy affecting drug metabolism, pharmacokinetics, anti-tumor effects and toxicity. In conclusion, breast harbors a community of microbes that can communicate with the host cells inducing downstream signaling pathways and modulating various aspects of breast cancer growth and metastatic progression and an improved understanding of microbial dysbiosis can potentially reduce breast cancer risk and improve outcomes of breast cancer patients. The human microbiome, now referred to as, the &quot;forgotten organ&quot; contains a metagenome that is 100-fold more diverse compared to the human genome, thereby, is critically associated with human health [1,2]. With the revelations of the human microbiome project and advent of deep sequencing techniques, a plethora of information has been acquired in recent years. Body sites like stomach, bladder and lungs, once thought to be sterile, are now known to harbor millions of indigenous microbial species. Approximately 80% of the healthy microbiome consists of Firmicutes and Bacteroidetes accompanied by Verrucomicrobia, Actinobacteria, Proteobacteria, Tenericutes and Cyanobacteria [2-7]. The role of microbiome in diabetes, obesity and even neurodegenerative diseases was greatly appreciated in the last decade [1,7-14] and now it has been established that microbiome significantly contributes to many organ specific cancers [1,15,16].}, }
@article {pmid30979072, year = {2019}, author = {Lerner, A and Shoenfeld, Y and Matthias, T}, title = {Probiotics: If It Does Not Help It Does Not Do Any Harm. Really?.}, journal = {Microorganisms}, volume = {7}, number = {4}, pages = {}, pmid = {30979072}, issn = {2076-2607}, abstract = {Probiotics per definition should have beneficial effects on human health, and their consumption has tremendously increased in the last decades. In parallel, the amount of published material and claims for their beneficial efficacy soared continuously. Recently, multiple systemic reviews, meta-analyses, and expert opinions expressed criticism on their claimed effects and safety. The present review describes the dark side of the probiotics, in terms of problematic research design, incomplete reporting, lack of transparency, and under-reported safety. Highlighted are the potential virulent factors and the mode of action in the intestinal lumen, risking the physiological microbiome equilibrium. Finally, regulatory topics are discussed to lighten the heterogeneous guidelines applied worldwide. The shift in the scientific world towards a better understanding of the human microbiome, before consumption of the probiotic cargo, is highly endorsed. It is hoped that better knowledge will extend the probiotic repertoire, re-confirm efficacy or safety, establish their efficacy and substantiate their beneficial effects.}, }
@article {pmid30976019, year = {2019}, author = {Jeong, H and Arif, B and Caetano-Anollés, G and Kim, KM and Nasir, A}, title = {Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {5953}, pmid = {30976019}, issn = {2045-2322}, support = {20140428//Ministry of Oceans and Fisheries (MOF)/ ; 21 519/SRGP/R&amp;D/HEC/2014//Higher Education Commission, Pakistan (HEC)/ ; }, abstract = {Horizontal gene transfer (HGT) is widespread in the evolution of prokaryotes, especially those associated with the human body. Here, we implemented large-scale gene-species phylogenetic tree reconstructions and reconciliations to identify putative HGT-derived genes in the reference genomes of microbiota isolated from six major human body sites by the NIH Human Microbiome Project. Comparisons with a control group representing microbial genomes from diverse natural environments indicated that HGT activity increased significantly in the genomes of human microbiota, which is confirmatory of previous findings. Roughly, more than half of total genes in the genomes of human-associated microbiota were transferred (donated or received) by HGT. Up to 60% of the detected HGTs occurred either prior to the colonization of the human body or involved bacteria residing in different body sites. The latter could suggest 'genetic crosstalk' and movement of bacterial genes within the human body via hitherto poorly understood mechanisms. We also observed that HGT activity increased significantly among closely-related microorganisms and especially when they were united by physical proximity, suggesting that the 'phylogenetic effect' can significantly boost HGT activity. Finally, we identified several core and widespread genes least influenced by HGT that could become useful markers for building robust 'trees of life' and address several outstanding technical challenges to improve the phylogeny-based genome-wide HGT detection method for future applications.}, }
@article {pmid30959425, year = {2019}, author = {Shetty, SA and Smidt, H and de Vos, WM}, title = {Reconstructing functional networks in the human intestinal tract using synthetic microbiomes.}, journal = {Current opinion in biotechnology}, volume = {58}, number = {}, pages = {146-154}, doi = {10.1016/j.copbio.2019.03.009}, pmid = {30959425}, issn = {1879-0429}, mesh = {*Gastrointestinal Microbiome ; Humans ; Intestines ; }, abstract = {The human intestinal tract harbors one of the most densely populated and open microbial ecosystems. The application of multi-omics approaches has provided insight into a wide array of complex interactions between the various groups of mainly anaerobic colonic microbes as well as the host-microbe dialogue. Integration of multi-omics techniques in cultivation based experiments that vary in complexity from monocultures to synthetic microbial communities identified key metabolic players in the trophic interactions as well as their ecological dynamics. A synergy between these approaches will be of utmost importance to reconstruct the functional interaction networks at the ecosystem level within the human intestinal microbiome. The improved understanding of microbiome functioning at ecosystem level will further aid in developing better predictive models and design of effective microbiome modulation strategies for health benefits.}, }
@article {pmid30958298, year = {2019}, author = {Algazina, T and Yermekbayeva, B and Batpenova, G and Kushugulova, A}, title = {FEATURES OF MICROBIOTA IN PSORIATIC DISEASE: FROM SKIN AND GUT PERSPECTIVES (REVIEW).}, journal = {Georgian medical news}, volume = {}, number = {287}, pages = {98-104}, pmid = {30958298}, issn = {1512-0112}, mesh = {Arthritis, Psoriatic/*microbiology/pathology ; Dermatitis, Atopic ; Humans ; *Microbiota ; Psoriasis/*microbiology/pathology ; Skin/*microbiology/pathology ; }, abstract = {Psoriatic disease is a chronic inflammatory disease characterized by skin lesions. Psoriasis development has been associated both with genetic and environmental factors. Though skin and gut microbiota has been implicated in number of pathologies including atopic dermatitis, inflammatory bowel disease, Crohn's disease, allergy, and obesity, its role has been poorly studied in psoriatic disease, which incorporates both psoriasis and psoriatic arthritis. This literature review summarizes the most recent and major findings on microbiota features in psoriatic disease. Despite conflicting findings, psoriasis patients were frequently found to have distinct microbial composition in both skin and guts especially in the major bacterial phyla, Firmicutes, Bacteroidetes, and genus Akkermansia. Furthermore, bacterial DNA has been found in psoriatic patients both locally and systemically, and altogether suggesting a crucial role of bacteria in psoriatic disease and future studies in this field.}, }
@article {pmid30955503, year = {2019}, author = {Checinska Sielaff, A and Urbaniak, C and Mohan, GBM and Stepanov, VG and Tran, Q and Wood, JM and Minich, J and McDonald, D and Mayer, T and Knight, R and Karouia, F and Fox, GE and Venkateswaran, K}, title = {Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {50}, pmid = {30955503}, issn = {2049-2618}, mesh = {Bacteria/*classification/genetics/isolation &amp; purification ; Confined Spaces ; Environmental Microbiology ; Fungi/*classification/genetics/isolation &amp; purification ; Humans ; Microbiological Techniques/*methods ; Phylogeny ; Sequence Analysis, DNA/*methods ; Spacecraft ; Weightlessness ; }, abstract = {BACKGROUND: The International Space Station (ISS) is a closed system inhabited by microorganisms originating from life support systems, cargo, and crew that are exposed to unique selective pressures such as microgravity. To date, mandatory microbial monitoring and observational studies of spacecraft and space stations have been conducted by traditional culture methods, although it is known that many microbes cannot be cultured with standard techniques. To fully appreciate the true number and diversity of microbes that survive in the ISS, molecular and culture-based methods were used to assess microbial communities on ISS surfaces. Samples were taken at eight pre-defined locations during three flight missions spanning 14 months and analyzed upon return to Earth.<br><br>RESULTS: The cultivable bacterial and fungal population ranged from 104 to 109 CFU/m2 depending on location and consisted of various bacterial (Actinobacteria, Firmicutes, and Proteobacteria) and fungal (Ascomycota and Basidiomycota) phyla. Amplicon sequencing detected more bacterial phyla when compared to the culture-based analyses, but both methods identified similar numbers of fungal phyla. Changes in bacterial and fungal load (by culture and qPCR) were observed over time but not across locations. Bacterial community composition changed over time, but not across locations, while fungal community remained the same between samplings and locations. There were no significant differences in community composition and richness after propidium monoazide sample treatment, suggesting that the analyzed DNA was extracted from intact/viable organisms. Moreover, approximately 46% of intact/viable bacteria and 40% of intact/viable fungi could be cultured.<br><br>CONCLUSIONS: The results reveal a diverse population of bacteria and fungi on ISS environmental surfaces that changed over time but remained similar between locations. The dominant organisms are associated with the human microbiome and may include opportunistic pathogens. This study provides the first comprehensive catalog of both total and intact/viable bacteria and fungi found on surfaces in closed space systems and can be used to help develop safety measures that meet NASA requirements for deep space human habitation. The results of this study can have significant impact on our understanding of other confined built environments on the Earth such as clean rooms used in the pharmaceutical and medical industries.}, }
@article {pmid30946154, year = {2019}, author = {Sessa, L and Reddel, S and Manno, E and Quagliariello, A and Cotugno, N and Del Chierico, F and Amodio, D and Capponi, C and Leone, F and Bernardi, S and Rossi, P and Putignani, L and Palma, P}, title = {Distinct gut microbiota profile in antiretroviral therapy-treated perinatally HIV-infected patients associated with cardiac and inflammatory biomarkers.}, journal = {AIDS (London, England)}, volume = {33}, number = {6}, pages = {1001-1011}, doi = {10.1097/QAD.0000000000002131}, pmid = {30946154}, issn = {1473-5571}, abstract = {OBJECTIVE: Persistent inflammation and higher risk to develop cardiovascular diseases still represent a major complication for HIV-infected patients despite effective antiretroviral therapy (ART). We investigated the correlation between the gut microbiota profile, markers of inflammation, vascular endothelial activation (VEA) and microbial translocation (MT) in perinatally HIV-infected patients (PHIV) under ART.<br><br>DESIGN: Cross-sectional study including 61 ART-treated PHIV (age range 3-30 years old) and 71 age-matched healthy controls. Blood and stool sample were collected at the same time and analyzed for gut microbiota composition and plasma biomarkers.<br><br>METHODS: Gut microbiota composition was determined by 16S rRNA targeted-metagenomics. Soluble markers of MT, inflammation and VEA were quantified by ELISA or Luminex assay. Markers of immune activation were analyzed by flow cytometry on CD4 and CD8T cells.<br><br>RESULTS: We identified two distinct gut microbiota profiles (groups A and B) among PHIV. No different clinical parameters (age, sex, ethnicity, clinical class), dietary and sexual habits were found between the groups. The group A showed a relative dominance of Akkermansia muciniphila, whereas gut microbiota of group B was characterized by a higher biodiversity. The analysis of soluble markers revealed a significantly higher level of soluble E-selectine (P = 0.0296), intercellular adhesion molecule-1 (P = 0.0028), vascular adhesion molecule-1 (P = 0.0230), IL-6 (P = 0.0247) and soluble CD14 (P = 0.0142) in group A compared with group B.<br><br>CONCLUSION: Distinctive gut microbiota profiles are differently associated with inflammation, microbial translocation and VEA. Future studies are needed to understand the role of A. muciniphila and risk to develop cardiovascular diseases in PHIV.}, }
@article {pmid30942867, year = {2019}, author = {Brown, SM and Chen, H and Hao, Y and Laungani, BP and Ali, TA and Dong, C and Lijeron, C and Kim, B and Wultsch, C and Pei, Z and Krampis, K}, title = {MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs.}, journal = {GigaScience}, volume = {8}, number = {4}, pages = {}, pmid = {30942867}, issn = {2047-217X}, support = {UH3 CA140233/CA/NCI NIH HHS/United States ; UL1 TR000457/TR/NCATS NIH HHS/United States ; G12 MD007599/MD/NIMHD NIH HHS/United States ; R01 AI110372/AI/NIAID NIH HHS/United States ; U54 CA221705/CA/NCI NIH HHS/United States ; R01 CA159036/CA/NCI NIH HHS/United States ; R21 DE025352/DE/NIDCR NIH HHS/United States ; U01 CA182370/CA/NCI NIH HHS/United States ; }, mesh = {Algorithms ; Cloud Computing ; Computational Biology/*methods ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiology ; Microbiota ; Molecular Sequence Annotation ; Reproducibility of Results ; *Software ; Workflow ; }, abstract = {BACKGROUND: Current methods used for annotating metagenomics shotgun sequencing (MGS) data rely on a computationally intensive and low-stringency approach of mapping each read to a generic database of proteins or reference microbial genomes.<br><br>RESULTS: We developed MGS-Fast, an analysis approach for shotgun whole-genome metagenomic data utilizing Bowtie2 DNA-DNA alignment of reads that is an alternative to using the integrated catalog of reference genes database of well-annotated genes compiled from human microbiome data. This method is rapid and provides high-stringency matches (>90% DNA sequence identity) of the metagenomics reads to genes with annotated functions. We demonstrate the use of this method with data from a study of liver disease and synthetic reads, and Human Microbiome Project shotgun data, to detect differentially abundant Kyoto Encyclopedia of Genes and Genomes gene functions in these experiments. This rapid annotation method is freely available as a Galaxy workflow within a Docker image.<br><br>CONCLUSIONS: MGS-Fast can confidently transfer functional annotations from gene databases to metagenomic reads, with speed and accuracy.}, }
@article {pmid30939512, year = {2019}, author = {Chernikova, D and Yuan, I and Shaker, M}, title = {Prevention of allergy with diverse and healthy microbiota: an update.}, journal = {Current opinion in pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1097/MOP.0000000000000766}, pmid = {30939512}, issn = {1531-698X}, abstract = {PURPOSE OF REVIEW: Microbiota consist of symbiotic microscopic neighbors that interact on and within our bodies in diverse and incompletely understood ways throughout our lifetime. Though various associations with allergic disease have been described, clear effective therapeutic interventions to prevent allergy have been elusive.<br><br>RECENT FINDINGS: The human microbiome is influenced by multiple factors, including: mode of infant delivery (vaginal vs. cesarean section), breastfeeding, diet, presence of siblings and pets, exposure to antibiotics and other medications (particularly antacids), lifestyle, and developmental context. Microbial species promoting atopic responses and tolerance have been described. Specific microbiota likely act through distinct metabolic pathways to promote the health of their human hosts, optimally directing the developing immune system away from pro-allergic, Th2-dominated responses to more T-regulatory-influenced behaviors.<br><br>SUMMARY: Evidence suggests that specific healthy infant microbiome signatures may influence development of some components of the allergic march of childhood by decreasing atopic dermatitis, asthma, and food allergy. Further understanding of factors that influence healthy microbiota may lead to specific strategies tailored for early intervention and disease prevention.}, }
@article {pmid30938174, year = {2019}, author = {Sander, MA and Sander, MS and Isaac-Renton, JL and Croxen, MA}, title = {The Cutaneous Microbiome: Implications for Dermatology Practice.}, journal = {Journal of cutaneous medicine and surgery}, volume = {23}, number = {4}, pages = {436-441}, doi = {10.1177/1203475419839939}, pmid = {30938174}, issn = {1615-7109}, mesh = {Genomics ; Humans ; *Microbiota/genetics ; Precision Medicine ; Skin/*microbiology ; Skin Diseases/drug therapy/*microbiology ; }, abstract = {The human integument is inhabited by a vast array of microorganisms known collectively as the cutaneous microbiome. As a result of advances in laboratory science, our understanding of the diversity and complexity of the human microbiome is rapidly evolving. In particular, advances in the field of genomics have enabled the study of the cutaneous microbiome with a hitherto unimaginable level of detail, resulting in a maturation of our understanding of cutaneous health and disease. Herein, we review current microbiology concepts and highlight the key features of recent laboratory advances, particularly with respect to genomics. We provide a summary of new findings related to normal skin flora, interactions between host immunity and microbial communities, and microbial relationships with common skin disorders. Finally, we review the implications for dermatologists.}, }
@article {pmid30937887, year = {2019}, author = {Sharma, A and Buschmann, MM and Gilbert, JA}, title = {Pharmacomicrobiomics: The Holy Grail to Variability in Drug Response?.}, journal = {Clinical pharmacology and therapeutics}, volume = {106}, number = {2}, pages = {317-328}, doi = {10.1002/cpt.1437}, pmid = {30937887}, issn = {1532-6535}, abstract = {The human body, with 3.0 × 1013 cells and more than 3.8 × 1013 microorganisms, has nearly a one-to-one ratio of resident microbes to human cells. Initiatives like the Human Microbiome Project, American Gut, and Flemish Gut have identified associations between microbial taxa and human health. The study of interactions between microbiome and pharmaceutical agents, i.e., pharmacomicrobiomics, has revealed an instrumental role of the microbiome in modulating drug response that alters the therapeutic outcomes. In this review, we present our current comprehension of the relationship of the microbiome, host biology, and pharmaceutical agents such as cardiovascular drugs, analgesics, and chemotherapeutic agents to human disease and treatment outcomes. We also discuss the significance of studying diet-gene-drug interactions and further address the key challenges associated with pharmacomicrobiomics. Finally, we examine proposed models employing systems biology for the application of pharmacomicrobiomics and other -omics data, and provide approaches to elucidate microbiome-drug interactions to improve future translation to personalized medicine.}, }
@article {pmid30935409, year = {2019}, author = {Hamidi, B and Wallace, K and Vasu, C and Alekseyenko, AV}, title = {W∗d -test: robust distance-based multivariate analysis of variance.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {51}, pmid = {30935409}, issn = {2049-2618}, support = {R01 LM012517/LM/NLM NIH HHS/United States ; U54 CA210962/CA/NCI NIH HHS/United States ; UL1 TR001450/TR/NCATS NIH HHS/United States ; }, mesh = {Computational Biology/*methods ; Computer Simulation ; Humans ; *Microbiota ; Multivariate Analysis ; Software ; }, abstract = {BACKGROUND: Community-wide analyses provide an essential means for evaluation of the effect of interventions or design variables on the composition of the microbiome. Applications of these analyses are omnipresent in microbiome literature, yet some of their statistical properties have not been tested for robustness towards common features of microbiome data. Recently, it has been reported that PERMANOVA can yield wrong results in the presence of heteroscedasticity and unbalanced sample sizes.<br><br>FINDINGS: We develop a method for multivariate analysis of variance, [Formula: see text], based on Welch MANOVA that is robust to heteroscedasticity in the data. We do so by extending a previously reported method that does the same for two-level independent factor variables. Our approach can accommodate multi-level factors, stratification, and multiple post hoc testing scenarios. An R language implementation of the method is available at https://github.com/alekseyenko/WdStar .<br><br>CONCLUSION: Our method resolves potential for confounding of location and dispersion effects in multivariate analyses by explicitly accounting for the differences in multivariate dispersion in the data tested. The methods based on [Formula: see text] have general applicability in microbiome and other 'omics data analyses.}, }
@article {pmid30935126, year = {2019}, author = {Massari, F and Mollica, V and Di Nunno, V and Gatto, L and Santoni, M and Scarpelli, M and Cimadamore, A and Lopez-Beltran, A and Cheng, L and Battelli, N and Montironi, R and Brandi, G}, title = {The Human Microbiota and Prostate Cancer: Friend or Foe?.}, journal = {Cancers}, volume = {11}, number = {4}, pages = {}, pmid = {30935126}, issn = {2072-6694}, abstract = {The human microbiome is gaining increasing attention in the medical community, as knowledge on its role not only in health but also in disease development and response to therapies is expanding. Furthermore, the connection between the microbiota and cancer, especially the link between the gut microbiota and gastrointestinal tumors, is becoming clearer. The interaction between the microbiota and the response to chemotherapies and, more recently, to immunotherapy has been widely studied, and a connection between a peculiar type of microbiota and a better response to these therapies and a different incidence in toxicities has been hypothesized. As knowledge on the gut microbiota increases, interest in the residing microbial population in other systems of our body is also increasing. Consequently, the urinary microbiota is under evaluation for its possible implications in genitourinary diseases, including cancer. Prostate cancer is the most common cancer in the male population; thus, research regarding its etiology and possible factors correlated to disease progression or the response to specific therapies is thriving. This review has the purpose to recollect the current knowledge on the relationship between the human microbiota and prostate cancer.}, }
@article {pmid30935109, year = {2019}, author = {Nava Lara, RA and Aguilera-Mendoza, L and Brizuela, CA and Peña, A and Del Rio, G}, title = {Heterologous Machine Learning for the Identification of Antimicrobial Activity in Human-Targeted Drugs.}, journal = {Molecules (Basel, Switzerland)}, volume = {24}, number = {7}, pages = {}, pmid = {30935109}, issn = {1420-3049}, support = {FOIN-219//Consejo Nacional de Ciencia y Tecnología/ ; CB-252316//Consejo Nacional de Ciencia y Tecnología/ ; IG100416//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica, UNAM, Mexico/ ; IN208014//Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica, UNAM, Mexico/ ; }, mesh = {Anti-Infective Agents/*chemistry/*pharmacology ; Bacteria/drug effects ; *Drug Discovery/methods ; Gastrointestinal Microbiome/drug effects ; Humans ; *Machine Learning ; Microbial Sensitivity Tests ; }, abstract = {The emergence of microbes resistant to common antibiotics represent a current treat to human health. It has been recently recognized that non-antibiotic labeled drugs may promote antibiotic-resistance mechanisms in the human microbiome by presenting a secondary antibiotic activity; hence, the development of computer-assisted procedures to identify antibiotic activity in human-targeted compounds may assist in preventing the emergence of resistant microbes. In this regard, it is worth noting that while most antibiotics used to treat human infectious diseases are non-peptidic compounds, most known antimicrobials nowadays are peptides, therefore all computer-based models aimed to predict antimicrobials either use small datasets of non-peptidic compounds rendering predictions with poor reliability or they predict antimicrobial peptides that are not currently used in humans. Here we report a machine-learning-based approach trained to identify gut antimicrobial compounds; a unique aspect of our model is the use of heterologous training sets, in which peptide and non-peptide antimicrobial compounds were used to increase the size of the training data set. Our results show that combining peptide and non-peptide antimicrobial compounds rendered the best classification of gut antimicrobial compounds. Furthermore, this classification model was tested on the latest human-approved drugs expecting to identify antibiotics with broad-spectrum activity and our results show that the model rendered predictions consistent with current knowledge about broad-spectrum antibiotics. Therefore, heterologous machine learning rendered an efficient computational approach to classify antimicrobial compounds.}, }
@article {pmid30930963, year = {2018}, author = {Jaja-Chimedza, A and Zhang, L and Wolff, K and Graf, BL and Kuhn, P and Moskal, K and Carmouche, R and Newman, S and Salbaum, JM and Raskin, I}, title = {A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome.}, journal = {Journal of functional foods}, volume = {47}, number = {}, pages = {376-385}, pmid = {30930963}, issn = {1756-4646}, support = {P20 RR021945/RR/NCRR NIH HHS/United States ; P30 DK072476/DK/NIDDK NIH HHS/United States ; T32 AT004094/AT/NCCIH NIH HHS/United States ; P20 GM103528/GM/NIGMS NIH HHS/United States ; P50 AT002776/AT/NCCIH NIH HHS/United States ; P30 GM118430/GM/NIGMS NIH HHS/United States ; }, abstract = {Moringa oleifera (moringa) has been traditionally used for the treatment of diabetes and in water purification. We previously showed that moringa seed extract (MSE), standardized to its primary bioactive isothiocyanate (MIC-1), modulated inflammatory and antioxidant signaling pathways in vitro. To understand the efficacy and mechanisms of action of MSE in vivo, we incorporated MSE into the diets of normal and obese C57Bl/6J male mice fed a standard low-fat diet or a very high-fat diet for 12 wk, respectively. MSE supplementation resulted in reduced body weight, decreased adiposity, improved glucose tolerance, reduced inflammatory gene expression, and increased antioxidant gene expression. 16S rRNA gene sequencing and quantitative PCR of fecal/cecal samples showed major modulation of the gut microbial community and a significantly reduced bacterial load, similar to an antibiotic response. This suggests that MSE improves metabolic health by its intracellular anti-inflammatory and antioxidant activities, and/or its antibiotic-like restructuring of the gut microbiota.}, }
