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19 Apr 2021 at 01:34
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Bibliography on: Microbiome


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RJR: Recommended Bibliography 19 Apr 2021 at 01:34 Created: 


It has long been known that every multicellular organism coexists with large prokaryotic ecosystems — microbiomes — that completely cover its surfaces, external and internal. Recent studies have shown that these associated microbiomes are not mere contamination, but instead have profound effects upon the function and fitness of the multicellular organism. We now know that all MCEs are actually functional composites, holobionts, composed of more prokaryotic cells than eukaryotic cells and expressing more prokaryotic genes than eukaryotic genes. A full understanding of the biology of "individual" eukaryotes will now depend on an understanding of their associated microbiomes.

Created with PubMed® Query: microbiome[tiab] NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-04-17

Rimkus A, Gudrā D, Dubova L, et al (2021)

Stimulation of sewage sludge treatment by carbon sources and bioaugmentation with a sludge-derived microbial consortium.

The Science of the total environment, 783:146989 pii:S0048-9697(21)02059-3 [Epub ahead of print].

Recently, sewage sludge (SS) disposal has become one of the greatest global challenges. In this study, we aimed to evaluate the effect of faba bean straw (Straw-B), wheat straw (Straw-W), and wood-chip pellets (WCP) amended to SS, as well as bioaugmentation (BA), on the physicochemical characteristics and structure of the microbial community of the treated SS. Sixteen days of incubation of SS-containing mixtures revealed the highest efficiency of Straw-W(BA) in terms of SS stabilisation, i.e., the highest and most stable respiration intensity, the lowest ammonia emission, and the highest stimulation effect on the cress seedling growth. Shotgun sequencing data analysis showed that Proteobacteria dominated in the raw SS with 60.17% reads, which consisted of 16.40%, 29.18%, and 12.33% of Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, respectively. All treated samples were characterised by an increased abundance of Firmicutes (32.70-53.84%). A remarkable increase in virus abundance (0.34% reads) was detected in the treated SS, which was incubated without C amendment and bioaugmentation. The addition of C sources to the SS changed some physicochemical characteristics of the mixture. All of these findings provide novel insights toward a mechanistic understanding of the fate of the human sewage microbiome in wastewater and other environments.

RevDate: 2021-04-17

Jia Y, Niu CT, Zheng FY, et al (2021)

Development of a defined autochthonous starter through dissecting the seasonal microbiome of broad bean paste.

Food chemistry, 357:129625 pii:S0308-8146(21)00631-2 [Epub ahead of print].

Bean-based fermentation foods are usually ripened in open environment, which would lead to inconsistencies in flavor and quality between batches. The physicochemical metabolism and microbial community of seasonal broad bean paste (BBP) were compared to distinguish discriminant metabolites and unique taxa, as well as their specific reasons for different flavor and quality in this study. Here, we found that environmental variables led to the seasonal distribution of microbiota, and differential microorganisms further contributed to the inconsistency of flavor quality, in which Lactobacillales was responsible for the higher titratable acid and amino acid nitrogen concentration in winter pei, while Saccharomycetales benefited the formation of volatile flavor substances in autumn pei. Additionally, we compared the effect of different combinations of Lactobacillales with Zygosaccharomyces rouxii on the quality of BBP, and found that W. confusa was more suitable for BBP fermentation rather than T. halophilus in terms of sensory characteristics and physicochemical metabolites.

RevDate: 2021-04-17

Tavasolian F, RD Inman (2021)

Gut microbiota-microRNA interactions in ankylosing spondylitis.

Autoimmunity reviews pii:S1568-9972(21)00099-9 [Epub ahead of print].

Ankylosing spondylitis (AS) is a chronic autoimmune inflammatory disability that is part of the rheumatic disease group of spondyloarthropathies. AS commonly influences the joints of the axial skeleton. The contributions to AS pathogenesis of genetic susceptibility (particularly HLA-B27 and ERAP-1) and epigenetic modifications, like non-coding RNAs, as well as environmental factors, have been investigated over the last few years. But the fundamental etiology of AS remains elusive to date. The evidence summarized here indicates that in the immunopathogenesis of AS, microRNAs and the gut microbiome perform critical functions. We discuss significant advances in the immunological mechanisms underlying AS and address potential cross-talk between the gut microbiome and host microRNAs. This critical interaction implicates a co-evolutionary symbiotic link between host immunity and the gut microbiome.

RevDate: 2021-04-17

Qiang W, Xuan H, Yu S, et al (2021)

Impact of the gut microbiota on heat stroke rat mediated by Xuebijing metabolism.

Microbial pathogenesis pii:S0882-4010(21)00133-9 [Epub ahead of print].

The goal of the present study was to evaluate the fecal microbiome and serum metabolites in Xuebijing (XBJ)-injected rats after heat stroke using 16S rRNA gene sequencing and gas chromatography-mass spectrometry (GC-MS) metabolomics. Eighteen rats were divided into the control group (CON), heat stroke group (HS), and XBJ group. The 16S rRNA gene sequencing results revealed that the abundance of Bacteroidetes was overrepresented in the XBJ group compared to the HS group, while Actinobacteria was underrepresented. Metabolomic profiling showed that the pyrimidine metabolism pathway, pentose phosphate pathway, and glycerophospholipid metabolism pathway were upregulated in the XBJ group compared to the HS group. Taken together, these results demonstrated that heat stroke not only altered the gut microbiome community structure of rats but also greatly affected metabolic functions, leading to gut microbiome toxicity.

RevDate: 2021-04-17

Oka A, Kidoguchi M, Kariya S, et al (2021)

Role of salivary microbiome in IL-10 production and efficacy of sublingual immunotherapy.

RevDate: 2021-04-17

Li R, Boer CG, Oei L, et al (2021)

The Gut Microbiome: a New Frontier in Musculoskeletal Research.

Current osteoporosis reports [Epub ahead of print].

PURPOSE OF THE REVIEW: The human gut harbors a complex community of microbes that influence many processes regulating musculoskeletal development and homeostasis. This review gives an update on the current knowledge surrounding the impact of the gut microbiota on musculoskeletal health, with an emphasis on research conducted over the last three years.

RECENT FINDINGS: The gut microbiota and their metabolites are associated with sarcopenia, osteoporosis, osteoarthritis, and rheumatoid arthritis. The field is moving fast from describing simple correlations to pursue establishing causation through clinical trials. The gut microbiota and their microbial-synthesized metabolites hold promise for offering new potential alternatives for the prevention and treatment of musculoskeletal diseases given its malleability and response to environmental stimuli.

RevDate: 2021-04-17

Fadlelmola FM, Ghedira K, Hamdi Y, et al (2021)

H3ABioNet genomic medicine and microbiome data portals hackathon proceedings.

Database : the journal of biological databases and curation, 2021:.

African genomic medicine and microbiome datasets are usually not well characterized in terms of their origin, making it difficult to find and extract data for specific African ethnic groups or even countries. The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized the need for developing data portals for African genomic medicine and African microbiomes to address this and ran a hackathon to initiate their development. The two portals were designed and significant progress was made in their development during the hackathon. All the participants worked in a very synergistic and collaborative atmosphere in order to achieve the hackathon's goals. The participants were divided into content and technical teams and worked over a period of 6 days. In response to one of the survey questions of what the participants liked the most during the hackathon, 55% of the hackathon participants highlighted the familial and friendly atmosphere, the team work and the diversity of team members and their expertise. This paper describes the preparations for the portals hackathon and the interaction between the participants and reflects upon the lessons learned about its impact on successfully developing the two data portals as well as building scientific expertise of younger African researchers. Database URL: The code for developing the two portals was made publicly available in GitHub repositories: [https://github.com/codemeleon/Database; https://github.com/codemeleon/AfricanMicrobiomePortal].

RevDate: 2021-04-17

Li R, Meng X, Chen B, et al (2021)

Gut Microbiota in Lupus: a Butterfly Effect?.

Current rheumatology reports, 23(4):27.

PURPOSE OF REVIEW: Systemic lupus erythematosus (SLE) is a prototypic autoimmune disease that typically displays chronic inflammatory tissue damage and miscellaneous circulatory autoantibodies, as well as distinctive type 1 interferon signatures. The etiology of SLE is unclear and currently is attributed to genetic predisposition and environmental triggers. Gut microbiota has recently been considered a critical environmental pathogenic factor in immune-related disorders, and studies are ongoing to uncover the key pathogens and the imputative mechanisms. Fundamental advancements on the role of the microbiota in SLE pathology have been achieved in recent years and are summarized in this review.

RECENT FINDINGS: Recent findings suggested that gut commensals could propagate autoimmunity via molecular mimicry in which ortholog-carrying microbes cross-activate autoreactive T/B cells and trigger the response against host autoantigens, or via bystander activation by stimulating antigen-presenting cells that present autoantigens and enhancing the expression of co-stimulatory molecules and cytokines, thus leading to the loss of self-tolerance and the production of autoantibodies. Additionally, the break of gut barrier and the translocation of gut commensals to inner organs can trigger immune dysregulation and inappropriate systemic inflammation. All these microbiota-mediated mechanisms could contribute to lupus immunopathogenesis and promote disease development in susceptible individuals. Evidence of the causative role of disturbed gut microbiome in SLE is still limited, and the related molecular mechanisms and pathways are largely elusive. However, the modification of gut microbiota, such as pathobiont vaccine, special diet, restricted consortium transplantation, as well as regulatory metabolites supplementation, might be promising strategies for lupus prophylaxis and treatment.

RevDate: 2021-04-17

Zipkin M (2021)

Fecal microbiota potentiate checkpoint inhibitors, unleash microbiome startups.

RevDate: 2021-04-17

Afroz KF, Reyes N, Young K, et al (2021)

Altered gut microbiome and autism like behavior are associated with parental high salt diet in male mice.

Scientific reports, 11(1):8364.

Neurodevelopmental disorders are conditions caused by the abnormal development of the central nervous system. Autism spectrum disorder (ASD) is currently the most common form of such disorders, affecting 1% of the population worldwide. Despite its prevalence, the mechanisms underlying ASD are not fully known. Recent studies have suggested that the maternal gut microbiome can have profound effects on neurodevelopment. Considering that the gut microbial composition is modulated by diet, we tested the hypothesis that ASD-like behavior could be linked to maternal diet and its associated gut dysbiosis. Therefore, we used a mouse model of parental high salt diet (HSD), and specifically evaluated social and exploratory behaviors in their control-fed offspring. Using 16S genome sequencing of fecal samples, we first show that (1) as expected, HSD changed the maternal gut microbiome, and (2) this altered gut microbiome was shared with the offspring. More importantly, behavioral analysis of the offspring showed hyperactivity, increased repetitive behaviors, and impaired sociability in adult male mice from HSD-fed parents. Taken together, our data suggests that parental HSD consumption is strongly associated with offspring ASD-like behavioral abnormalities via changes in gut microbiome.

RevDate: 2021-04-17

Li X, Su C, Jiang Z, et al (2021)

Berberine attenuates choline-induced atherosclerosis by inhibiting trimethylamine and trimethylamine-N-oxide production via manipulating the gut microbiome.

NPJ biofilms and microbiomes, 7(1):36.

Trimethylamine-N-oxide (TMAO), a derivative from the gut microbiota metabolite trimethylamine (TMA), has been identified to be an independent risk factor for promoting atherosclerosis. Evidences suggest that berberine (BBR) could be used to treat obesity, diabetes and atherosclerosis, however, its mechanism is not clear mainly because of its poor oral bioavailability. Here, we show that BBR attenuated TMA/TMAO production in the C57BL/6J and ApoE KO mice fed with choline-supplemented chow diet, and mitigated atherosclerotic lesion areas in ApoE KO mice. Inhibition of TMA/TMAO production by BBR-modulated gut microbiota was proved by a single-dose administration of d9-choline in vivo. Metagenomic analysis of cecal contents demonstrated that BBR altered gut microbiota composition, microbiome functionality, and cutC/cntA gene abundance. Furthermore, BBR was shown to inhibit choline-to-TMA conversion in TMA-producing bacteria in vitro and in gut microbial consortium from fecal samples of choline-fed mice and human volunteers, and the result was confirmed by transplantation of TMA-producing bacteria in mice. These results offer new insights into the mechanisms responsible for the anti-atherosclerosis effects of BBR, which inhibits commensal microbial TMA production via gut microbiota remodeling.

RevDate: 2021-04-17

Ashrafi M, Kuhn KA, MH Weisman (2021)

The arthritis connection to inflammatory bowel disease (IBD): why has it taken so long to understand it?.

RMD open, 7(1):.

Inflammatory bowel disease (IBD) associated arthritis is a subgroup of spondyloarthritis (SpA) that has suffered from lack of recognition in rheumatology clinical and research circles for over 100 years. Although clinically distinguishable from rheumatoid arthritis and ankylosing spondylitis, it took advances in detection systems in the middle of the last century (rheumatoid factor, HLA-B27) to convincingly make the final separations. We now know that significant numbers of patients with SpA have associated clinical IBD and almost half of them show subclinical gut inflammation, yet the connection between the gut and the musculoskeletal system has remained a vexing problem. Two publications from Nathan Zvaifler (one in 1960, the other in 1975) presciently described the relationship between the gut and the spine/peripheral joints heralding much of the work present today in laboratories around the world trying to examine basic mechanisms for the connections (there are likely to be many) between the gut, the environment (presumably our intestinal flora) and the downstream effect on the musculoskeletal system. The role of dysregulated microbiome along with microbiome-driven T helper 17 cell expansion and immune cell migration to the joints has been recognised, all of which occur in the appropriate context of genetic background inside and outside of the human leucocyte antigen system. Moreover, different adhesion molecules that mediate immune cells homing to the gut and joints have been noted. In this review, we studied the origins and evolution of IBD-arthritis, proposed pathogenic mechanisms and the current gaps that need to be filled for a complete understanding of IBD-arthritis.

RevDate: 2021-04-17

Chen L, Zhai Y, Wang Y, et al (2021)

Altering the microbiome inhibits tumorigenesis in a mouse model of oviductal high-grade serous carcinoma.

Cancer research pii:0008-5472.CAN-21-0106 [Epub ahead of print].

Studies have shown bacteria influence the initiation and progression of cancers arising in sites that harbor rich microbial communities, such as the colon. Little is known about the potential for the microbiome to influence tumorigenesis at sites considered sterile, including the upper female genital tract. The recent identification of distinct bacterial signatures associated with ovarian carcinomas suggests microbiota in the gut, vagina, or elsewhere might contribute to ovarian cancer pathogenesis. Here, we tested whether altering the microbiome affects tumorigenesis in a mouse model of high-grade serous carcinoma (HGSC) based on conditional oviduct-specific inactivation of the Brca1, Trp53, Rb1, and Nf1 tumor suppressor genes. Cohorts of control (n=20) and antibiotic-treated (n=23) mice were treated with tamoxifen to induce tumor formation and then monitored for 12 months. The antibiotic cocktail was administered for the first 5 months of the monitoring period in the treatment group. Antibiotic-treated mice had significantly fewer and less advanced tumors than control mice at study endpoint. Antibiotics induced changes in the composition of the intestinal and vaginal microbiota, which were durable in the fecal samples. Clustering analysis showed particular groups of microbiota are associated with the development of HGSC in this model. These findings demonstrate the microbiome influences HGSC pathogenesis in an in vivo model that closely recapitulates the human disease. Because the microbiome can modulate efficacy of cancer chemo- and immunotherapy, our genetically engineered mouse model system may prove useful for testing whether altering the microbiota can improve the heretofore poor response of HGSC to immunotherapies.

RevDate: 2021-04-17

Jungles KN, Jungles KM, Greenfield L, et al (2021)

The Infant Microbiome and Its Impact on Development of Food Allergy.

Immunology and allergy clinics of North America, 41(2):285-299.

The prevalence of food allergy (FA) has been increasing over the past few decades; recent statistics suggest that FA has an impact on up to 10% of the population and 8% of children. Although the pathogenesis of FA is unclear, studies suggest gut microbiome plays a role in the development of FA. The gut microbiome is influenced by infant feeding method, infant diet, and maternal diet during lactation. Breastfeeding, Mediterranean diet, and probiotics are associated with commensal gut microbiota that protect against FA. This area of research is essential to discovering potential preventive methods or therapeutic targets against FA.

RevDate: 2021-04-17

Albuhairi S, R Rachid (2021)

Biologics and Novel Therapies for Food Allergy.

Immunology and allergy clinics of North America, 41(2):271-283.

Food allergy is a significant public health burden affecting around 10% of adults and 8% of children. Although the first peanut oral immunotherapy product received Food and Drug Administration approval in 2020, there is still an unmet need for more effective therapeutic options that minimize the risk of anaphylaxis, nutritional deficiencies, and patient's quality of life. Biologics are promising modalities, as they may improve compliance, target multiple food allergies, and treat other concomitant atopic diseases. Although omalizumab has been evaluated extensively, most biologics are more novel and have broader immunologic impact. Careful evaluation of their safety profile should therefore be conducted.

RevDate: 2021-04-17

Strickland BA, Patel MC, Shilts MH, et al (2021)

Microbial community structure and composition is associated with host species and sex in Sigmodon cotton rats.

Animal microbiome, 3(1):29.

BACKGROUND: The cotton rat (genus Sigmodon) is an essential small animal model for the study of human infectious disease and viral therapeutic development. However, the impact of the host microbiome on infection outcomes has not been explored in this model, partly due to the lack of a comprehensive characterization of microbial communities across different cotton rat species. Understanding the dynamics of their microbiome could significantly help to better understand its role when modeling viral infections in this animal model.

RESULTS: We examined the bacterial communities of the gut and three external sites (skin, ear, and nose) of two inbred species of cotton rats commonly used in research (S. hispidus and S. fulviventer) by using 16S rRNA gene sequencing, constituting the first comprehensive characterization of the cotton rat microbiome. We showed that S. fulviventer maintained higher alpha diversity and richness than S. hispidus at external sites (skin, ear, nose), but there were no differentially abundant genera. However, S. fulviventer and S. hispidus had distinct fecal microbiomes composed of several significantly differentially abundant genera. Whole metagenomic shotgun sequencing of fecal samples identified species-level differences between S. hispidus and S. fulviventer, as well as different metabolic pathway functions as a result of differential host microbiome contributions. Furthermore, the microbiome composition of the external sites showed significant sex-based differences while fecal communities were not largely different.