@article {pmid30930939, year = {2019}, author = {Guo, M and Xu, E and Ai, D}, title = {Inferring Bacterial Infiltration in Primary Colorectal Tumors From Host Whole Genome Sequencing Data.}, journal = {Frontiers in genetics}, volume = {10}, number = {}, pages = {213}, pmid = {30930939}, issn = {1664-8021}, abstract = {Colorectal cancer is the third most common cancer worldwide with abysmal survival, thus requiring novel therapy strategies. Numerous studies have frequently observed infiltrating bacteria within the primary tumor tissues derived from patients. These studies have implicated the relative abundance of these bacteria as a contributing factor in tumor progression. Infiltrating bacteria are believed to be among the major drivers of tumorigenesis, progression, and metastasis and, hence, promising targets for new treatments. However, measuring their abundance directly remains challenging. One potential approach is to use the unmapped reads of host whole genome sequencing (hWGS) data, which previous studies have considered as contaminants and discarded. Here, we developed rigorous bioinformatics and statistical procedures to identify tumor-infiltrating bacteria associated with colorectal cancer from such whole genome sequencing data. Our approach used the reads of whole genome sequencing data of colon adenocarcinoma tissues not mapped to the human reference genome, including unmapped paired-end read pairs and single-end reads, the mates of which were mapped. We assembled the unmapped read pairs, remapped all those reads to the collection of human microbiome reference, and then computed their relative abundance of microbes by maximum likelihood (ML) estimation. We analyzed and compared the relative abundance and diversity of infiltrating bacteria between primary tumor tissues and associated normal blood samples. Our results showed that primary tumor tissues contained far more diverse total infiltrating bacteria than normal blood samples. The relative abundance of Bacteroides fragilis, Bacteroides dorei, and Fusobacterium nucleatum was significantly higher in primary colorectal tumors. These three bacteria were among the top ten microbes in the primary tumor tissues, yet were rarely found in normal blood samples. As a validation step, most of these bacteria were also closely associated with colorectal cancer in previous studies with alternative approaches. In summary, our approach provides a new analytic technique for investigating the infiltrating bacterial community within tumor tissues. Our novel cloud-based bioinformatics and statistical pipelines to analyze the infiltrating bacteria in colorectal tumors using the unmapped reads of whole genome sequences can be freely accessed from GitHub at https://github.com/gutmicrobes/UMIB.git.}, }
@article {pmid30930863, year = {2019}, author = {Reid, G and Gadir, AA and Dhir, R}, title = {Probiotics: Reiterating What They Are and What They Are Not.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {424}, pmid = {30930863}, issn = {1664-302X}, abstract = {It has been over seventeen years since the scientific definition of probiotics was crafted, along with guidelines ensuring the appropriate use of the term. This definition is now used globally, yet on a consistent basis scientists, media and industry misrepresent probiotics or make generalized statements that illustrate a misunderstanding of their utility and limitations. The rate of discovery of novel organisms with potentially therapeutic benefit for both human and environmental health is progressing at an unprecedented rate. However, the term &quot;probiotic&quot; is often misapplied to describe any microbe with plausible therapeutic utility in the human host. It is argued that strict compliance to the scientific definition of the term &quot;probiotic&quot; and avoidance of generalizations to the whole field of probiotics based upon studies of one product, will help advance the development and validation of microbial therapies, and applications to improve human health.}, }
@article {pmid30925932, year = {2019}, author = {van der Veer, C and Hertzberger, RY and Bruisten, SM and Tytgat, HLP and Swanenburg, J and de Kat Angelino-Bart, A and Schuren, F and Molenaar, D and Reid, G and de Vries, H and Kort, R}, title = {Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: implications for in vivo dominance of the vaginal microbiota.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {49}, pmid = {30925932}, issn = {2049-2618}, mesh = {Bacterial Proteins/genetics ; Dysbiosis/*microbiology ; Female ; Genome, Bacterial ; Genomics/*methods ; Glycogen/*metabolism ; Glycosylation ; Glycosyltransferases/genetics ; Humans ; Lactobacillus crispatus/genetics/*isolation &amp; purification/metabolism ; Neisseria gonorrhoeae/growth &amp; development ; Phenotype ; Phylogeny ; Sequence Analysis, DNA ; Vagina/*microbiology ; }, abstract = {BACKGROUND: A vaginal microbiota dominated by lactobacilli (particularly Lactobacillus crispatus) is associated with vaginal health, whereas a vaginal microbiota not dominated by lactobacilli is considered dysbiotic. Here we investigated whether L. crispatus strains isolated from the vaginal tract of women with Lactobacillus-dominated vaginal microbiota (LVM) are pheno- or genotypically distinct from L. crispatus strains isolated from vaginal samples with dysbiotic vaginal microbiota (DVM).<br><br>RESULTS: We studied 33 L. crispatus strains (n = 16 from LVM; n = 17 from DVM). Comparison of these two groups of strains showed that, although strain differences existed, both groups degraded various carbohydrates, produced similar amounts of organic acids, inhibited Neisseria gonorrhoeae growth, and did not produce biofilms. Comparative genomics analyses of 28 strains (n = 12 LVM; n = 16 DVM) revealed a novel, 3-fragmented glycosyltransferase gene that was more prevalent among strains isolated from DVM. Most L. crispatus strains showed growth on glycogen-supplemented growth media. Strains that showed less-efficient (n = 6) or no (n = 1) growth on glycogen all carried N-terminal deletions (respectively, 29 and 37 amino acid deletions) in a putative pullulanase type I protein.<br><br>DISCUSSION: L. crispatus strains isolated from LVM were not phenotypically distinct from L. crispatus strains isolated from DVM; however, the finding that the latter were more likely to carry a 3-fragmented glycosyltransferase gene may indicate a role for cell surface glycoconjugates, which may shape vaginal microbiota-host interactions. Furthermore, the observation that variation in the pullulanase type I gene is associated with growth on glycogen discourages previous claims that L. crispatus cannot directly utilize glycogen.}, }
@article {pmid30923584, year = {2018}, author = {Li, Z and Lee, K and Karagas, MR and Madan, JC and Hoen, AG and O'Malley, AJ and Li, H}, title = {Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data.}, journal = {Statistics in biosciences}, volume = {10}, number = {3}, pages = {587-608}, pmid = {30923584}, issn = {1867-1764}, support = {R01 GM123056/GM/NIGMS NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; R01 GM123014/GM/NIGMS NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; K01 LM011985/LM/NLM NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; UG3 OD023275/OD/NIH HHS/United States ; R01 CA127334/CA/NCI NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, abstract = {The human microbiome plays critical roles in human health and has been linked to many diseases. While advanced sequencing technologies can characterize the composition of the microbiome in unprecedented detail, it remains challenging to disentangle the complex interplay between human microbiome and disease risk factors due to the complicated nature of microbiome data. Excessive numbers e f zero values, high dimensionality, the hierarchical phylogenetic tree and compositional structure are compounded and consequently make existing methods inadequate to appropriately address these issues. We propose a multivariate two-part zero-inflated logistic normal (MZILN) model to analyze the association of disease risk factors with individual microbial taxa and overall microbial community composition. This approach can naturally handle excessive numbers e f zeros and the compositional data structure with the discrete part and the logistic-normal part e f the model. For parameter estimation, an estimating equations approach is employed that enables us to address the complex inter-taxa correlation structure induced by the hierarchical phylogenetic tree structure and the compositional data structure. This model is able to incorporate standard regularization approaches to deal with high dimensionality. Simulation shews that our model outperforms existing methods. Our approach is also compared to ethers using the analysis of real microbiome data.}, }
@article {pmid30920647, year = {2019}, author = {Hidalgo-Cantabrana, C and Gómez, J and Delgado, S and Requena-López, S and Queiro-Silva, R and Margolles, A and Coto, E and Sánchez, B and Coto-Segura, P}, title = {Gut microbiota dysbiosis in a cohort of patients with psoriasis.}, journal = {The British journal of dermatology}, volume = {181}, number = {6}, pages = {1287-1295}, doi = {10.1111/bjd.17931}, pmid = {30920647}, issn = {1365-2133}, support = {AGL2013-44039R//Spanish 'Programa Estatal de Investigación, Desarrollo e Innovación Orientada a los Retos de la Sociedad'/ ; PS-2016//Fundación Científica Asociación Española Contra el Cáncer/ ; PI16/01792//'Fondo de Investigaciones Sanitarias' (FIS)/ ; }, abstract = {BACKGROUND: There is increasing evidence of the key role that the gut microbiota plays in inflammatory diseases.<br><br>OBJECTIVES: To identify differences in the faecal microbial composition of patients with psoriasis compared with healthy individuals in order to unravel the microbiota profiling in this autoimmune disease.<br><br>METHODS: 16S rRNA gene sequencing and bioinformatic analyses were performed with the total DNA extracted from the faecal microbiota of 19 patients with psoriasis and 20 healthy individuals from the same geographic location.<br><br>RESULTS: Gut microbiota composition of patients with psoriasis displayed a lower diversity and different relative abundance of certain bacterial taxa compared with healthy individuals.<br><br>CONCLUSIONS: The gut microbiota profile of patients with psoriasis displayed a clear dysbiosis that can be targeted for microbiome-based therapeutic approaches. What's already known about this topic? Psoriasis is a chronic inflammatory immune-mediated skin disease, the aetiology of which remains unclear. The human microbiota is a complex microbial community that inhabits our body and has been related with the maintenance of a healthy status. Several studies have focused on the skin microbiome and its connection with psoriasis although less attention has been focused on the potential role of the gut microbiota in psoriatic disease. What does this study add? This study unravels the gut microbiome dysbiosis present in a cohort of patients with psoriasis, compared with a healthy control group from the same geographical location. This study shows a lower bacterial diversity and different relative abundance of certain bacterial taxa in patients with psoriasis. We gain knowledge and insight into the microbiome alterations in psoriatic disease, opening new avenues for therapeutic approaches to reshape the human microbiome towards a healthy status.}, }
@article {pmid30919073, year = {2019}, author = {Ames, NJ and Barb, JJ and Ranucci, A and Kim, H and Mudra, SE and Cashion, AK and Townsley, DM and Childs, R and Paster, BJ and Faller, LL and Wallen, GR}, title = {The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study.}, journal = {Annals of hematology}, volume = {98}, number = {6}, pages = {1351-1365}, doi = {10.1007/s00277-019-03599-w}, pmid = {30919073}, issn = {1432-0584}, mesh = {Adult ; Aged ; Anemia, Aplastic/drug therapy/*microbiology/therapy ; Anti-Bacterial Agents/pharmacology ; Antilymphocyte Serum/therapeutic use ; Benzoates/pharmacology/therapeutic use ; Biodiversity ; Cyclosporine/therapeutic use ; DNA, Bacterial/analysis ; Dental Health Surveys ; Female ; Graft vs Host Disease/etiology/microbiology ; Hematopoietic Stem Cell Transplantation ; Humans ; Hydrazines/pharmacology/therapeutic use ; Immunocompromised Host ; Immunosuppressive Agents/therapeutic use ; Male ; *Microbiota/drug effects ; Middle Aged ; Mouth/*microbiology ; Pilot Projects ; Pyrazoles/pharmacology/therapeutic use ; Ribotyping ; Sequence Analysis, DNA ; Smoking/epidemiology ; T-Lymphocytes/immunology ; Tongue/microbiology ; Young Adult ; }, abstract = {The microbiome, an intriguing component of the human body, composed of trillions of microorganisms, has prompted scientific exploration to identify and understand its function and role in health and disease. As associations between microbiome composition, disease, and symptoms accumulate, the future of medicine hinges upon a comprehensive knowledge of these microorganisms for patient care. The oral microbiome may provide valuable and efficient insight for predicting future changes in disease status, infection, or treatment course. The main aim of this pilot study was to characterize the oral microbiome in patients with severe aplastic anemia (SAA) during their therapeutic course. SAA is a hematologic disease characterized by bone marrow failure which if untreated is fatal. Treatment includes either hematopoietic stem cell transplantation (HSCT) or immunosuppressive therapy (IST). In this study, we examined the oral microbiome composition of 24 patients admitted to the National Institutes of Health (NIH) Clinical Center for experimental SAA treatment. Tongue brushings were collected to assess the effects of treatment on the oral microbiome. Twenty patients received standard IST (equine antithymocyte globulin and cyclosporine) plus eltrombopag. Four patients underwent HSCT. Oral specimens were obtained at three time points during treatment and clinical follow-up. Using a novel approach to 16S rRNA gene sequence analysis encompassing seven hypervariable regions, results demonstrated a predictable decrease in microbial diversity over time among the transplant patients. Linear discriminant analysis or LefSe reported a total of 14 statistically significant taxa (p < 0.05) across time points in the HSCT patients. One-way plots of relative abundance for two bacterial species (Haemophilus parainfluenzae and Rothia mucilaginosa) in the HSCT group, show the differences in abundance between time points. Only one bacterial species (Prevotella histicola) was noted in the IST group with a p value of 0.065. The patients receiving immunosuppressive therapy did not exhibit a clear change in diversity over time; however, patient-specific changes were noted. In addition, we compared our findings to tongue dorsum samples from healthy participants in the Human Microbiome Project (HMP) database and found among HSCT patients, approximately 35% of bacterial identifiers (N = 229) were unique to this study population and were not present in tongue dorsum specimens obtained from the HMP. Among IST-treated patients, 45% (N = 351) were unique to these patients and not identified by the HMP. Although antibiotic use may have likely influenced bacterial composition and diversity, some literature suggests a decreased impact of antimicrobials on the oral microbiome as compared to their effect on the gut microbiome. Future studies with larger sample sizes that focus on the oral microbiome and the effects of antibiotics in an immunosuppressed patient population may help establish these potential associations.}, }
@article {pmid30918980, year = {2019}, author = {Shannon, MB and Limeira, R and Johansen, D and Gao, X and Lin, H and Dong, Q and Wolfe, AJ and Mueller, ER}, title = {Bladder urinary oxygen tension is correlated with urinary microbiota composition.}, journal = {International urogynecology journal}, volume = {30}, number = {8}, pages = {1261-1267}, pmid = {30918980}, issn = {1433-3023}, abstract = {INTRODUCTION AND HYPOTHESIS: Presence of microbial communities (microbiota) in an organ system depends on environmental factors, such as oxygen availability. We describe a novel technique to measure bladder urine oxygen tension (BUOT) in ambulatory women and use that technique to compare BUOT values to female urinary microbiota and participant urinary signs and symptoms.<br><br>METHODS: Ambulatory female urogynecology patients presenting for clinical care who were willing to undergo transurethral catheterization underwent BUOT determination with a non-invasive flow-through oxygen sensor. To detect urinary microbiota in the bladder, 16S rRNA gene sequencing was performed on catheterized urine. Multivariate statistical analyses were performed to examine potential correlations among BUOT, urinary microbiota compositions and clinical variables.<br><br>RESULTS: Significant variation in BUOT existed between individuals (range: 0.47-51.5 mmHg; median: 23.1 ± 13.5). Microbiota compositions were associated with BUOT (p = 0.03). BUOT was significantly lower in urines that were nitrite negative on dipstick analysis (p = 0.0001) and in participants who answered yes to having urinary leakage on the validated Urinary Distress Inventory (p = 0.01).<br><br>CONCLUSIONS: BUOTs can be measured in ambulatory women. For urogynecology patients, a wide range of values exist. BUOT may be associated with the presence of urinary microbiota and resultant signs and symptoms.}, }
@article {pmid30917589, year = {2019}, author = {George, A}, title = {Antimicrobial Resistance (AMR) in the Food Chain: Trade, One Health and Codex.}, journal = {Tropical medicine and infectious disease}, volume = {4}, number = {1}, pages = {}, pmid = {30917589}, issn = {2414-6366}, abstract = {Strategies that take on a One Health approach to addressing antimicrobial resistance (AMR) focused on reducing human use of antimicrobials, but policy-makers now have to grapple with a different set of political, economic, and highly sensitive trade interests less amenable to government direction, to tackle AMR in the food chain. Understanding the importance and influence of the intergovernmental Codex negotiations underway on AMR in the Food Chain is very weak but essential for AMR public policy experts. National and global food producing industries are already under pressure as consumers learn about the use of antimicrobials in food production and more so when the full impact of AMR microorganisms in the food chain and on the human microbiome is better understood. Governments will be expected to respond. Trade-related negotiations on access and use made of antimicrobials is political: the relevance of AMR 'evidence' is already contested and not all food producers or users of antimicrobials in the food chain are prepared to, or capable of, moving at the same pace. In trade negotiations governments defend their interpretation of national interest. Given AMR in the global food chain threatens national interest, both AMR One Health and zoonotic disease experts should understand and participate in all trade-related AMR negotiations to protect One Health priorities. To help facilitate this an overview and analysis of Codex negotiations is provided.}, }
@article {pmid30911403, year = {2019}, author = {El-Awady, A and de Sousa Rabelo, M and Meghil, MM and Rajendran, M and Elashiry, M and Stadler, AF and Foz, AM and Susin, C and Romito, GA and Arce, RM and Cutler, CW}, title = {Polymicrobial synergy within oral biofilm promotes invasion of dendritic cells and survival of consortia members.}, journal = {NPJ biofilms and microbiomes}, volume = {5}, number = {}, pages = {11}, pmid = {30911403}, issn = {2055-5008}, support = {R01 DE014328/DE/NIDCR NIH HHS/United States ; }, abstract = {Years of human microbiome research have confirmed that microbes rarely live or function alone, favoring diverse communities. Yet most experimental host-pathogen studies employ single species models of infection. Here, the influence of three-species oral microbial consortium on growth, virulence, invasion and persistence in dendritic cells (DCs) was examined experimentally in human monocyte-derived dendritic cells (DCs) and in patients with periodontitis (PD). Cooperative biofilm formation by Streptococcus gordonii, Fusobacterium nucleatum and Porphyromonas gingivalis was documented in vitro using growth models and scanning electron microscopy. Analysis of growth rates by species-specific 16s rRNA probes revealed distinct, early advantages to consortium growth for S. gordonii and F. nucleatum with P. gingivalis, while P. gingivalis upregulated its short mfa1 fimbriae, leading to increased invasion of DCs. F. nucleatum was only taken up by DCs when in consortium with P. gingivalis. Mature consortium regressed DC maturation upon uptake, as determined by flow cytometry. Analysis of dental plaques of PD and healthy subjects by 16s rRNA confirmed oral colonization with consortium members, but DC hematogenous spread was limited to P. gingivalis and F. nucleatum. Expression of P. gingivalis mfa1 fimbriae was increased in dental plaques and hematogenous DCs of PD patients. P. gingivalis in the consortium correlated with an adverse clinical response in the gingiva of PD subjects. In conclusion, we have identified polymicrobial synergy in a three-species oral consortium that may have negative consequences for the host, including microbial dissemination and adverse peripheral inflammatory responses.}, }
@article {pmid30911128, year = {2019}, author = {Brito, IL and Gurry, T and Zhao, S and Huang, K and Young, SK and Shea, TP and Naisilisili, W and Jenkins, AP and Jupiter, SD and Gevers, D and Alm, EJ}, title = {Transmission of human-associated microbiota along family and social networks.}, journal = {Nature microbiology}, volume = {4}, number = {6}, pages = {964-971}, doi = {10.1038/s41564-019-0409-6}, pmid = {30911128}, issn = {2058-5276}, mesh = {Bacteria/genetics ; *Family ; Female ; Fiji ; Gastrointestinal Microbiome/genetics ; Genomics ; Genotype ; Host Specificity ; Humans ; Interspersed Repetitive Sequences ; Male ; *Microbiota/genetics ; Polymorphism, Single Nucleotide ; *Social Networking ; }, abstract = {The human microbiome, described as an accessory organ because of the crucial functions it provides, is composed of species that are uniquely found in humans1,2. Yet, surprisingly little is known about the impact of routine interpersonal contacts in shaping microbiome composition. In a relatively 'closed' cohort of 287 people from the Fiji Islands, where common barriers to bacterial transmission are absent, we examine putative bacterial transmission in individuals' gut and oral microbiomes using strain-level data from both core single-nucleotide polymorphisms and flexible genomic regions. We find a weak signal of transmission, defined by the inferred sharing of genotypes, across many organisms that, in aggregate, reveals strong transmission patterns, most notably within households and between spouses. We were unable to determine the directionality of transmission nor whether it was direct. We further find that women harbour strains more closely related to those harboured by their familial and social contacts than men, and that transmission patterns of oral-associated and gut-associated microbiota need not be the same. Using strain-level data alone, we are able to confidently predict a subset of spouses, highlighting the role of shared susceptibilities, behaviours or social interactions that distinguish specific links in the social network.}, }
@article {pmid30910274, year = {2019}, author = {Leynaert, B and Le Moual, N and Neukirch, C and Siroux, V and Varraso, R}, title = {[Environmental risk factors for asthma developement].}, journal = {Presse medicale (Paris, France : 1983)}, volume = {48}, number = {3 Pt 1}, pages = {262-273}, doi = {10.1016/j.lpm.2019.02.022}, pmid = {30910274}, issn = {2213-0276}, mesh = {Air Pollution, Indoor/adverse effects ; Allergens/adverse effects ; Animals ; Asthma/*etiology/microbiology ; Environmental Exposure/*adverse effects ; Humans ; Risk Factors ; }, abstract = {The prevalence of asthma has increased rapidly since the early 1970s, and only changes in exposure to environmental factors; which go together with changes in lifestyle, are likely to explain such a rapid increase. Exposure to allergens is a risk factor for allergic sensitization, and allergic sensitization is a risk factor for allergic asthma. However, apart from indoor mold exposure as a risk factor for childhood asthma, there is insufficient evidence to conclude that the associations between allergen exposure and asthma development are causal. A new challenge for research is to analyze the huge amount of data derived from the metagenomic characterization of the environmental and human microbiome, to understand the role of interactions between viruses, bacteria and allergens in the development of asthma. It is recognized that prenatal and postnatal exposure to air pollution and maternal smoking increase the risk of developing asthma in children. In adults, the data are scarce and the results remain controversial as regards these exposures and asthma incidence. Further research is needed to appraise the effect of exposure to phenols, phthalates and perfluorinated compounds, which are widespread in the environment and may be associated with asthma, especially in children. Frequent use of chemicals for home cleaning especially in the form of sprays - which is a common practice at the population level - is a risk factor for the development of adult asthma. The domestic use of cleaning products might also be a risk factor for asthma in children exposed at home. The chemicals involved in these relationships are still to be identified. Occupational asthma is a major phenotype of adult asthma. A significant part of these asthma cases might relate to occupational exposure to cleaning products. While there is evidence of associations between diet during pregnancy or during childhood and the risk of developing asthma in children, the data in adults are insufficient. Beyond genetic factors, body composition is influenced by dietary choices and physical activity. Further research is needed to clarify the complex interplay between these nutritional factors and asthma development. The new challenge for research is to decipher the role of all the environmental factors to which the individual is exposed since conception (&quot;exposome&quot;) in the development of asthma, using a holistic approach.}, }
@article {pmid30908947, year = {2019}, author = {Ahern, GJ and Hennessy, AA and Ryan, CA and Ross, RP and Stanton, C}, title = {Advances in Infant Formula Science.}, journal = {Annual review of food science and technology}, volume = {10}, number = {}, pages = {75-102}, doi = {10.1146/annurev-food-081318-104308}, pmid = {30908947}, issn = {1941-1421}, abstract = {Human milk contains a plethora of nutrients and bioactive components to help nourish the developing neonate and is considered the &quot;gold standard&quot; for early life nutrition-as befits the only food &quot;designed&quot; by evolution to feed human infants. Over the past decade, there is considerable evidence that highlights the &quot;intelligence&quot; contained in milk components that contribute to infant health beyond basic nutrition-in areas such as programming the developing microbiome and immune system and protecting against infection. Such discoveries have led to new opportunities for infant milk formula (IMF) manufacturers to refine nutritional content in order to simulate the functionality of breast milk. These include the addition of specialized protein fractions as well as fatty acid and complex carbohydrate components-all of which have mechanistic supporting evidence in terms of improving the health and nutrition of the infant. Moreover, IMF is the single most important dietary intervention whereby the human microbiome can be influenced at a crucial early stage of development. In this respect, it is expected that the complexity of IMF will continue to increase as we get a greater understanding of how it can modulate microbiota development (including the development of probiotics, prebiotics, and synbiotics) and influence long-term health. This review provides a scientific evaluation of key features of importance to infant nutrition, including differences in milk composition and emerging &quot;humanized&quot; ingredients.}, }
@article {pmid30899033, year = {2019}, author = {Reddel, S and Del Chierico, F and Quagliariello, A and Giancristoforo, S and Vernocchi, P and Russo, A and Fiocchi, A and Rossi, P and Putignani, L and El Hachem, M}, title = {Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {4996}, pmid = {30899033}, issn = {2045-2322}, support = {201502P003534//Ministero della Salute (Ministry of Health, Italy)/ ; 201602P00370//Ministero della Salute (Ministry of Health, Italy)/ ; 201503X003570//Ministero della Salute (Ministry of Health, Italy)/ ; }, abstract = {Atopic dermatitis (AD) has been hypothesised to be associated with gut microbiota (GM) composition. We performed a comparative study of the GM profile of 19 AD children and 18 healthy individuals aimed at identifying bacterial biomarkers associated with the disease. The effect of probiotic intake (Bifidobacterium breve plus Lactobacillus salivarius) on the modulation of GM and the probiotic persistence in the GM were also evaluated. Faecal samples were analysed by real-time PCR and 16S rRNA targeted metagenomics. Although the probiotics, chosen for this study, did not shape the entire GM profile, we observed the ability of these species to pass through the gastrointestinal tract and to persist (only B. breve) in the GM. Moreover, the GM of patients compared to CTRLs showed a dysbiotic status characterised by an increase of Faecalibacterium, Oscillospira, Bacteroides, Parabacteroides and Sutterella and a reduction of short-chain fatty acid (SCFA)-producing bacteria (i.e., Bifidobacterium, Blautia, Coprococcus, Eubacterium and Propionibacterium). Taken togheter these results show an alteration in AD microbiota composition with the depletion or absence of some species, opening the way to future probiotic intervention studies.}, }
@article {pmid30895406, year = {2019}, author = {Nguyen, VD and Nguyen, TT and Pham, TT and Packianather, M and Le, CH}, title = {Molecular screening and genetic diversity analysis of anticancer Azurin-encoding and Azurin-like genes in human gut microbiome deduced through cultivation-dependent and cultivation-independent studies.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {22}, number = {4}, pages = {437-449}, doi = {10.1007/s10123-019-00070-8}, pmid = {30895406}, issn = {1618-1905}, support = {106-YS.04-2014.40//National Foundation for Science and Technology Development/ ; }, mesh = {Adolescent ; Adult ; Azurin/*genetics/metabolism ; Child ; Culture Media/metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genetic Variation ; Humans ; Male ; Phylogeny ; Pseudomonas aeruginosa/*genetics/growth &amp; development/*isolation &amp; purification/metabolism ; Young Adult ; }, abstract = {Azurin, a bacteriocin produced by a human gut bacterium Pseudomonas aeruginosa, can reveal selectively cytotoxic and induce apoptosis in cancer cells. After overcoming two phase I trials, a functional region of Azurin called p28 has been approved as a drug for the treatment of brain tumor glioma by FDA. The present study aims to improve a screening procedure and assess genetic diversity of Azurin genes in P. aeruginosa and Azurin-like genes in the gut microbiome of a specific population in Vietnam and global populations. Firstly, both cultivation-dependent and cultivation-independent techniques based on genomic and metagenomic DNAs extracted from fecal samples of the healthy specific population were performed and optimized to detect Azurin genes. Secondly, the Azurin gene sequences were analyzed and compared with global populations by using bioinformatics tools. Finally, the screening procedure improved from the first step was applied for screening Azurin-like genes, followed by the protein synthesis and NCI in vitro screening for anticancer activity. As a result, this study has successfully optimized the annealing temperatures to amplify DNAs for screening Azurin genes and applying to Azurin-like genes from human gut microbiota. The novelty of this study is the first of its kind to classify Azurin genes into five different genotypes at a global scale and confirm the potential anticancer activity of three Azurin-like synthetic proteins (Cnazu1, Dlazu11, and Ruazu12). The results contribute to the procedure development applied for screening anticancer proteins from human microbiome and a comprehensive understanding of their therapeutic response at a genetic level.}, }
@article {pmid30894847, year = {2019}, author = {Brown, EEF and Cooper, A and Carrillo, C and Blais, B}, title = {Selection of Multidrug-Resistant Bacteria in Medicated Animal Feeds.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {456}, pmid = {30894847}, issn = {1664-302X}, abstract = {Exposure to antimicrobial resistant (AMR) bacteria is a major public health issue which may, in part, have roots in food production practices that are conducive to the selection of AMR bacteria ultimately impacting the human microbiome through food consumption. Of particular concern is the prophylactic use of antibiotics in animal husbandry, such as the medication of feeds with sulfonamides and other antibiotics not considered clinically relevant, but which may nonetheless co-select for multi-drug resistant (MDR) bacteria harboring resistance to medically important antibiotics. Using a MDR Klebsiella pneumoniae strain exhibiting resistance to sulfonamides and beta-lactams (including carbapenem) as a model, we examined the ability of non-medicated and commercially medicated (sulfonamide) animal feeds to select for the model strain when inoculated at low levels by measuring its recovery along with key AMR markers, sul1(sulfonamide) and blaKPC-3 (meropenem), under different incubation conditions. When non-medicated feeds were supplemented with defined amounts of sulfadiazine the model strain was significantly enriched after incubation in Mueller Hinton Broth at 37°C overnight, or in same at room temperature for a week, with consistent detection of both the sul1 and blaKPC-3 markers as determined by polymerase chain reaction (PCR) techniques to screen colony isolates recovered on plating media. Significant recoveries of the inoculated strain and the sul1 and blaKPC-3 markers were observed with one of three commercially medicated (sulfamethazine) feeds tested under various incubation conditions. These results demonstrate that under certain conditions the prophylactic use of so-called non-priority antibiotics in feeds can potentially lead to co-selection of environmental AMR bacteria with resistance to medically important antibiotics, which may have far-reaching implications for human health.}, }
@article {pmid30894688, year = {2019}, author = {Ma, ZS and Li, L and Gotelli, NJ}, title = {Diversity-disease relationships and shared species analyses for human microbiome-associated diseases.}, journal = {The ISME journal}, volume = {13}, number = {8}, pages = {1911-1919}, pmid = {30894688}, issn = {1751-7370}, mesh = {Bacteria/classification/genetics/*isolation &amp; purification ; Biodiversity ; Disease ; Health ; Humans ; *Microbiota ; }, abstract = {Diversity indices have been routinely computed in the study of human microbiome-associated diseases (MADs). However, it is still unclear whether there is a consistent diversity-disease relationship (DDR) for the human MADs, and whether there are consistent differences in the taxonomic composition of microbiomes sampled from healthy versus diseased individuals. Here we reanalyzed raw data and used a meta-analysis to compare the microbiome diversity and composition of healthy versus diseased individuals in 41 comparisons extracted from 27 previously published studies of human MADs. In the DDR analysis, the average effect size across studies did not differ from zero for a comparison of healthy versus diseased individuals. In 30 of 41 comparisons (73%) there was no significant difference in microbiome diversity of healthy versus diseased individuals, or of different disease classes. For the species composition analysis (shared species analysis), the effect sizes were significantly different from zero. In 33 of 41 comparisons (80%), there were fewer OTUs (operational taxonomic units) shared between healthy and diseased individuals than expected by chance, but with 49% (20 of 41 comparisons) statistically significant. These results imply that the taxonomic composition of disease-associated microbiomes is often distinct from that of healthy individuals. Because species composition changes with disease state, some microbiome OTUs may serve as potential diagnostic indicators of disease. However, the overall species diversity of human microbiomes is not a reliable indicator of disease.}, }
@article {pmid30890301, year = {2019}, author = {Chen, QL and Cui, HL and Su, JQ and Penuelas, J and Zhu, YG}, title = {Antibiotic Resistomes in Plant Microbiomes.}, journal = {Trends in plant science}, volume = {24}, number = {6}, pages = {530-541}, doi = {10.1016/j.tplants.2019.02.010}, pmid = {30890301}, issn = {1878-4372}, abstract = {Microorganisms associated with plants may alter the traits of the human microbiome important for human health, but this alteration has largely been overlooked. The plant microbiome is an interface between plants and the environment, and provides many ecosystem functions such as improving nutrient uptake and protecting against biotic and abiotic stress. The plant microbiome also represents a major pathway by which humans are exposed to microbes and genes consumed with food, such as pathogenic bacteria, antibiotic-resistant bacteria, and antibiotic-resistance genes. In this review we highlight the main findings on the composition and function of the plant microbiome, and underline the potential of plant microbiomes in the dissemination of antibiotic resistance via food consumption or direct contact.}, }
@article {pmid30890187, year = {2019}, author = {Tovaglieri, A and Sontheimer-Phelps, A and Geirnaert, A and Prantil-Baun, R and Camacho, DM and Chou, DB and Jalili-Firoozinezhad, S and de Wouters, T and Kasendra, M and Super, M and Cartwright, MJ and Richmond, CA and Breault, DT and Lacroix, C and Ingber, DE}, title = {Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {43}, pmid = {30890187}, issn = {2049-2618}, support = {K08 DK106562/DK/NIDDK NIH HHS/United States ; T32 CA009216/CA/NCI NIH HHS/United States ; R01 DK084056/DK/NIDDK NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bacteria/*metabolism ; Benzoates/pharmacology ; Caproates/pharmacology ; Cells, Cultured ; Enterohemorrhagic Escherichia coli/metabolism/*pathogenicity ; Escherichia coli Infections/microbiology/*pathology ; Female ; Gastrointestinal Microbiome ; Heptanoic Acids/pharmacology ; Humans ; Intestines/*cytology/microbiology ; Male ; Mice ; Microchip Analytical Procedures ; Organ Culture Techniques/*methods ; Species Specificity ; }, abstract = {BACKGROUND: Species-specific differences in tolerance to infection are exemplified by the high susceptibility of humans to enterohemorrhagic Escherichia coli (EHEC) infection, whereas mice are relatively resistant to this pathogen. This intrinsic species-specific difference in EHEC infection limits the translation of murine research to human. Furthermore, studying the mechanisms underlying this differential susceptibility is a difficult problem due to complex in vivo interactions between the host, pathogen, and disparate commensal microbial communities.<br><br>RESULTS: We utilize organ-on-a-chip (Organ Chip) microfluidic culture technology to model damage of the human colonic epithelium induced by EHEC infection, and show that epithelial injury is greater when exposed to metabolites derived from the human gut microbiome compared to mouse. Using a multi-omics approach, we discovered four human microbiome metabolites-4-methyl benzoic acid, 3,4-dimethylbenzoic acid, hexanoic acid, and heptanoic acid-that are sufficient to mediate this effect. The active human microbiome metabolites preferentially induce expression of flagellin, a bacterial protein associated with motility of EHEC and increased epithelial injury. Thus, the decreased tolerance to infection observed in humans versus other species may be due in part to the presence of compounds produced by the human intestinal microbiome that actively promote bacterial pathogenicity.<br><br>CONCLUSION: Organ-on-chip technology allowed the identification of specific human microbiome metabolites modulating EHEC pathogenesis. These identified metabolites are sufficient to increase susceptibility to EHEC in our human Colon Chip model and they contribute to species-specific tolerance. This work suggests that higher concentrations of these metabolites could be the reason for higher susceptibility to EHEC infection in certain human populations, such as children. Furthermore, this research lays the foundation for therapeutic-modulation of microbe products in order to prevent and treat human bacterial infection.}, }
@article {pmid30885720, year = {2019}, author = {LaPierre, N and Ju, CJ and Zhou, G and Wang, W}, title = {MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.}, journal = {Methods (San Diego, Calif.)}, volume = {166}, number = {}, pages = {74-82}, pmid = {30885720}, issn = {1095-9130}, support = {R01 GM115833/GM/NIGMS NIH HHS/United States ; T32 EB016640/EB/NIBIB NIH HHS/United States ; }, abstract = {The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a number of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Consequently, there have been growing efforts to predict disease status from metagenomic sequencing data, with a proliferation of new approaches in the last few years. Some of these efforts have explored utilizing a powerful form of machine learning called deep learning, which has been applied successfully in several biological domains. Here, we review some of these methods and the algorithms that they are based on, with a particular focus on deep learning methods. We also perform a deeper analysis of Type 2 Diabetes and obesity datasets that have eluded improved results, using a variety of machine learning and feature extraction methods. We conclude by offering perspectives on study design considerations that may impact results and future directions the field can take to improve results and offer more valuable conclusions. The scripts and extracted features for the analyses conducted in this paper are available via GitHub:https://github.com/nlapier2/metapheno.}, }
@article {pmid30880022, year = {2019}, author = {Cohen, LJ and Cho, JH and Gevers, D and Chu, H}, title = {Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-Based Therapies for Inflammatory Bowel Diseases.}, journal = {Gastroenterology}, volume = {156}, number = {8}, pages = {2174-2189}, pmid = {30880022}, issn = {1528-0012}, support = {U01 DK062429/DK/NIDDK NIH HHS/United States ; U01 DK062422/DK/NIDDK NIH HHS/United States ; K08 DK109287/DK/NIDDK NIH HHS/United States ; R00 DK110534/DK/NIDDK NIH HHS/United States ; R01 DK106593/DK/NIDDK NIH HHS/United States ; R01 DK092235/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Drugs, Investigational/*administration &amp; dosage/pharmacology ; Gastrointestinal Microbiome/*genetics/*immunology ; Genome, Human ; Humans ; Immunotherapy/*methods ; Inflammatory Bowel Diseases/microbiology/pathology/*therapy ; Mice ; Models, Animal ; *Practice Guidelines as Topic ; Prognosis ; Treatment Outcome ; }, abstract = {The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis and physiology. Imbalances in the microbiome and aberrant immune responses to gut bacteria can disrupt homeostasis and are associated with inflammatory bowel diseases (IBDs) in humans and colitis in mice. We review genetic variants associated with IBD and their effects on the intestinal microbiome, the immune response, and disease pathogenesis. The intestinal microbiome, which includes microbial antigens, adjuvants, and metabolic products, affects the development and function of the intestinal mucosa, influencing inflammatory responses in the gut. Therefore, strategies to manipulate the microbiome might be used in treatment of IBD. We review microbe-based therapies for IBD and the potential to engineer patients' intestinal microbiota. We discuss how studies of patients with IBD and mouse models have advanced our understanding of the interactions between genetic factors and the gut microbiome, and challenges to the development of microbe-based therapies for IBD.}, }
@article {pmid30877283, year = {2019}, author = {Shaw, LP and Bassam, H and Barnes, CP and Walker, AS and Klein, N and Balloux, F}, title = {Modelling microbiome recovery after antibiotics using a stability landscape framework.}, journal = {The ISME journal}, volume = {13}, number = {7}, pages = {1845-1856}, pmid = {30877283}, issn = {1751-7370}, support = {//Wellcome Trust/United Kingdom ; 209409//Wellcome Trust/United Kingdom ; 097319/Z/11/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents/*pharmacology ; Bayes Theorem ; Dysbiosis/*microbiology ; Gastrointestinal Microbiome/drug effects/physiology ; Humans ; Microbiota/*drug effects/physiology ; *Models, Theoretical ; }, abstract = {Treatment with antibiotics is one of the most extreme perturbations to the human microbiome. Even standard courses of antibiotics dramatically reduce the microbiome's diversity and can cause transitions to dysbiotic states. Conceptually, this is often described as a 'stability landscape': the microbiome sits in a landscape with multiple stable equilibria, and sufficiently strong perturbations can shift the microbiome from its normal equilibrium to another state. However, this picture is only qualitative and has not been incorporated in previous mathematical models of the effects of antibiotics. Here, we outline a simple quantitative model based on the stability landscape concept and demonstrate its success on real data. Our analytical impulse-response model has minimal assumptions with three parameters. We fit this model in a Bayesian framework to data from a previous study of the year-long effects of short courses of four common antibiotics on the gut and oral microbiomes, allowing us to compare parameters between antibiotics and microbiomes, and further validate our model using data from another study looking at the impact of a combination of last-resort antibiotics on the gut microbiome. Using Bayesian model selection we find support for a long-term transition to an alternative microbiome state after courses of certain antibiotics in both the gut and oral microbiomes. Quantitative stability landscape frameworks are an exciting avenue for future microbiome modelling.}, }
@article {pmid30876799, year = {2019}, author = {Douillard, FP and de Vos, WM}, title = {Biotechnology of health-promoting bacteria.}, journal = {Biotechnology advances}, volume = {37}, number = {6}, pages = {107369}, doi = {10.1016/j.biotechadv.2019.03.008}, pmid = {30876799}, issn = {1873-1899}, mesh = {Bifidobacterium ; *Biotechnology ; *Gastrointestinal Microbiome ; Humans ; *Probiotics ; }, abstract = {Over the last decade, there has been an increasing scientific and public interest in bacteria that may positively contribute to human gut health and well-being. This interest is reflected by the ever-increasing number of developed functional food products containing health-promoting bacteria and reaching the market place as well as by the growing revenue and profits of notably bacterial supplements worldwide. Traditionally, the origin of probiotic-marketed bacteria was limited to a rather small number of bacterial species that mostly belong to lactic acid bacteria and bifidobacteria. Intensifying research efforts on the human gut microbiome offered novel insights into the role of human gut microbiota in health and disease, while also providing a deep and increasingly comprehensive understanding of the bacterial communities present in this complex ecosystem and their interactions with the gut-liver-brain axis. This resulted in rational and systematic approaches to select novel health-promoting bacteria or to engineer existing bacteria with enhanced probiotic properties. In parallel, the field of gut microbiomics developed into a fertile framework for the identification, isolation and characterization of a phylogenetically diverse array of health-promoting bacterial species, also called next-generation therapeutic bacteria. The present review will address these developments with specific attention for the selection and improvement of a selected number of health-promoting bacterial species and strains that are extensively studied or hold promise for future food or pharma product development.}, }
@article {pmid30871856, year = {2019}, author = {Minot, SS}, title = {De novo Assembly Vastly Expands the Known Microbial Universe.}, journal = {Trends in microbiology}, volume = {27}, number = {5}, pages = {385-386}, doi = {10.1016/j.tim.2019.02.007}, pmid = {30871856}, issn = {1878-4380}, abstract = {The study of the human microbiome relies heavily on the genomes of bacterial isolates that can be grown in culture. A recent study (Pasolli et al. Cell 2019;176:649-662) of stool microbiome samples generated over 150 000 microbial genomes without any culture, vastly expanding our knowledge of the biases in existing reference databases.}, }
@article {pmid30871469, year = {2019}, author = {Perz, AI and Giles, CB and Brown, CA and Porter, H and Roopnarinesingh, X and Wren, JD}, title = {MNEMONIC: MetageNomic Experiment Mining to create an OTU Network of Inhabitant Correlations.}, journal = {BMC bioinformatics}, volume = {20}, number = {Suppl 2}, pages = {96}, pmid = {30871469}, issn = {1471-2105}, support = {P20 GM103636/GM/NIGMS NIH HHS/United States ; P30 AG050911/AG/NIA NIH HHS/United States ; T32 AG052363/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Metagenomics/*methods ; Microbiota/*genetics ; }, abstract = {BACKGROUND: The number of publicly available metagenomic experiments in various environments has been rapidly growing, empowering the potential to identify similar shifts in species abundance between different experiments. This could be a potentially powerful way to interpret new experiments, by identifying common themes and causes behind changes in species abundance.<br><br>RESULTS: We propose a novel framework for comparing microbial shifts between conditions. Using data from one of the largest human metagenome projects to date, the American Gut Project (AGP), we obtain differential abundance vectors for microbes using experimental condition information provided with the AGP metadata, such as patient age, dietary habits, or health status. We show it can be used to identify similar and opposing shifts in microbial species, and infer putative interactions between microbes. Our results show that groups of shifts with similar effects on microbiome can be identified and that similar dietary interventions display similar microbial abundance shifts.<br><br>CONCLUSIONS: Without comparison to prior data, it is difficult for experimentalists to know if their observed changes in species abundance have been observed by others, both in their conditions and in others they would never consider comparable. Yet, this can be a very important contextual factor in interpreting the significance of a shift. We've proposed and tested an algorithmic solution to this problem, which also allows for comparing the metagenomic signature shifts between conditions in the existing body of data.}, }
@article {pmid30870464, year = {2019}, author = {Burcham, ZM and Schmidt, CJ and Pechal, JL and Brooks, CP and Rosch, JW and Benbow, ME and Jordan, HR}, title = {Detection of critical antibiotic resistance genes through routine microbiome surveillance.}, journal = {PloS one}, volume = {14}, number = {3}, pages = {e0213280}, pmid = {30870464}, issn = {1932-6203}, mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/drug effects/*genetics ; Bacterial Infections/*diagnosis/epidemiology/genetics/microbiology ; Cadaver ; Drug Resistance, Microbial/*genetics ; *Genes, Bacterial ; Humans ; *Metagenome ; Microbiota ; *Population Surveillance ; United States/epidemiology ; }, abstract = {Population-based public health data on antibiotic resistance gene carriage is poorly surveyed. Research of the human microbiome as an antibiotic resistance reservoir has primarily focused on gut associated microbial communities, but data have shown more widespread microbial colonization across organs than originally believed, with organs previously considered as sterile being colonized. Our study demonstrates the utility of postmortem microbiome sampling during routine autopsy as a method to survey antibiotic resistance carriage in a general population. Postmortem microbial sampling detected pathogens of public health concern including genes for multidrug efflux pumps, carbapenem, methicillin, vancomycin, and polymixin resistances. Results suggest that postmortem assessments of host-associated microbial communities are useful in acquiring community specific data while reducing selective-participant biases.}, }