CONCLUSIONS: Our study shows that host genetic background potentially exerts homeostatic pressures, resulting in distinct microbiomes for two different inbred cotton rat species. Because of the numerous studies that have uncovered strong relationships between host microbiome, viral infection outcomes, and immune responses, our findings represent a strong contribution for understanding the impact of different microbial communities on viral pathogenesis. Furthermore, we provide novel cotton rat microbiome data as a springboard to uncover the full therapeutic potential of the microbiome against viral infections.

RevDate: 2021-04-17

Tzeng A, Sangwan N, Jia M, et al (2021)

Human breast microbiome correlates with prognostic features and immunological signatures in breast cancer.

Genome medicine, 13(1):60.

BACKGROUND: Currently, over half of breast cancer cases are unrelated to known risk factors, highlighting the importance of discovering other cancer-promoting factors. Since crosstalk between gut microbes and host immunity contributes to many diseases, we hypothesized that similar interactions could occur between the recently described breast microbiome and local immune responses to influence breast cancer pathogenesis.

METHODS: Using 16S rRNA gene sequencing, we characterized the microbiome of human breast tissue in a total of 221 patients with breast cancer, 18 individuals predisposed to breast cancer, and 69 controls. We performed bioinformatic analyses using a DADA2-based pipeline and applied linear models with White's t or Kruskal-Wallis H-tests with Benjamini-Hochberg multiple testing correction to identify taxonomic groups associated with prognostic clinicopathologic features. We then used network analysis based on Spearman coefficients to correlate specific bacterial taxa with immunological data from NanoString gene expression and 65-plex cytokine assays.

RESULTS: Multiple bacterial genera exhibited significant differences in relative abundance when stratifying by breast tissue type (tumor, tumor adjacent normal, high-risk, healthy control), cancer stage, grade, histologic subtype, receptor status, lymphovascular invasion, or node-positive status, even after adjusting for confounding variables. Microbiome-immune networks within the breast tended to be bacteria-centric, with sparse structure in tumors and more interconnected structure in benign tissues. Notably, Anaerococcus, Caulobacter, and Streptococcus, which were major bacterial hubs in benign tissue networks, were absent from cancer-associated tissue networks. In addition, Propionibacterium and Staphylococcus, which were depleted in tumors, showed negative associations with oncogenic immune features; Streptococcus and Propionibacterium also correlated positively with T-cell activation-related genes.

CONCLUSIONS: This study, the largest to date comparing healthy versus cancer-associated breast microbiomes using fresh-frozen surgical specimens and immune correlates, provides insight into microbial profiles that correspond with prognostic clinicopathologic features in breast cancer. It additionally presents evidence for local microbial-immune interplay in breast cancer that merits further investigation and has preventative, diagnostic, and therapeutic potential.

RevDate: 2021-04-17

Bastianelli C, Farris M, Bianchi P, et al (2021)

The effect of different contraceptive methods on the vaginal microbiome.

Expert review of clinical pharmacology [Epub ahead of print].

Introduction: Following a historical overview, the effect of different contraceptive methods on vaginal microbiome has been reviewed and summarized.Areas covered: Effects of: combined hormonal contraceptives (oral or vaginal) and of progestin only (injectable and implantable), intrauterine devices/systems (copper- or levonorgestrel-releasing), on vaginal microbiome. In addition, mention is made of vaginal rings releasing antiviral drugs and lactic acid.Expert opinion: The vaginal microbiota (VM) is unique in that it is normally dominated by Lactobacillus species providing a degree of protection against infections; this however may vary, depending on the species and strains of Lactobacillus. Bacterial Vaginosis represents the most common dysbiosis of the VM and its prevalence can be influenced by use of contraception.Available evidence indicates that, under the influence of oral or systemically administered female sex hormones there is a promotion of vaginal eubiosis, with a prevalence of a healthy VM in which lactobacilli predominate.

RevDate: 2021-04-16

Patil SM, Kurade MB, Basak B, et al (2021)

Anaerobic co-digester microbiome during food waste valorization reveals Methanosaeta mediated methanogenesis with improved carbohydrate and lipid metabolism.

Bioresource technology, 332:125123 pii:S0960-8524(21)00462-4 [Epub ahead of print].

This study determines the optimum food waste (FW) loading in an anaerobic digester for methane production. Interrelation between the degradation mechanism and microbial community composition was assessed through in-depth metabolic pathway analysis and gene quantification. Higher methane production and short lag phase were observed in the FW reactors with low substrate loadings (<4% v/v) while extended lag phase and incomplete substrate utilization were observed in the reactors fed with higher substrates (>6% v/v). The long-chain fatty acids (LCFAs) degradation was influenced by initial FW loading, and up to 99% LCFA degradation occurred at 4% FW reactor. The addition of 8 to 10% FW substrate inhibited methanogenesis due to the accumulation of volatile fatty acids (VFA) and low LCFA degradation. Under optimal conditions of substrate loading, Methanosaeta and Methanosarcina were abundant, indicating their role in methanogenesis and syntrophic acetogenesis, along with enhanced metabolic pathways specific for carbohydrate and lipid metabolism.

RevDate: 2021-04-16

Molton JS, Lee IR, Bertrand D, et al (2021)

Stool metagenome analysis of patients with Klebsiella pneumoniae liver abscess and their domestic partners.

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases pii:S1201-9712(21)00323-4 [Epub ahead of print].

OBJECTIVES: Hypermucoviscous Klebsiella pneumoniae is an emerging cause of community-acquired liver abscess. We aimed to investigate if hypermucoviscous strains could be shared among households.

METHODS: We genotyped the clinical K. pneumoniae isolates in a cohort of 24 patients with Klebsiella liver abscess and analyzed the stool metagenomes of the index patients and their cohabiting domestic partners.

RESULTS: We identified K. pneumoniae in 33% of index patient's stools and identified one index patient's clinical isolate in their domestic partner's stool.

CONCLUSIONS: This could represent a transmission event or could represent exposure to a common environmental source.

RevDate: 2021-04-16

Hu C, van Meel ER, Medina-Gomez C, et al (2021)

A population-based study on associations of stool microbiota with atopic diseases in school-age children.

The Journal of allergy and clinical immunology pii:S0091-6749(21)00563-7 [Epub ahead of print].

BACKGROUND: Infants with less diverse gut microbiota seem to have higher risks of atopic diseases in early life, but any associations at school age are unclear.

OBJECTIVE: To examine the associations of diversity, relative abundance and functional pathways of stool microbiota with atopic diseases in school-aged children.

METHODS: We performed a cross-sectional study within an existing population-based prospective cohort among 1,440 children aged 10 years. On stool samples, 16S rRNA gene sequencing was performed, and taxonomic and functional tables were produced. Physician-diagnosed eczema, allergy and asthma were measured by questionnaires, allergic sensitization by skin prick tests, and lung function by spirometry.

RESULTS: Alpha diversity of stool microbiota was associated with a decreased risk of eczema (OR (95%CI): 0.98 (0.97, 1.00)), and beta diversity was associated with physician-diagnosed inhalant allergy (R2 (p-value): 0.001 (0.047)). Lachnospiraceae, Ruminococcaceae_UCG-005 and Christensenellaceae_R-7_group species were associated with decreased risks of eczema, inhalant allergic sensitization, and physician-diagnosed inhalant allergy (OR range (95%CI): 0.88 (0.79, 0.96) - 0.94 (0.88, 0.98)), while Agathobacter species was associated with an increased risk of physician-diagnosed inhalant allergy (1.23 (1.08, 1.42)). Functional pathways related to heme and terpenoid biosynthesis were associated with decreased risks of physician-diagnosed inhalant allergy and asthma (OR range (95%CI): 0.89 (0.80, 0.99) - 0.86 (0.73, 1.02)). No associations of stool microbiota with lung function were observed.

CONCLUSIONS: The diversity, relative abundance and functional pathways of stool microbiota were most consistently associated with physician-diagnosed inhalant allergy in school-aged children, and less consistent with other atopic diseases.

RevDate: 2021-04-16

Caragata EP, Otero LM, Tikhe CV, et al (2021)

Microbial Diversity of Adult Aedes aegypti and Water Collected from Different Mosquito Aquatic Habitats in Puerto Rico.

Microbial ecology [Epub ahead of print].

Mosquitoes, the major vectors of viruses like dengue, are naturally host to diverse microorganisms, which play an important role in their development, fecundity, immunity, and vector competence. The composition of their microbiota is strongly influenced by the environment, particularly their aquatic larval habitat. In this study, we used 2×300 bp 16s Illumina sequencing to compare the microbial profiles of emerging adult Aedes aegypti mosquitoes and the water collected from common types of aquatic habitat containers in Puerto Rico, which has endemic dengue transmission. We sequenced 141 mosquito and 46 water samples collected from plastic containers, septic tanks, discarded tires, underground trash cans, tree holes, or water meters. We identified 9 bacterial genera that were highly prevalent in the mosquito microbiome, and 77 for the microbiome of the aquatic habitat. The most abundant mosquito-associated bacterial OTUs were from the families Burkholderiaceae, Pseudomonadaceae, Comamonadaceae, and Xanthomonadaceae. Microbial profiles varied greatly between mosquitoes, and there were few major differences explained by container type; however, the microbiome of mosquitoes from plastic containers was more diverse and contained more unique taxa than the other groups. Container water was significantly more diverse than mosquitoes, and our data suggest that mosquitoes filter out many bacteria, with Alphaproteobacteria in particular being far more abundant in water. These findings provide novel insight into the microbiome of mosquitoes in the region and provide a platform to improve our understanding of the fundamental mosquito-microbe interactions.

RevDate: 2021-04-16

Menozzi E, Macnaughtan J, AHV Schapira (2021)

The gut-brain axis and Parkinson disease: clinical and pathogenetic relevance.

Annals of medicine, 53(1):611-625.

Gastrointestinal disorders are one of the most significant non-motor problems affecting people with Parkinson disease (PD). Pathogenetically, the gastrointestinal tract has been proposed to be the initial site of pathological changes in PD. Intestinal inflammation and alterations in the gut microbiota may contribute to initiation and progression of pathology in PD. However, the mechanisms underlying this "gut-brain" axis in PD remain unclear. PD patients can display a large variety of gastrointestinal symptoms, leading to reduced quality of life and psychological distress. Gastrointestinal disorders can also limit patients' response to medications, and consequently negatively impact on neurological outcomes. Despite an increasing research focus, gastrointestinal disorders in PD remain poorly understood and their clinical management often suboptimal. This review summarises our understanding of the relevance of the "gut-brain" axis to the pathogenesis of PD, discusses the impact of gastrointestinal disorders in patients with PD, and provides clinicians with practical guidance to their management.

RevDate: 2021-04-16

Simeone R, Sayes F, Lawaree E, et al (2021)

Breaching the phagosome, the case of the tuberculosis agent (Phagosome/invasion dynamics).

Cellular microbiology [Epub ahead of print].

The interactions between microbes and their hosts are among the most complex biological phenomena known today. The interaction may reach from overall beneficial interaction, as observed for most microbiome/microbiota related interactions to interaction with virulent pathogens, against which host cells have evolved sophisticated defense strategies. Amongst the latter, the confinement of invading pathogens in a phagosome plays a key role, which often results in the destruction of the invader, whereas some pathogens may counteract phagosomal arrest and survive by gaining access to the cytosol of the host cell. In the current review we will discuss recent insights into this dynamic process of host-pathogen interaction, using Mycobacterium tuberculosis and related pathogenic mycobacteria as main examples. This article is protected by copyright. All rights reserved.

RevDate: 2021-04-16

El-Sayed A, Aleya L, M Kamel (2021)

The link among microbiota, epigenetics, and disease development.

Environmental science and pollution research international [Epub ahead of print].

The microbiome is a community of various microorganisms that inhabit or live on the skin of humans/animals, sharing the body space with their hosts. It is a sort of complex ecosystem of trillions of commensals, symbiotic, and pathogenic microorganisms, including trillions of bacteria, archaea, protozoa, fungi, and viruses. The microbiota plays a role in the health and disease status of the host. Their number, species dominance, and viability are dynamic. Their long-term disturbance is usually accompanied by serious diseases such as metabolic disorders, cardiovascular diseases, or even cancer. While epigenetics is a term that refers to different stimuli that induce modifications in gene expression patterns without structural changes in the inherited DNA sequence, these changes can be reversible or even persist for several generations. Epigenetics can be described as cell memory that stores experience against internal and external factors. Results from multiple institutions have contributed to the role and close interaction of both microbiota and epigenetics in disease induction. Understanding the mechanisms of both players enables a better understanding of disease induction and development and also opens the horizon to revolutionary therapeutic approaches. The present review illustrates the roles of diet, microbiome, and epigenetics in the induction of several chronic diseases. In addition, it discusses the application of epigenetic data to develop diagnostic biomarkers and therapeutics and evaluate their safety for patients. Understanding the interaction among all these elements enables the development of innovative preventive/therapeutic approaches for disease control.

RevDate: 2021-04-16

Ding J, Ma X, Han L, et al (2021)

Gut microbial alterations in neonatal jaundice pre- and post-treatment.

Bioscience reports pii:228373 [Epub ahead of print].

Neonatal jaundice is a common disease that affects up to 60% of new-borns. Herein, we performed a comparative analysis of the gut microbiome in neonatal jaundice and non-neonatal jaundice infants and identified gut microbial alterations in neonatal jaundice pre- and post-treatment. We prospectively collected 232 faecal samples from 51 infants at 5 time points (0, 1, 3, 6 and 12 months). Finally, 114 samples from 6 neonatal jaundice infants (NJI) and 19 non-NJI completed MiSeq sequencing and analysis. We characterized the gut microbiome and identified microbial differences and gene functions. Meconium microbial diversity from NJI was decreased compared with that from non-NJI. The genus Gemella was decreased in NJI versus non-NJI. Eleven predicted microbial functions, including fructose 1,6-bisphosphatase III and pyruvate carboxylase subunit B, decreased, while 3 functions, including acetyl-CoA acyltransferase, increased in NJI. After treatments, the microbial community presented significant alteration-based beta diversity. The phyla Firmicutes and Actinobacteria were increased, while Proteobacteria and Fusobacteria were decreased. Microbial alterations were also analysed between 6 recovered NJI and 19 non-NJI. The gut microbiota was unique in the meconium microbiome from NJI, implying that early gut microbiome intervention could be promising for the management of neonatal jaundice. Alterations of gut microbiota from NJI can be of great value to bolster evidence-based prevention against 'bacterial dysbiosis'.

RevDate: 2021-04-16

Shoji M, Sasaki Y, Abe Y, et al (2021)

Characteristics of the gut microbiome profile in obese patients with colorectal cancer.

JGH open : an open access journal of gastroenterology and hepatology, 5(4):498-507 pii:JGH312529.

Background and Aim: Obesity affects the gut microbiome, which in turn increases the risk for colorectal cancer. Several studies have shown the mechanisms by which some bacteria may influence the development of colorectal cancer; however, gut microbiome characteristics in obese patients with colorectal cancer remain unclear. Therefore, this study evaluated their gut microbiome profile and its relationship with metabolic markers.

Methods: The study assessed fecal samples from 36 consecutive patients with colorectal cancer and 38 controls without colorectal cancer. To identify microbiotic variations between patients with colorectal cancer and controls, as well as between nonobese and obese individuals, 16S rRNA gene amplicon sequencing was performed.

Results: Principal coordinate analysis showed significant differences in the overall structure of the microbiome among the study groups. The α-diversity, assessed by the Chao1 index or Shannon index, was higher in patients with colorectal cancer versus controls. The relative abundance of the genera Enterococcus, Capnocytophaga, and Polaribacter was significantly altered in obese patients with colorectal cancer, whose serum low-density lipoprotein concentrations were positively correlated with the abundance of the genus Enterococcus; among the most abundant species was Enterococcus faecalis, observed at lower levels in obese versus nonobese patients.

Conclusions: This study demonstrated several compositional alterations of the gut microbiome in patients with colorectal cancer and showed that a reduced presence of E. faecalis may be associated with obesity-related colorectal cancer development. The gut microbiome may provide novel insights into the potential mechanisms in obesity-related colorectal carcinogenesis.

RevDate: 2021-04-16

Tan AH, Hor JW, Chong CW, et al (2021)

Probiotics for Parkinson's disease: Current evidence and future directions.

JGH open : an open access journal of gastroenterology and hepatology, 5(4):414-419 pii:JGH312450.

The gut-brain axis is a hot topic in Parkinson's disease (PD). It has been postulated that gut pathogens and dysbiosis can contribute to peripheral inflammatory states or trigger downstream metabolic effects that exacerbate the neurodegenerative process in PD. Several preclinical and clinical studies have demonstrated disrupted intestinal permeability, intestinal inflammation, altered gut microbiome, and reduced fecal short-chain fatty acids in PD. In this regard, microbial-directed therapies such as probiotics are emerging as potential therapeutic options. Probiotic supplementation is postulated to confer a variety of health benefits due to the diverse functions of these live microorganisms, including inhibition of pathogen colonization, modulation/"normalization" of the microbiome and/or its function, immunomodulatory effects (e.g. reducing inflammation), and improved host epithelial barrier function. Interestingly, several PD animal model studies have demonstrated the potential neuroprotective effects of probiotics in reducing dopaminergic neuronal degeneration. Notably, two randomized placebo-controlled trials have provided class I evidence for probiotics as a treatment for constipation in PD. However, the effects of probiotics on other PD aspects, such as motor disability and cognitive function, and its long-term efficacy (including effects on PD drug absorption in the gut) have not been investigated adequately. Further targeted animal and human studies are also warranted to understand the mechanisms of actions of probiotics in PD and to tailor probiotic therapy based on individual host profiles to improve patient outcomes in this disabling disorder.

RevDate: 2021-04-16

Jégousse C, Vannier P, Groben R, et al (2021)

A total of 219 metagenome-assembled genomes of microorganisms from Icelandic marine waters.