@article {pmid30867232, year = {2019}, author = {Elzinga, J and van der Oost, J and de Vos, WM and Smidt, H}, title = {The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {83}, number = {2}, pages = {}, pmid = {30867232}, issn = {1098-5557}, mesh = {Animals ; Bacteria/classification ; Cell Culture Techniques ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Genomics/methods ; *Host Microbial Interactions ; Humans ; Mice ; *Microbiota ; *Models, Animal ; }, abstract = {The human intestinal ecosystem is characterized by a complex interplay between different microorganisms and the host. The high variation within the human population further complicates the quest toward an adequate understanding of this complex system that is so relevant to human health and well-being. To study host-microbe interactions, defined synthetic bacterial communities have been introduced in gnotobiotic animals or in sophisticated in vitro cell models. This review reinforces that our limited understanding has often hampered the appropriate design of defined communities that represent the human gut microbiota. On top of this, some communities have been applied to in vivo models that differ appreciably from the human host. In this review, the advantages and disadvantages of using defined microbial communities are outlined, and suggestions for future improvement of host-microbe interaction models are provided. With respect to the host, technological advances, such as the development of a gut-on-a-chip system and intestinal organoids, may contribute to more-accurate in vitro models of the human host. With respect to the microbiota, due to the increasing availability of representative cultured isolates and their genomic sequences, our understanding and controllability of the human gut &quot;core microbiota&quot; are likely to increase. Taken together, these advancements could further unravel the molecular mechanisms underlying the human gut microbiota superorganism. Such a gain of insight would provide a solid basis for the improvement of pre-, pro-, and synbiotics as well as the development of new therapeutic microbes.}, }
@article {pmid30863868, year = {2019}, author = {Plantinga, AM and Chen, J and Jenq, RR and Wu, MC}, title = {pldist: ecological dissimilarities for paired and longitudinal microbiome association analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {35}, number = {19}, pages = {3567-3575}, pmid = {30863868}, issn = {1367-4811}, support = {R01 GM129512/GM/NIGMS NIH HHS/United States ; S10 OD020069/OD/NIH HHS/United States ; }, abstract = {MOTIVATION: The human microbiome is notoriously variable across individuals, with a wide range of 'healthy' microbiomes. Paired and longitudinal studies of the microbiome have become increasingly popular as a way to reduce unmeasured confounding and to increase statistical power by reducing large inter-subject variability. Statistical methods for analyzing such datasets are scarce.<br><br>RESULTS: We introduce a paired UniFrac dissimilarity that summarizes within-individual (or within-pair) shifts in microbiome composition and then compares these compositional shifts across individuals (or pairs). This dissimilarity depends on a novel transformation of relative abundances, which we then extend to more than two time points and incorporate into several phylogenetic and non-phylogenetic dissimilarities. The data transformation and resulting dissimilarities may be used in a wide variety of downstream analyses, including ordination analysis and distance-based hypothesis testing. Simulations demonstrate that tests based on these dissimilarities retain appropriate type 1 error and high power. We apply the method in two real datasets.<br><br>The R package pldist is available on GitHub at https://github.com/aplantin/pldist.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid30843443, year = {2019}, author = {Salvucci, E}, title = {The human-microbiome superorganism and its modulation to restore health.}, journal = {International journal of food sciences and nutrition}, volume = {70}, number = {7}, pages = {781-795}, doi = {10.1080/09637486.2019.1580682}, pmid = {30843443}, issn = {1465-3478}, mesh = {Bifidobacterium/physiology ; Brain/microbiology ; Dysbiosis ; Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; *Health ; Host Microbial Interactions/immunology/*physiology ; Humans ; Microbiota/immunology/*physiology ; Neurodevelopmental Disorders/microbiology/prevention &amp; control ; Prebiotics ; Probiotics ; Synbiotics ; }, abstract = {Microbiome is the community of microorganism that co-live with a host. The human being is the result of the integration of its genome and the coexistence with millions of microorganisms throughout its evolutionary history. Human-microbiome association can be considered a step of integration in evolution, constituting a superorganism. Many emergent diseases are related to the loss of part of this microbiome and its restoration can be achieved by different strategies. Gut microbiome imbalance is particularly associated with numerous inflammatory, immune and nervous system-related diseases by a communication pathway called microbiome-brain axis. Modulation of microbiome by administering prebiotics, like arabinoxylans, and synbiotics is a plausible treatment for dysbiosis, the regulation of neurotransmitters and alleviation of neurological manifestations.}, }
@article {pmid30835837, year = {2019}, author = {Haahtela, T}, title = {A biodiversity hypothesis.}, journal = {Allergy}, volume = {74}, number = {8}, pages = {1445-1456}, doi = {10.1111/all.13763}, pmid = {30835837}, issn = {1398-9995}, abstract = {Biodiversity hypothesis states that contact with natural environments enriches the human microbiome, promotes immune balance and protects from allergy and inflammatory disorders. We are protected by two nested layers of biodiversity, microbiota of the outer layer (soil, natural waters, plants, animals) and inner layer (gut, skin, airways). The latter inhabits our body and is colonized from the outer layer. Explosion of human populations along with cultural evolution is profoundly changing our environment and lifestyle. Adaptive immunoregulatory circuits and dynamic homeostasis are at stake in the newly emerged urban surroundings. In allergy, and chronic inflammatory disorders in general, exploring the determinants of immunotolerance is the key for prevention and more effective treatment. Loss of immunoprotective factors, derived from nature, is a new kind of health risk poorly acknowledged until recently. The paradigm change has been implemented in the Finnish allergy programme (2008-2018), which emphasized tolerance instead of avoidance. The first results are promising, as allergy burden has started to reduce. The rapidly urbanizing world is facing serious biodiversity loss with global warming, which are interconnected. Biodiversity hypothesis of health and disease has societal impact, for example, on city planning, food and energy production and nature conservation. It has also a message for individuals for health and well-being: take nature close, to touch, eat, breathe, experience and enjoy. Biodiverse natural environments are dependent on planetary health, which should be a priority also among health professionals.}, }
@article {pmid30835680, year = {2019}, author = {Wallace, DJ and Sayre, NL and Patterson, TT and Nicholson, SE and Hilton, D and Grandhi, R}, title = {Spinal cord injury and the human microbiome: beyond the brain-gut axis.}, journal = {Neurosurgical focus}, volume = {46}, number = {3}, pages = {E11}, doi = {10.3171/2018.12.FOCUS18206}, pmid = {30835680}, issn = {1092-0684}, support = {IK2 BX003240/BX/BLRD VA/United States ; }, abstract = {In addition to standard management for the treatment of the acute phase of spinal cord injury (SCI), implementation of novel neuroprotective interventions offers the potential for significant reductions in morbidity and long-term health costs. A better understanding of the systemic changes after SCI could provide insight into mechanisms that lead to secondary injury. An emerging area of research involves the complex interplay of the gut microbiome and the CNS, i.e., a brain-gut axis, or perhaps more appropriately, a CNS-gut axis. This review summarizes the relevant literature relating to the gut microbiome and SCI. Experimental models in stroke and traumatic brain injury demonstrate the bidirectional communication of the CNS to the gut with postinjury dysbiosis, gastrointestinal-associated lymphoid tissue-mediated neuroinflammatory responses, and bacterial-metabolite neurotransmission. Similar findings are being elucidated in SCI as well. Experimental interventions in these areas have shown promise in improving functional outcomes in animal models. This commensal relationship between the human body and its microbiome, particularly the gut microbiome, represents an exciting frontier in experimental medicine.}, }
@article {pmid30832730, year = {2019}, author = {Meyer, F and Bremges, A and Belmann, P and Janssen, S and McHardy, AC and Koslicki, D}, title = {Assessing taxonomic metagenome profilers with OPAL.}, journal = {Genome biology}, volume = {20}, number = {1}, pages = {51}, pmid = {30832730}, issn = {1474-760X}, mesh = {Classification/methods ; Humans ; Metagenomics/methods/*standards ; *Software ; }, abstract = {The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiative for the Critical Assessment of Metagenome Interpretation (CAMI), together with convenient visualizations. In addition, we perform in-depth performance comparisons with seven profilers on datasets of CAMI and the Human Microbiome Project. OPAL is freely available at https://github.com/CAMI-challenge/OPAL .}, }
@article {pmid30830433, year = {2019}, author = {Piersigilli, F and Lam, TT and Vernocchi, P and Quagliariello, A and Putignani, L and Aghai, ZH and Bhandari, V}, title = {Identification of new biomarkers of bronchopulmonary dysplasia using metabolomics.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {15}, number = {2}, pages = {20}, pmid = {30830433}, issn = {1573-3890}, abstract = {OBJECTIVE: To identify new biomarkers of bronchopulmonary dysplasia (BPD) in preterm neonates.<br><br>STUDY DESIGN: Metabolomic study of prospectively collected tracheal aspirate (TA) samples from preterm neonates admitted in 2 neonatal intensive care units measured by a mass spectroscopy-based assay and analysed using partial least squares-discriminant analysis.<br><br>RESULTS: We evaluated 160 TA samples from 68 neonates, 44 with BPD and 24 without BPD in the first week of life. A cluster of 53 metabolites was identified as characteristic of BPD, with 18 select metabolites being highly significant in the separation of BPD versus No BPD. To control for the gestational age (GA) differences, we did a sub-group analyses, and noted that the amino acids histidine, glutamic acid, citrulline, glycine and isoleucine levels were higher in neonates with BPD. In addition, acylcarnitines C16-OH and C18:1-OH were also higher in neonates who developed BPD, but especially in the most preterm infants (neonates with GA < 27 weeks).<br><br>CONCLUSION: Metabolomics is a promising approach to identify novel specific biomarkers for BPD.}, }
@article {pmid30828318, year = {2019}, author = {Reid, G}, title = {Disentangling What We Know About Microbes and Mental Health.}, journal = {Frontiers in endocrinology}, volume = {10}, number = {}, pages = {81}, pmid = {30828318}, issn = {1664-2392}, abstract = {Much has been written in recent years about the gut-brain axis. Exciting pilot studies suggest probiotic applications to the gut can reduce anxiety and depression via the vagus nerve. But not to diminish such findings, much still needs to be considered, including the fact that the vagus nerve links to many other body sites that also host a microbiome. Questions remain that touch the core of being human: (i) Do our microbes influence happiness and to what extent? (ii) What components of the gut microbiota and their function, including as it relates to mental health, are critical and how do they differ between agile, fit hunter gatherers and obese westerners or Danes described as the happiest people on the planet? (iii) What role do environmental pollutants play in this microbes-host ecosystem? While approaching life from a reductionist perspective has a long history in science, we need to try to interrogate these health and disease issues from a wider perspective. For verification of a link between the gut microbiota and brain, and to test new therapies, human studies are needed, and are long overdue.}, }
@article {pmid30814984, year = {2019}, author = {Song, Z and Wang, X and Zhou, X and Jiang, S and Li, Y and Ahmad, O and Qi, L and Li, P and Li, J}, title = {Taxonomic Distribution of FosB in Human-Microbiota and Activity Comparison of Fosfomycin Resistance.}, journal = {Frontiers in microbiology}, volume = {10}, number = {}, pages = {200}, pmid = {30814984}, issn = {1664-302X}, abstract = {FosB, a Mg2+ dependent thioltransferase, confers antibiotic resistance to fosfomycin through enzymatic drug inactivation. Among all antibiotic resistant proteins in the Antibiotic Resistance Genes Database and the Comprehensive Antibiotic Resistance Database, FosB is within 5% of the most number of ARPs identified in Human Microbiome Project reference database but mainly distributed in limited genera, i.e., 122 of total 133 FosB homologues are found from Bacillus and Staphylococcus. Furthermore, these FosB sequences could be divided into three clusters based on their phylogenetic relationship, i.e., two groups of FosB were mainly from Bacillus, and another was mainly from Staphylococcus. Finally, we confirmed that FosB from the group of Staphylococcus presented the highest resistance ability to fosfomycin by in silico and in vitro comparisons. In summary, this study elaborates the specific taxonomic characteristics and resistant abilities of FosB in human microbiota, which might help in developing more promising fosfomycin-like antibiotics.}, }
@article {pmid30811000, year = {2019}, author = {Shan, Y and Wu, W and Fan, W and Haahtela, T and Zhang, G}, title = {House dust microbiome and human health risks.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {22}, number = {3}, pages = {297-304}, doi = {10.1007/s10123-019-00057-5}, pmid = {30811000}, issn = {1618-1905}, mesh = {Bacteria/classification/*isolation &amp; purification ; *Dust ; *Environmental Microbiology ; Fungi/classification/*isolation &amp; purification ; Humans ; *Microbiota ; *Risk Assessment ; }, abstract = {People spend a lot of time indoors and the indoor microbiome is a major part of the environment that we are exposed to. However, awareness of the exposure to the indoor microbiome and its health effects remains poor. Outdoor environment (soil and air), indoor sources (ventilation, dampness and building materials), human occupants, and pets compose the indoor microbial community. It has been estimated that up to 500-1000 different species can be present in house dust. House dust is a major source and reservoir of indoor microbiome, which influences human microbiome and determines health and disease. Herein, we review the origins and the components of the fungal and bacterial communities in house dust and their possible effect on human health, in particular on allergic disorders, intestinal microbiome, and immune responses. We expect to lay a solid foundation for the further study on the mechanisms of how the house dust microbes interact with the host microbiome and the human immune system.}, }
@article {pmid30810508, year = {2019}, author = {Falony, G and Vandeputte, D and Caenepeel, C and Vieira-Silva, S and Daryoush, T and Vermeire, S and Raes, J}, title = {The human microbiome in health and disease: hype or hope.}, journal = {Acta clinica Belgica}, volume = {74}, number = {2}, pages = {53-64}, doi = {10.1080/17843286.2019.1583782}, pmid = {30810508}, issn = {2295-3337}, mesh = {Colon/microbiology ; Disease ; Fecal Microbiota Transplantation ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {OBJECTIVES: The prognostic, diagnostic, and therapeutic potential of the human gut microbiota is widely recognised. However, translation of microbiome findings to clinical practice is challenging. Here, we discuss current knowledge and applications in the field.<br><br>METHODS: We revisit some recent advances in the field of faecal microbiome analyses with a focus on covariate analyses and ecological interpretation.<br><br>RESULTS: Population-level characterization of gut microbiota variation among healthy volunteers has allowed identifying microbiome covariates required for clinical studies. Currently, microbiome research is moving from relative to quantitative approaches that will shed a new light on microbiota-host interactions in health and disease.<br><br>CONCLUSIONS: Covariate characterization and technical advances increase reproducibility of microbiome research. Targeted in vitro/in vivo intervention studies will accelerate clinical implementation of microbiota findings.}, }
@article {pmid30808411, year = {2019}, author = {, }, title = {A review of 10 years of human microbiome research activities at the US National Institutes of Health, Fiscal Years 2007-2016.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {31}, pmid = {30808411}, issn = {2049-2618}, mesh = {Biomedical Research/*economics/*organization &amp; administration ; Humans ; Metagenomics/economics/organization &amp; administration ; Microbiota ; National Institutes of Health (U.S.) ; United States ; }, abstract = {The National Institutes of Health (NIH) is the primary federal government agency for biomedical research in the USA. NIH provides extensive support for human microbiome research with 21 of 27 NIH Institutes and Centers (ICs) currently funding this area through their extramural research programs. This analysis of the NIH extramural portfolio in human microbiome research briefly reviews the early history of this field at NIH, summarizes the program objectives and the resources developed in the recently completed 10-year (fiscal years 2007-2016) $215 M Human Microbiome Project (HMP) program, evaluates the scope and range of the $728 M NIH investment in extramural human microbiome research activities outside of the HMP over fiscal years 2012-2016, and highlights some specific areas of research which emerged from this investment. This analysis closes with a few comments on the technical needs and knowledge gaps which remain for this field to be able to advance over the next decade and for the outcomes of this research to be able to progress to microbiome-based interventions for treating disease and supporting health.}, }
@article {pmid30808401, year = {2019}, author = {, }, title = {2017 NIH-wide workshop report on &quot;The Human Microbiome: Emerging Themes at the Horizon of the 21st Century&quot;.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {32}, pmid = {30808401}, issn = {2049-2618}, support = {U54 HD080784/HD/NICHD NIH HHS/United States ; U54 DK102557/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DE023789/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Internet ; *Microbiota ; National Institutes of Health (U.S.) ; United States ; }, abstract = {The National Institutes of Health (NIH) organized a three-day human microbiome research workshop, August 16-18, 2017, to highlight the accomplishments of the 10-year Human Microbiome Project program, the outcomes of the investments made by the 21 NIH Institutes and Centers which now fund this area, and the technical challenges and knowledge gaps which will need to be addressed in order for this field to advance over the next 10 years. This report summarizes the key points in the talks, round table discussions, and Joint Agency Panel from this workshop.}, }
@article {pmid30804923, year = {2018}, author = {Ma, Z and Li, L}, title = {Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3333}, pmid = {30804923}, issn = {1664-302X}, abstract = {Investigating inter-subject heterogeneity (or spatial distribution) of human semen microbiome diversity is of important significance. Theoretically, the spatial distribution of biodiversity constitutes the core of microbiome biogeography. Practically, the inter-subject heterogeneity is crucial for understanding the normal (healthy) flora of semen microbiotas as well as their possible changes associated with abnormal fertility. In this article, we analyze the scaling (changes) of semen microbiome diversity across individuals with DAR (diversity-area relationship) analysis, a recent extension to classic SAR (species-area relationship) law in biogeography and ecology. Specifically, the unit of &quot;area&quot; is individual subject, and the microbial diversity in seminal fluid of an individual (area) is assessed via metagenomic DNA sequencing technique and measured in the Hill numbers. The DAR models were then fitted to the accrued diversity across different number of individuals (area size). We further tested the difference in DAR parameters among the healthy, subnormal, and abnormal microbiome samples in terms of their fertility status based on a cross-sectional study of a Chinese cohort. Given that no statistically significant differences in the DAR parameters were detected among the three groups, we built unified DAR models for semen microbiome by combining the healthy, subnormal, and abnormal groups. The model parameters were used to (i) estimate the microbiome diversity scaling in a population (cohort), and construct the so-termed DAR profile; (ii) predict/construct the maximal accrual diversity (MAD) profile in a population; (iii) estimate the pair-wise diversity overlap (PDO) between two individuals and construct the PDO profile; (iv) assess the ratio of individual diversity to population (RIP) accrual diversity. The last item (RIP) is a new concept we propose in this study, which is essentially a ratio of local diversity to regional or global diversity (LRD/LGD), applicable to general biodiversity investigation beyond human microbiome.}, }
@article {pmid30801627, year = {2019}, author = {McSkimming, DI and Banack, HR and Genco, R and Wactawski-Wende, J and LaMonte, MJ}, title = {RE: &quot;QUANTIFICATION OF HUMAN MICROBIOME STABILITY OVER 6 MONTHS: IMPLICATIONS FOR EPIDEMIOLOGIC STUDIES&quot;.}, journal = {American journal of epidemiology}, volume = {188}, number = {4}, pages = {807-808}, doi = {10.1093/aje/kwz021}, pmid = {30801627}, issn = {1476-6256}, mesh = {Epidemiologic Studies ; Humans ; *Microbiota ; }, }
@article {pmid30799264, year = {2019}, author = {De Filippis, F and Pasolli, E and Tett, A and Tarallo, S and Naccarati, A and De Angelis, M and Neviani, E and Cocolin, L and Gobbetti, M and Segata, N and Ercolini, D}, title = {Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {3}, pages = {444-453.e3}, doi = {10.1016/j.chom.2019.01.004}, pmid = {30799264}, issn = {1934-6069}, mesh = {Diet/*methods ; *Feeding Behavior ; Female ; Gastrointestinal Microbiome ; Genome, Bacterial ; Genotype ; Healthy Volunteers ; Humans ; Italy ; Male ; *Microbiota ; Phenotype ; Prevalence ; Prevotella/*classification/genetics/*isolation &amp; purification/physiology ; }, abstract = {The role of intestinal Prevotella species in human health is controversial, with both positive and negative associations. Strain-level diversity may contribute to discrepancies in genus and species associations with health and disease. We dissected the gut metagenomes of Italians with varying dietary habits, investigating the presence of distinct Prevotella copri strains. Fiber-rich diets were linked to P. copri types with enhanced potential for carbohydrate catabolism. P. copri strains associated with an omnivore diet had a higher prevalence of the leuB gene-involved in branched-chain amino acid biosynthesis-a risk factor for glucose intolerance and type 2 diabetes. These P. copri pangenomes were compared to existing cohorts, providing evidence of distinct gene repertoires characterizing different P. copri populations, with drug metabolism and complex carbohydrate degradation significantly associated with Western and non-Western individuals, respectively. Strain-level P. copri diversity in gut microbiomes is affected by diet and should be considered when examining host-microbe associations.}, }
@article {pmid30799003, year = {2019}, author = {Rogers, GB and Ward, J and Brown, A and Wesselingh, SL}, title = {Inclusivity and equity in human microbiome research.}, journal = {Lancet (London, England)}, volume = {393}, number = {10173}, pages = {728-729}, doi = {10.1016/S0140-6736(18)33204-5}, pmid = {30799003}, issn = {1474-547X}, mesh = {Biomedical Research/*standards ; Continental Population Groups ; Health Status Disparities ; Humans ; Microbiota/*genetics ; Oceanic Ancestry Group ; }, }
@article {pmid30777586, year = {2019}, author = {Araos, R and D'Agata, EMC}, title = {The human microbiota and infection prevention.}, journal = {Infection control and hospital epidemiology}, volume = {40}, number = {5}, pages = {585-589}, doi = {10.1017/ice.2019.28}, pmid = {30777586}, issn = {1559-6834}, support = {K24 AI119158/AI/NIAID NIH HHS/United States ; }, abstract = {The human microbiome participates in numerous aspects of human physiology and disease states. Recently, studies have begun to explore the role of the microbiome in colonization, infection and transmission of pathogens. This review provides a summary of the methodological principles used in microbiome studies and the published evidence of the impact of microbiome dysbiosis in infection prevention.}, }
@article {pmid30772579, year = {2019}, author = {Li, H and Zhou, XY and Yang, XR and Zhu, YG and Hong, YW and Su, JQ}, title = {Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China.}, journal = {The Science of the total environment}, volume = {665}, number = {}, pages = {61-68}, doi = {10.1016/j.scitotenv.2019.01.367}, pmid = {30772579}, issn = {1879-1026}, mesh = {*Air Microbiology ; Air Pollutants/*analysis ; Air Pollution/*statistics &amp; numerical data ; Bacteria ; China ; Cities ; Climate ; *Environmental Monitoring ; Firmicutes ; *Microbiota ; Proteobacteria ; RNA, Ribosomal, 16S ; Seasons ; Urbanization ; }, abstract = {Exposure to airborne microbes (AM) can affect the human microbiome and has various consequences for human health. Investigating the profiles of AM and the potential bacterial pathogens within, along with the factors influencing their community, is pivotal for understanding the impact of AM on human health. In this study, we collected AM during spring and summer from 11 sites with various levels of urbanization in the city of Xiamen, China. Bacterial community compositions of the AM were determined based on 16S rRNA gene amplicon sequencing. Firmicutes and Proteobacteria were the predominating phyla in the airborne bacterial communities, and a higher (P < 0.05) diversity of AM was found during the summer as compared to the spring. Significant differences in the community structure of the AM and the potential bacterial pathogens within airborne microbes were observed among the seasons and the sites with different levels of urbanization. Increases and/or decreases in the abundance of Bacillus and Acinetobacter could explain a major part of the variations in the AM community compositions. The proportion of potential bacterial pathogens during the summer was significantly higher (P < 0.01) than in the spring, and the relative abundance of several bacterial pathogens (i.e. Burkholderia multivoran, Enterococcus faecium and Streptococcus thermophilus) related to human diseases (39.8% of total pathogens on average) increased with increasing urbanization levels, suggesting that urbanization can increase the AM-associated human health risk.}, }
@article {pmid30767956, year = {2019}, author = {Bai, J and Jhaney, I and Daniel, G and Watkins Bruner, D}, title = {Pilot Study of Vaginal Microbiome Using QIIME 2™ in Women With Gynecologic Cancer Before and After Radiation Therapy.}, journal = {Oncology nursing forum}, volume = {46}, number = {2}, pages = {E48-E59}, doi = {10.1188/19.ONF.E48-E59}, pmid = {30767956}, issn = {1538-0688}, mesh = {Adult ; Aged ; Female ; Genital Neoplasms, Female/*microbiology/*radiotherapy ; Georgia ; Humans ; Microbiota/*genetics/*radiation effects ; Middle Aged ; Pilot Projects ; RNA, Ribosomal, 16S/*analysis ; Vagina/*microbiology ; }, abstract = {OBJECTIVES: To characterize the vaginal microbiome using QIIME 2™ (Quantitative Insights Into Microbial Ecology 2) in women with gynecologic cancer.<br><br>SAMPLE &amp;AMP; SETTING: 19 women with gynecologic cancer before and after radiation therapy at a comprehensive cancer center in Atlanta, Georgia.<br><br>METHODS &amp;AMP; VARIABLES: This pilot study analyzed vaginal microbiome communities using a microbiome analysis pipeline, beginning with 16S rRNA gene sequencing and processing through use of a bioinformatics pipeline to downstream microbial statistical analysis.<br><br>RESULTS: The findings showed the methods to be robust, and most women with gynecologic cancer showed depletion of Lactobacillus. Compared to those pre-radiation therapy, women post-radiation therapy showed higher abundances of Mobiluncus, Atopobium, and Prevotella but lower abundances of Lactobacillus, Gardnerella, and Peptostreptococcus, which are associated with bacterial vaginosis.<br><br>IMPLICATIONS FOR NURSING: This study presents the fundamentals of human microbiome data collection and analysis methods to inform nursing science. Assessing the vaginal microbiome provides a potential pathway to develop interventions to ameliorate dysbiosis of the vaginal microbiome.}, }
@article {pmid30764863, year = {2019}, author = {Luo, Z and Li, M and Wu, Y and Meng, Z and Martin, L and Zhang, L and Ogunrinde, E and Zhou, Z and Qin, S and Wan, Z and Westerink, MAJ and Warth, S and Liu, H and Jin, P and Stroncek, D and Li, QZ and Wang, E and Wu, X and Heath, SL and Li, Z and Alekseyenko, AV and Jiang, W}, title = {Systemic translocation of Staphylococcus drives autoantibody production in HIV disease.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {25}, pmid = {30764863}, issn = {2049-2618}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; R01 AI091526/AI/NIAID NIH HHS/United States ; R01 AI128864/AI/NIAID NIH HHS/United States ; R01 AI114380/AI/NIAID NIH HHS/United States ; R01 CA213290/CA/NCI NIH HHS/United States ; P01 CA186866/CA/NCI NIH HHS/United States ; R01 LM012517/LM/NLM NIH HHS/United States ; I01 CX001211/CX/CSRD VA/United States ; R01 AG045973/AG/NIA NIH HHS/United States ; UL1 TR001450/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Autoantibodies/blood/*metabolism ; *Bacterial Translocation ; DNA, Bacterial/blood ; DNA, Ribosomal/blood ; Disease Models, Animal ; Germinal Center/immunology ; HIV Infections/*immunology ; Hep G2 Cells ; Humans ; Immunity, Innate ; Influenza Vaccines/*immunology ; Influenza, Human/prevention &amp; control ; Lymphocyte Activation ; Male ; Mice ; Single-Cell Analysis ; Staphylococcus/genetics/immunology/*physiology ; Up-Regulation ; }, abstract = {BACKGROUND: Increased autoreactive antibodies have been reported in HIV disease; however, the mechanism accounting for autoantibody induction in HIV remains unknown.<br><br>RESULTS: Herein, we show that seasonal influenza vaccination induces autoantibody production (e.g., IgG anti-nuclear antibody (ANA) and anti-double-stranded DNA antibody (anti-dsDNA)) in some viral-suppressed antiretroviral therapy (ART)-treated HIV+ subjects, but not in healthy controls. These autoantibodies were not derived from antigen-specific B cells but from activated &quot;bystander&quot; B cells analyzed by single-cell assay and by study of purified polyclonal ANAs from plasma. To explore the mechanism of autoantibody generation in HIV+ subjects, plasma level of microbial products, gene expression profile of B cells, and B cell receptor (BCR) repertoires were analyzed. We found that autoantibody production was associated with increased plasma level of microbial translocation; the patients with high autoantibodies had skewed B cell repertoires and upregulation of genes related to innate immune activation in response to microbial translocation. By analyzing circulating microbial 16S rDNA in plasma, the relative abundance of Staphylococcus was found to be associated with autoantibody production in HIV+ subjects. Finally, we found that injection of heat-killed Staphylococcus aureus promoted germinal center B cell responses and autoantibody production in mice, consistent with the notion that autoantibody production in HIV+ patients is triggered by microbial products.<br><br>CONCLUSIONS: Our results showed that translocation of Staphylococcus can promote B cell activation through enhancing germinal center response and induces autoantibody production. It uncovers a potential mechanism linking microbial translocation and autoimmunity in HIV+ disease and provides a strong rationale for targeting Staphylococcus to prevent autoantibody production.}, }
@article {pmid30763534, year = {2019}, author = {Shkoporov, AN and Hill, C}, title = {Bacteriophages of the Human Gut: The &quot;Known Unknown&quot; of the Microbiome.}, journal = {Cell host &amp; microbe}, volume = {25}, number = {2}, pages = {195-209}, doi = {10.1016/j.chom.2019.01.017}, pmid = {30763534}, issn = {1934-6069}, mesh = {Bacteria/*virology ; Bacteriophages/*classification/*growth &amp; development ; Gastrointestinal Tract/*microbiology/*virology ; Host-Parasite Interactions ; Humans ; *Microbiota ; Population Dynamics ; }, abstract = {The human gut microbiome is a dense and taxonomically diverse consortium of microorganisms. While the bacterial components of the microbiome have received considerable attention, comparatively little is known about the composition and physiological significance of human gut-associated bacteriophage populations (phageome). By extrapolating our knowledge of phage-host interactions from other environments, one could expect that >1012 viruses reside in the human gut, and we can predict that they play important roles in regulating the complex microbial networks operating in this habitat. Before delving into their function, we need to first overcome the challenges associated with studying and characterizing the phageome. In this Review, we summarize the available methods and main findings regarding taxonomic composition, community structure, and population dynamics in the human gut phageome. We also discuss the main challenges in the field and identify promising avenues for future research.}, }
@article {pmid30759766, year = {2019}, author = {Reddel, S and Putignani, L and Del Chierico, F}, title = {The Impact of Low-FODMAPs, Gluten-Free, and Ketogenic Diets on Gut Microbiota Modulation in Pathological Conditions.}, journal = {Nutrients}, volume = {11}, number = {2}, pages = {}, pmid = {30759766}, issn = {2072-6643}, mesh = {*Diet, Gluten-Free ; *Diet, Ketogenic ; *Dietary Carbohydrates ; Gastrointestinal Diseases/*diet therapy/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {The gut microbiota performs several essential protective, structural, and metabolic functions for host health. The maintenance of a beneficial microbiota requires a homeostatic equilibrium within microbial communities, and between the microorganisms and the host. The gut microbiota composition may be affected by external factors, among them diet habits may be considered most important. In some pathological conditions such as irritable bowel syndrome (IBS), celiac disease (CD), or neurological disorders (ND), specific dietary regimens as low-fermentable, oligo-, di-, mono-saccharides and polyols (FODMAPs), ketogenic (KD), and gluten-free (GFD) diets are considered therapeutic. These kinds of diets are characterized by a reduction or exclusion of a specific nutrient from the entire dietary pattern. Despite these alimentary regimens showing beneficial effects on disease symptoms, they can affect microbiota composition, especially if they are protracted for a long time. To date, only a few studies have reported the effects of these diets on gut microbiota. In this review, we discuss the effects of low-FODMAPs, KD, and GFD on gut microbiota modulation in pathological conditions, advancing the possibility of depicting a balanced diet and developing personalized dietary intervention protocols.}, }
@article {pmid30744677, year = {2019}, author = {Blakeley-Ruiz, JA and Erickson, AR and Cantarel, BL and Xiong, W and Adams, R and Jansson, JK and Fraser, CM and Hettich, RL}, title = {Metaproteomics reveals persistent and phylum-redundant metabolic functional stability in adult human gut microbiomes of Crohn's remission patients despite temporal variations in microbial taxa, genomes, and proteomes.}, journal = {Microbiome}, volume = {7}, number = {1}, pages = {18}, pmid = {30744677}, issn = {2049-2618}, support = {UH2 DK083991/DK/NIDDK NIH HHS/United States ; }, mesh = {Acetylglucosamine/analysis ; Adult ; Bacteria/genetics/*metabolism ; Crohn Disease/*microbiology/surgery ; Cytidine Monophosphate N-Acetylneuraminic Acid/analysis ; Fatty Acids, Volatile/analysis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Male ; Middle Aged ; Proteome/*metabolism ; Proteomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The gut microbiome plays a fundamental role in the human host's overall health by contributing key biological functions such as expanded metabolism and pathogen defense/immune control. In a healthy individual, the gut microbiome co-exists within the human host in a symbiotic, non-inflammatory relationship that enables mutual benefits, such as microbial degradation of indigestible food products into small molecules that the host can utilize, and enhanced pathogen defense. In abnormal conditions, such as Crohn's disease, this favorable metabolic relationship breaks down and a variety of undesirable activities result, including chronic inflammation and other health-related issues. It has been difficult, however, to elucidate the overall functional characteristics of this relationship because the microbiota can vary substantially in composition for healthy humans and possibly even more in individuals with gut disease conditions such as Crohn's disease. Overall, this suggests that microbial membership composition may not be the best way to characterize a phenotype. Alternatively, it seems to be more informative to examine and characterize the functional composition of a gut microbiome. Towards that end, this study examines 25 metaproteomes measured in several Crohn's disease patients' post-resection surgery across the course of 1 year, in order to examine persistence of microbial taxa, genes, proteins, and metabolic functional distributions across time in individuals whose microbiome might be more variable due to the gut disease condition.<br><br>RESULTS: The measured metaproteomes were highly personalized, with all the temporally-related metaproteomes clustering most closely by individual. In general, the metaproteomes were remarkably distinct between individuals and to a lesser extent within individuals. This prompted a need to characterize the metaproteome at a higher functional level, which was achieved by annotating identified protein groups with KEGG orthologous groups to infer metabolic modules. At this level, similar and redundant metabolic functions across multiple phyla were observed across time and between individuals. Tracking through these various metabolic modules revealed a clear path from carbohydrate, lipid, and amino acid degradation to central metabolism and finally the production of fermentation products.<br><br>CONCLUSIONS: The human gut metaproteome can vary quite substantially across time and individuals. However, despite substantial intra-individual variation in the metaproteomes, there is a clear persistence of conserved metabolic functions across time and individuals. Additionally, the persistence of these core functions is redundant across multiple phyla but is not always observable in the same sample. Finally, the gut microbiome's metabolism is not driven by a set of discrete linear pathways but a web of interconnected reactions facilitated by a network of enzymes that connect multiple molecules across multiple pathways.}, }
@article {pmid30732955, year = {2019}, author = {Healy, CM and Moran, GP}, title = {The microbiome and oral cancer: More questions than answers.}, journal = {Oral oncology}, volume = {89}, number = {}, pages = {30-33}, doi = {10.1016/j.oraloncology.2018.12.003}, pmid = {30732955}, issn = {1879-0593}, mesh = {Carcinoma, Squamous Cell/*genetics/pathology ; Humans ; Microbiota/*genetics ; Mouth Neoplasms/*genetics/pathology ; }, abstract = {Recent advances in DNA sequencing technology have facilitated rapid advances in the analysis of the human microbiome and its role in human disease. Several studies have now shown that OSCC and some oral premalignant conditions are associated with alterations in the oral microbiome. These studies raise questions regarding the role of the oral microbiome in the progression of oral malignancies and whether microbiome change is a significant risk factor in the development of oral cancer. This short review summarises current knowledge in the field and highlights questions that require further investigation.}, }
@article {pmid30731251, year = {2019}, author = {Bekker, V and Zwittink, RD and Knetsch, CW and Sanders, IMJG and Berghuis, D and Heidt, PJ and Vossen, JMJJ and de Vos, WM and Belzer, C and Bredius, RGM and Van't Hof, PJ and Lankester, AC and Kuijper, EJ}, title = {Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment during Hematopoietic Stem Cell Transplantation.}, journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation}, volume = {25}, number = {6}, pages = {1164-1171}, doi = {10.1016/j.bbmt.2019.01.037}, pmid = {30731251}, issn = {1523-6536}, abstract = {Bloodstream infections and graft-versus-host disease are common complications after hematopoietic stem cell transplantation (HSCT) procedures, associated with the gut microbiota that acts as a reservoir for opportunistic pathogens. Selective gut decontamination (SGD) and total gut decontamination (TGD) during HSCT have been associated with a decreased risk of developing these complications after transplantation. However, because studies have shown conflicting results, the use of these treatments remains subject of debate. In addition, their impact on the gut microbiota is not well studied. The aim of this study was to elucidate the dynamics of the microbiota during and after TGD and to compare these with the dynamics of SGD. In this prospective, observational, single-center study fecal samples were longitudinally collected from 19 children eligible for allogenic HSCT (TGD, n=12; SGD, n=7), weekly during hospital admission and monthly after discharge. In addition, fecal samples were collected from 3 family stem cell donors. Fecal microbiota structure of patients and donors was determined by 16S rRNA gene amplicon sequencing. Microbiota richness and diversity markedly decreased during SGD and TGD and gradually increased after cessation of decontamination treatment. During SGD, gut microbiota composition was relatively stable and dominated by Bacteroides, whereas it showed high inter- and intraindividual variation and low Bacteroides abundance during TGD. In some children TGD allowed the genera Enterococcus and Streptococcus to thrive during treatment. A gut microbiota dominated by Bacteroides was associated with increased predicted activity of several metabolic processes. Comparing the microbiota of recipients and their donors indicated that receiving an SCT did not alter the patient's microbiota to become more similar to that of its donor. Overall, our findings indicate that SGD and TGD affect gut microbiota structure in a treatment-specific manner. Whether these treatments affect clinical outcomes via interference with the gut microbiota needs to be further elucidated.}, }
@article {pmid30728915, year = {2019}, author = {Lu, H and Ren, Z and Li, A and Li, J and Xu, S and Zhang, H and Jiang, J and Yang, J and Luo, Q and Zhou, K and Zheng, S and Li, L}, title = {Tongue coating microbiome data distinguish patients with pancreatic head cancer from healthy controls.}, journal = {Journal of oral microbiology}, volume = {11}, number = {1}, pages = {1563409}, pmid = {30728915}, issn = {2000-2297}, abstract = {Background: The microbiota plays a critical role in the process of human carcinogenesis. Pancreatic head carcinoma (PHC)-associated tongue coating microbiome dysbiosis has not yet been clearly defined.Objective: Our aim is to reveal the bacterial composition shifts in the microbiota of the tongue coat of PHC patients.Design: The tongue coating microbiota was analyzed in 30 PHC patients and 25 healthy controls using 16S rRNA gene sequencing technology.Results: The microbiome diversity of the tongue coat in PHC patients was significantly increased, as shown by the Shannon, Simpson, inverse Simpson, Obs and incidence-based coverage estimators. Principal component analysis revealed that PHC patients were colonized by remarkably different tongue coating microbiota than healthy controls and liver cancer patients. Linear discriminant analysis effect size revealed that Leptotrichia, Fusobacterium,Rothia, Actinomyces, Corynebacterium, Atopobium, Peptostreptococcus, Catonella, Oribacterium, Filifactor, Campylobacter, Moraxella and Tannerella were overrepresented in the tongue coating of PHC patients, and Haemophilus, Porphyromonas and Paraprevotella were enriched in the tongue coating microbiota of healthy controls. Strikingly, Haemophilus, Porphyromonas, Leptotrichia and Fusobacterium could distinguish PHC patients from healthy subjects, and Streptococcus and SR1 could distinguish PHC patients from liver cancer patients. Conclusions: These findings identified the microbiota dysbiosis of the tongue coat in PHC patients, and provide insight into the association between the human microbiome and pancreatic cancer.}, }
@article {pmid30725462, year = {2019}, author = {Morales, E and Chen, J and Greathouse, KL}, title = {Compositional Analysis of the Human Microbiome in Cancer Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {1928}, number = {}, pages = {299-335}, doi = {10.1007/978-1-4939-9027-6_16}, pmid = {30725462}, issn = {1940-6029}, mesh = {Biological Evolution ; Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Polymerase Chain Reaction ; RNA, Ribosomal, 16S ; *Research ; }, abstract = {Gut microbial composition has shown to be associated with obesity, diabetes mellitus, inflammatory bowel disease, colitis, autoimmune disorders, and cancer, among other diseases. Microbiome research has significantly evolved through the years and continues to advance as we develop new and better strategies to more accurately measure its composition and function. Careful selection of study design, inclusion and exclusion criteria of participants, and methodology are paramount to accurately analyze microbial structure. Here we present the most up-to-date available information on methods for gut microbial collection and analysis.}, }
@article {pmid30718869, year = {2019}, author = {Forster, SC and Kumar, N and Anonye, BO and Almeida, A and Viciani, E and Stares, MD and Dunn, M and Mkandawire, TT and Zhu, A and Shao, Y and Pike, LJ and Louie, T and Browne, HP and Mitchell, AL and Neville, BA and Finn, RD and Lawley, TD}, title = {A human gut bacterial genome and culture collection for improved metagenomic analyses.}, journal = {Nature biotechnology}, volume = {37}, number = {2}, pages = {186-192}, pmid = {30718869}, issn = {1546-1696}, support = {//Wellcome Trust/United Kingdom ; }, mesh = {Bacteria/classification ; Computational Biology/methods ; Contig Mapping ; Gastrointestinal Microbiome ; *Genome, Bacterial ; Genome, Human ; Humans ; *Metagenome ; *Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.}, }
@article {pmid30710104, year = {2019}, author = {Du Toit, A}, title = {Expanding diversity of the human microbiome.}, journal = {Nature reviews. Microbiology}, volume = {17}, number = {3}, pages = {126}, doi = {10.1038/s41579-019-0154-0}, pmid = {30710104}, issn = {1740-1534}, }
@article {pmid30705670, year = {2018}, author = {Whittle, E and Leonard, MO and Harrison, R and Gant, TW and Tonge, DP}, title = {Multi-Method Characterization of the Human Circulating Microbiome.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3266}, pmid = {30705670}, issn = {1664-302X}, abstract = {The term microbiome describes the genetic material encoding the various microbial populations that inhabit our body. Whilst colonization of various body niches (e.g., the gut) by dynamic communities of microorganisms is now universally accepted, the existence of microbial populations in other &quot;classically sterile&quot; locations, including the blood, is a relatively new concept. The presence of bacteria-specific DNA in the blood has been reported in the literature for some time, yet the true origin of this is still the subject of much deliberation. The aim of this study was to investigate the phenomenon of a &quot;blood microbiome&quot; by providing a comprehensive description of bacterially derived nucleic acids using a range of complementary molecular and classical microbiological techniques. For this purpose we utilized a set of plasma samples from healthy subjects (n = 5) and asthmatic subjects (n = 5). DNA-level analyses involved the amplification and sequencing of the 16S rRNA gene. RNA-level analyses were based upon the de novo assembly of unmapped mRNA reads and subsequent taxonomic identification. Molecular studies were complemented by viability data from classical aerobic and anaerobic microbial culture experiments. At the phylum level, the blood microbiome was predominated by Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key phyla detected were consistent irrespective of molecular method (DNA vs. RNA), and consistent with the results of other published studies. In silico comparison of our data with that of the Human Microbiome Project revealed that members of the blood microbiome were most likely to have originated from the oral or skin communities. To our surprise, aerobic and anaerobic cultures were positive in eight of out the ten donor samples investigated, and we reflect upon their source. Our data provide further evidence of a core blood microbiome, and provide insight into the potential source of the bacterial DNA/RNA detected in the blood. Further, data reveal the importance of robust experimental procedures, and identify areas for future consideration.}, }
@article {pmid30701191, year = {2019}, author = {Leviatan, S and Segal, E}, title = {A Significant Expansion of Our Understanding of the Composition of the Human Microbiome.}, journal = {mSystems}, volume = {4}, number = {1}, pages = {}, pmid = {30701191}, issn = {2379-5077}, abstract = {Shotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set. This is particularly true for non-Western populations and for samples that do not originate from the gut. Pasolli et al. (E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, et al., Cell, 2019, https://doi.org/10.1016/j.cell.2019.01.001) perform a grand effort to expand the reference set, and to better classify its members, revealing a wider pangenome of existing species as well as identifying new species of previously unknown taxonomic branches.}, }
@article {pmid30700742, year = {2019}, author = {Tejesvi, MV and Nissi, R and Saravesi, K and Pirttilä, AM and Markkola, A and Talvensaari-Mattila, A and Ruotsalainen, AL}, title = {Association of prevalent vaginal microbiome of mother with occurrence of type I diabetes in child.}, journal = {Scientific reports}, volume = {9}, number = {1}, pages = {959}, pmid = {30700742}, issn = {2045-2322}, support = {138309//Suomen Akatemia | Biotieteiden ja Ymp&amp;#x00E4;rist&amp;#x00F6;n Tutkimuksen Toimikunta (Research Council for Biosciences and Environment)/ ; }, abstract = {Type I diabetes (T1D) is a rapidly increasing autoimmune disease especially in the Western countries and poses a serious global health problem. Incidence of T1D cannot be fully explained by genetic background, and environmental factors have been assumed to play a role. Environmental conditions and composition of human microbiome have been found to correlate with the incidence of T1D. We asked whether mothers' prevalent vaginal microbiome could correlate with the incidence of T1D in child. To test this hypothesis, we collected samples of vaginal microbiomes from eight mothers that had at least one child with T1D (child age maximum of 11 years at the time of sampling), born with a vaginal delivery. Eight control mothers had child/children with vaginal delivery and no diabetic child/children. The microbiomes were studied by using 16S rRNA Ion Torrent high throughput sequencing. We found that composition of total and Lactobacillus microbiome was altered, and saw an indication that diversity of vaginal microbiomes of the mothers with a diabetic child could be higher. Based on these pilot observations, we strongly encourage a larger population study to verify whether mother vaginal microbiome diversity and composition are linked to the prevalence of T1D in children.}, }
@article {pmid30697198, year = {2018}, author = {Naradasu, D and Miran, W and Sakamoto, M and Okamoto, A}, title = {Isolation and Characterization of Human Gut Bacteria Capable of Extracellular Electron Transport by Electrochemical Techniques.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3267}, pmid = {30697198}, issn = {1664-302X}, abstract = {Microorganisms are known to exhibit extracellular electron transfer (EET) in a wide variety of habitats. However, as for the human microbiome which significantly impacts our health, the role and importance of EET has not been widely investigated. In this study, we enriched and isolated the EET-capable bacteria from human gut microbes using an electrochemical enrichment method and examined whether the isolates couple EET with anaerobic respiration or fermentation. Upon the use of energy-rich or minimum media (with acetate or lactate) for electrochemical enrichment with the human gut sample at an electrode potential of +0.4 V [vs. the standard hydrogen electrode (SHE)], both culture conditions showed significant current production. However, EET-capable pure strains were enriched specifically with minimum media, and subsequent incubation using the δ-MnO2-agar plate with lactate or acetate led to the isolation of two EET-capable microbial strains, Gut-S1 and Gut-S2, having 99% of 16S rRNA gene sequence identity with Enterococcus avium (E. avium) and Klebsiella pneumoniae (K. pneumoniae), respectively. While the enrichment involved anaerobic respiration with acetate and lactate, further electrochemistry with E. avium and K. pneumoniae revealed that the glucose fermentation was also coupled with EET. These results indicate that EET couples not only with anaerobic respiration as found in environmental bacteria, but also with fermentation in the human gut.}, }