PeerJ, 9:e11112 pii:11112.

Marine microorganisms contribute to the health of the global ocean by supporting the marine food web and regulating biogeochemical cycles. Assessing marine microbial diversity is a crucial step towards understanding the global ocean. The waters surrounding Iceland are a complex environment where relatively warm salty waters from the Atlantic cool down and sink down to the deep. Microbial studies in this area have focused on photosynthetic micro- and nanoplankton mainly using microscopy and chlorophyll measurements. However, the diversity and function of the bacterial and archaeal picoplankton remains unknown. Here, we used a co-assembly approach supported by a marine mock community to reconstruct metagenome-assembled genomes (MAGs) from 31 metagenomes from the sea surface and seafloor of four oceanographic sampling stations sampled between 2015 and 2018. The resulting 219 MAGs include 191 bacterial, 26 archaeal and two eukaryotic MAGs to bridge the gap in our current knowledge of the global marine microbiome.

RevDate: 2021-04-16

Su L, Li D, Su J, et al (2021)

Polysaccharides of Sporoderm-Broken Spore of Ganoderma lucidum Modulate Adaptive Immune Function via Gut Microbiota Regulation.

Evidence-based complementary and alternative medicine : eCAM, 2021:8842062.

Ganoderma lucidum (Leyss.Fr.) Karst is one of the well-known medicinal macrofungi all over the world, and mounting researches have focused on the polysaccharides derived from the spores of G. lucidum. In the present study, BALB/c mice (n = 8-10) were administered with crude polysaccharides of G. lucidum spores (CPGS) and the refined polysaccharides of G. lucidum spores (RPGS) for 30 days to investigate their effect on the adaptive immune system. Results showed that CPGS and RPGS displayed diverse effects on the lymphocyte activity in the spleen. The splenocyte proliferation activity upon mitogen was suppressed by CPGS and RPGS, while the NK cell's tumor-killing ability was promoted by CPGS. Both CPGS and RPGS could increase the proportion of naïve T cells in thymus, but only RPGS significantly uplifted the percentage of T cells, as well as the T cell subsets, in peripheral blood, and promoted the activation by upregulating the expression of costimulatory factor CD28. Moreover, 16S sequencing results showed that the effects of CPGS and RPGS were closely related to the regulation of gut microbiota. β-diversity of the microbiome was evidently changed by CPGS and RPGS. The phytoestrogen/polysaccharide-metabolizing bacteria (Adlercreutzia, Parabacteroides, and Prevotella), and an unclassified Desulfovibrionaceae, were remarkably enriched by CPGS or RPGS, and functions involving carbohydrate metabolism, membrane transport, and lipid metabolism were regulated. Moreover, the enrichments of Adlercreutzia, Prevotella, and Desulfovibrionaceae were positively related to the immune regulation by CPGS and RPGS, while that of Parabacteroides displayed a negative correlation. These findings suggested a promising effect of the polysaccharide from sporoderm-broken spore of G. lucidum in immune regulation to promote health control.

RevDate: 2021-04-16

Schmitt H, Neurath MF, R Atreya (2021)

Role of the IL23/IL17 Pathway in Crohn's Disease.

Frontiers in immunology, 12:622934.

Crohn's disease (CD) is a chronic relapsing disorder of the gastrointestinal tract and represents one of the main entities of inflammatory bowel disease (IBD). CD affects genetically susceptible patients that are influenced by environmental factors and the intestinal microbiome, which results in excessive activation of the mucosal immune system and aberrant cytokine responses. Various studies have implicated the pro-inflammatory cytokines IL17 and IL23 in the pathogenesis of CD. IL23 is a member of the IL12 family of cytokines and is able to enhance and affect the expansion of pathogenic T helper type 17 (Th17) cells through various mechanisms, including maintenance of Th17 signature genes, upregulation of effector genes or suppression of repressive factors. Moreover, IL17 and IL23 signaling is able to induce a cascade of pro-inflammatory molecules like TNF, IFNγ, IL22, lymphotoxin, IL1β and lipopolysaccharide (LPS). Here, IL17A and TNF are known to mediate signaling synergistically to drive expression of inflammatory genes. Recent advances in understanding the immunopathogenetic mechanisms underlying CD have led to the development of new biological therapies that selectively intervene and inhibit inflammatory processes caused by pro-inflammatory mediators like IL17 and IL23. Recently published data demonstrate that treatment with selective IL23 inhibitors lead to markedly high response rates in the cohort of CD patients that failed previous anti-TNF therapy. Macrophages are considered as a main source of IL23 in the intestine and are supposed to play a key role in the molecular crosstalk with T cell subsets and innate lymphoid cells in the gut. The following review focuses on mechanisms, pathways and specific therapies in Crohn's disease underlying the IL23/IL17 pathway.

RevDate: 2021-04-16

Liu D, He X, Chater CCC, et al (2021)

Microbiome Community Structure and Functional Gene Partitioning in Different Micro-Niches Within a Sporocarp-Forming Fungus.

Frontiers in microbiology, 12:629352.

Thelephora ganbajun is a wild edible mushroom highly appreciated throughout China. The microbiomes of some fungal sporocarps have been studied, however, their potential functional roles currently remain uncharacterized. Here, functional gene microarrays (GeoChip 5.0) and amplicon sequencing were employed to define the taxonomic and functional attributes within three micro-niches of T. ganbajun. The diversity and composition of bacterial taxa and their functional genes differed significantly (p < 0.01) among the compartments. Among 31,117 functional genes detected, some were exclusively recorded in one sporocarp compartment: 1,334 genes involved in carbon (mdh) and nitrogen fixation (nifH) in the context; 524 genes influencing carbon (apu) and sulfite reduction (dsrB, dsra) in the hymenophore; and 255 genes involved in sulfur oxidation (soxB and soxC) and polyphosphate degradation (ppx) in the pileipellis. These results shed light on a previously unknown microbiome and functional gene partitioning in sporome compartments of Basidiomycota. This also has great implications for their potential ecological and biogeochemical functions, demonstrating a higher genomic complexity than previously thought.

RevDate: 2021-04-16

Grimm M, Grube M, Schiefelbein U, et al (2021)

The Lichens' Microbiota, Still a Mystery?.

Frontiers in microbiology, 12:623839.

Lichens represent self-supporting symbioses, which occur in a wide range of terrestrial habitats and which contribute significantly to mineral cycling and energy flow at a global scale. Lichens usually grow much slower than higher plants. Nevertheless, lichens can contribute substantially to biomass production. This review focuses on the lichen symbiosis in general and especially on the model species Lobaria pulmonaria L. Hoffm., which is a large foliose lichen that occurs worldwide on tree trunks in undisturbed forests with long ecological continuity. In comparison to many other lichens, L. pulmonaria is less tolerant to desiccation and highly sensitive to air pollution. The name-giving mycobiont (belonging to the Ascomycota), provides a protective layer covering a layer of the green-algal photobiont (Dictyochloropsis reticulata) and interspersed cyanobacterial cell clusters (Nostoc spec.). Recently performed metaproteome analyses confirm the partition of functions in lichen partnerships. The ample functional diversity of the mycobiont contrasts the predominant function of the photobiont in production (and secretion) of energy-rich carbohydrates, and the cyanobiont's contribution by nitrogen fixation. In addition, high throughput and state-of-the-art metagenomics and community fingerprinting, metatranscriptomics, and MS-based metaproteomics identify the bacterial community present on L. pulmonaria as a surprisingly abundant and structurally integrated element of the lichen symbiosis. Comparative metaproteome analyses of lichens from different sampling sites suggest the presence of a relatively stable core microbiome and a sampling site-specific portion of the microbiome. Moreover, these studies indicate how the microbiota may contribute to the symbiotic system, to improve its health, growth and fitness.

RevDate: 2021-04-16

Maas RM, Deng Y, Dersjant-Li Y, et al (2021)

Exogenous enzymes and probiotics alter digestion kinetics, volatile fatty acid content and microbial interactions in the gut of Nile tilapia.

Scientific reports, 11(1):8221.

Sustainable aquafeed production requires fishmeal replacement, leading to an increasing use of plant-derived ingredients. As a consequence, higher levels of antinutritional substances, such as non-starch polysaccharides and phytate, are present in aquafeeds, with negative effects on fish performance, nutrient digestibility and overall gut health. To alleviate these negative effects, providing exogenous digestive enzymes and/or probiotics can be an effective solution. In this study, we tested the effect of dietary supplementation of enzymes (phytase and xylanase) and probiotics (three strains of Bacillus amyloliquefaciens) on nutrient digestion kinetics and volatile fatty acid content along the gut, and the distal gut microbiome diversity in Nile tilapia. Chyme volatile fatty content was increased with probiotic supplementation in the proximal gut, while lactate content, measured for the first time in vivo in fish, decreased with enzymes along the gut. Enzyme supplementation enhanced crude protein, Ca and P digestibility in proximal and middle gut. Enzymes and probiotics supplementation enhanced microbial interactions as shown by network analysis, while increased the abundance of lactic acid bacteria and Bacillus species. Such results suggest that supplementation with exogenous enzymes and probiotics increases nutrient availability, while at the same time benefits gut health and contributes to a more stable microbiome environment.

RevDate: 2021-04-16

Roscioli JR, Meredith LK, Shorter JH, et al (2021)

Soil gas probes for monitoring trace gas messengers of microbial activity.

Scientific reports, 11(1):8327.

Soil microbes vigorously produce and consume gases that reflect active soil biogeochemical processes. Soil gas measurements are therefore a powerful tool to monitor microbial activity. Yet, the majority of soil gases lack non-disruptive subsurface measurement methods at spatiotemporal scales relevant to microbial processes and soil structure. To address this need, we developed a soil gas sampling system that uses novel diffusive soil probes and sample transfer approaches for high-resolution sampling from discrete subsurface regions. Probe sampling requires transferring soil gas samples to above-ground gas analyzers where concentrations and isotopologues are measured. Obtaining representative soil gas samples has historically required balancing disruption to soil gas composition with measurement frequency and analyzer volume demand. These considerations have limited attempts to quantify trace gas spatial concentration gradients and heterogeneity at scales relevant to the soil microbiome. Here, we describe our new flexible diffusive probe sampling system integrated with a modified, reduced volume trace gas analyzer and demonstrate its application for subsurface monitoring of biogeochemical cycling of nitrous oxide (N2O) and its site-specific isotopologues, methane, carbon dioxide, and nitric oxide in controlled soil columns. The sampling system observed reproducible responses of soil gas concentrations to manipulations of soil nutrients and redox state, providing a new window into the microbial response to these key environmental forcings. Using site-specific N2O isotopologues as indicators of microbial processes, we constrain the dynamics of in situ microbial activity. Unlocking trace gas messengers of microbial activity will complement -omics approaches, challenge subsurface models, and improve understanding of soil heterogeneity to disentangle interactive processes in the subsurface biome.

RevDate: 2021-04-16

Couch CE, Stagaman K, Spaan RS, et al (2021)

Diet and gut microbiome enterotype are associated at the population level in African buffalo.

Nature communications, 12(1):2267.

Studies in humans and laboratory animals link stable gut microbiome "enterotypes" with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease.

RevDate: 2021-04-16

Huang J, Chen W, Zhou F, et al (2021)

Tissue-specific reprogramming of host tRNA transcriptome by the microbiome.

Genome research pii:gr.272153.120 [Epub ahead of print].

Transfer RNAs (tRNAs) are essential for translation, and tRNA expression and modifications are regulated by many factors. However, the interplay between the microbiome and host tRNA profiles through host-microbiome interactions has not been explored. In this study, we investigated host-microbiome interactions via the tRNA profiling of four tissue types from germ-free and specific pathogen-free mice. Our analyses reveal that cytosolic and mitochondrial tRNA expression and tRNA modifications in the host are reprogrammed in a tissue-specific and microbiome-dependent manner. In terms of tRNA expression, the intestines and brains are more sensitive to the influence of the microbiome than the livers and kidneys. In terms of tRNA modifications, cytosolic tRNAs show more obvious changes in the livers and kidneys in the presence of the microbiome. Our findings reveal a previously unexplored relationship among the microbiome, tRNA abundance, and epitranscriptome in a mammalian host.

RevDate: 2021-04-16

Upadhaya SD, Ahn JM, Cho JH, et al (2021)

Bacteriophage cocktail supplementation improves growth performance, gut microbiome and production traits in broiler chickens.

Journal of animal science and biotechnology, 12(1):49.

BACKGROUND: Effective antibiotic alternatives are urgently needed in the poultry industry to control disease outbreaks. Phage therapy mainly utilizes lytic phages to kill their respective bacterial hosts and can be an attractive solution to combating the emergence of antibiotic resistance in livestock.

METHODS: Five hundred and four, one-day-old broilers (Ross 308) were allotted to 1 of 4 treatment groups in a completely randomized design. Treatments consisted of CON (basal diet), PC (CON + 0.025% Avilamax®), BP 0.05 (CON + 0.05% bacteriophage), and BP 0.10 (CON + 0.10% bacteriophage).

RESULTS: A significant linear effect on body weight gain (BWG) was observed during days 1-7, days 22-35, and cumulatively in bacteriophage (BP) supplemented groups. The BWG tended to be higher (P = 0.08) and the feed intake (FI) was increased (P = 0.017) in the PC group over CON group. A greater (P = 0.016) BWG and trends in increased FI (P = 0.06) were observed in the experiment in birds fed PC than CON diet. At the genus level, the relative abundance of Lactobacillus was decreased in PC (65.28%), while it was similar in BP 0.05 and BP 0.10 (90.65%, 86.72%) compared to CON (90.19%). At the species level, the relative abundance of Lactobacillus salivarus was higher in BP 0.05 (40.15%) and BP 0.10 (38.58%) compared to the CON (20.04%) and PC (18.05%). A linear reduction in the weight of bursa of Fabricius (P = 0.022) and spleen (P = 0.052) was observed in birds fed graded level of BP and an increase (P = 0.059) in the weight of gizzard was observed in birds fed PC over BP diets. Linear and quadratic responses were observed in redness of breast muscle color in birds fed graded level of BP.

CONCLUSIONS: The inclusion of the 0.05% and 0.1% BP cocktail linearly improved broiler weight during the first 7 days, 22-35 days and cumulatively, whereas 0.05% BP addition was sufficient for supporting immune organs, bursa and spleen as well as enhancing gut microbiome, indicating the efficacy of 0.05% BP as a substitute antibiotic growth promoter in broiler diets.

RevDate: 2021-04-16

Behary J, Raposo AE, Amorim NML, et al (2021)

Defining the temporal evolution of gut dysbiosis and inflammatory responses leading to hepatocellular carcinoma in Mdr2 -/- mouse model.

BMC microbiology, 21(1):113.

BACKGROUND: Emerging evidence implicates the gut microbiome in liver inflammation and hepatocellular carcinoma (HCC) development. We aimed to characterize the temporal evolution of gut dysbiosis, in relation to the phenotype of systemic and hepatic inflammatory responses leading to HCC development. In the present study, Mdr2 -/- mice were used as a model of inflammation-based HCC. Gut microbiome composition and function, in addition to serum LPS, serum cytokines/chemokines and intrahepatic inflammatory genes were measured throughout the course of liver injury until HCC development.

RESULTS: Early stages of liver injury, inflammation and cirrhosis, were characterized by dysbiosis. Microbiome functional pathways pertaining to gut barrier dysfunction were enriched during the initial phase of liver inflammation and cirrhosis, whilst those supporting lipopolysaccharide (LPS) biosynthesis increased as cirrhosis and HCC ensued. In parallel, serum LPS progressively increased during the course of liver injury, corresponding to a shift towards a systemic Th1/Th17 proinflammatory phenotype. Alongside, the intrahepatic inflammatory gene profile transitioned from a proinflammatory phenotype in the initial phases of liver injury to an immunosuppressed one in HCC. In established HCC, a switch in microbiome function from carbohydrate to amino acid metabolism occurred.

CONCLUSION: In Mdr2 -/- mice, dysbiosis precedes HCC development, with temporal evolution of microbiome function to support gut barrier dysfunction, LPS biosynthesis, and redirection of energy source utilization. A corresponding shift in systemic and intrahepatic inflammatory responses occurred supporting HCC development. These findings support the notion that gut based therapeutic interventions could be beneficial early in the course of liver disease to halt HCC development.

RevDate: 2021-04-16

Cross AS, Opal SM, Palardy JE, et al (2021)

A pilot study of an anti-endotoxin Ig-enriched bovine colostrum to prevent experimental sepsis.

Innate immunity, 27(3):266-274.

Despite the dramatic increase in antimicrobial resistance, there is a dearth of antibiotics in development and few pharmaceutical companies working in the field. Further, any new antibiotics are likely to have a short shelf life. Ab-based interventions offer alternatives that are not likely to be circumvented by the widely prevalent antibiotic resistance genes. Bovine colostrum (BC)-the first milk after parturition, rich in nutrients and immune components-promotes gut integrity and modulates the gut microbiome. We developed a hyperimmune BC (HBC) enriched in Abs to a highly conserved LOS core region of Gram-negative bacteria by immunizing pregnant cows with a vaccine comprised of detoxified LOS from Escherichia coli O111 Rc (J5) mutant non-covalently complexed to group B meningococcal outer membrane protein (J5dLOS/OMP). This vaccine generated robust levels of anti-J5 LOS Ab in the colostrum. When given orally to neutropenic rats challenged orally with Pseudomonas aeruginosa, administration of HBC improved survival compared to non-immune rats, while both BC preparations improved survival compared to PBS controls. Elevated circulating endotoxin levels correlated with mortality. HBC and to a lesser extent non-immune BC reduced bacterial burden from the liver, lung, and spleen. We conclude that HBC and to a lesser extent BC may be effective supplements that improve outcome from lethal gut-derived disseminated infection and may reduce transmission of Gram-negative bacilli from the gastrointestinal tract.

RevDate: 2021-04-16

Lu Q, Liu J, He H, et al (2021)

Waste activated sludge stimulates in situ microbial reductive dehalogenation of organohalide-contaminated soil.