@article {pmid30692672, year = {2019}, author = {Devoto, AE and Santini, JM and Olm, MR and Anantharaman, K and Munk, P and Tung, J and Archie, EA and Turnbaugh, PJ and Seed, KD and Blekhman, R and Aarestrup, FM and Thomas, BC and Banfield, JF}, title = {Megaphages infect Prevotella and variants are widespread in gut microbiomes.}, journal = {Nature microbiology}, volume = {4}, number = {4}, pages = {693-700}, pmid = {30692672}, issn = {2058-5276}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R21 AG055777/AG/NIA NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteria/*virology ; Bacteriophages/classification/genetics/*isolation &amp; purification ; Female ; *Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Male ; Metagenome ; *Microbiota ; Middle Aged ; Papio/*microbiology ; Phylogeny ; Prevotella/classification/genetics/*virology ; Swine/*microbiology ; }, abstract = {Bacteriophages (phages) dramatically shape microbial community composition, redistribute nutrients via host lysis and drive evolution through horizontal gene transfer. Despite their importance, much remains to be learned about phages in the human microbiome. We investigated the gut microbiomes of humans from Bangladesh and Tanzania, two African baboon social groups and Danish pigs; many of these microbiomes contain phages belonging to a clade with genomes >540 kilobases in length, the largest yet reported in the human microbiome and close to the maximum size ever reported for phages. We refer to these as Lak phages. CRISPR spacer targeting indicates that Lak phages infect bacteria of the genus Prevotella. We manually curated to completion 15 distinct Lak phage genomes recovered from metagenomes. The genomes display several interesting features, including use of an alternative genetic code, large intergenic regions that are highly expressed and up to 35 putative transfer RNAs, some of which contain enigmatic introns. Different individuals have distinct phage genotypes, and shifts in variant frequencies over consecutive sampling days reflect changes in the relative abundance of phage subpopulations. Recent homologous recombination has resulted in extensive genome admixture of nine baboon Lak phage populations. We infer that Lak phages are widespread in gut communities that contain the Prevotella species, and conclude that megaphages, with fascinating and underexplored biology, may be common but largely overlooked components of human and animal gut microbiomes.}, }
@article {pmid30687300, year = {2018}, author = {Woods, DF and Kozak, IM and Flynn, S and O'Gara, F}, title = {The Microbiome of an Active Meat Curing Brine.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3346}, pmid = {30687300}, issn = {1664-302X}, abstract = {Traditional food products are important to our culture and heritage, and to the continued success of the food industry. Many of the production processes associated with these products have not been subjected to an in-depth microbial compositional analysis. The traditional process of curing meat, both preserves a natural protein source, as well as increasing its organoleptic qualities. One of the most important salting processes is known as Wiltshire curing. The Wiltshire process involves injecting pork with a curing solution and immersing the meat into microbial-rich brine which promotes the development of the distinct organoleptic characteristics. The important microbial component of Wiltshire brine has not been extensively characterized. We analyzed the key microbial component of Wiltshire brine by performing microbiome analysis using Next Generation Sequencing (NGS) technologies. This analysis identified the genera, Marinilactibacillus, Carnobacterium, Leuconostoc, and Vibrio as the core microflora present in Wiltshire curing brine. The important food industrial applications of these bacteria were also assessed. The bacterial diversity of the brine was investigated, and the community composition of the brine was demonstrated to change over time. New knowledge on the characterization of key microbiota associated with a productive Wiltshire brine is an important development linked to promoting enhanced quality and safety of meat processing in the food industry.}, }
@article {pmid30687254, year = {2018}, author = {Forbes, JD and Bernstein, CN and Tremlett, H and Van Domselaar, G and Knox, NC}, title = {A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease?.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3249}, pmid = {30687254}, issn = {1664-302X}, abstract = {The human microbiome has received decades of attention from scientific and medical research communities. The human gastrointestinal tract is host to immense populations of microorganisms including bacteria, viruses, archaea, and fungi (the gut microbiota). High-throughput sequencing and computational advancements provide unprecedented ability to investigate the structure and function of microbial communities associated with the human body in health and disease. Most research to date has largely focused on elucidating the bacterial component of the human gut microbiota. Study of the gut &quot;mycobiota,&quot; which refers to the diverse array of fungal species, is a relatively new and rapidly progressing field. Though omnipresent, the number and abundance of fungi occupying the human gut is orders of magnitude smaller than that of bacteria. Recent insights however, have suggested that the gut mycobiota may be intricately linked to health and disease. Evaluation of the gut mycobiota has shown that not only are the fungal communities altered in disease, but they also play a role in maintaining intestinal homeostasis and influencing systemic immunity. In addition, it is now widely accepted that host-fungi and bacteria-fungi associations are critical to host health. While research of the gut mycobiota in health and disease is on the rise, little research has been performed in the context of neuroimmune and neurodegenerative conditions. Gut microbiota dysbiosis (specifically bacteria and archaea) have been reported in neurological diseases such as multiple sclerosis, amyotrophic lateral sclerosis, and Alzheimer's, among others. Given the widely accepted bacteria-fungi associations and paucity of mycobiota-specific studies in neurological disease, this review discusses the potential role fungi may play in multiple sclerosis and other neurological diseases. Herein, we provide an overview of recent advances in gut mycobiome research and discuss the plausible role of both intestinal and non-intestinal fungi in the context of neuroimmune and neurodegenerative conditions.}, }
@article {pmid30675064, year = {2019}, author = {Tanoue, T and Morita, S and Plichta, DR and Skelly, AN and Suda, W and Sugiura, Y and Narushima, S and Vlamakis, H and Motoo, I and Sugita, K and Shiota, A and Takeshita, K and Yasuma-Mitobe, K and Riethmacher, D and Kaisho, T and Norman, JM and Mucida, D and Suematsu, M and Yaguchi, T and Bucci, V and Inoue, T and Kawakami, Y and Olle, B and Roberts, B and Hattori, M and Xavier, RJ and Atarashi, K and Honda, K}, title = {A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.}, journal = {Nature}, volume = {565}, number = {7741}, pages = {600-605}, doi = {10.1038/s41586-019-0878-z}, pmid = {30675064}, issn = {1476-4687}, support = {DK43351/NH/NIH HHS/United States ; AT009708/NH/NIH HHS/United States ; }, mesh = {Adenocarcinoma/*immunology/pathology/*therapy ; Animals ; Antigens, CD/metabolism ; Bacteria/*classification/immunology/isolation &amp; purification ; CD8-Positive T-Lymphocytes/cytology/*immunology ; Cell Line, Tumor ; Dendritic Cells/immunology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Healthy Volunteers ; Histocompatibility Antigens Class I/immunology ; Humans ; Integrin alpha Chains/metabolism ; Interferon-gamma/biosynthesis/immunology ; Listeria monocytogenes/immunology ; Listeriosis/immunology/microbiology/*prevention &amp; control ; Male ; Mice ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/immunology ; Symbiosis/*immunology ; Xenograft Model Antitumor Assays ; }, abstract = {There is a growing appreciation for the importance of the gut microbiota as a therapeutic target in various diseases. However, there are only a handful of known commensal strains that can potentially be used to manipulate host physiological functions. Here we isolate a consortium of 11 bacterial strains from healthy human donor faeces that is capable of robustly inducing interferon-γ-producing CD8 T cells in the intestine. These 11 strains act together to mediate the induction without causing inflammation in a manner that is dependent on CD103+ dendritic cells and major histocompatibility (MHC) class Ia molecules. Colonization of mice with the 11-strain mixture enhances both host resistance against Listeria monocytogenes infection and the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumour models. The 11 strains primarily represent rare, low-abundance components of the human microbiome, and thus have great potential as broadly effective biotherapeutics.}, }
@article {pmid30671046, year = {2018}, author = {Zhang, C and Thakkar, PV and Powell, SE and Sharma, P and Vennelaganti, S and Betel, D and Shah, MA}, title = {A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3246}, pmid = {30671046}, issn = {1664-302X}, abstract = {Identification of the human microbiome has proven to be of utmost importance with the emerging role of bacteria in various physiological and pathological processes. High throughput sequencing strategies have evolved to assess the composition of the microbiome. To identify possible bias that may exist in the processing of tissue for whole genome sequencing (WGS), it is important to evaluate the extraction method on the overall microbial content and composition. Here we compare two different methods of extraction, homogenization vs. enzymatic lysis, on gastric, esophageal and colorectal biopsies and survey the microbial content and composition using WGS and quantitative PCR (qPCR). We examined total bacterial content using universal 16S rDNA qPCR as well as the abundance of three phyla (Actinobacter, Firmicutes, Bacteroidetes) and one genus (Fusobacterium). We found minimal differences between the two extraction methods in the overall community structure. Furthermore, based on our qPCR analysis, neither method demonstrated preferential extraction of any particular clade of bacteria, nor significantly altered the detection of Gram-positive or Gram-negative organisms. However, although the overall microbial composition remained very similar and the most prevalent bacteria could be detected effectively using either method, the precise community structure and microbial abundances between the two methods were different, primarily due to variations in detection of low abundance genus. We also demonstrate that the homogenization extraction method provides higher microbial DNA content and higher read counts from human tissue biopsy samples of the gastrointestinal tract.}, }
@article {pmid30670574, year = {2019}, author = {Dominguez-Bello, MG and Godoy-Vitorino, F and Knight, R and Blaser, MJ}, title = {Role of the microbiome in human development.}, journal = {Gut}, volume = {68}, number = {6}, pages = {1108-1114}, pmid = {30670574}, issn = {1468-3288}, mesh = {Biological Evolution ; Female ; Fetal Development/*physiology ; *Health Status ; *Human Development ; Humans ; Infant, Newborn ; Male ; Microbiota/*genetics/physiology ; }, abstract = {The host-microbiome supraorganism appears to have coevolved and the unperturbed microbial component of the dyad renders host health sustainable. This coevolution has likely shaped evolving phenotypes in all life forms on this predominantly microbial planet. The microbiota seems to exert effects on the next generation from gestation, via maternal microbiota and immune responses. The microbiota ecosystems develop, restricted to their epithelial niches by the host immune system, concomitantly with the host chronological development, providing early modulation of physiological host development and functions for nutrition, immunity and resistance to pathogens at all ages. Here, we review the role of the microbiome in human development, including evolutionary considerations, and the maternal/fetal relationships, contributions to nutrition and growth. We also discuss what constitutes a healthy microbiota, how antimicrobial modern practices are impacting the human microbiota, the associations between microbiota perturbations, host responses and diseases rocketing in urban societies and potential for future restoration.}, }
@article {pmid30666529, year = {2019}, author = {Bilen, M and Fonkou, MDM and Caputo, A and Nguyen, TT and Di Pinto, F and Bittar, F and Daoud, Z and Levasseur, A and Fournier, PE and Raoult, D and Cadoret, F}, title = {Phoenicibacter congonensis gen. nov., sp. nov., a new genus isolated from the human gut and its description using a taxonogenomic approach.}, journal = {Antonie van Leeuwenhoek}, volume = {112}, number = {5}, pages = {775-784}, doi = {10.1007/s10482-018-01211-1}, pmid = {30666529}, issn = {1572-9699}, support = {10-IAHU- 03//Agence Nationale de la Recherche/ ; FEDER PRIMI//Conseil R?gional Provence-Alpes-C?te d'Azur/ ; }, mesh = {Actinobacteria/*classification/genetics/*isolation &amp; purification ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Feces ; Female ; Gastrointestinal Microbiome ; Humans ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Culturomics has recently allowed the isolation and description of previously uncultured bacteria from the human microbiome at different body sites. As part of a project aiming to describe the human gut microbiota by culturomics, Phoenicibacter congonensis strain Marseille-P3241T was isolated from the gut of a 45 years old Pygmy female. In the present work, we aim to describe this strain via the taxonogenomics approach. The major phenotypic, genomic and biochemical characteristics of this strain were analysed. Strain Marseille-P3241T is an anaerobic, Gram-positive and motile coccobacillus that grows optimally at 37 °C. The genome of strain Marseille-P3241T is 1,447,956 bp long with 43.44% GC content and its 16S rRNA gene sequence exhibited 89% sequence similarity with that of Denitrobacterium detoxificans strain NPOH1T, the phylogenetically closest related species with current standing in nomenclature. After performing a phylogenetic and genomic analysis, we conclude that strain Marseille-P3241T (= CCUG 70681T = CSUR P3241T) represents the type species of a new genus, for which we propose the name Phoenicibacter congonensis gen. nov., sp. nov.}, }
@article {pmid30666248, year = {2018}, author = {Malla, MA and Dubey, A and Kumar, A and Yadav, S and Hashem, A and Abd Allah, EF}, title = {Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {2868}, pmid = {30666248}, issn = {1664-3224}, mesh = {Communicable Diseases/etiology/*microbiology ; Computational Biology/trends ; Dysbiosis/complications ; Forecasting ; High-Throughput Nucleotide Sequencing/instrumentation/*trends ; Host Microbial Interactions/*genetics ; Host-Pathogen Interactions/*genetics ; Humans ; Metagenomics/*trends ; Microbiota/*physiology ; Nanotechnology/methods ; }, abstract = {The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.}, }
@article {pmid30664484, year = {2019}, author = {Lauwers, L and Bastiaens, H and Remmen, R and Keune, H}, title = {The Integration of Interlinkages Between Nature and Human Health in Primary Health Care: Protocol for a Scoping Review.}, journal = {JMIR research protocols}, volume = {8}, number = {1}, pages = {e12510}, pmid = {30664484}, issn = {1929-0748}, abstract = {BACKGROUND: International overview reports and the majority of scientific publications on interlinkages between nature and human health (NHI) do not seem to focus on the role of the health care sector. Primary health care (PHC) is often the first point of contact people have with the health care system and provides comprehensive, accessible, and community-based care that meets the health needs of individuals throughout their life. PHC is a vital backbone for linking knowledge and practice within the organization of health care. This scoping review aims to focus on the potential role of PHC in relation to NHI.<br><br>OBJECTIVE: The objective of this protocol is to present the method used to scope international overview reports and scientific publications on what is mentioned on the integration of NHI in PHC.<br><br>METHODS: The international overview reports have been screened for keywords relating to PHC. We developed a specific search strategy to scope scientific literature on NHI in relation to PHC. The scientific literature search ran in Web of Science (WOS) and PubMed from inception to May 2017. The scientific publications are screened by 2 independent reviewers, which will result in a list of relevant publications that meet eligibility and inclusion criteria.<br><br>RESULTS: On the basis of a first screen on the title of the first 200 results in both search engines, we decided to restrict to WOS. First insights in the international overview reports and the quantitative overview of the results in WOS give a first impression of a missing link between NHI and PHC. The findings are expected to identify knowledge gaps in the translation of evidence on NHI in PHC practices and the role of PHC regarding the application of that evidence in health care practice.<br><br>CONCLUSIONS: This is, to our knowledge, the first study that seeks to relate existing knowledge on NHI to PHC. The presentation of our method through this protocol allows researchers to build upon and improve our work in future research on the practical implementation of NIH. The findings of the scoping review are expected to guide future scientific research, international policy directives, and PHC workers to fill the gaps in the integration of NHI in PHC.<br><br>DERR1-10.2196/12510.}, }
@article {pmid30664014, year = {2019}, author = {Joris, BR and Gloor, GB}, title = {Unaccounted risk of cardiovascular disease: the role of the microbiome in lipid metabolism.}, journal = {Current opinion in lipidology}, volume = {30}, number = {2}, pages = {125-133}, doi = {10.1097/MOL.0000000000000582}, pmid = {30664014}, issn = {1473-6535}, abstract = {PURPOSE OF REVIEW: Not all of the risk of cardiovascular disease can be explained by diet and genetics, and the human microbiome, which lies at the interface of these two factors, may help explain some of the unaccounted risk. This review examines some of the well established links between the microbiome and cardiovascular health, and proposes relatively unexplored associations.<br><br>RECENT FINDINGS: Byproducts of microbial metabolism are associated with health and disease: Trimethylamine N oxide is associated with atherosclerosis; whereas short-chain fatty acids are associated with decreased inflammation and increased energy expenditure. More broadly, a large number of association studies have been conducted to explore the connections between bacterial taxa and metabolic syndrome. In contrast, the relationship between the microbiome and triglycerides levels remains poorly understood.<br><br>SUMMARY: We suggest that deeper understanding of the molecular mechanisms that drive linkages between the microbiome and disease can be determined by replacing 16S rRNA gene sequencing with shotgun metagenomic sequencing or other functional approaches. Furthermore, to ensure translatability and reproducibility of research findings, a combination of multiple different complementary '-omic' approaches should be employed.}, }
@article {pmid30661755, year = {2019}, author = {Pasolli, E and Asnicar, F and Manara, S and Zolfo, M and Karcher, N and Armanini, F and Beghini, F and Manghi, P and Tett, A and Ghensi, P and Collado, MC and Rice, BL and DuLong, C and Morgan, XC and Golden, CD and Quince, C and Huttenhower, C and Segata, N}, title = {Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.}, journal = {Cell}, volume = {176}, number = {3}, pages = {649-662.e20}, pmid = {30661755}, issn = {1097-4172}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/M50161X/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Big Data ; Genetic Variation/genetics ; Geography ; Humans ; Life Style ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; }, abstract = {The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.}, }
@article {pmid30660785, year = {2019}, author = {Marsh, RL and Smith-Vaughan, HC and Chen, ACH and Marchant, JM and Yerkovich, ST and Gibson, PG and Pizzutto, SJ and Hodge, S and Upham, JW and Chang, AB}, title = {Multiple Respiratory Microbiota Profiles Are Associated With Lower Airway Inflammation in Children With Protracted Bacterial Bronchitis.}, journal = {Chest}, volume = {155}, number = {4}, pages = {778-786}, doi = {10.1016/j.chest.2019.01.002}, pmid = {30660785}, issn = {1931-3543}, mesh = {Bacteria/*isolation &amp; purification ; Bronchitis, Chronic/diagnosis/*microbiology ; Bronchoalveolar Lavage Fluid/*microbiology ; Bronchoscopy ; Child ; Child, Preschool ; Female ; Follow-Up Studies ; Humans ; Infant ; Male ; Microbiota/*physiology ; Neutrophils/pathology ; Prospective Studies ; }, abstract = {BACKGROUND: Effective management of protracted bacterial bronchitis (PBB) is needed to prevent chronic disease (eg, bronchiectasis). Understanding the contributions of ongoing airway infection and inflammation is important to achieving optimal PBB treatments. The aim of this study was to compare BAL microbiota, bacterial biomass, and inflammatory markers in children with PBB and age-matched control patients.<br><br>METHODS: BAL was prospectively collected from 28 children with PBB (median age, 1.7 years; range, 0.6-7.4) and 8 control patients (median age, 1.9 years; range, 0.4-4.7). BAL microbiology was determined using culture, 16S ribosomal RNA gene sequencing and bacterial biomass quantification. BAL inflammatory cells, IL-8, and IL-1β were used to assess lower airway inflammation.<br><br>RESULTS: Bacterial biomass, neutrophil percentage, IL-8, and IL-1β levels were significantly higher in children with PBB compared with control patients. BAL microbiota in children with PBB was significantly different to that of control patients (permutational multivariate analysis of variance P = .001) and clustered into four distinct profiles that were either dominated by a respiratory pathogen or contained a more diverse microbiota including Prevotella species. Alpha diversity was unrelated to bacterial biomass, culture of recognized respiratory pathogens, or inflammatory markers.<br><br>CONCLUSIONS: Neutrophilic inflammation in children with PBB was associated with multiple BAL microbiota profiles. Significant associations between inflammatory markers and bacterial biomass, but not alpha diversity, suggest that inflammation in children with PBB is not driven by single pathogenic species. Understanding the role of the entire respiratory microbiota in PBB pathogenesis may be important to determining whether bacteria other than the recognized pathogens contribute to disease recurrence and progression to bronchiectasis.}, }
@article {pmid30658055, year = {2019}, author = {Pellock, SJ and Walton, WG and Ervin, SM and Torres-Rivera, D and Creekmore, BC and Bergan, G and Dunn, ZD and Li, B and Tripathy, A and Redinbo, MR}, title = {Discovery and Characterization of FMN-Binding β-Glucuronidases in the Human Gut Microbiome.}, journal = {Journal of molecular biology}, volume = {431}, number = {5}, pages = {970-980}, pmid = {30658055}, issn = {1089-8638}, support = {R01 CA098468/CA/NCI NIH HHS/United States ; R01 CA161879/CA/NCI NIH HHS/United States ; R01 CA207416/CA/NCI NIH HHS/United States ; T32 GM008570/GM/NIGMS NIH HHS/United States ; }, mesh = {Catalytic Domain/physiology ; Clostridiales/metabolism ; Flavin Mononucleotide/*metabolism ; Gastrointestinal Microbiome/*physiology ; Glucuronidase/*metabolism ; Humans ; Kinetics ; Metagenome/physiology ; Microbiota/physiology ; Ruminococcus/metabolism ; }, abstract = {The human gut microbiota encodes β-glucuronidases (GUSs) that play key roles in health and disease via the metabolism of glucuronate-containing carbohydrates and drugs. Hundreds of putative bacterial GUS enzymes have been identified by metagenomic analysis of the human gut microbiome, but less than 10% have characterized structures and functions. Here we describe a set of unique gut microbial GUS enzymes that bind flavin mononucleotide (FMN). First, we show using mass spectrometry, isothermal titration calorimetry, and x-ray crystallography that a purified GUS from the gut commensal microbe Faecalibacterium prausnitzii binds to FMN on a surface groove located 30 Å away from the active site. Second, utilizing structural and functional data from this FMN-binding GUS, we analyzed the 279 unique GUS sequences from the Human Microbiome Project database and identified 14 putative FMN-binding GUSs. We characterized four of these hits and solved the structure of two, the GUSs from Ruminococcus gnavus and Roseburia hominis, which confirmed that these are FMN binders. Third, binding and kinetic analysis of the FMN-binding site mutants of these five GUSs show that they utilize a conserved site to bind FMN that is not essential for GUS activity, but can affect KM. Lastly, a comprehensive structural review of the PDB reveals that the FMN-binding site employed by these enzymes is unlike any structurally characterized FMN binders to date. These findings reveal the first instance of an FMN-binding glycoside hydrolase and suggest a potential link between FMN and carbohydrate metabolism in the human gut microbiota.}, }
@article {pmid30657195, year = {2019}, author = {Espin-Garcia, O and Croitoru, K and Xu, W}, title = {A finite mixture model for X-chromosome association with an emphasis on microbiome data analysis.}, journal = {Genetic epidemiology}, volume = {43}, number = {4}, pages = {427-439}, doi = {10.1002/gepi.22190}, pmid = {30657195}, issn = {1098-2272}, support = {145546//CIHR/Canada ; GET-101831//CIHR/Canada ; CMF108031//CIHR/Canada ; }, mesh = {*Chromosomes, Human, X/genetics ; Cohort Studies ; Crohn Disease/epidemiology/genetics/microbiology ; Data Analysis ; Family ; Female ; Finite Element Analysis ; Gene-Environment Interaction ; Genetic Association Studies/statistics &amp; numerical data ; Genotype ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Microbiota/*genetics ; Models, Genetic ; X Chromosome Inactivation ; }, abstract = {Analysis of the X chromosome has been largely neglected in genetic studies mainly because of complex underlying biological mechanisms. On the other hand, the study of human microbiome data (typically over-dispersed counts with an excess of zeros) has generated great interest recently because of advancements in next-generation sequencing technologies. We propose a novel approach to infer the association between host genetic variants in the X-chromosome and microbiome data. The method accounts for random X-chromosome inactivation (XCI), skewed (or nonrandom) XCI (XCI-S), and escape of XCI (XCI-E). The inference is performed through a finite mixture model (FMM), in which an indicator variable denoting the &quot;true&quot; biological mechanism is treated as missing data. An expectation-maximization algorithm on zero-inflated and two-part models is implemented to estimate genetic effects. We investigate the performance of the FMM along with strategies that assume XCI and XCI-E mechanisms for all subjects compared with alternative approaches. Briefly, an XCI mechanism codes males' genotypes as homozygous females, whereas under XCI-E, males are treated as heterozygous females. By comprehensive simulations, we evaluate tests of the hypothesis under a computationally efficient score statistic. In summary, the FMM renders reduced bias and commensurate power compared to XCI, XCI-E, and alternative strategies while maintaining adequate Type 1 error control. The proposed method has far-reaching applications. In particular, we illustrate its usage on a large-scale human microbiome study, the Genetic, Environmental and Microbial (GEM) project, to test for the genetic association on the X chromosome.}, }