Journal of hazardous materials, 411:125189.

Due to its enriched organic matter, nutrients and growth cofactors, as well as a diverse range of microorganisms, waste activated sludge (WAS) might be an ideal additive to stimulate organohalide respiration for in situ bioremediation of organohalide-contaminated sites. In this study, we investigated the biostimulation and bioaugmentation impacts of WAS-amendment on the performance and microbiome in tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) dechlorinating microcosms. Results demonstrated that WAS-amendment increased PCE- and PCBs-dechlorination rate as much as 6.06 and 10.67 folds, respectively. The presence of WAS provided a favorable growth niche for organohalide-respiring bacteria (OHRB), including redox mediation and generation of electron donors and carbon sources. Particularly for the PCE dechlorination, indigenous Geobacter and WAS-derived Dehalococcoides were identified to play key roles in PCE-to-dichloroethene (DCE) and DCE-to-ethene dechlorination, respectively. Similar biostimulation and bioaugmentation effects of WAS-amendment were observed on both PCE- and PCBs-dechlorination in three different soils, i.e., laterite, brown loam and paddy soil. Risk assessment suggested low potential ecological risk of WAS amendment in remediation of organohalide-contaminated soil. Overall, this study provided an economic and efficient strategy to stimulate the organohalide respiration-based bioremediation in field applications.

RevDate: 2021-04-16

Zeng H, Xu H, Liu G, et al (2021)

Physiological and metagenomic strategies uncover the rhizosphere bacterial microbiome succession underlying three common environmental stresses in cassava.

Journal of hazardous materials, 411:125143.

The most common environmental pollutants such as cadmium (Cd), glyphosate and tetracycline have led to profoundly adverse impacts on plant productivity. However, how tropical crops such as cassava sense these pollutants via roots and how rhizosphere microbiome interacts with the host and pollutants remain largely unknown. In this study, we found these stresses significantly inhibited plant growth and triggered cell damage in a dosage-dependent manner, and the toxic effect on redox homeostasis was correlated with antioxidant metabolism. Using metagenomics technique, we found the rhizosphere microbiomes dynamically altered as the dose of these stresses increased. We also identified stressor-associated metagenome-assembled genomes and microbial metabolic pathways as well as mobile genetic elements in the rhizosphere microbiomes. Next, a co-occurrence network of both physiological and microbiome features was constructed to explore how these pollutants derived oxidative damage through the microbiome succession. Notably, phyllosphere transplantation of Agrobacterium tumefaciens or Pseudomonas stutzeri can significantly alleviate the negative effects of stresses on cassava growth and redox homeostasis. Collectively, this study demonstrated the dynamics of rhizosphere bacterial microbiome of cassava under three common environmental stresses, and A. tumefaciens and P. stutzeri could be developed as potential beneficial bacteria to alleviate Cd, glyphosate and tetracycline-triggered damage to cassava.

RevDate: 2021-04-16

Qu Q, Li Y, Zhang Z, et al (2021)

Effects of S-metolachlor on wheat (Triticum aestivum L.) seedling root exudates and the rhizosphere microbiome.

Journal of hazardous materials, 411:125137.

S-metolachlor (S-ME) is a common chloroacetanilide herbicide. Here, we investigated the effects of S-ME on wheat seedling growth and explored via metabolomics the driver through which S-ME changes the rhizosphere microbiome. The results indicated that 4 mg/kg S-ME had a strong inhibitory effect on plant growth by inducing hydrogen peroxide (H2O2) levels. The richness of the rhizosphere microbiome markedly decreased after S-ME treatment, although the abundance of some potential beneficial rhizobacteria, such as Rhizobiaceae and Burkholderiaceae, increased suggesting that plants recruited potential beneficial microorganisms to resist S-ME-induced stress. Spearman correlation analysis revealed that Rhizobiaceae and Burkholderiaceae were positively correlated with organic acids secreted by plants after S-ME treatment, implying that potential beneficial microorganisms may be attracted mainly by organic acids. Our results demonstrated the phytotoxicity of S-ME on crop growth and indicated both that S-ME could influence rhizosphere microorganism abundance and that recruitment of potential beneficial microorganisms could be the result of root exudate regulation.

RevDate: 2021-04-15

de Groot GA, Geisen S, Wubs ERJ, et al (2021)

The aerobiome uncovered: Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air.

Environment international, 154:106551 pii:S0160-4120(21)00176-8 [Epub ahead of print].

Air is a major conduit for the dispersal of organisms at the local and the global scale. Most research has focused on the dispersal of plants, vertebrates and human disease agents. However, the air represents a key dispersal medium also for bacteria, fungi and protists. Many of those represent potential pathogens of animals and plants and have until now gone largely unrecorded. Here we studied the turnover in composition of the entire aerobiome, the collective diversity of airborne microorganisms. For that we performed daily analyses of all prokaryotes and eukaryotes (including plants) using multi-marker high-throughput sequencing for a total of three weeks. We linked the resulting communities to local weather conditions, to assess determinants of aerobiome composition and distribution. We observed hundreds of microbial taxa, mostly belonging to spore-forming organisms including fungi, but also protists. Additionally, we detected many potential human- and plant-pathogens. Community composition fluctuated on a daily basis and was linked to concurrent weather conditions, particularly air pressure and temperature. Using network analyses, we identified taxonomically diverse groups of organisms with correlated temporal dynamics. In part, this was due to co-variation with environmental conditions, while we could also detect specific host-parasite interactions. This study provides the first full inventory of the aerobiome and identifies putative drivers of its dynamics in terms of taxon composition. This knowledge can help develop early warning systems against pathogens and improve our understanding of microbial dispersal.

RevDate: 2021-04-15

Bindas AJ, Kulkarni S, Koppes RA, et al (2021)

Parkinson's Disease and the Gut: Models of an Emerging Relationship.

Acta biomaterialia pii:S1742-7061(21)00229-4 [Epub ahead of print].

Parkinson's disease (PD) is a common neurodegenerative disease characterized by a progressive loss of fine motor function that impacts 1-2 out of 1,000 people. PD occurs predominately late in life and lacks a definitive biomarker for early detection. Recent cross-disciplinary progress has implicated the gut as a potential origin of PD pathogenesis. The gut-origin hypothesis has motivated research on gut PD pathology and transmission to the brain, especially during the prodromal stage (10-20 years before motor symptom onset). Early findings have revealed several possible triggers for Lewy pathology - the pathological hallmark of PD - in the gut, suggesting that microbiome and epithelial interactions may play a greater than appreciated role. But the mechanisms driving Lewy pathology and gut-brain transmission in PD remain unknown. Development of artificial α-Synuclein aggregates (α-Syn preformed fibrils) and animal disease models have recapitulated features of PD progression, enabling for the first time, controlled investigation of the gut-origin hypothesis. However, the role of specific cells in PD transmission, such as neurons, remains limited and requires in vitro models for controlled evaluation and perturbation. Human cell populations, three-dimensional organoids, and microfluidics as discovery platforms inch us closer to improving existing treatment for patients by providing platforms for discovery and screening. This review includes a discussion of PD pathology, conventional treatments, in vivo and in vitro models, and future directions.

RevDate: 2021-04-15

Shamsaddini A, Gillevet PM, Acharya C, et al (2021)

Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients with Cirrhosis.

Gastroenterology pii:S0016-5085(21)00634-X [Epub ahead of print].

BACKGROUND AND AIMS: Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear.

AIMS: Determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes.

METHODS: In cirrhotic outpatients who underwent metagenomics, we evaluated change in ARG abundances with progression and their multi-variable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre and 8-weeks post-rifaximin in compensated cirrhotics in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared to cirrhosis on machine learning.

RESULTS: 163 cirrhotics (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity. 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs.

CONCLUSIONS: Cirrhosis is associated with high gut microbial ARG gene burden compared to controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.

RevDate: 2021-04-15

Walker T, Quek S, Jeffries CL, et al (2021)

Stable high-density and maternally inherited Wolbachia infections in Anopheles moucheti and Anopheles demeilloni mosquitoes.

Current biology : CB pii:S0960-9822(21)00429-2 [Epub ahead of print].

Wolbachia, a widespread bacterium that can reduce pathogen transmission in mosquitoes, has recently been reported to be present in Anopheles (An.) species. In wild populations of the An. gambiae complex, the primary vectors of Plasmodium malaria in Sub-Saharan Africa, Wolbachia DNA sequences at low density and infection frequencies have been detected. As the majority of studies have used highly sensitive nested PCR as the only method of detection, more robust evidence is required to determine whether Wolbachia strains are established as endosymbionts in Anopheles species. Here, we describe high-density Wolbachia infections in geographically diverse populations of An. moucheti and An. demeilloni. Fluorescent in situ hybridization localized a heavy infection in the ovaries of An.moucheti, and maternal transmission was observed. Genome sequencing of both Wolbachia strains obtained genome depths and coverages comparable to those of other known infections. Notably, homologs of cytoplasmic incompatibility factor (cif) genes were present, indicating that these strains possess the capacity to induce the cytoplasmic incompatibility phenotype, which allows Wolbachia to spread through host populations. These strains should be further investigated as candidates for use in Wolbachia biocontrol strategies in Anopheles aiming to reduce the transmission of malaria.

RevDate: 2021-04-15

Pirolli NH, Bentley WE, SM Jay (2021)

Bacterial Extracellular Vesicles and the Gut-Microbiota Brain Axis: Emerging Roles in Communication and Potential as Therapeutics.

Advanced biology [Epub ahead of print].

Bacterial extracellular vesicles (BEVs) have emerged as candidate signaling vectors for long-distance interkingdom communication within the gut-microbiota brain axis. Most bacteria release these nanosized vesicles, capable of signaling to the brain via their abundant protein and small RNA cargo, possibly directly via crossing the blood-brain barrier. BEVs have been shown to regulate brain gene expression and induce pathology at most stages of neuroinflammation and neurodegeneration, and thus they may play a causal role in diseases such as Alzheimer's, Parkinson's, and depression/anxiety. On the other hand, BEVs have intrinsic therapeutic properties that may be relevant to probiotic therapy and can also be engineered to function as drug delivery vehicles and vaccines. Thus, BEVs may be both a cause of and solution to neuropathological conditions. In this review, current knowledge of the physiological roles of BEVs as well as state of the art pertaining to the development of therapeutic BEVs in the context of the microbiome-gut-brain axis are summarized.

RevDate: 2021-04-15

Vemulapally S, Villamizar A, Guerra T, et al (2021)

Mycobacteria In Skin Lesions and the Habitat of the Endangered Houston Toad (Anaxyrus houstonensis).

Journal of wildlife diseases pii:464125 [Epub ahead of print].

Head-starting of the federally endangered Houston toad (Anaxyrus houstonensis), that is, the release of egg strands, tadpoles, and metamorphic juveniles produced in captivity into the original breeding ponds, requires assessment of potential threats for the transmission of pathogens from captive to free-ranging toads. We used Illumina-based 16S rRNA V3 amplicon sequencing to investigate the community structure of bacteria from skin lesions of captive Houston toad and habitat (pond) samples. Proteobacteria, alone or together with Actinobacteria and, in some samples, Cyanobacteria represented virtually all reads in tissue lesion samples, whereas pond samples were much more diverse, with Acidobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Cyanobacteria, Firmicutes, Planctomycetes, Proteobacteria, and Verrucomicrobia present with little variation between samples. If present in lesions, Actinobacteria were largely represented by Mycobacteriaceae, and here mainly by one sequence identical to sequences of members of the Mycobacterium chelonae-abscessus complex. In pond samples, mycobacteria represented only a small portion of the actinobacteria, although at higher diversity with six distinct reads. Sequences for reads obtained from pond samples were identical to those representing the M. chelonae-abscessus complex, a group with Mycobacterium marinum, Mycobacterium kansasii, Mycobacterium avium, a group with Mycobacterium vaccae, Mycobacterium fortuitum, Mycobacterium poriferae, and a group with Mycobacterium elephantis and Mycobacterium celeriflavum, whereas sequences of high similarity were detected for reads related to those of Mycobacterium holsaticum, Mycobacterium pallens, and Mycobacterium obuense, and Mycobacterium goodii. Our results indicated that lesions observed on the Houston toad in captivity are not the result of mycobacteria in every case, and that the presence of mycobacteria in the captive colony does not represent a novel pathogen threat to the wild populations because such bacteria are also seen in the natural pond habitats for the Houston toad.

RevDate: 2021-04-15

Mori G, Morrison M, A Blumenthal (2021)

Microbiome-immune interactions in tuberculosis.

PLoS pathogens, 17(4):e1009377 pii:PPATHOGENS-D-20-02636.

Tuberculosis (TB) remains an infectious disease of global significance and a leading cause of death in low- and middle-income countries. Significant effort has been directed towards understanding Mycobacterium tuberculosis genomics, virulence, and pathophysiology within the framework of Koch postulates. More recently, the advent of "-omics" approaches has broadened our appreciation of how "commensal" microbes have coevolved with their host and have a central role in shaping health and susceptibility to disease. It is now clear that there is a diverse repertoire of interactions between the microbiota and host immune responses that can either sustain or disrupt homeostasis. In the context of the global efforts to combatting TB, such findings and knowledge have raised important questions: Does microbiome composition indicate or determine susceptibility or resistance to M. tuberculosis infection? Is the development of active disease or latent infection upon M. tuberculosis exposure influenced by the microbiome? Does microbiome composition influence TB therapy outcome and risk of reinfection with M. tuberculosis? Can the microbiome be actively managed to reduce risk of M. tuberculosis infection or recurrence of TB? Here, we explore these questions with a particular focus on microbiome-immune interactions that may affect TB susceptibility, manifestation and progression, the long-term implications of anti-TB therapy, as well as the potential of the host microbiome as target for clinical manipulation.

RevDate: 2021-04-15

Khanna S (2021)

Microbiota restoration for recurrent Clostridioides difficile: Getting one step closer every day!.

Journal of internal medicine [Epub ahead of print].

Clostridioides difficile infection (CDI) is an urgent health threat being the most common healthcare-associated infection, and its management is a clinical conundrum. Over 450 000 infections are seen in the United States with similar incidence seen in the rest of the developed world. The majority of infections seen are mild-moderate with fulminant disease and mortality being rare complications seen in the elderly and in those with comorbidities. The most common complication of CDI is recurrent infection with rates as high as 60% after three or more infections. A dilemma in the management of primary and recurrent CDI is testing due to the high sensitivity of the nucleic acid amplification tests such as the polymerase chain reaction, which leads to clinical false positives if patients are not chosen carefully (with symptoms) before testing. A newer testing regimen involving a 2-step strategy is emerging using glutamate dehydrogenase as a screening strategy followed by enzyme immunoassay for the C. difficile toxin. Microbiota restoration therapies are the cornerstone of management of recurrent CDI to prevent future recurrences. The most common modality of microbiota restoration is faecal microbiota transplantation, which has been tainted with heterogeneity and adverse events such as serious infectious transmission. The success rates for recurrence prevention from microbiota restoration therapies are over 90% compared with less than 50% of recurrence prevention with courses of antibiotics. This has led to development and emergence of standardized microbiota restoration therapies in capsule and enema forms. Capsule-based therapies include CP101 (positive phase II results), RBX7455 (positive phase I results), SER-109 (positive phase III results) and VE303 (ongoing phase II trial). Enema-based therapy includes RBX2660 (positive phase III data). This review summarizes the principles of management and diagnosis of CDI and focuses on emerging and existing data on faecal microbiota transplantation and standardized microbiota restoration therapies.

RevDate: 2021-04-15

Lu H, Yao Y, Yang J, et al (2021)

Microbiome-miRNA interactions in the progress from undifferentiated arthritis to rheumatoid arthritis: evidence, hypotheses, and opportunities.

Rheumatology international [Epub ahead of print].

The human microbiome has attracted attention for its potential utility in precision medicine. Increasingly, more researchers are recognizing changes in intestinal microbiome can upset the balance between pro- and anti-inflammatory factors of host immune system, potentially contributing to arthritis immunopathogenesis. Patients who develop rheumatoid arthritis from undifferentiated arthritis can face multiple irreversible joint lesions and even deformities. Strategies for identifying undifferentiated arthritis patients who have a tendency to develop rheumatoid arthritis and interventions to prevent rheumatoid arthritis development are urgently needed. Intestinal microbiome dysbiosis and shifts in the miRNA profile affect undifferentiated arthritis progression, and may play an important role in rheumatoid arthritis pathophysiologic process via stimulating inflammatory cytokines and disturbing host and microbial metabolic functions. However, a causal relationship between microbiome-miRNA interactions and rheumatoid arthritis development from undifferentiated arthritis has not been uncovered yet. Changes in the intestinal microbiome and miRNA profiles of undifferentiated arthritis patients with different disease outcomes should be studied together to uncover the role of the intestinal microbiome in rheumatoid arthritis development and to identify potential prognostic indicators of rheumatoid arthritis in undifferentiated arthritis patients. Herein, we discuss the possibility of microbiome-miRNA interactions contributing to rheumatoid arthritis development and describe the gaps in knowledge regarding their influence on undifferentiated arthritis prognosis that should be addressed by future studies.

RevDate: 2021-04-16

Thomas S, Lappin DF, Nile CJ, et al (2021)

Microbiome analysis of feline odontoclastic resorptive lesion (FORL) and feline oral health.

Journal of medical microbiology, 70(4):.

Introduction. Feline odontoclastic resorptive lesion (FORL) is one of the most common and painful oral diseases of the cat. It is characterised by tooth resorption due to destructive activity of odontoclasts. FORL can result in tooth loss. While the aetiology of FORL is not clearly understood, it is thought to be multifactorial and bacteria are likely to play a major role.Hypothesis. Dysbiosis of the normal feline oral microbiota leads to an alteration in commensal bacteria populations, which results in the development of FORL.Aim. The purpose of the current study was to determine the composition of the microbiomes associated with feline oral health and FORL.Methodology. Supragingival plaque was collected from 25 cats with a healthy oral cavity and 40 cats with FORL. DNA was extracted from each sample, the V4 region of the 16S rRNA gene amplified by polymerase chain reaction and amplicons sequenced. Diversity and species richness analyses were performed, principal component analysis was used to explore differences between the oral microbiomes of healthy cats and those with FORL, and linear discriminant analysis effect size was used to assess differences between the groups.Results. The six most abundant bacterial genera identified were Bergeyella, Capnocytophaga, Lampropedia, Morexella, Porphyromonas and Treponema. Two-step cluster analysis of the data identified two FORL sub-groups (FORL-1, FORL-2). The FORL-2 sub-group was very similar to the healthy group, whilst the FORL-1 sub-group was clearly different from both the FORL-2 sub-group and the healthy groups. In this analysis, Capnocytophaga (P <0.001) and Lampropedia (P <0.01) were found at significantly lower levels and Porphyromonas at a slightly higher level in the FORL-1 sub-group compared to the healthy and FORL-2 sub-groups. Microbial diversity was found to be less in the FORL-1 sub-group than in the healthy group. Lampropedia sp., a phosphate-accumulating oral commensal species, was significantly lower in the FORL-1 sub-group.Conclusion. The oral microbiota associated with the FORL-1 sub-group is distinct from that found in the healthy group and FORL-2 sub-group. Lampropedia species may influence the local calcium-phosphate ratio, which could be a factor in tooth and bone resorption observed in FORL.

RevDate: 2021-04-15

Xie H, Jallow A, Yue X, et al (2021)

Aspergillus flavus's Response to Antagonism Bacterial Stress Sheds Light on a Regulation and Metabolic Trade-Off Mechanism for Adversity Survival.

Journal of agricultural and food chemistry [Epub ahead of print].

Biocontrol to combat the menace of Aspergillus flavus has gained considerable attention. However, the molecular mechanisms of A. flavus 's response to antagonism biotic stress are poorly deciphered. Here, we discovered that A. flavus switches an adaptive metabolic reprogramming to ensure its adversity survival by multiomics analyses (including four omics platform). Antifungal "weapons" lipopeptides and antibacterial metabolites of imizoquin were identified. The central metabolism fluxes were significantly depleted but the expressions of most corresponding genes were considerably increased in A. flavus. Secondary metabolism that does not contribute to stress was markedly suppressed. In contrast, A. flavus antibacterial "weapon arsenal" was activated to occupy an ecological niche. Our results revealed that interlinked mitochondrial central metabolism and secondary metabolism are central to A. flavus antagonism biotic stress response. This discovery contributes to the targeted design of biocontrol agents and smart regularization of rhizosphere microbiome homeostasis to realize long-term fungi pathogen control and mitigation mycotoxin contamination.

RevDate: 2021-04-15

Luo Y, T Zhou (2021)

Connecting the dots: Targeting the microbiome in drug toxicity.

Medicinal research reviews [Epub ahead of print].

The gut microbiota has a vast influence on human health and its role in initiating, aggravating, or ameliorating diseases is beginning to emerge. Recently, its contribution to heterogeneous toxicological responses is also gaining attention, especially in drug-induced toxicity. Whether they are orally administered or not, drugs may interact with the gut microbiota directly or indirectly, which leads to altered toxicity. Present studies focus more on the unidirectional influence of how xenobiotics disturb intestinal microbial composition and functions, and thus induce altered homeostasis. However, interactions between the gut microbiota and xenobiotics are bidirectional and the impact of the gut microbiota on xenobiotics, especially on drugs, should not be neglected. Thus, in this review, we focus on how the gut microbiota modulates drug toxicity by highlighting the microbiome, microbial enzyme, and microbial metabolites. We connect the dots between drugs, the microbiome, microbial enzymes or metabolites, drug metabolites, and host toxicological responses to facilitate the discovery of microbial targets and mechanisms associated with drug toxicity. Besides this, current mainstream strategies to manipulate drug toxicity by targeting the microbiome are summarized and discussed. The review provides technical reference for the evaluation of medicinal properties in the research and development of innovative drugs, and for the future exploitation of strategies to reduce drug toxicity by targeting the microbiome.

RevDate: 2021-04-15

Dunnack HJ, Judge MP, Cong X, et al (2021)

An Integrative Review of the Role of the Oral and Gut Microbiome in Oral Health Symptomatology During Cancer Therapy.

Oncology nursing forum, 48(3):317-331.

PROBLEM IDENTIFICATION: Both chemotherapy and radiation therapy cause considerable symptom burden on patients' oral health, influencing nutritional status and quality of life. The role of the oral and gut microbiome in oral health alterations during cancer therapy is an emerging area of science in symptom management.

LITERATURE SEARCH: PubMed®, CINAHL®, and Scopus® were searched for articles published from January 2000 through July 2020.

DATA EVALUATION: Articles published in English that were focused on chemotherapy and/or radiation therapy were included in the review.

SYNTHESIS: Of the 22 identified studies, 12 described oral health symptoms during chemotherapy and radiation therapy for head and neck cancer. Ten studies assessed symptoms during treatment for a variety of solid tumors and blood cancers, with four of these describing microbial interventions for the management of oral mucositis. Interventions varied, but the results supported the benefits of probiotics and synbiotics in reducing mucositis severity. Overall, less diverse oral and gut microbiome environments were associated with increased severity of oral health symptomatology.

IMPLICATIONS FOR PRACTICE: Additional research is needed to determine how the oral and gut microbiome and microbial interventions may be used to improve oral health management during cancer treatment.

RevDate: 2021-04-15

U'Ren JM, NB Zimmerman (2021)

Oaks provide new perspective on seed microbiome assembly.

The New phytologist, 230(4):1293-1295.

RevDate: 2021-04-15

Faw LR, Raymann K, Romo Bechara N, et al (2021)

Larval Conditioning and Aging of Sand Fly Rearing Medium Affect Oviposition Site Selection in Phlebotomus papatasi (Diptera: Psychodidae) Sand Flies.

Journal of medical entomology pii:6226034 [Epub ahead of print].

Sand fly larvae develop in sheltered humid habitats containing decaying organic matter on which they feed. Previously, we showed that gravid females of Phlebotomus papatasi Scopoli (Diptera: Psychodidae) are attracted to and stimulated to lay eggs on larval rearing medium containing larvae. That study, however, did not control for the possible effect of medium aging. Our goal in this study was to evaluate the effect of larval substrate conditioning on attraction and oviposition responses of Ph. papatasi sand flies while controlling for the effect of substrate aging. Initially, we confirmed that the pretreatment fresh larval food sources (to be used as larval conditioned and unconditioned media) did not differ with respect to their effect on attraction and oviposition responses. The larval conditioned medium was produced by rearing larvae to the second/third-instar stage over 3 wk using the same larval food source. To produce larval unconditioned medium, the same amount of fresh larval food was added to a control rearing cup that did not contain larvae but was aged under identical time and conditions. Two-choice bioassays were conducted to evaluate gravid female's attraction and oviposition response to larval conditioned and unconditioned media. We found that gravid females were significantly attracted (P < 0.05) to larval conditioned medium when compared with unconditioned medium under the same amount of time and conditions. However, no such difference was found with respect to oviposition response. Both attraction and oviposition responses were significantly increased for larval conditioned and unconditioned media in comparison to the initial fresh larval food source.

RevDate: 2021-04-16

Zhu B, Zheng S, Lin K, et al (2021)

Effects of Infant Formula Supplemented With Prebiotics and OPO on Infancy Fecal Microbiota: A Pilot Randomized Clinical Trial.

Frontiers in cellular and infection microbiology, 11:650407.

Several lines of evidence suggest that the intestinal microbiota plays crucial roles in infant development, and that it is highly influenced by extrinsic and intrinsic factors. Prebiotic-containing infant formula may increase gastrointestinal tolerance and improve commensal microbiota composition. However, it remains unknown whether supplementation of milk-formulas with prebiotics and 1,3-olein-2-palmitin (OPO) can achieve feeding outcomes similar to those of breastfeeding. In the present study, we investigated the effects of two kinds of infant formula with different additives on the overall diversity and composition of the fecal microbiota, to determine which was closer to breastfeeding. A total of 108 infants were enrolled, including breastfeeding (n=59) and formula feeding group (n=49). The formula feeding infants were prospectively randomly divided into a standard formula group (n=18), and a supplemented formula group(n=31). The fecal samples were collected at 4 months after intervention. Fecal microbiota analysis targeting the V4 region of the 16S rRNA gene was performed using MiSeq sequencing. The overall bacterial diversity and composition, key functional bacteria, and predictive functional profiles in the two different formula groups were compared with breastfeeding group. We found that the alpha diversity of the gut microbiota was not significantly different between the OPO and breastfeeding groups with Chaos 1 index (p=0.346). The relative abundances of Enhydrobacter and Akkermansia in the OPO group were more similar to those of the breastfeeding group than to those of the standard formula group. The gut microbiota metabolism function prediction analysis showed that the supplemented formula group was similar to the breastfeeding group in terms of ureolysis (p=0.297). These findings suggest that, when formula supplemented with prebiotics and OPO was given, the overall bacterial diversity and parts of the composition of the fecal microbiota would be similar to that of breastfeeding infants.

RevDate: 2021-04-16

Owagboriaye F, Mesnage R, Dedeke G, et al (2021)

Impacts of a glyphosate-based herbicide on the gut microbiome of three earthworm species (Alma millsoni, Eudrilus eugeniae and Libyodrilus violaceus): A pilot study.

Toxicology reports, 8:753-758.

While the impact of glyphosate-based herbicides (GBHs) on earthworms has been studied, little is known about their effects on the earthworm gut microbiome. This study investigated the impact of a GBH on the gut microbial communities of three earthworm species (Alma millsoni, Eudrilus eugeniae and Libyodrilus violaceus). Earthworm species accommodated in soil were sprayed with 115.49 mL/m² of Roundup® Alphée or water. Gut microbiome composition was analysed using 16S rRNA Bacterial Tag-Encoded FLX Amplicon Pyrosequencing (bTEFAP) at the 8th week post-herbicide application. A profound shift in bacterial populationswas observed in all exposed earthworms with Proteobacteria becoming the dominant phylum. Affected bacteria were mostly from the genus Enterobacter, Pantoea and Pseudomonas, which together represented approximately 80 % of the total abundance assigned at the genus level in exposed earthworms, while they were present at a minor abundance (∼1%) in unexposed earthworms. Although consistent results were observed between the three groups of worm species, it is not possible to generalize these outcomes due to a lack of biological replicates, which does not allow for inferential statistical analysis. Nevertheless, our study is the first to report the effects of a GBH on the earthworm gut microbiome and paves the way for future more comprehensive investigations.

RevDate: 2021-04-16

Gong Y, Xue Y, Li X, et al (2021)

Inter- and Transgenerational Effects of Paternal Exposure to Inorganic Arsenic.

Advanced science (Weinheim, Baden-Wurttemberg, Germany), 8(7):2002715.

The rise of metabolic disorders in modern times is mainly attributed to the environment. However, heritable effects of environmental chemicals on mammalian offsprings' metabolic health are unclear. Inorganic arsenic (iAs) is the top chemical on the Agency for Toxic Substances and Disease Registry priority list of hazardous substances. Here, we assess cross-generational effects of iAs in an exclusive male-lineage transmission paradigm. The exposure of male mice to 250 ppb iAs causes glucose intolerance and hepatic insulin resistance in F1 females, but not males, without affecting body weight. Hepatic expression of glucose metabolic genes, glucose output, and insulin signaling are disrupted in F1 females. Inhibition of the glucose 6-phosphatase complex masks the intergenerational effect of iAs, demonstrating a causative role of hepatic glucose production. F2 offspring from grandpaternal iAs exposure show temporary growth retardation at an early age, which diminishes in adults. However, reduced adiposity persists into middle age and is associated with altered gut microbiome and increased brown adipose thermogenesis. In contrast, F3 offspring of the male-lineage iAs exposure show increased adiposity, especially on a high-calorie diet. These findings have unveiled sex- and generation-specific heritable effects of iAs on metabolic physiology, which has broad implications in understanding gene-environment interactions.

RevDate: 2021-04-16

Oliveira de Almeida M, Carvalho R, Figueira Aburjaile F, et al (2021)

Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil.

PeerJ, 9:e11079.

Background: Lactobacillus crispatus is the dominant species in the vaginal microbiota associated with health and considered a homeostasis biomarker. Interestingly, some strains are even used as probiotics. However, the genetic mechanisms of L. crispatus involved in the control of the vaginal microbiome and protection against bacterial vaginosis (BV) are not entirely known. To further investigate these mechanisms, we sequenced and characterized the first four L. crispatus genomes from vaginal samples from Brazilian women and used genome-wide association study (GWAS) and comparative analyses to identify genetic mechanisms involved in healthy or BV conditions and selective pressures acting in the vaginal microbiome.

Methods: The four genomes were sequenced, assembled using ten different strategies and automatically annotated. The functional characterization was performed by bioinformatics tools comparing with known probiotic strains. Moreover, it was selected one representative strain (L. crispatus CRI4) for in vitro detection of phages by electron microscopy. Evolutionary analysis, including phylogeny, GWAS and positive selection were performed using 46 public genomes strains representing health and BV conditions.

Results: Genes involved in probiotic effects such as lactic acid production, hydrogen peroxide, bacteriocins, and adhesin were identified. Three hemolysins and putrescine production were predicted, although these features are also present in other probiotic strains. The four genomes presented no plasmids, but 14 known families insertion sequences and several prophages were detected. However, none of the mobile genetic elements contained antimicrobial resistance genes. The genomes harbor a CRISPR-Cas subtype II-A system that is probably inactivated due to fragmentation of the genes csn2 and cas9. No genomic feature was associated with a health condition, perhaps due to its multifactorial characteristic. Five genes were identified as under positive selection, but the selective pressure remains to be discovered. In conclusion, the Brazilian strains investigated in this study present potential protective properties, although in vitro and in vivo studies are required to confirm their efficacy and safety to be considered for human use.

RevDate: 2021-04-16

Gavriliuc S, Stothart MR, Henry A, et al (2021)

Long-term storage of feces at -80 °C versus -20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome.

PeerJ, 9:e10837.

The development of next-generation sequencing technologies has spurred a surge of research on bacterial microbiome diversity and function. But despite the rapid growth of the field, many uncertainties remain regarding the impact of differing methodologies on downstream results. Sample storage temperature is conventionally thought to be among the most important factors for ensuring reproducibility across marker gene studies, but to date much of the research on this topic has focused on short-term storage in the context of clinical applications. Consequently, it has remained unclear if storage at -80 °C, widely viewed as the gold standard for long-term archival of feces, is truly required for maintaining sample integrity in amplicon-based studies. A better understanding of the impacts of long-term storage conditions is important given the substantial cost and limited availability of ultra-low temperature freezers. To this end, we compared bacterial microbiome profiles inferred from 16S V3-V4 amplicon sequencing for paired fecal samples obtained from a feral horse population from Sable Island, Nova Scotia, Canada, stored at either -80 °C or -20 °C for 4 years. We found that storage temperature did not significantly affect alpha diversity measures, including amplicon sequence variant (ASV) richness and evenness, and abundance of rare sequence variants, nor presence/absence, relative abundances and phylogenetic diversity weighted measures of beta diversity. These results indicate that storage of equine feces at -20 °C for periods ranging from a few months to a few years is equivalent to storage at -80 °C for amplicon-based microbiome studies, adding to accumulating evidence indicating that standard domestic freezers are both economical and effective for microbiome research.

RevDate: 2021-04-16

Liu YCG, Lan SJ, Hirano H, et al (2021)

Update and review of the gerodontology prospective for 2020's: Linking the interactions of oral (hypo)-functions to health vs. systemic diseases.

Journal of dental sciences, 16(2):757-773.

New lines of evidence suggest that the oral-systemic medical links and oral hypo-function are progressively transcending beyond the traditional clinical signs and symptoms of oral diseases. Research into the dysbiotic microbiome, host immune/inflammatory regulations and patho-physiologic changes and subsequent adaptations through the oral-systemic measures under ageism points to pathways leading to mastication deficiency, dysphagia, signature brain activities for (neuro)-cognition circuitries, dementia and certain cancers of the digestive system as well. Therefore, the coming era of oral health-linked systemic disorders will likely reshape the future of diagnostics in oral geriatrics, treatment modalities and professional therapies in clinical disciplines. In parallel to these highlights, a recent international symposium was jointly held by the International Association of Gerontology and Geriatrics (IAGG), Japanese Society of Gerodontology (JSG), the representative of USA and Taiwan Academy of Geriatric Dentistry (TAGD) on Oct 25th, 2019. Herein, specific notes are briefly addressed and updated for a summative prospective from this symposium and the recent literature.

RevDate: 2021-04-16

Yang C, Kwon DI, Kim M, et al (2021)

Commensal Microbiome Expands Tγδ17 Cells in the Lung and Promotes Particulate Matter-Induced Acute Neutrophilia.

Frontiers in immunology, 12:645741.

Particulate matter (PM) induces neutrophilic inflammation and deteriorates the prognosis of diseases such as cardiovascular diseases, cancers, and infections, including COVID-19. Here, we addressed the role of γδ T cells and intestinal microbiome in PM-induced acute neutrophilia. γδ T cells are a heterogeneous population composed of Tγδ1, Tγδ2, Tγδ17, and naïve γδ T cells (TγδN) and commensal bacteria promote local expansion of Tγδ17 cells, particularly in the lung and gut without affecting their Vγ repertoire. Tγδ17 cells are more tissue resident than Tγδ1 cells, while TγδN cells are circulating cells. IL-1R expression in Tγδ17 cells is highest in the lung and they outnumber all the other type 17 cells such as Th17, ILC3, NKT17, and MAIT17 cells. Upon PM exposure, IL-1β-secreting neutrophils and IL-17-producing Tγδ17 cells attract each other around the airways. Accordingly, PM-induced neutrophilia was significantly relieved in γδ T- or IL-17-deficient and germ-free mice. Collectively, these findings show that the commensal microbiome promotes PM-induced neutrophilia in the lung via Tγδ17 cells.