@article {pmid30650377, year = {2019}, author = {Britton, GJ and Contijoch, EJ and Mogno, I and Vennaro, OH and Llewellyn, SR and Ng, R and Li, Z and Mortha, A and Merad, M and Das, A and Gevers, D and McGovern, DPB and Singh, N and Braun, J and Jacobs, JP and Clemente, JC and Grinspan, A and Sands, BE and Colombel, JF and Dubinsky, MC and Faith, JJ}, title = {Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt+ Regulatory T Cells and Exacerbate Colitis in Mice.}, journal = {Immunity}, volume = {50}, number = {1}, pages = {212-224.e4}, pmid = {30650377}, issn = {1097-4180}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; F30 DK108487/DK/NIDDK NIH HHS/United States ; UL1 TR000124/TR/NCATS NIH HHS/United States ; P30 CA016042/CA/NCI NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; R01 DK085691/DK/NIDDK NIH HHS/United States ; R01 GM108505/GM/NIGMS NIH HHS/United States ; F31 DK112679/DK/NIDDK NIH HHS/United States ; P01 DK046763/DK/NIDDK NIH HHS/United States ; P50 AT008661/AT/NCCIH NIH HHS/United States ; U24 AI118644/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Cell Differentiation ; Colitis/chemically induced/immunology/*microbiology ; Disease Models, Animal ; Disease Progression ; Gastrointestinal Microbiome/*genetics ; Homeostasis ; Humans ; Inflammatory Bowel Diseases/*immunology/*microbiology ; Mice ; Mice, Inbred C57BL ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; RNA, Ribosomal, 16S/*genetics ; T-Lymphocytes, Regulatory/*immunology ; Th17 Cells/*metabolism ; }, abstract = {Microbiota are thought to influence the development and progression of inflammatory bowel disease (IBD), but determining generalizable effects of microbiota on IBD etiology requires larger-scale functional analyses. We colonized germ-free mice with intestinal microbiotas from 30 healthy and IBD donors and determined the homeostatic intestinal T cell response to each microbiota. Compared to microbiotas from healthy donors, transfer of IBD microbiotas into germ-free mice increased numbers of intestinal Th17 cells and Th2 cells and decreased numbers of RORγt+ Treg cells. Colonization with IBD microbiotas exacerbated disease in a model where colitis is induced upon transfer of naive T cells into Rag1-/- mice. The proportions of Th17 and RORγt+ Treg cells induced by each microbiota were predictive of human disease status and accounted for disease severity in the Rag1-/- colitis model. Thus, an impact on intestinal Th17 and RORγt+ Treg cell compartments emerges as a unifying feature of IBD microbiotas, suggesting a general mechanism for microbial contribution to IBD pathogenesis.}, }
@article {pmid30649168, year = {2019}, author = {Griffith, JC and Morgan, XC}, title = {Invited Commentary: Improving the Accessibility of Human Microbiome Project Data Through Integration With R/Bioconductor.}, journal = {American journal of epidemiology}, volume = {188}, number = {6}, pages = {1027-1030}, doi = {10.1093/aje/kwz007}, pmid = {30649168}, issn = {1476-6256}, mesh = {Computational Biology ; Humans ; Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference data set of the &quot;normal&quot; human microbiome of 242 healthy adults at 5 major body sites. The HMP used both 16S ribosomal RNA gene sequencing and whole-genome metagenomic sequencing to profile the subjects' microbial communities. However, accessing and analyzing the HMP data set still presents technical and bioinformatic challenges, given that researchers must import the microbiome data, integrate phylogenetic trees, and access and merge public and restricted metadata. The HMP16SData R/Bioconductor package developed by Schiffer et al. (Am J Epidemiol. 2019;188(6):1023-1026) greatly simplifies access to the HMP data by combining 16S taxonomic abundance data, public patient metadata, and phylogenetic trees as a single data object. The authors also provide an interface for users with approved Database of Genotypes and Phenotypes (dbGaP) projects to easily retrieve and merge the controlled-access HMP metadata. This package has a broad range of appeal to researchers across disciplines and with various levels of expertise in using R and/or other statistical tools, which translates to improved data accessibility for public health research, with data from healthy individuals serving as a reference for disease-associated studies.}, }
@article {pmid30649166, year = {2019}, author = {Schiffer, L and Azhar, R and Shepherd, L and Ramos, M and Geistlinger, L and Huttenhower, C and Dowd, JB and Segata, N and Waldron, L}, title = {HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor.}, journal = {American journal of epidemiology}, volume = {188}, number = {6}, pages = {1023-1026}, pmid = {30649166}, issn = {1476-6256}, support = {R01 HG005220/HG/NHGRI NIH HHS/United States ; R21 AI121784/AI/NIAID NIH HHS/United States ; U24 CA180996/CA/NCI NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Computational Biology ; Databases, Genetic/*statistics &amp; numerical data ; Female ; Humans ; Male ; Microbiota/*physiology ; RNA, Ribosomal, 16S/*metabolism ; Young Adult ; }, abstract = {Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 242 healthy American adults to produce the first comprehensive reference for the composition and variation of the &quot;healthy&quot; human microbiome. Publicly available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.}, }
@article {pmid30644740, year = {2019}, author = {Brasili, E and Hassimotto, NMA and Del Chierico, F and Marini, F and Quagliariello, A and Sciubba, F and Miccheli, A and Putignani, L and Lajolo, F}, title = {Daily Consumption of Orange Juice from Citrus sinensis L. Osbeck cv. Cara Cara and cv. Bahia Differently Affects Gut Microbiota Profiling as Unveiled by an Integrated Meta-Omics Approach.}, journal = {Journal of agricultural and food chemistry}, volume = {67}, number = {5}, pages = {1381-1391}, doi = {10.1021/acs.jafc.8b05408}, pmid = {30644740}, issn = {1520-5118}, mesh = {Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Brazil ; Citrus sinensis/chemistry/classification/*metabolism ; Female ; Fruit/chemistry/classification ; Fruit and Vegetable Juices/*analysis ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism/microbiology ; Humans ; Male ; Middle Aged ; Young Adult ; }, abstract = {We have investigated the effect of intake of two different orange juices from Citrus sinensis cv. &quot;Cara Cara&quot; and cv. &quot;Bahia&quot; on faecal microbiota and metabolome using an integrated meta-omics approach. Following a randomized crossover design, healthy subjects daily consumed 500 mL of orange juice from Cara Cara or Bahia juices or an isocaloric control drink. Stools were collected at baseline (T0) and after a week (T7) of intervention. Operational taxonomic units (OTUs) were pyrosequenced targeting 16S rRNA, and faecal metabolites were analyzed by an untargeted metabolomics approach based on 1H NMR spectroscopy. The major shift observed in microbiota composition after orange juice intake was the increased abundance of a network of Clostridia OTUs from Mogibacteriaceae, Tissierellaceae, Veillonellaceae, Odoribacteraceae, and Ruminococcaceae families, whose members were differently affected by Cara Cara or Bahia juice consumption. A core of six metabolites such as inositol, choline, lysine, arginine, urocanic acid, and formate significantly increased in Cara Cara compared to the Bahia group.}, }
@article {pmid30643895, year = {2019}, author = {Gutiérrez-Barranquero, JA and Parages, ML and Dobson, ADW and Reen, FJ and O'Gara, F}, title = {Genome Sequence of Paracoccus sp. JM45, a Bacterial Strain Isolated from a Marine Sponge with a Dual Quorum Sensing Inhibition Activity.}, journal = {Microbiology resource announcements}, volume = {8}, number = {2}, pages = {}, pmid = {30643895}, issn = {2576-098X}, abstract = {The draft genome sequence of Paracoccus sp. strain JM45, isolated from a marine sponge harvested off the west coast of Ireland, is reported here. Quorum sensing and quorum sensing inhibition activities have been reported recently for this bacterium, and genomic analysis supports its potential use for novel therapeutic development.}, }
@article {pmid30635376, year = {2019}, author = {Feng, S and McLellan, SL}, title = {Highly Specific Sewage-Derived Bacteroides Quantitative PCR Assays Target Sewage-Polluted Waters.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {6}, pages = {}, pmid = {30635376}, issn = {1098-5336}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteroides/classification/genetics/*isolation &amp; purification ; DNA, Bacterial/genetics ; Feces/microbiology ; Fresh Water/*microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction/*methods ; Sensitivity and Specificity ; Sewage/*microbiology ; Water Pollution/analysis ; }, abstract = {The identification of sewage contamination in water has primarily relied on the detection of human-associated Bacteroides using markers within the V2 region of the 16S rRNA gene. Despite the establishment of multiple assays that target the HF183 cluster (i.e., Bacteroides dorei) and other Bacteroides organisms (e.g., Bacteroides thetaiotaomicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined the Bacteroides population structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near-full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in the V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of the HF183 cluster. The most abundant Bacteroides in untreated sewage was not human associated but pipe derived. Two TaqMan quantitative PCR (qPCR) assays targeting the V4V5 and V6 regions of this organism were developed. Validation studies using fecal samples from seven animal hosts (n = 76) and uncontaminated water samples (n = 30) demonstrated the high specificity of the assays for sewage. Freshwater Bacteroides were also identified in uncontaminated water samples, demonstrating that measures of total Bacteroides do not reflect fecal pollution. A comparison of two previously described human Bacteroides assays (HB and HF183/BacR287) in municipal wastewater influent and sewage-contaminated urban water samples revealed identical results, illustrating the assays target the same organism. The detection of sewage-derived Bacteroides provided an independent measure of sewage-impacted waters.IMPORTANCEBacteroides are major members of the gut microbiota, and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of Bacteroides within sewage to contextualize the well-studied HF183 marker for a human-associated Bacteroides The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are nonspecific but other potential human-associated markers are present. Furthermore, we show the most abundant Bacteroides in sewage is free living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organisms specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.}, }
@article {pmid30626617, year = {2019}, author = {Rowan-Nash, AD and Korry, BJ and Mylonakis, E and Belenky, P}, title = {Cross-Domain and Viral Interactions in the Microbiome.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {83}, number = {1}, pages = {}, pmid = {30626617}, issn = {1098-5557}, support = {P20 GM109035/GM/NIGMS NIH HHS/United States ; P20 GM121344/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Archaea/metabolism/pathogenicity ; Bacteria/metabolism/pathogenicity ; Fungi/metabolism/pathogenicity ; Gastrointestinal Microbiome/*physiology ; *Gastrointestinal Tract/microbiology/parasitology/virology ; Helminths/metabolism/pathogenicity ; Host-Parasite Interactions/*physiology ; Humans ; Models, Animal ; Specific Pathogen-Free Organisms ; *Viruses/metabolism/pathogenicity ; }, abstract = {The importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.}, }
@article {pmid30619299, year = {2018}, author = {Satitsuksanoa, P and Jansen, K and Głobińska, A and van de Veen, W and Akdis, M}, title = {Regulatory Immune Mechanisms in Tolerance to Food Allergy.}, journal = {Frontiers in immunology}, volume = {9}, number = {}, pages = {2939}, pmid = {30619299}, issn = {1664-3224}, mesh = {Animals ; Cytokines/immunology/metabolism ; Dendritic Cells/immunology ; Dietary Proteins/*immunology/metabolism ; Epithelial Cells/immunology ; Food Hypersensitivity/*immunology ; Gastrointestinal Microbiome/immunology ; Humans ; Immune Tolerance/*immunology ; T-Lymphocytes, Regulatory/*immunology/metabolism ; }, abstract = {Oral tolerance can develop after frequent exposure to food allergens. Upon ingestion, food is digested into small protein fragments in the gastrointestinal tract. Small food particles are later absorbed into the human body. Interestingly, some of these ingested food proteins can cause allergic immune responses, which can lead to food allergy. So far it has not been completely elucidated how these proteins become immunogenic and cause food allergies. In contrast, oral tolerance helps to prevent the pathologic reactions against different types of food antigens from animal or plant origin. Tolerance to food is mainly acquired by dendritic cells, epithelial cells in the gut, and the gut microbiome. A subset of CD103+ DCs is capable of inducing T regulatory cells (Treg cells) that express anti-inflammatory cytokines. Anergic T cells also contribute to oral tolerance, by reducing the number of effector cells. Similar to Treg cells, B regulatory cells (Breg cells) suppress effector T cells and contribute to the immune tolerance to food allergens. Furthermore, the human microbiome is an essential mediator in the induction of oral tolerance or food allergy. In this review, we outline the current understanding of regulatory immune mechanisms in oral tolerance. The biological changes reflecting early consequences of immune stimulation with food allergens should provide useful information for the development of novel therapeutic treatments.}, }
@article {pmid30619188, year = {2018}, author = {Xiao, J and Chen, L and Yu, Y and Zhang, X and Chen, J}, title = {A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data.}, journal = {Frontiers in microbiology}, volume = {9}, number = {}, pages = {3112}, pmid = {30619188}, issn = {1664-302X}, support = {U01 FD005875/FD/FDA HHS/United States ; }, abstract = {Fueled by technological advancement, there has been a surge of human microbiome studies surveying the microbial communities associated with the human body and their links with health and disease. As a complement to the human genome, the human microbiome holds great potential for precision medicine. Efficient predictive models based on microbiome data could be potentially used in various clinical applications such as disease diagnosis, patient stratification and drug response prediction. One important characteristic of the microbial community data is the phylogenetic tree that relates all the microbial taxa based on their evolutionary history. The phylogenetic tree is an informative prior for more efficient prediction since the microbial community changes are usually not randomly distributed on the tree but tend to occur in clades at varying phylogenetic depths (clustered signal). Although community-wide changes are possible for some conditions, it is also likely that the community changes are only associated with a small subset of &quot;marker&quot; taxa (sparse signal). Unfortunately, predictive models of microbial community data taking into account both the sparsity and the tree structure remain under-developed. In this paper, we propose a predictive framework to exploit sparse and clustered microbiome signals using a phylogeny-regularized sparse regression model. Our approach is motivated by evolutionary theory, where a natural correlation structure among microbial taxa exists according to the phylogenetic relationship. A novel phylogeny-based smoothness penalty is proposed to smooth the coefficients of the microbial taxa with respect to the phylogenetic tree. Using simulated and real datasets, we show that our method achieves better prediction performance than competing sparse regression methods for sparse and clustered microbiome signals.}, }
@article {pmid30604388, year = {2019}, author = {Osman, AEG and Luke, JJ}, title = {The Impact of the Fecal Microbiome on Cancer Immunotherapy.}, journal = {BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy}, volume = {33}, number = {1}, pages = {1-7}, doi = {10.1007/s40259-018-0328-8}, pmid = {30604388}, issn = {1179-190X}, support = {W81XWH-17-1-0265//U.S. Department of Defense/ ; }, mesh = {Gastrointestinal Microbiome/*immunology ; Graft vs Host Disease ; Humans ; Immunotherapy/methods ; Neoplasms/*microbiology/*therapy ; }, abstract = {Recent advances in culture-free methods of studying the human microbiome, coupled with strong bioinformatics tools, have provided new insights on the role of the human microbiome in health and disease. The human gut, in particular, houses a vast number and diverse variety of microbes. A plethora of evidence has demonstrated the significant effects of the gut microbiome on local and systemic immunity. Studies in hematopoietic stem cell transplantation recipients provided early evidence of the involvement of the gut microbiome in the development of graft-versus-host disease and its related mortality. Cancer immunotherapy and checkpoint inhibitors, in particular, harness the power of the host's immune system to fight a range of malignancies. Resistance to immunotherapy and fatal immune-related adverse events both continue to be challenges in the field. The role of the human gut microbiome in affecting the response to immunotherapy was recently uncovered through a series of preclinical and clinical studies. The evidence presented in these studies provides tremendous potential for gut microbes to be used for biomarker development and therapeutic intervention trials.}, }
@article {pmid30588567, year = {2019}, author = {Wei, F and Wu, Q and Hu, Y and Huang, G and Nie, Y and Yan, L}, title = {Conservation metagenomics: a new branch of conservation biology.}, journal = {Science China. Life sciences}, volume = {62}, number = {2}, pages = {168-178}, doi = {10.1007/s11427-018-9423-3}, pmid = {30588567}, issn = {1869-1889}, mesh = {Animals ; Animals, Wild/*microbiology/physiology ; Biological Coevolution ; Conservation of Natural Resources/*trends ; Humans ; *Metagenomics ; Microbiota/genetics/*physiology ; }, abstract = {Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.}, }
@article {pmid30584647, year = {2019}, author = {Zhang, J and Zhang, F and Zhao, C and Xu, Q and Liang, C and Yang, Y and Wang, H and Shang, Y and Wang, Y and Mu, X and Zhu, D and Zhang, C and Yang, J and Yao, M and Zhang, L}, title = {Dysbiosis of the gut microbiome is associated with thyroid cancer and thyroid nodules and correlated with clinical index of thyroid function.}, journal = {Endocrine}, volume = {64}, number = {3}, pages = {564-574}, pmid = {30584647}, issn = {1559-0100}, support = {31471202//the National Natural Science Foundation of China/International ; 81670822//the National Natural Science Foundation of China/International ; 2016YYSP009//the Shandong Provincial Key Research and Development Program/International ; 2016GNS023//Weihai Technique Extension Project/International ; 17-3-3-10-nsh//Qingdao Key Research Project/International ; tshw20120206//the Taishan Scholars Program of Shandong Province/International ; }, abstract = {PURPOSE: Thyroid cancer and thyroid nodules are the most prevalent form of thyroid endocrine disorder. The balance of gut microbiome is highly crucial for a healthy human body, especially for the immune and endocrine system. However, the relationship between gut microbiome and the thyroid endocrine disorders such as thyroid cancer and thyroid nodules has not been reported yet.<br><br>METHODS: A cohort of 74 patients was recruited for this study. Among them, 20 patients had thyroid cancer, 18 patients had thyroid nodules, and 36 were matched healthy controls. Gut microbiome composition was analyzed by 16S rRNA (16S ribosomal RNA) gene-based sequencing protocol.<br><br>RESULTS: We compared the gut microbiome results of 74 subjects and established the correlation between gut microbiome and thyroid endocrine function for both thyroid cancer and thyroid nodules. The results inferred that alpha and beta diversity were different for patients with thyroid tumor than the healthy controls (p < 0.01). In comparison to healthy controls, the relative abundance of Neisseria (p < 0.001) and Streptococcus (p < 0.001) was significantly higher for thyroid cancer and thyroid nodules. Butyricimonas (p < 0.001) and Lactobacillus (p < 0.001) displayed notably lower relative abundance for thyroid cancer and thyroid nodules, respectively. It was also found that the clinical indexes were correlated with gut microbiome.<br><br>CONCLUSION: Our results indicate that both thyroid cancer and thyroid nodules are associated with the composition of gut microbiome. These results may support further clinical diagnosis to a great extent and help in developing potential probiotics to facilitate the treatment of thyroid cancer and thyroid nodules.}, }
@article {pmid30578461, year = {2019}, author = {Nobili, V and Mosca, A and Alterio, T and Cardile, S and Putignani, L}, title = {Fighting Fatty Liver Diseases with Nutritional Interventions, Probiotics, Symbiotics, and Fecal Microbiota Transplantation (FMT).}, journal = {Advances in experimental medicine and biology}, volume = {1125}, number = {}, pages = {85-100}, doi = {10.1007/5584_2018_318}, pmid = {30578461}, issn = {0065-2598}, mesh = {*Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Humans ; Non-alcoholic Fatty Liver Disease/*therapy ; Probiotics/*therapeutic use ; Randomized Controlled Trials as Topic ; }, abstract = {Pediatric obesity is rising worldwide leading the worrying phenomenon of nonalcoholic fatty liver disease (NAFLD) to shift into one of the most frequent causes of chronic liver illness in childhood. Occurrence of NAFLD depends on several factors such as the geographical area and the diagnostic modalities used; overall it ranges between 3% and 10% of pediatric population, increasing up to 70% in patients with metabolic comorbidities (Manco M, Bottazzo G, DeVito R et al, J Am Coll Nutr 27:667-676, 2008).Recent findings have related the intestinal microbiota to a plethora of pathological conditions, including type 2 diabetes (T2D), obesity, and nonalcoholic steatohepatitis (NASH). One of the emerging areas of the study is the link between liver diseases and gut microbiome, which has added new information to the understanding of the so-called gut-liver axis.In order to address the role of gut microbiome in NAFLD onset and progression, it is necessary to &quot;decipher&quot; operational codes for microbiome investigation within the context of advanced laboratory medicine to capture microbiome features and, hence, to address the function of the intestinal microbiome within the gut microbiota-liver axis.Results of these investigations have allowed the beginning of implementing the usage of probiotics and symbiotics in the medical approach of obesity and NAFLD in adults and children. Several randomized clinical trials (RCTs) have been already published on fecal microbiota transplantation (FMT), T2D, NASH, and inflammatory bowel disease (IBD).This review proposes to describe the current state of knowledge on the ways fatty liver diseases can be addressed with nutritional interventions, probiotics, symbiotics, and FMT.}, }
@article {pmid30578265, year = {2019}, author = {Stubbendieck, RM and May, DS and Chevrette, MG and Temkin, MI and Wendt-Pienkowski, E and Cagnazzo, J and Carlson, CM and Gern, JE and Currie, CR}, title = {Competition among Nasal Bacteria Suggests a Role for Siderophore-Mediated Interactions in Shaping the Human Nasal Microbiota.}, journal = {Applied and environmental microbiology}, volume = {85}, number = {10}, pages = {}, pmid = {30578265}, issn = {1098-5336}, support = {P01 HL070831/HL/NHLBI NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; U19 AI109673/AI/NIAID NIH HHS/United States ; }, abstract = {Resources available in the human nasal cavity are limited. Therefore, to successfully colonize the nasal cavity, bacteria must compete for scarce nutrients. Competition may occur directly through interference (e.g., antibiotics) or indirectly by nutrient sequestration. To investigate the nature of nasal bacterial competition, we performed coculture inhibition assays between nasal Actinobacteria and Staphylococcus spp. We found that isolates of coagulase-negative staphylococci (CoNS) were sensitive to growth inhibition by Actinobacteria but that Staphylococcus aureus isolates were resistant to inhibition. Among Actinobacteria, we observed that Corynebacterium spp. were variable in their ability to inhibit CoNS. We sequenced the genomes of 10 Corynebacterium species isolates, including 3 Corynebacterium propinquum isolates that strongly inhibited CoNS and 7 other Corynebacterium species isolates that only weakly inhibited CoNS. Using a comparative genomics approach, we found that the C. propinquum genomes were enriched in genes for iron acquisition and harbored a biosynthetic gene cluster (BGC) for siderophore production, absent in the noninhibitory Corynebacterium species genomes. Using a chrome azurol S assay, we confirmed that C. propinquum produced siderophores. We demonstrated that iron supplementation rescued CoNS from inhibition by C. propinquum, suggesting that inhibition was due to iron restriction through siderophore production. Through comparative metabolomics and molecular networking, we identified the siderophore produced by C. propinquum as dehydroxynocardamine. Finally, we confirmed that the dehydroxynocardamine BGC is expressed in vivo by analyzing human nasal metatranscriptomes from the NIH Human Microbiome Project. Together, our results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness.IMPORTANCE Within the nasal cavity, interference competition through antimicrobial production is prevalent. For instance, nasal Staphylococcus species strains can inhibit the growth of other bacteria through the production of nonribosomal peptides and ribosomally synthesized and posttranslationally modified peptides. In contrast, bacteria engaging in exploitation competition modify the external environment to prevent competitors from growing, usually by hindering access to or depleting essential nutrients. As the nasal cavity is a nutrient-limited environment, we hypothesized that exploitation competition occurs in this system. We determined that Corynebacterium propinquum produces an iron-chelating siderophore, and this iron-sequestering molecule correlates with the ability to inhibit the growth of coagulase-negative staphylococci. Furthermore, we found that the genes required for siderophore production are expressed in vivo Thus, although siderophore production by bacteria is often considered a virulence trait, our work indicates that bacteria may produce siderophores to compete for limited iron in the human nasal cavity.}, }