RevDate: 2021-04-16

Tegtmeier D, Hurka S, Klüber P, et al (2021)

Cottonseed Press Cake as a Potential Diet for Industrially Farmed Black Soldier Fly Larvae Triggers Adaptations of Their Bacterial and Fungal Gut Microbiota.

Frontiers in microbiology, 12:634503.

Black soldier fly larvae (Hermetia illucens, Diptera: Stratiomyidae) are used for the bioconversion of organic side products into valuable compounds such as proteins, lipids and chitin. However, the economic competitiveness of farmed insects compared to conventional protein production systems in agriculture and aquaculture depends on the availability of large quantities of inexpensive insect feed. Cottonseed press cake (CPC) is a side-stream of cotton production that is rich in proteins and lipids but unsuitable as feed for several farmed animals, except ruminants, due to the presence of the anti-nutritional sesquiterpenoid gossypol. Here, we tested CPC as a feed for black soldier fly larvae and studied the impact of this diet on the gut microbiome. Larvae reared on CPC developed normally and even showed a shorter life-cycle, but were smaller at the end of larval development than control larvae reared on chicken feed. The adaptability of the larvae to different diets is mediated by their versatile gut microbiome, which facilitates digestion and detoxification. We therefore used amplicon sequencing to analyze the bacterial and fungal communities associated with larvae reared on each diet, revealing differences between the larval guts and frass (residual feed substrate) as well as differences between the two diet groups. For example, Actinomycetaceae and Aspergillaceae were significantly enriched in guts of the CPC diet group and may help to metabolize compounds such as gossypol. Potentially probiotic yeasts and beneficial Enterobacteriaceae, which presumably belong to the core microbiota, were detected in high relative abundance in the gut and frass, indicating a functional role of these microbes, especially the protection against pathogens. We conclude that CPC may be suitable as an inexpensive and environmentally sustainable feed for the industrial rearing of black soldier flies.

RevDate: 2021-04-15

Carrier TJ, Leigh BA, Deaker DJ, et al (2021)

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history.

Proceedings of the National Academy of Sciences of the United States of America, 118(16):.

Animal gastrointestinal tracts harbor a microbiome that is integral to host function, yet species from diverse phyla have evolved a reduced digestive system or lost it completely. Whether such changes are associated with alterations in the diversity and/or abundance of the microbiome remains an untested hypothesis in evolutionary symbiosis. Here, using the life history transition from planktotrophy (feeding) to lecithotrophy (nonfeeding) in the sea urchin Heliocidaris, we demonstrate that the lack of a functional gut corresponds with a reduction in microbial community diversity and abundance as well as the association with a diet-specific microbiome. We also determine that the lecithotroph vertically transmits a Rickettsiales that may complement host nutrition through amino acid biosynthesis and influence host reproduction. Our results indicate that the evolutionary loss of a functional gut correlates with a reduction in the microbiome and the association with an endosymbiont. Symbiotic transitions can therefore accompany life history transitions in the evolution of developmental strategies.

RevDate: 2021-04-15

Peña-Cearra A, Belanche A, Gonzalez-Lopez M, et al (2021)

Peripheral blood mononuclear cells (PBMC) microbiome is not affected by colon microbiota in healthy goats.

Animal microbiome, 3(1):28.

BACKGROUND: The knowledge about blood circulating microbiome and its functional relevance in healthy individuals remains limited. An assessment of changes in the circulating microbiome was performed by sequencing peripheral blood mononuclear cells (PBMC) bacterial DNA from goats supplemented or not in early life with rumen liquid transplantation.

RESULTS: Most of the bacterial DNA associated to PBMC was identified predominantly as Proteobacteria (55%) followed by Firmicutes (24%), Bacteroidetes (11%) and Actinobacteria (8%). The predominant genera found in PBMC samples were Pseudomonas, Prevotella, Sphingomonas, Acinetobacter, Corynebacterium and Ruminococcus. Other genera such as Butyrivibrivio, Bifidobacterium, Dorea and Coprococcus were also present in lower proportions. Several species known as blood pathogens or others involved in gut homeostasis such as Faecalibacterium prausnitzii were also identified. However, the PBMC microbiome phylum composition differed from that in the colon of goats (P ≤ 0.001), where Firmicutes was the predominant phylum (83%). Although, rumen liquid administration in early-life altered bacterial community structure and increased Tlr5 expression (P = 0.020) in colon pointing to higher bacterial translocation, less than 8% of OTUs in colon were also observed in PBMCs.

CONCLUSIONS: Data suggest that in physiological conditions, PBMC microbiome differs from and is not affected by colon gut microbiota in small ruminants. Although, further studies with larger number of animals and covering other animal tissues are required, results point to a common circulating bacterial profile on mammals being phylum Proteobacteria, and genera Pseudomonas and Prevotella the most abundants. All suggest that PBMC microbiome in healthy ruminants could be implicated in homeostatic condition. This study expands our knowledge about PBMC microbiome contribution to health in farm animals.

RevDate: 2021-04-15

Mu A, McDonald D, Jarmusch AK, et al (2021)

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection.

Microbiome, 9(1):92.

BACKGROUND: Infectious bacterial diseases exhibiting increasing resistance to antibiotics are a serious global health issue. Bacteriophage therapy is an anti-microbial alternative to treat patients with serious bacterial infections. However, the impacts to the host microbiome in response to clinical use of phage therapy are not well understood.

RESULTS: Our paper demonstrates a largely unchanged microbiota profile during 4 weeks of phage therapy when added to systemic antibiotics in a single patient with Staphylococcus aureus device infection. Metabolomic analyses suggest potential indirect cascading ecological impacts to the host (skin) microbiome. We did not detect genomes of the three phages used to treat the patient in metagenomic samples taken from saliva, stool, and skin; however, phages were detected using endpoint-PCR in patient serum.

CONCLUSION: Results from our proof-of-principal study supports the use of bacteriophages as a microbiome-sparing approach to treat bacterial infections. Video abstract.

RevDate: 2021-04-16
CmpDate: 2021-04-16

Kobzová Š, Vacek L, Lipový B, et al (2021)

Enzyme-based treatment of skin and soft tissue infections.

Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceske lekarske spolecnosti J.E. Purkyne, 70(1):52-61.

Inflammatory diseases of the skin and soft tissues are an important group of human infections. The most common causes are the bacteria Staphylococcus aureus and Streptococcus pyogenes. Given the growing resistance of these pathogens to antimicrobials, the current research focuses on the search for novel therapeutic options that would be effective against infections refractory to conventional antimicrobials. A promising alternative is the use of enzyme-based antimicrobials (enzybiotics) that degrade the bacterial cell wall. They target the specific pathogen but do not affect the skin microbiome, thus helping the healing process. As enzymes can be poorly soluble, unstable, or subject to rapid elimination from the body, efforts are made to create biobetters, i.e., enzymes with improved characteristics. Emphasis is also put on the development of novel enzybiotic carriers or wound healing dressings with integrated enzymes.

RevDate: 2021-04-14

Oyetibo GO, Ige OO, Obinani PK, et al (2021)

Ecological risk potentials of petroleum hydrocarbons and heavy metals shape the bacterial communities of marine hydrosphere at Atlantic Ocean, Atlas Cove, Nigeria.

Journal of environmental management, 289:112563 pii:S0301-4797(21)00625-3 [Epub ahead of print].

Trans-Atlantic voyage of petroleum often leads to marine pollution with petroleum hydrocarbons (PHs) and heavy metals (HMs) that defines structures of autochthonous bacteria in the hydrosphere. Bacterial taxa of marine sediments exposed to petroleum transport activities were profiled using 16S rDNA metagenomics and correlated with the geochemistry to establish their impact on the microbiome. The physico-chemistry of the marine systems revealed varied degrees of contamination with PHs and HMs exceeding recommended threshold for aquatic life. Ecological risk assessment based on organic carbon of the sediment established phenanthrene, anthracene, and pyrene posed high risks (index risk quotient >32) to marine life. The most dominant phylum of the 44 bacterial phyla in the marine-sphere was Proteobacteria with relative abundance of 45-77% in the sampling locations. Relative dominance of Proteobacteria in the sediments spanned Gammaproteobacteria (17-25%), Deltaproteobacteria (12-20%), and Alphaproteobacteria (7-14%). Whereas, more operational taxonomic units (OTUs) belonging to Epsilonproteobacteria (19 ± 2.4%) were found in estuarine sediment unlike < 0.5% relative abundances obtained from oceanic sediments. Sulfurimonas apparently dominated the bacterial genera with up to 2.16 ± 0.19% abundance in oceanic sediments. Canonical correspondence analysis revealed that PHs shaped the structure of bacterial OTUs in oceanic sediments where petroleum loading/offloading occurs unlike in some kilometres a yonder where HMs correlated with the bacteria structure. The dominant bacteria might possibly pivotal to ecophysiologies of hydrocarbon contaminated marine environment, and would be pertinent to biotechnological applications for possible bioremediation campaign.

RevDate: 2021-04-14

Kwon AHK, SA Liddelow (2021)

Astrocytes have a license to kill inflammatory T cells.

Immunity, 54(4):614-616.

Microbiome-induced interferon signaling through gut-derived natural killer cells is integral to minimize peripheral inflammatory responses in the brain and spinal cord. In a recent issue of Nature, Sanmarco, Wheeler, et al. define how interferon signaling induces LAMP1+TRAIL+ astrocytes, which cause death of inflammatory T cells, mitigating degeneration in a mouse model of demyealination.

RevDate: 2021-04-14

Gutiérrez-Salmerón M, Lucena SRR, Chocarro-Calvo A, et al (2021)

Remodelling of colorectal cancer cell signaling by microbiota and immunity in diabetes.

Endocrine-related cancer pii:ERC-20-0315.R2 [Epub ahead of print].

Obesity is the strongest known risk factor to develop Type 2 diabetes (T2D) and both share a state of chronic, diffuse and low-grade inflammation, impaired immune responses and alterations in the composition and function of the microbiome. Notably, these hallmarks are shared with colorectal cancer (CRC), which is epidemiologically associated to obesity and T2D. Gut barrier damages in T2D, destabilize the microbiome that metabolizes the diet and modulates the host immune response triggering inflammatory and proliferative pathways. In this review, we discuss the pathways altered by defects in the immune response and microbiota that may link T2D to CRC development. Stressed adipocytes, metabolic incongruity in blood and gut barrier failure with dysbiosis cooperate to establish imbalances between immune innate and adaptive cells and cytokines such as interleukin 6 (IL-6) or tumour necrosis factor α (TNF-α) that define low-grade diffuse inflammation in T2D. Inflammation drives tissue repair through proliferation and migration (critical mechanisms for tumourigenesis) and under physiological conditions feeds anti-inflammatory cytokine production to resolve the process. The disproportion in pro- versus anti-inflammatory cells and cytokines imposed by T2D will impact the tumour micro- and macro-environment, favouring tumour proliferation, angiogenesis and decreased immune responses. Complex bidirectional relationships between the metabolic environment of T2D, gut microbiota, and immune dysfunctions may favour tumour cell demands and will define the outcome. Animal models developed to study the relationships between T2D and CRC in the context of microbiota and immune system are discussed.

RevDate: 2021-04-15

Baldwin H, Alexis AF, Andriessen A, et al (2021)

Evidence of Barrier Deficiency in Rosacea and the Importance of Integrating OTC Skincare Products into Treatment Regimens.

Journal of drugs in dermatology : JDD, 20(4):384-392.

BACKGROUND: Rosacea, an inflammatory skin disease that leads to an impaired skin barrier function commonly involves the face. Symptoms of rosacea can be bothersome and include pain, stinging, burning, itching, and facial flushing. This review explored skin barrier impairment in rosacea and reduced symptomatology when using over the counter (OTC) skincare products.

METHODS: Nine dermatologists (the panel) completed a survey on OTC products they recommend for rosacea. The survey results were summarized, presented, and discussed during the online meeting, together with the results of a literature review. The outcome of these discussions, coupled with the panel's expert opinion and experience, is shown in the current review.

RESULTS: Addressing barrier dysfunction by use of moisturizer and cleanser formulations that restore skin hydration, normalize skin pH, restore the microbiome, and skin lipids can assist in improving rosacea signs and symptoms. The panel's consensus was that in addition to the use of prescription medications, skincare recommendations are a crucial part of successful rosacea therapy. In addition to occlusives and humectants, barrier restoring ingredients such as ceramides, hyaluronic acid, and niacinamide were considered beneficial. Equally important was the absence of potentially irritating substances.

CONCLUSIONS: The use of OTC products can improve rosacea symptomatology and signs. As adjuncts, these products are recommended before and during prescription therapy and as part of a maintenance regimen. J Drugs Dermatol. 20(4):384-392. doi:10.36849/JDD.5861 THIS ARTICLE HAD BEEN MADE AVAILABLE FREE OF CHARGE. PLEASE SCROLL DOWN TO ACCESS THE FULL fTEXT OF THIS ARTICLE WITHOUT LOGGING IN. NO PURCHASE NECESSARY. PLEASE CONTACT THE PUBLISHER WITH ANY QUESTIONS.

RevDate: 2021-04-14

Yang Y, Chi L, Lai Y, et al (2021)

The gut microbiome and arsenic-induced disease-iAs metabolism in mice.

Current environmental health reports [Epub ahead of print].

PURPOSE OF REVIEW: This review summarizes inorganic arsenic (iAs) metabolism and toxicity in mice and the gut microbiome and how iAs and the gut microbiome interact to induce diseases.

RECENT FINDINGS: Recently, a variety of studies have started to reveal the interactions between iAs and the gut microbiome. Evidence shows that gut bacteria can influence iAs biotransformation and disease risks. The gut microbiome can directly metabolize iAs, and it can also indirectly be involved in iAs metabolism through the host, such as altering iAs absorption, cofactors, and genes related to iAs metabolism. Many factors, such as iAs metabolism influenced by the gut microbiome, and microbiome metabolites perturbed by iAs can lead to different disease risks. iAs is a widespread toxic metalloid in environment, and iAs toxicity has become a global health issue. iAs is subject to metabolic reactions after entering the host body, including methylation, demethylation, oxidation, reduction, and thiolation. Different arsenic species, including trivalent and pentavalent forms and inorganic and organic forms, determine their toxicity. iAs poisoning is predominately caused by contaminated drinking water and food, and chronic arsenic toxicity can cause various diseases. Therefore, studies of iAs metabolism are important for understanding iAs associated disease risks.

RevDate: 2021-04-16

Hochstedler BR, Burnett L, Price TK, et al (2021)

Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods.

International urogynecology journal [Epub ahead of print].

INTRODUCTION AND HYPOTHESIS: Many clinicians utilize standard culture of voided urine to guide treatment for women with recurrent urinary tract infections (RUTI). However, despite antibiotic treatment, symptoms may persist and events frequently recur. The cyclic nature and ineffective treatment of RUTI suggest that underlying uropathogens pass undetected because of the preferential growth of Escherichia coli. Expanded quantitative urine culture (EQUC) detects more clinically relevant microbes. The objective of this study was to assess how urine collection and culture methods influence microbial detection in RUTI patients.

METHODS: This cross-sectional study enrolled symptomatic adult women with an established RUTI diagnosis. Participants contributed both midstream voided and catheterized urine specimens for culture via both standard urine culture (SUC) and EQUC. Presence and abundance of microbiota were compared between culture and collection methods.

RESULTS: Forty-three symptomatic women participants (mean age 67 years) contributed specimens. Compared to SUC, EQUC detected more unique bacterial species and consistently detected more uropathogens from catheterized and voided urine specimens. For both collection methods, the most commonly detected uropathogens by EQUC were E. coli (catheterized: n = 8, voided: n = 12) and E. faecalis (catheterized: n = 7, voided: n = 17). Compared to catheterized urine samples assessed by EQUC, SUC often missed uropathogens, and culture of voided urines by either method yielded high false-positive rates.

CONCLUSIONS: In women with symptomatic RUTI, SUC and assessment of voided urines have clinically relevant limitations in uropathogen detection. These results suggest that, in this population, catheterized specimens analyzed via EQUC provide clinically relevant information for appropriate diagnosis.

RevDate: 2021-04-14

Liu Q, Tian X, Maruyama D, et al (2021)

Lung Immune Tone via Gut-Lung Axis: Gut-derived LPS and Short-chain Fatty Acids' immunometabolic regulation of Lung IL-1β, FFAR2 and FFAR3 Expression.

American journal of physiology. Lung cellular and molecular physiology [Epub ahead of print].

Microbial metabolites produced by the gut microbiome, e.g. short-chain fatty acids (SCFA), have been found to influence lung physiology and injury responses. However, how lung immune activity is regulated by SCFA is unknown. We examined fresh human lung tissue and observed the presence of SCFA with inter-individual variability. In vitro, SCFA were capable of modifying the metabolic programming in LPS-exposed alveolar macrophages (AM). We hypothesized that lung immune tone could be defined by baseline detection of lung intracellular IL-1β. Therefore, we interrogated naïve mouse lungs with intact gut microbiota for IL-1β mRNA expression and localized its presence within alveolar spaces, specifically within AM subsets. We established that metabolically active gut microbiota, that produce SCFA, can transmit LPS and SCFA to the lung and thereby could create primed lung immunometabolic tone. To understand how murine lung cells sensed and upregulated IL-1β in response to gut microbiome-derived factors, we determined that, in vitro, AM and AT2 cells expressed SCFA receptors, FFAR2, FFAR3, and IL-1β but with distinct expression patterns and different responses to LPS. Finally, we observed that IL-1β, FFAR2 and FFAR3 were expressed in isolated human AM and AT2 cells ex-vivo, but in fresh human lung sections in situ, only AM expressed IL-1β at rest and after LPS challenge. Together, this translational study using mouse and human lung tissue and cells point to an important role for the gut microbiome and their SCFA in establishing and regulating lung immune tone.

RevDate: 2021-04-15

D'Alterio MN, Giuliani C, Scicchitano F, et al (2021)

Possible role of microbiome in the pathogenesis of endometriosis.

Minerva obstetrics and gynecology, 73(2):193-214.