@article {pmid30577530, year = {2018}, author = {Yang, AJ and Marito, S and Yang, JJ and Keshari, S and Chew, CH and Chen, CC and Huang, CM}, title = {A Microtube Array Membrane (MTAM) Encapsulated Live Fermenting Staphylococcus epidermidis as a Skin Probiotic Patch against Cutibacterium acnes.}, journal = {International journal of molecular sciences}, volume = {20}, number = {1}, pages = {}, pmid = {30577530}, issn = {1422-0067}, support = {106-2320-B-008, 105-2314-B-008-001, 101-2221-E-038-009-, 107-2314-B-008 -001, 107-2622-B-008-002-CC1 and 106/107-2622-B-008-001-CC1//Ministry of Science and Technology, Taiwan/ ; NHRI-EX106-10607SI//NHRI/ ; }, mesh = {Animals ; *Antibiosis ; Chemokine CXCL2/metabolism ; Dermatitis/metabolism/microbiology ; Fermentation ; Glycerol/metabolism ; Humans ; Mice ; *Probiotics ; Propionibacteriaceae/*physiology ; Skin/*microbiology ; Staphylococcus epidermidis/*physiology ; }, abstract = {Antibiotics without selectivity for acne treatment may destroy the beneficial microbes in the human microbiome that helps to fight Cutibacterium acnes (C. acnes), a bacterium associated with inflammatory acne vulgaris. Probiotic treatment by direct application of live Staphylococcus epidermidis (S. epidermidis) onto the open acne lesions may run the risk of bloodstream infections. Here, we fabricated the polysulfone microtube array membranes (PSF MTAM) to encapsulate probiotic S.epidermidis. We demonstrate that the application of the encapsulation of S.epidermidis in PSF MTAM enhanced the glycerol fermentation activities of S. epidermidis. To mimic the granulomatous type of acne inflammatory acne vulgaris, the ears of mice were injected intradermally with C.acnes to induce the secretion of macrophage inflammatory protein-2 (MIP-2), a murine counterpart of human interleukin (IL)-8. The C. acnes-injected mouse ears were covered with a PST MTAM encapsulated with or without S.epidermidis in the presence of glycerol. The application of S.epidermidis-encapsulated PST MTAM plus glycerol onto the C.acnes-injected mouse ears considerably reduced the growth of C. acnes and the production of MIP-2. Furthermore, no S. epidermidis leaked from PSF MTAM into mouse skin. The S. epidermidis-encapsulated PST MTAM functions as a probiotic acne patch.}, }
@article {pmid30575732, year = {2018}, author = {Coryell, M and McAlpine, M and Pinkham, NV and McDermott, TR and Walk, ST}, title = {The gut microbiome is required for full protection against acute arsenic toxicity in mouse models.}, journal = {Nature communications}, volume = {9}, number = {1}, pages = {5424}, pmid = {30575732}, issn = {2041-1723}, support = {F31 ES026884/ES/NIEHS NIH HHS/United States ; R01 CA215784/CA/NCI NIH HHS/United States ; R21 ES026411/ES/NIEHS NIH HHS/United States ; }, mesh = {Adult ; Animals ; Arsenic/metabolism ; Arsenic Poisoning/*prevention &amp; control ; Faecalibacterium prausnitzii/*physiology ; *Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; *Germ-Free Life ; Humans ; Inactivation, Metabolic ; Male ; Methyltransferases/physiology ; Mice, Inbred C57BL ; Mice, Transgenic ; Young Adult ; }, abstract = {Arsenic poisons an estimated 200 million people worldwide through contaminated food and drinking water. Confusingly, the gut microbiome has been suggested to both mitigate and exacerbate arsenic toxicity. Here, we show that the microbiome protects mice from arsenic-induced mortality. Both antibiotic-treated and germ-free mice excrete less arsenic in stool and accumulate more arsenic in organs compared to control mice. Mice lacking the primary arsenic detoxification enzyme (As3mt) are hypersensitive to arsenic after antibiotic treatment or when derived germ-free, compared to wild-type and/or conventional counterparts. Human microbiome (stool) transplants protect germ-free As3mt-KO mice from arsenic-induced mortality, but protection depends on microbiome stability and the presence of specific bacteria, including Faecalibacterium. Our results demonstrate that both a functional As3mt and specific microbiome members are required for protection against acute arsenic toxicity in mouse models. We anticipate that the gut microbiome will become an important explanatory factor of disease (arsenicosis) penetrance in humans, and a novel target for prevention and treatment strategies.}, }
@article {pmid30573380, year = {2019}, author = {Altomare, A and Putignani, L and Del Chierico, F and Cocca, S and Angeletti, S and Ciccozzi, M and Tripiciano, C and Dalla Piccola, B and Cicala, M and Guarino, MPL}, title = {Gut mucosal-associated microbiota better discloses inflammatory bowel disease differential patterns than faecal microbiota.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {51}, number = {5}, pages = {648-656}, doi = {10.1016/j.dld.2018.11.021}, pmid = {30573380}, issn = {1878-3562}, mesh = {Bacteria/*classification ; Case-Control Studies ; Colon/pathology ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Intestinal Mucosa/*microbiology/pathology ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Growing evidence supports the potential role of intestinal microbiota in the pathophysiology of inflammatory bowel diseases (IBD) even if the literature does not reveal uniform alterations. The aim of the study was to evaluate the mucosal (MM) and faecal microbiota (FM) composition in a cohort of IBD patients compared to healthy controls (CTRLs).<br><br>METHODS: Faecal and mucosal samples were collected from 14 IBD patients and 11 CTRLs. The V1-V3 region of 16S rRNA locus was amplified on a 454-Junior Genome Sequencer. Reads were grouped into operational taxonomic units (OTUs) at a sequence similarity level of 97% for taxonomic assignment, and aligned for OTUs matching against Greengenes database.<br><br>RESULTS: Irrespective of disease localization and activity, in the MM of IBD patients a statistically significant increase of Proteobacteria (especially Enterobacteriaceae, Acidaminococcus, Veillonella dispar) and decrease of Firmicutes (especially Roseburia and Faecalibacterium prausnitzii) and Actinobacteria was found compared to CTRLs. In the colon district some specific bacterial biomarkers were identified: Enterobacteriaceae for IBD stools, Bacteroides for IBD biopsies, Mogibacteriaceae, Ruminococcaceae and Prevotella for CTRL stools, Ruminococcaceae for CTRL biopsies.<br><br>CONCLUSIONS: The profiles of FM were more similar to CTRLs, suggesting that microbiota adhering to the gut mucosa better discriminates patients from controls, with the identification of some interesting biomarkers.}, }
@article {pmid30572622, year = {2018}, author = {Sánchez-Ponce, Y and Varela-Fascinetto, G and Romo-Vázquez, JC and López-Martínez, B and Sánchez-Huerta, JL and Parra-Ortega, I and Fuentes-Pananá, EM and Morales-Sánchez, A}, title = {Simultaneous Detection of Beta and Gamma Human Herpesviruses by Multiplex qPCR Reveals Simple Infection and Coinfection Episodes Increasing Risk for Graft Rejection in Solid Organ Transplantation.}, journal = {Viruses}, volume = {10}, number = {12}, pages = {}, pmid = {30572622}, issn = {1999-4915}, mesh = {Adolescent ; Child ; Coinfection/*diagnosis/virology ; DNA Primers/genetics ; DNA, Viral/blood ; Epstein-Barr Virus Infections/*diagnosis/virology ; Female ; Graft Rejection/*etiology/virology ; Herpesvirus 4, Human/genetics ; Herpesvirus 6, Human/genetics ; Herpesvirus 7, Human/genetics ; Humans ; Male ; Multiplex Polymerase Chain Reaction ; Organ Transplantation/*adverse effects ; Prospective Studies ; Roseolovirus Infections/*diagnosis/virology ; Sensitivity and Specificity ; Viral Load ; }, abstract = {Herpesviruses are common components of the human microbiome that become clinically relevant when a competent immunosurveillance is compromised, such as in transplantation. Members of the beta and gamma subfamilies are associated with a wide diversity of pathologies, including end-organ disease and cancer. In this study, we developed a multiplex qPCR technique with high specificity, sensitivity, efficiency and predictability that allowed the simultaneous detection and quantification of beta and gamma human herpesviruses. The technique was tested in a cohort of 34 kidney- or liver-transplanted pediatric patients followed up for up to 12 months post-transplant. Viral load was determined in 495 leukocyte-plasma paired samples collected bi-weekly or monthly. Human herpesvirus (HHV) 7 was the herpesvirus most frequently found in positive samples (39%), followed by Epstein-Barr virus (EBV) (20%). Also, EBV and HHV7 were present in the majority of coinfection episodes (62%). The share of positive samples exclusively detected either in leukocytes or plasma was 85%, suggesting that these herpesviruses tended to take a latent or lytic path in an exclusive manner. Infection by human cytomegalovirus (HCMV) and HHV6, as well as coinfection by EBV/HHV7 and EBV/HHV6/HHV7, were associated with graft rejection (RR = 40.33 (p = 0.0013), 5.60 (p = 0.03), 5.60 (p = 0.03) and 17.64 (p = 0.0003), respectively). The routine monitoring of beta and gamma herpesviruses should be mandatory in transplant centers to implement preventive strategies.}, }
@article {pmid30564562, year = {2018}, author = {Proal, A and Marshall, T}, title = {Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity.}, journal = {Frontiers in pediatrics}, volume = {6}, number = {}, pages = {373}, pmid = {30564562}, issn = {2296-2360}, abstract = {The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.}, }
@article {pmid30559213, year = {2018}, author = {Tedijanto, C and Olesen, SW and Grad, YH and Lipsitch, M}, title = {Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {E11988-E11995}, pmid = {30559213}, issn = {1091-6490}, support = {R01 AI132606/AI/NIAID NIH HHS/United States ; U01 CK000538/CK/NCEZID CDC HHS/United States ; U01CK000538//ACL HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Anti-Bacterial Agents/immunology/*pharmacology ; Bacteria/classification/*drug effects/immunology ; Child ; Child, Preschool ; Drug Resistance, Bacterial/*drug effects/immunology ; Escherichia coli/drug effects ; Humans ; Infant ; Infant, Newborn ; Microbial Sensitivity Tests/methods ; Microbiota/*drug effects/immunology ; Pneumococcal Infections ; Pneumococcal Vaccines/immunology ; Species Specificity ; Staphylococcus aureus/drug effects ; Streptococcus pneumoniae/drug effects ; United States ; Vaccination ; Vaccines, Conjugate/immunology ; Young Adult ; }, abstract = {Bystander selection-the selective pressure for resistance exerted by antibiotics on microbes that are not the target pathogen of treatment-is critical to understanding the total impact of broad-spectrum antibiotic use on pathogenic bacterial species that are often carried asymptomatically. However, to our knowledge, this effect has never been quantified. We quantify bystander selection for resistance for a range of clinically relevant antibiotic-species pairs as the proportion of all antibiotic exposures received by a species for conditions in which that species was not the causative pathogen (&quot;proportion of bystander exposures&quot;). Data sources include the 2010-2011 National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey, the Human Microbiome Project, and additional carriage and etiological data from existing literature. For outpatient prescribing in the United States, we find that this proportion over all included antibiotic classes is over 80% for eight of nine organisms of interest. Low proportions of bystander exposure are often associated with infrequent bacterial carriage or concentrated prescribing of a particular antibiotic for conditions caused by the species of interest. Applying our results, we roughly estimate that pneumococcal conjugate vaccination programs result in nearly the same proportional reduction in total antibiotic exposures of Streptococcus pneumoniae, Staphylococcus aureus, and Escherichia coli, despite the latter two organisms not being targeted by the vaccine. These results underscore the importance of considering antibiotic exposures of bystanders, in addition to the target pathogen, in measuring the impact of antibiotic resistance interventions.}, }
@article {pmid30559176, year = {2018}, author = {Relman, DA and Lipsitch, M}, title = {Microbiome as a tool and a target in the effort to address antimicrobial resistance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {115}, number = {51}, pages = {12902-12910}, pmid = {30559176}, issn = {1091-6490}, support = {R01 AI112401/AI/NIAID NIH HHS/United States ; R01 GM099534/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Infective Agents/*pharmacology ; Communicable Disease Control/*methods ; Communicable Diseases/drug therapy ; Drug Resistance, Microbial/*drug effects/genetics ; Host Microbial Interactions/drug effects/genetics/immunology ; Humans ; Microbiota/*drug effects ; Vaccines/*therapeutic use ; }, abstract = {Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.}, }
@article {pmid30551740, year = {2018}, author = {Romani, L and Pane, S and Severini, C and Menegon, M and Foglietta, G and Bernardi, S and Tchidjou, HK and Onetti Muda, A and Palma, P and Putignani, L}, title = {Challenging diagnosis of congenital malaria in non-endemic areas.}, journal = {Malaria journal}, volume = {17}, number = {1}, pages = {470}, pmid = {30551740}, issn = {1475-2875}, support = {RC2018//Bambino Gesù Children's Hospital/ ; }, mesh = {Communicable Diseases, Imported/*diagnosis/parasitology ; Fetal Diseases/*diagnosis/parasitology ; Humans ; Infant ; Italy ; Malaria, Falciparum/*diagnosis/epidemiology ; Male ; Plasmodium falciparum/isolation &amp; purification ; Polymerase Chain Reaction ; }, abstract = {BACKGROUND: Congenital malaria is usually defined as the detection of asexual forms of Plasmodium spp. in a blood sample of a neonate during perinatal age if there is no possibility of postpartum infection by a mosquito bite. The incidence of congenital malaria is highly variable and seems related to several factors, such as different diagnostic methods for Plasmodium spp. detection, and area in which the epidemiologic analyses are performed. In non-endemic countries, cases of congenital malaria are rare. Hereby, a case of a congenital malaria in an HIV exposed child is reported.<br><br>CASE PRESENTATION: A 2-month-old male child was admitted to Bambino Gesù Children's Hospital due to anaemia and exposure to HIV. He was born prematurely in Italy by cesarean section at 34 weeks' gestation after a bicorial, biamniotic pregnancy by a migrant woman from Nigeria. He was the first of non-identical twins. Combined with anaemia, spleen and liver enlargement was noted, malaria was hypothesized. Malaria laboratory panel was performed on the newborn, mother and other twin blood samples, as follows: (i) malaria rapid diagnostic test (RDT); (ii) Giemsa-stained thick and thin blood smears for Plasmodium spp. identification and parasitaemia titration; (iii) molecular screening and typing of Plasmodium spp. by multiplex qualitative PCR assay based on 18S rRNA gene. Genotyping of Plasmodium falciparum isolates from mother and child was performed by neutral microsatellite and highly polymorphic marker amplification.<br><br>CONCLUSIONS: The maternal RDT sample was negative, while the infant RDT was positive; in both cases microscopy of blood smears and PCR showed infection with P. falciparum. Two of the genotypic molecular markers displayed different allelic variants between the two samples. This difference could imply infection multiplicity of the mother during the pregnancy, possibly harbouring more than one isolate, only one of them being transmitted to the newborn while the other persisting in the mother's blood. Because of the increasing number of pregnant women coming from endemic areas for malaria, an accurate anamnesis of infant's mother, and the inclusion of Plasmodium spp. research into TORCH screenings for mother-infant pair at birth, aiming at reducing morbidity and mortality associated to the disease might be suitable.}, }
@article {pmid30544936, year = {2018}, author = {D'Argenio, V}, title = {The Prenatal Microbiome: A New Player for Human Health.}, journal = {High-throughput}, volume = {7}, number = {4}, pages = {}, pmid = {30544936}, issn = {2571-5135}, abstract = {The last few years have featured an increasing interest in the study of the human microbiome and its correlations with health status. Indeed, technological advances have allowed the study of microbial communities to reach a previously unthinkable sensitivity, showing the presence of microbes also in environments usually considered as sterile. In this scenario, microbial communities have been described in the amniotic fluid, the umbilical blood cord, and the placenta, denying a dogma of reproductive medicine that considers the uterus like a sterile womb. This prenatal microbiome may play a role not only in fetal development but also in the predisposition to diseases that may develop later in life, and also in adulthood. Thus, the aim of this review is to report the current knowledge regarding the prenatal microbiome composition, its association with pathological processes, and the future perspectives regarding its manipulation for healthy status promotion and maintenance.}, }
@article {pmid30524957, year = {2018}, author = {Yang, J and Mu, X and Wang, Y and Zhu, D and Zhang, J and Liang, C and Chen, B and Wang, J and Zhao, C and Zuo, Z and Heng, X and Zhang, C and Zhang, L}, title = {Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers.}, journal = {Frontiers in oncology}, volume = {8}, number = {}, pages = {520}, pmid = {30524957}, issn = {2234-943X}, abstract = {Background: Association between oral bacteria and increased risk of lung cancer have been reported in several previous studies, however, the potential association between salivary microbiome and lung cancer in non-smoking women have not been evaluated. There is also no report on the relationship between immunocytochemistry markers and salivary microbiota. Method: In this study, we assessed the salivary microbiome of 75 non-smoking female lung cancer patients and 172 matched healthy individuals using 16S rRNA gene amplicon sequencing. We also calculated the Spearman's rank correlation coefficient between salivary microbiota and three immunohistochemical markers (TTF-1, Napsin A and CK7). Result: We analyzed the salivary microbiota of 247 subjects and found that non-smoking female lung cancer patients exhibited oral microbial dysbiosis. There was significantly lower microbial diversity and richness in lung cancer patients when compared to the control group (Shannon index, P < 0.01; Ace index, P < 0.0001). Based on the analysis of similarities, the composition of the microbiota in lung cancer patients also differed from that of the control group (r = 0.454, P < 0.001, unweighted UniFrac; r = 0.113, P < 0.01, weighted UniFrac). The bacterial genera Sphingomonas (P < 0.05) and Blastomonas (P < 0.0001) were relatively higher in non-smoking female lung cancer patients, whereas Acinetobacter (P < 0.001) and Streptococcus (P < 0.01) were higher in controls. Based on Spearman's correlation analysis, a significantly positive correlation can be observed between CK7 and Enterobacteriaceae (r = 0.223, P < 0.05). At the same time, Napsin A was positively associated with genera Blastomonas (r = 0.251, P < 0.05). TTF-1 exhibited a significantly positive correlation with Enterobacteriaceae (r = 0.262, P < 0.05). Functional analysis from inferred metagenomes indicated that oral microbiome in non-smoking female lung cancer patients were related to cancer pathways, p53 signaling pathway, apoptosis and tuberculosis. Conclusions: The study identified distinct salivary microbiome profiles in non-smoking female lung cancer patients, revealed potential correlations between salivary microbiome and immunocytochemistry markers used in clinical diagnostics, and provided proof that salivary microbiota can be an informative source for discovering non-invasive lung cancer biomarkers.}, }
@article {pmid30534599, year = {2018}, author = {Escapa, IF and Chen, T and Huang, Y and Gajare, P and Dewhirst, FE and Lemon, KP}, title = {New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract.}, journal = {mSystems}, volume = {3}, number = {6}, pages = {}, pmid = {30534599}, issn = {2379-5077}, support = {R01 AI101018/AI/NIAID NIH HHS/United States ; R01 DE024468/DE/NIDCR NIH HHS/United States ; R37 DE016937/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; }, abstract = {The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.}, }
@article {pmid30532649, year = {2018}, author = {Lim, MY and Cho, Y and Rho, M}, title = {Diverse Distribution of Resistomes in the Human and Environmental Microbiomes.}, journal = {Current genomics}, volume = {19}, number = {8}, pages = {701-711}, pmid = {30532649}, issn = {1389-2029}, abstract = {The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.}, }
@article {pmid30530088, year = {2019}, author = {Ben, Y and Fu, C and Hu, M and Liu, L and Wong, MH and Zheng, C}, title = {Human health risk assessment of antibiotic resistance associated with antibiotic residues in the environment: A review.}, journal = {Environmental research}, volume = {169}, number = {}, pages = {483-493}, doi = {10.1016/j.envres.2018.11.040}, pmid = {30530088}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents ; *Bacteria ; *Drug Resistance, Microbial ; Humans ; Risk Assessment ; }, abstract = {The extensive use of antibiotics leading to the rapid spread of antibiotic resistance poses high health risks to humans, but to date there is still lack of a quantitative model to properly assess the risks. Concerns over the health risk of antibiotic residues in the environment are mainly (1) the potential hazard of ingested antibiotic residues in the environment altering the human microbiome and promoting emergence and selection for bacteria resistance inhabiting the human body, and (2) the potential hazard of creating a selection pressure on environmental microbiome and leading to reservoirs of antibiotic resistance in the environment. We provide a holistic view of health risk assessment of antibiotic resistance associated with antibiotic residues in the environment in contrast with that of the antibiotic resistant bacteria and discuss the main knowledge gaps and the future research that should be prioritized to achieve the quantitative risk assessment. We examined and summarized the available data and information on the four core elements of antibiotic resistance associated with antibiotic residues in the environment: hazard identification, exposure assessment, dose-response assessment, and risk characterization. The data required to characterize the risks of antibiotic residues in the environment is severely limited. The main future research needs have been identified to enable better assessments of antibiotic resistance associated with antibiotic residues in the environment: (1) establishment of a standardized monitoring guide of antibiotic residues and antibiotic resistance in the environment, (2) derivation of the relationship between antibiotic levels and pathogenic antibiotic-resistance development in different settings, and (3) establishment of the dose-response relationship between pathogenic antibiotic resistant bacteria and various infection diseases. After identification of key risk determinant parameters, we propose a conceptual framework of human health risk assessments of antibiotic residues in the environment. CAPSULE: A holistic view of human health risk assessment of antibiotic residues in the environment was provided.}, }
@article {pmid30529020, year = {2019}, author = {Robertson, RC and Manges, AR and Finlay, BB and Prendergast, AJ}, title = {The Human Microbiome and Child Growth - First 1000 Days and Beyond.}, journal = {Trends in microbiology}, volume = {27}, number = {2}, pages = {131-147}, doi = {10.1016/j.tim.2018.09.008}, pmid = {30529020}, issn = {1878-4380}, support = {108065/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 206455/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; MR/M007367/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Bacteria/classification ; Child, Preschool ; Environment ; Female ; Gastrointestinal Microbiome/immunology/physiology ; Gastrointestinal Tract/*microbiology ; Growth and Development/immunology/*physiology ; *Host Microbial Interactions/immunology/physiology ; Humans ; Infant ; Infant, Newborn ; Infections ; Malnutrition ; *Microbiota/immunology/physiology ; Pregnancy ; }, abstract = {The assembly of microbial communities within the gastrointestinal tract during early life plays a critical role in immune, endocrine, metabolic, and other host developmental pathways. Environmental insults during this period, such as food insecurity and infections, can disrupt this optimal microbial succession, which may contribute to lifelong and intergenerational deficits in growth and development. Here, we review the human microbiome in the first 1000 days - referring to the period from conception to 2 years of age - and using a developmental model, we examine the role of early microbial succession in growth and development. We propose that an 'undernourished' microbiome is intergenerational, thereby perpetuating growth impairments into successive generations. We also identify and discuss the intertwining host-microbe-environment interactions occurring prenatally and during early infancy, which may impair the trajectories of healthy growth and development, and explore their potential as novel microbial targets for intervention.}, }
@article {pmid30526758, year = {2018}, author = {Blaser, MJ}, title = {Our missing microbes: Short-term antibiotic courses have long-term consequences.}, journal = {Cleveland Clinic journal of medicine}, volume = {85}, number = {12}, pages = {928-930}, doi = {10.3949/ccjm.85gr.18005}, pmid = {30526758}, issn = {1939-2869}, mesh = {Anti-Bacterial Agents/*adverse effects ; Humans ; Long Term Adverse Effects/*chemically induced/microbiology ; Microbiota/*drug effects ; }, }
@article {pmid30521647, year = {2018}, author = {Jeżewska-Frąckowiak, J and Seroczyńska, K and Banaszczyk, J and Jedrzejczak, G and Żylicz-Stachula, A and Skowron, PM}, title = {The promises and risks of probiotic Bacillus species.}, journal = {Acta biochimica Polonica}, volume = {65}, number = {4}, pages = {509-519}, doi = {10.18388/abp.2018_2652}, pmid = {30521647}, issn = {1734-154X}, mesh = {Bacillus/classification/genetics/*physiology ; Biofilms ; Drug Resistance, Bacterial ; Gastrointestinal Diseases/*microbiology/*prevention &amp; control ; *Gastrointestinal Microbiome ; Humans ; Probiotics/*administration &amp; dosage/*adverse effects/standards ; RNA, Ribosomal, 16S/genetics ; Risk ; }, abstract = {Supplementing the human microbiome