INTRODUCTION: There is an urgent necessity to explore the complex pathophysiological nature of endometriosis, which may enable the rationale for new diagnostic and therapeutic strategies to be discovered. This systematic review aimed to clarify the bidirectional relationship between endometriosis and the microbiome and evaluate if the microbiome may be involved in endometriosis's pathogenesis, establishing a potential connection between the different studies.

EVIDENCE ACQUISITION: Studies were identified through a systematic literature search of papers that evaluated the microbiomes of human or other animal species with endometriosis and of those without in the electronic database PubMed/Medline, and Embase without a date restriction. We included all cohort studies focusing on the interaction between endometriosis and the microbiomes of humans or other mammals, evaluating if the microbiome may be involved in endometriosis's pathogenesis.

EVIDENCE SYNTHESIS: Endometriosis appears to be associated with elevated levels of different microorganisms across various microbiome sites. An ineffective immune response seems to play a key role in endometriosis pathogenesis, and there is some scientific proof to state that the immune response may be modulated by the microbiome. Interestingly, nine studies of our review detected species belonging to the phyla Proteobacteria, Bacteroidetes, and Negativicutes characterized by Gram-negative staining, that were significantly increased in endometriosis cohorts.

CONCLUSIONS: Laboratory and clinical investigations indicate that hosts' microbiome profiles with and without endometriosis can be significantly different. To further our understanding of the relationships between endometriosis and the host microbiome, more studies are necessary.

RevDate: 2021-04-14

Hysa E, Cutolo CA, Gotelli E, et al (2021)

Immunopathophysiology and clinical impact of uveitis in inflammatory rheumatic diseases: an update.

European journal of clinical investigation [Epub ahead of print].

BACKGROUND: Uveitis is one of the most frequent ophthalmologic manifestations in rheumatology. Uveal inflammation can underlie a systemic inflammatory rheumatic disease (SIRD) in approximately 30 % of cases with a significant burden on the quality of life since it represents a cause of blindness in up to 20 % of cases in Western countries.

METHODS: In this review, we provide a comprehensive overview of the pathophysiology of uveitis associated with SIRDs. According to our literature survey on the epidemiology of uveitis among SIRDs, spondyloarthritides, Behçet's disease and sarcoidosis get the major impact.

RESULTS: In Behçet's uveitis, the key players are highly polarized Th1 and Th17 lymphocytes, natural killer T cells and γδ T cells. All contribute to a great destructive inflammatory environment with the most serious visual damage resulting from the involvement of the posterior segment of the eye. In contrast, spondyloarthritides-related uveitis derives from a complex interaction between genetic background and extra-ocular inflammatory mediators originating from enthesitis, arthritis, psoriatic lesions and microbiome pro-inflammatory alterations. In such conditions, the immune infiltration of CD4+ T cells, Th17 and natural killer cells along with pro-inflammatory cytokines, TNF-α amongst all, lead to intraocular inflammation. Lastly, granuloma formation represents the primary hallmark lesion in sarcoid uveitis. This suggests a profound link between the innate system that mainly recruits activated macrophages and adaptive system involving by Th1, Th17 and Th17.1 cells.

CONCLUSIONS: Awareness amongst rheumatologists of a potential severe ocular involvement generates new insights into targeted therapeutic approaches and personalized treatments for each patient.

RevDate: 2021-04-14

Merenstein C, Liang G, Whiteside SA, et al (2021)

Signatures of COVID-19 severity and immune response in the respiratory tract microbiome.

medRxiv : the preprint server for health sciences.

Rationale: Viral infection of the respiratory tract can be associated with propagating effects on the airway microbiome, and microbiome dysbiosis may influence viral disease.

Objective: To define the respiratory tract microbiome in COVID-19 and relationship disease severity, systemic immunologic features, and outcomes.

Methods and Measurements: We examined 507 oropharyngeal, nasopharyngeal and endotracheal samples from 83 hospitalized COVID-19 patients, along with non-COVID patients and healthy controls. Bacterial communities were interrogated using 16S rRNA gene sequencing, commensal DNA viruses Anelloviridae and Redondoviridae were quantified by qPCR, and immune features were characterized by lymphocyte/neutrophil (L/N) ratios and deep immune profiling of peripheral blood mononuclear cells (PBMC).

Main Results: COVID-19 patients had upper respiratory microbiome dysbiosis, and greater change over time than critically ill patients without COVID-19. Diversity at the first time point correlated inversely with disease severity during hospitalization, and microbiome composition was associated with L/N ratios and PBMC profiles in blood. Intubated patients showed patient-specific and dynamic lung microbiome communities, with prominence of Staphylococcus . Anelloviridae and Redondoviridae showed more frequent colonization and higher titers in severe disease. Machine learning analysis demonstrated that integrated features of the microbiome at early sampling points had high power to discriminate ultimate level of COVID-19 severity.

Conclusions: The respiratory tract microbiome and commensal virome are disturbed in COVID-19, correlate with systemic immune parameters, and early microbiome features discriminate disease severity. Future studies should address clinical consequences of airway dysbiosis in COVID-19, possible use as biomarkers, and role of bacterial and viral taxa identified here in COVID-19 pathogenesis.

RevDate: 2021-04-14

Malecki KMC, Nikodemova M, Schultz AA, et al (2021)

The Survey of the Health of Wisconsin (SHOW) Program: An infrastructure for Advancing Population Health Sciences.

medRxiv : the preprint server for health sciences.

Purpose: The Survey of the Health of Wisconsin (SHOW) was established in 2008 by the University of Wisconsin (UW) School of Medicine and Public Health (SMPH) with the goals of 1) providing a timely and accurate picture of the health of the state residents; and 2) serving as an agile resource infrastructure for ancillary studies. Today SHOW continues to serve as a vital population health research infrastructure.

Participants: SHOW currently includes 5,846 adult and 980 minor participants recruited between 2008-2019 in four primary waves. WAVE I (2008-2013) includes annual statewide representative samples of 3,380 adults ages 21 to 74 years. WAVE II (2014-2016) is a triannual statewide sample of 1957 adults (age ≥18 years) and 645 children. WAVE III (2017) consists of follow-up of 725 adults from the WAVE I and baseline surveys of 222 children in selected households. WAVEs II and III include stool samples collected as part of an ancillary study in a subset of 784 individuals. WAVE IV consist of 517 adults and 113 children recruited from traditionally under-represented populations in biomedical research including African Americans and Hispanics in Milwaukee county, WI.

Findings to Date: The SHOW provides extensive data to examine the intersectionality of multiple social determinants and population health. SHOW includes a large biorepository and extensive health data collected in a geographically diverse urban and rural population. Over 60 studies have been published covering a broad range of topics including, urban and rural disparities in cardio-metabolic disease and cancer, objective physical activity, sleep, green-space and mental health, transcriptomics, the gut microbiome, antibiotic resistance, air pollution, concentrated animal feeding operations and heavy metal exposures.

Future Plans: The SHOW cohort is available for continued longitudinal follow-up and ancillary studies including genetic, multi-omic and translational environmental health, aging, microbiome and COVID-19 research.

Article Summary: Strengths and limitations: The Survey of the Health of Wisconsin (SHOW) is an infrastructure to advance population health sciences including biological sample collection and broader data on individual and neighborhood social and environmental determinants of health.The extensive data from diverse urban and rural populations offers a unique study sample to compare how socio-economic gradients shape health outcomes in different contexts.The objective health data supports novel interdisciplinary research initiatives and is especially suited for research in causes and consequences of environmental exposures (physical, chemical, social) across the life course on cardiometabolic health, immunity, and aging related conditions.The extensive biorepository supports novel omics research into common biological mechanisms underlying numerous complex chronic conditions including inflammation, oxidative stress, metabolomics, and epigenetic modulation.Ancillary studies, such as the Wisconsin Microbiome Study, have expanded the utility of the study to examine human susceptibility to environmental exposures and opportunities for investigations of the role of microbiome in health and disease.Long-standing partnerships and recent participation among traditionally under-represented populations in biomedical research offer numerous opportunities to support community-driven health equity work.No biological samples were collected among children.The statewide sampling frame may limit generalizability to other regions in the United States.

RevDate: 2021-04-14

Prasad R, Patton MJ, Floyd JL, et al (2021)

Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis.

bioRxiv : the preprint server for biology.

The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria . The abundance of gram-negative bacteria (Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas) was higher than the gram-positive bacteria (Staphylococcus and Lactobacillus) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282±199.6 vs 838.1±91.33; p=0.0757), PGN (34.64±3.178 vs 17.53±2.12; p<0.0001), and LPS (405.5±48.37 vs 249.6±17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.

RevDate: 2021-04-16

Chen J, Xi Z, Shi Y, et al (2021)

Highly homogeneous microbial communities dominated by Mycoplasma pneumoniae instead of increased resistance to macrolide antibiotics is the characteristic of lower respiratory tract microbiome of children with refractory Mycoplasma pneumoniae pneumonia.

Translational pediatrics, 10(3):604-615.

Background: Although researchers have found that the microbiota changed during the lower respiratory tract (LRT) infection, little was known about the association between LRT microbiome and refractory M. pneumoniae pneumonia (RMPP).

Methods: From June 28th, 2019 to March 23rd, 2020, we enrolled fifty-two children diagnosed with RMPP or non-refractory M. pneumoniae pneumonia (NRMPP), and characterized the structure and function of microbiota in the bronchoalveolar lavage fluid (BALF) by metagenomic next generation sequencing (mNGS).

Results: Based on Bray-Curtis distance between samples, samples in RMPP group were highly homogeneous, and Shannon index in the RMPP group was much lower than NRMPP group while Simpson index, which presents the degree of dominance, was higher in RMPP group. The dominant taxon with relative abundance greater than 50% was merely Mycoplasma among RMPP and NRMPP patients, but the proportions of other taxonomic distribution were different. M. pneumoniae was the dominant species and occupied almost all niches in the vast majority of RMPP patients, whereas the other genera were dramatically lower. The NRMPP group was more enriched in antibiotic resistance genes (ARGs) than the RMPP group, and also exhibited a greater relative abundance of macrolide antibiotics resistance gene (macB) and fluoroquinolone antibiotic resistance genes (patA-B) in M. pneumoniae genome. In RMPP patients, higher relative abundance of Streptococcus pneumoniae had a strong correlation with increased hospitalization days while higher relative abundance of Streptococcus pneumoniae had a negative correlation with hospitalization days among NRMPP patients.

Conclusions: The microbiota of LRT in children with RMPP was much more homogeneous and simpler than that of the NRMPP group and with lower relative abundance of macrolide antibiotics resistance gene in M. pneumoniae genome. M. pneumoniae was absolutely dominant in the vast majority of RMPP patients. Prolonged hospitalization days was associated with relative abundance of M. pneumoniae in NRMPP patients while it was related with other pathogens' relative abundance (e.g., Streptococcus pneumoniae) in RMPP patients.

RevDate: 2021-04-14

Li JKM, Wang LL, Wong CYP, et al (2021)

A cross-sectional study on gut microbiota in prostate cancer patients with prostatectomy or androgen deprivation therapy.

Prostate cancer and prostatic diseases [Epub ahead of print].

BACKGROUND: Androgen deprivation therapy (ADT), either by medical or surgical castration, is the backbone for standard treatment of locally advanced or metastatic prostate cancer, yet it is also associated with various metabolic and cardiovascular complications. Recent evidence have shown that obesity, insulin resistance, or metabolic disturbances can be associated with changes in the gut microbiome, while animal studies also show that castration is associated with changes in the gut microbiome. This study aims to investigate whether the fecal microbiota in prostate cancer patients who had undergone prostatectomy or ADT are different, and explore changes in phylogeny and pathways that may lead to side effects from ADT.

METHODS: A total of 86 prostate cancer patients (56 patients on ADT and 30 patients with prostatectomy) were recruited. The fecal microbiota was analyzed by the 16S rRNA gene for alpha- and beta-diversities by QIIME2, as well as the predicted metabolic pathways by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2.

RESULTS: The alpha-diversity was significantly lower in the ADT group. The beta-diversity was significantly different between the groups, in which Ruminococcus gnavus and Bacteroides spp were having higher relative abundance in the ADT group, whereas Lachnospira and Roseburia were reduced. The Firmicutes-to-Bacteroidetes ratio is noted to be lower in the ADT group as well. The functional pathway prediction showed that the biosynthesis of lipopolysaccharide (endotoxin) and propanoate was enriched in the ADT as well as the energy cycle pathways. This study is limited by the cross-sectional design and the clinical heterogeneity.

CONCLUSIONS: There is a significant difference in gut microbiome between prostate cancer patients on ADT and prostatectomy. We theorize that this difference may contribute to the development of metabolic complications from ADT. Further longitudinal studies are awaited.

RevDate: 2021-04-14

Bent SM, Miller CA, Sharp KH, et al (2021)

Differential Patterns of Microbiota Recovery in Symbiotic and Aposymbiotic Corals following Antibiotic Disturbance.

mSystems, 6(2):.

Microbial relationships are critical to coral health, and changes in microbiomes are often exhibited following environmental disturbance. However, the dynamics of coral-microbial composition and external factors that govern coral microbiome assembly and response to disturbance remain largely uncharacterized. Here, we investigated how antibiotic-induced disturbance affects the coral mucus microbiota in the facultatively symbiotic temperate coral Astrangia poculata, which occurs naturally with high (symbiotic) or low (aposymbiotic) densities of the endosymbiotic dinoflagellate Breviolum psygmophilum We also explored how differences in the mucus microbiome of natural and disturbed A. poculata colonies affected levels of extracellular superoxide, a reactive oxygen species thought to have both beneficial and detrimental effects on coral health. Using a bacterial and archaeal small-subunit (SSU) rRNA gene sequencing approach, we found that antibiotic exposure significantly altered the composition of the mucus microbiota but that it did not influence superoxide levels, suggesting that superoxide production in A. poculata is not influenced by the mucus microbiota. In antibiotic-treated A. poculata exposed to ambient seawater, mucus microbiota recovered to its initial state within 2 weeks following exposure, and six bacterial taxa played a prominent role in this reassembly. Microbial composition among symbiotic colonies was more similar throughout the 2-week recovery period than that among aposymbiotic colonies, whose microbiota exhibited significantly more interindividual variability after antibiotic treatment and during recovery. This work suggests that the A. poculata mucus microbiome can rapidly reestablish itself and that the presence of B. psygmophilum, perhaps by supplying nutrients, photosynthate, or other signaling molecules, exerts influence on this process.IMPORTANCE Corals are animals whose health is often maintained by symbiotic microalgae and other microorganisms, yet they are highly susceptible to environmental-related disturbances. Here, we used a known disruptor, antibiotics, to understand how the coral mucus microbial community reassembles itself following disturbance. We show that the Astrangia poculata microbiome can recover from this disturbance and that individuals with algal symbionts reestablish their microbiomes in a more consistent manner compared to corals lacking symbionts. This work is important because it suggests that this coral may be able to recover its mucus microbiome following disturbance, it identifies specific microbes that may be important to reassembly, and it demonstrates that algal symbionts may play a previously undocumented role in microbial recovery and resilience to environmental change.

RevDate: 2021-04-14

Reiter T, Montpetit R, Byer S, et al (2021)

Transcriptomics Provides a Genetic Signature of Vineyard Site and Offers Insight into Vintage-Independent Inoculated Fermentation Outcomes.

mSystems, 6(2):.

Ribosomal DNA amplicon sequencing of grape musts has demonstrated that microorganisms occur nonrandomly and are associated with the vineyard of origin, suggesting a role for the vineyard, grape, and wine microbiome in shaping wine fermentation outcomes. Here, ribosomal DNA amplicon sequencing from grape musts and RNA sequencing of eukaryotic transcripts from primary fermentations inoculated with the wine yeast Saccharomyces cerevisiae RC212 were used to profile fermentations from 15 vineyards in California and Oregon across two vintages. These data demonstrate that the relative abundance of fungal organisms detected by ribosomal DNA amplicon sequencing correlated with neither transcript abundance from those same organisms within the RNA sequencing data nor gene expression of the inoculated RC212 yeast strain. These data suggest that the majority of the fungi detected in must by ribosomal DNA amplicon sequencing were not active during the primary stage of these inoculated fermentations and were not a major factor in determining RC212 gene expression. However, unique genetic signatures were detected within the ribosomal DNA amplicon and eukaryotic transcriptomic sequencing that were predictive of vineyard site and region. These signatures included S. cerevisiae gene expression patterns linked to nitrogen, sulfur, and thiamine metabolism. These genetic signatures of site offer insight into specific environmental factors to consider with respect to fermentation outcomes and vineyard site and regional wine characteristics.IMPORTANCE The wine industry generates billions of dollars of revenue annually, and economic productivity is in part associated with regional distinctiveness of wine sensory attributes. Microorganisms associated with grapes and wineries are influenced by region of origin, and given that some microorganisms play a role in fermentation, it is thought that microbes may contribute to the regional distinctiveness of wine. In this work, as in previous studies, it is demonstrated that specific bacteria and fungi are associated with individual wine regions and vineyard sites. However, this work further shows that their presence is not associated with detectable fungal gene expression during the primary fermentation or the expression of specific genes by the inoculate Saccharomyces cerevisiae strain RC212. The detected RC212 gene expression signatures associated with region and vineyard site also allowed the identification of flavor-associated metabolic processes and environmental factors that could impact primary fermentation outcomes. These data offer novel insights into the complexities and subtleties of vineyard-specific inoculated wine fermentation and starting points for future investigations into factors that contribute to regional wine distinctiveness.

RevDate: 2021-04-14

Chang ET, Ye W, Zeng YX, et al (2021)

The evolving epidemiology of nasopharyngeal carcinoma.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology pii:1055-9965.EPI-20-1702 [Epub ahead of print].

BACKGROUND: The epidemiology of nasopharyngeal carcinoma (NPC) has long been a source of fascination due to the malignancy's striking geographic distribution, the involvement of the oncogenic Epstein-Barr virus (EBV), the unique association with intake of Chinese-style salt-preserved fish, and etiologic heterogeneity by histological subtype.

METHODS: This review summarizes the current epidemiological literature on NPC, highlighting recent results from our population-based case-control study in southern China.

RESULTS: Findings from our case-control study provide new insight into the epidemiology of NPC, including a diminished role of Chinese-style salt-preserved fish, a profound impact of EBV genetic sequence variation, modest positive associations with passive smoking and household air pollution, and possible effects of oral health and the oral microbiome. Recent findings from other studies include a protective association with infectious mononucleosis, suggesting a causal role of early EBV infection; familial risk conferred by shared genetic variation in the host antibody-mediated immune response to EBV infection; and an unclear association with occupational exposure to formaldehyde.

CONCLUSIONS: To shed further light on the interplay of environmental, genetic, and viral causes of NPC, large pooled studies must accumulate sufficient cases with detailed exposure data.

IMPACT: New epidemiological findings have reshaped the causal model for NPC.

RevDate: 2021-04-14

Oberle A, Urban L, Falch-Leis S, et al (2021)

16S rRNA long-read nanopore sequencing is feasible and reliable for endometrial microbiome analysis.

Reproductive biomedicine online pii:S1472-6483(21)00144-9 [Epub ahead of print].

RESEARCH QUESTION: Full-length 16S rRNA gene sequencing using nanopore technology is a fast alternative to conventional short-read 16S rRNA gene sequencing with low initial investment costs that has been used for various microbiome studies but has not yet been investigated as an alternative approach for endometrial microbiome analysis. Is in-situ 16S rRNA gene long-read sequencing using portable nanopore sequencing technology feasible and reliable for endometrial microbiome analysis?

DESIGN: A prospective experimental study based on 33 patients seeking infertility treatment between January and October 2019. A 16S rRNA gene long-read nanopore sequencing protocol for analysing endometrial microbiome samples was established, including negative controls for contamination evaluation and positive controls for bias evaluation. Contamination caused by kit and exterior sources was identified and excluded from the analysis. Endometrial samples from 33 infertile patients were sequenced using the optimized long-read nanopore sequencing protocol and compared with conventional short-read sequencing carried out by external laboratories.

RESULTS: Of the 33 endometrial patient samples, 23 successfully amplified (69.7%) and their microbiome was assessed using nanopore sequencing. Of those 23 samples, 14 (60.9%) were Lactobacillus-dominated (>80% of reads mapping to Lactobacillus), with 10 samples resulting in more than 90% Lactobacillus reads. Our long-read nanopore sequencing revealed results similar to two conventional short-read sequencing approaches and to long-read sequencing validation carried out in external laboratories.

CONCLUSION: In this pilot study, 16S rRNA gene long-read nanopore sequencing was established to analyse the endometrial microbiome in situ that could be widely applied owing to its cost efficiency and portable character.

RevDate: 2021-04-14

Tan TC, Noviani M, Leung YY, et al (2021)

The microbiome and systemic sclerosis: A review of current evidence.

Best practice & research. Clinical rheumatology pii:S1521-6942(21)00029-2 [Epub ahead of print].

Systemic sclerosis (SSc) is characterized by immune dysregulation, vasculopathy, and fibrosis of multiple organs. The gastrointestinal (GI) tract is the most common internal organ manifestation, which contributes to significant morbidity and mortality in patients with SSc. Emerging reports have identified unique microbial taxa alterations in the GI microbiome of patients with SSc as compared to healthy controls (HC). These taxa alterations include differences at the phyla (e.g., Bacteroidetes) and genera (e.g., Bacteroides, Clostridium, Faecalibacterium, and Lactobacillus) level. In addition, some genera have been associated with more severe GI symptoms (e.g., Prevotella and Akkermansia). This review summarizes the current evidence on factors influencing the GI microbiome, GI microbiome alterations in SSc as compared to HC, and in SSc subgroups according to disease manifestations. Current exploration in therapeutic interventions that target the GI microbiome is discussed.

RevDate: 2021-04-16

Williamson KM, Wagner BD, Robertson CE, et al (2021)

Modified PCR protocol to increase sensitivity for determination of bacterial community composition.

Microbiome, 9(1):90.

BACKGROUND: The objective of this project was to increase the sensitivity of sequence-based bacterial community determination without impacting community composition or interfering with cluster formation during sequencing. Two PCR protocols (standard and modified) were examined in airway samples where we observed a large range in bacterial load (3.1-6.2 log10 16S rRNA gene copies/reaction). Tracheal aspirate (TA) samples (n = 99) were collected from sixteen children requiring mechanical ventilation at a single center. DNA was extracted, and total bacterial load (TBL) was assessed using qPCR. Amplification of 16S rRNA was attempted with both protocols in all samples.

RESULTS: PCR product was observed using both protocols in 52 samples and in 24 additional samples only with the modified protocol. TBL, diversity metrics, and prominent taxa were compared for samples in three groups based on success of the two protocols (successful with both, success with modified only, unsuccessful for both). TBL differed significantly across the three groups (p<0.001). Specifically, the modified protocol allowed amplification from samples with intermediate TBL. Shannon diversity was similar between the two protocols, and Morisita-Horn beta diversity index showed high agreement between the two protocols within samples (median value 0.9997, range 0.9947 to 1). We show that both protocols identify similar communities, and the technical variability of both protocols was very low. The use of limited PCR cycles was a key feature to limit impact of background by exclusion of 24% of samples with no evidence of bacterial DNA present in the sample.

CONCLUSION: The modified amplification protocol represents a viable approach that increased sensitivity of bacterial community analysis, which is important for study of the human airway microbiome where bacterial load is highly variable. Video abstract.

RevDate: 2021-04-16

Binyamin D, Nitzan O, Azrad M, et al (2021)

The microbial diversity following antibiotic treatment of Clostridioides difficile infection.

BMC gastroenterology, 21(1):166.

BACKGROUND: Clostridioides difficile (C. difficile) is a major nosocomial pathogen that infects the human gut and can cause diarrheal disease. A dominant risk factor is antibiotic treatment that disrupts the normal gut microbiota. The aim of the study was to examine the correlation between antibiotic treatment received prior to C. difficile infection (CDI) onset and patient gut microbiota.

METHODS: Stool samples were collected from patients with CDI, presenting at the Baruch Padeh Medical Center Poriya, Israel. Demographic and clinical information, including previous antibiotic treatments, was collected from patient charts, and CDI severity score was calculated. Bacteria were isolated from stool samples, and gut microbiome was analyzed by sequencing the 16S rRNA gene using the Illumina MiSeq platform and QIIME2.

RESULTS: In total, 84 patients with CDI were enrolled in the study; all had received antibiotics prior to disease onset. Due to comorbidities, 46 patients (55%) had received more than one class of antibiotics. The most common class of antibiotics used was cephalosporins (n = 44 cases). The intestinal microbiota of the patients was not uniform and was mainly dominated by Proteobacteria. Differences in intestinal microbiome were influenced by the different combinations of antibiotics that the patients had received (p = 0.022) CONCLUSIONS: The number of different antibiotics administered has a major impact on the CDI patients gut microbiome, mainly on bacterial richness.

RevDate: 2021-04-13

Arif M, Zhang C, Li X, et al (2021)

iNetModels 2.0: an interactive visualization and database of multi-omics data.

Nucleic acids research pii:6225230 [Epub ahead of print].

It is essential to reveal the associations between various omics data for a comprehensive understanding of the altered biological process in human wellness and disease. To date, very few studies have focused on collecting and exhibiting multi-omics associations in a single database. Here, we present iNetModels, an interactive database and visualization platform of Multi-Omics Biological Networks (MOBNs). This platform describes the associations between the clinical chemistry, anthropometric parameters, plasma proteomics, plasma metabolomics, as well as metagenomics for oral and gut microbiome obtained from the same individuals. Moreover, iNetModels includes tissue- and cancer-specific Gene Co-expression Networks (GCNs) for exploring the connections between the specific genes. This platform allows the user to interactively explore a single feature's association with other omics data and customize its particular context (e.g. male/female specific). The users can also register their data for sharing and visualization of the MOBNs and GCNs. Moreover, iNetModels allows users who do not have a bioinformatics background to facilitate human wellness and disease research. iNetModels can be accessed freely at https://inetmodels.com without any limitation.

RevDate: 2021-04-13

Rajeev AC, Sahu N, Arvind K, et al (2021)

Exploring prevalence of potential pathogens and fecal indicators in geographically distinct river systems through comparative metagenomics.

Environmental pollution (Barking, Essex : 1987), 282:117003 pii:S0269-7491(21)00585-6 [Epub ahead of print].

Microbial communities are considered as vital members to reflect the health of a riverine system. Among them, pathogenic and fecal indicators imply health risks involved with potability of river water. The present study explores the diverse microbial communities, distribution pattern of potential pathogens, and fecal indicators between the geographically distinct Himalayan and Peninsular river systems of India. It also inquires into the environmental factors associated with community variance and distribution pattern of microbial indicators. The application of high-throughput amplicon sequencing approach unveiled significant demarcation (p < 0.004, Anosim R = 0.62) of samples suggesting unique microbial diversities in these two river sediments. Random forest analysis revealed Desulfobulbulus, PSB_M_3, and Opitutus in Himalayan, while DA101, Bacillus, and Streptomyces in the Peninsular as significant contributors to develop overall dissimilarity between the river systems. Permutational multivariate analysis of variance and co-occurrence network analysis were used to study the relationships between microbial taxa and environmental factors. Amongst the various studied environmental parameters, pH, K, Ca, Mg, Ba, and Al in the Himalayan and salinity, Na, temperature, and Th in the Peninsular significantly influenced shaping of distinct microbial communities. Furthermore, the potential pathogenic genera, including Flavobacterium, Clostridium, Arcobacter, Pseudomonas, and Bacillus were highly prevalent in both the river systems. Arcobacter, Clostridium, Acinetobacter, Bacteroides, and Caloramator were the prominent fecal indicators in these river systems. Our findings provide salient information about the crucial role and interplay between various environmental factors and anthropogenic influences in framing the microbiome of the distinct river systems in India. Moreover, assessing potential pathogenic and fecal indicators suggest the public health risk associated with untreated sewage discharge into these water sources. The detection of various F/S indicators and potentially pathogenic bacteria in Himalayan and Peninsular river systems emphasize the urgent need for future monitoring and management of major riverine systems in India.

RevDate: 2021-04-15

Johns MS, NJ Petrelli (2021)

Microbiome and colorectal cancer: A review of the past, present, and future.

Surgical oncology, 37:101560 pii:S0960-7404(21)00049-9 [Epub ahead of print].

The gastrointestinal tract is home to diverse and abundant microorganisms, collectively referred to as the microbiome. This ecosystem typically contains trillions of microbial cells that play an important role in regulation of human health. The microbiome has been implicated in host immunity, nutrient absorption, digestion, and metabolism. In recent years, researchers have shown that alteration of the microbiome is associated with disease development, such as obesity, inflammatory bowel disease, and cancer. This review discusses the five decades of research into the human microbiome and the development of colorectal cancer - the historical context including experiments that sparked interest, the explosion of research that has occurred in the last decade, and finally the future of testing and treatment.

RevDate: 2021-04-13

de Meeûs d'Argenteuil C, Boshuizen B, Oosterlinck M, et al (2021)

Flexibility of equine bioenergetics and muscle plasticity in response to different types of training: An integrative approach, questioning existing paradigms.

PloS one, 16(4):e0249922 pii:PONE-D-20-29043.

Equine bioenergetics have predominantly been studied focusing on glycogen and fatty acids. Combining omics with conventional techniques allows for an integrative approach to broadly explore and identify important biomolecules. Friesian horses were aquatrained (n = 5) or dry treadmill trained (n = 7) (8 weeks) and monitored for: evolution of muscle diameter in response to aquatraining and dry treadmill training, fiber type composition and fiber cross-sectional area of the M. pectoralis, M. vastus lateralis and M. semitendinosus and untargeted metabolomics of the M. pectoralis and M. vastus lateralis in response to dry treadmill training. Aquatraining was superior to dry treadmill training to increase muscle diameter in the hindquarters, with maximum effect after 4 weeks. After dry treadmill training, the M. pectoralis showed increased muscle diameter, more type I fibers, decreased fiber mean cross sectional area, and an upregulated oxidative metabolic profile: increased β-oxidation (key metabolites: decreased long chain fatty acids and increased long chain acylcarnitines), TCA activity (intermediates including succinyl-carnitine and 2-methylcitrate), amino acid metabolism (glutamine, aromatic amino acids, serine, urea cycle metabolites such as proline, arginine and ornithine) and xenobiotic metabolism (especially p-cresol glucuronide). The M. vastus lateralis expanded its fast twitch profile, with decreased muscle diameter, type I fibers and an upregulation of glycolytic and pentose phosphate pathway activity, and increased branched-chain and aromatic amino acid metabolism (cis-urocanate, carnosine, homocarnosine, tyrosine, tryptophan, p-cresol-glucuronide, serine, methionine, cysteine, proline and ornithine). Trained Friesians showed increased collagen and elastin turn-over. Results show that branched-chain amino acids, aromatic amino acids and microbiome-derived xenobiotics need further study in horses. They feed the TCA cycle at steps further downstream from acetyl CoA and most likely, they are oxidized in type IIA fibers, the predominant fiber type of the horse. These study results underline the importance of reviewing existing paradigms on equine bioenergetics.

RevDate: 2021-04-13

Perez-Mon C, Qi W, Vikram S, et al (2021)

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps).

Microbial genomics, 7(4):.

The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.

RevDate: 2021-04-13

Huang W, MA Kane (2021)

MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis.

Journal of proteome research [Epub ahead of print].

Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. However, metaproteomics, which simultaneously analyzes all proteins from hundreds to thousands of species, faces significant challenges regarding database search and interpretation of results. To overcome these obstacles, we have developed a user-friendly microbiome analysis pipeline (MAPLE, freely downloadable at http://maple.rx.umaryland.edu/), which is able to define an optimal search space by inferring proteomes specific to samples following the principle of parsimony. MAPLE facilitates highly comparable or better peptide identification compared to a sample-specific metagenome-guided search. In addition, we implemented an automated peptide-centric enrichment analysis function in MAPLE to address issues of traditional protein-centric comparison, enabling straightforward and comprehensive comparison of taxonomic and functional makeup between microbiota.

RevDate: 2021-04-13

Borella F, Carosso AR, Cosma S, et al (2021)

Gut Microbiota and Gynecological Cancers: A Summary of Pathogenetic Mechanisms and Future Directions.

ACS infectious diseases [Epub ahead of print].

Over the past 20 years, important relationships between the microbiota and human health have emerged. A link between alterations of microbiota composition (dysbiosis) and cancer development has been recently demonstrated. In particular, the composition and the oncogenic role of intestinal bacterial flora has been extensively investigated in preclinical and clinical studies focusing on gastrointestinal tumors. Overall, the development of gastrointestinal tumors is favored by dysbiosis as it leads to depletion of antitumor substances (e.g., short-chain fatty acids) produced by healthy microbiota. Moreover, dysbiosis leads to alterations of the gut barrier, promotes a chronic inflammatory status through activation of toll-like receptors, and causes metabolic and hormonal dysregulations. However, the effects of these imbalances are not limited to the gastrointestinal tract and they can influence gynecological tumor carcinogenesis as well. The purpose of this Review is to provide a synthetic update about the mechanisms of interaction between gut microbiota and the female reproductive tract favoring the development of neoplasms. Furthermore, novel therapeutic approaches based on the modulation of microbiota and their role in gynecological oncology are discussed.

RevDate: 2021-04-13

Thompson TP, Kelly SA, Skvortsov T, et al (2021)

Microbiology of a NaCl stalactite 'salticle' formed within Triassic halite.

Environmental microbiology [Epub ahead of print].

Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. Some of these halophiles may have been preserved over geological timescales within hypersaline fluid inclusions, but ingresses of water and/or anthropogenic activities can lead to the formation of alternative habitats, including NaCl stalactites or speleothems. While the microbiology of ancient evaporites has been well-studied, the ecology of these recently formed structures is less-well understood. Here, the microbiology of a NaCl stalactite ('salticle') in a Triassic halite mine is characterised. The specific aims were to: determine the presence of fluid inclusions; determine the microbial structure of the salticle compared with a nearby brine-pool and surficial soil; and characterise the ecophysiological capabilities of this unique ecosystem. The salticle contained fluid inclusions, and their microbiome was composed of Euryarchaetota, Proteobacteria, and Actinobacteria, with Haloarchaea in greater abundance than brine-pool or soil microbiomes. The salticle metagenome exhibited a greater abundance of genes involved in osmoregulation, anaerobic respiration, UV resistance, oxidative stress, and stress-protein synthesis relative to the soil microbiome. We discuss the potential astrobiological implications of salticles as enclosed salt-saturated habitats that are protected from ionising radiation and have a stable water-activity. This article is protected by copyright. All rights reserved.

RevDate: 2021-04-13

Crudo F, Aichinger G, Mihajlovic J, et al (2021)

In vitro interactions of Alternaria mycotoxins, an emerging class of food contaminants, with the gut microbiota: a bidirectional relationship.

Archives of toxicology [Epub ahead of print].

The human gut microbiota plays an important role in the maintenance of human health. Factors able to modify its composition might predispose the host to the development of pathologies. Among the various xenobiotics introduced through the diet, Alternaria mycotoxins are speculated to represent a threat for human health. However, limited data are currently available about the bidirectional relation between gut microbiota and Alternaria mycotoxins. In the present work, we investigated the in vitro effects of different concentrations of a complex extract of Alternaria mycotoxins (CE; containing eleven mycotoxins; e.g. 0.153 µM alternariol and 2.3 µM altersetin, at the maximum CE concentration tested) on human gut bacterial strains, as well as the ability of the latter to metabolize or adsorb these compounds. Results from the minimum inhibitory concentration assay showed the scarce ability of CE to inhibit the growth of the tested strains. However, the growth kinetics of most of the strains were negatively affected by exposure to the various CE concentrations, mainly at the highest dose (50 µg/mL). The CE was also found to antagonize the formation of biofilms, already at concentrations of 0.5 µg/mL. LC-MS/MS data analysis of the mycotoxin concentrations found in bacterial pellets and supernatants after 24 h incubation showed the ability of bacterial strains to adsorb some Alternaria mycotoxins, especially the key toxins alternariol, alternariol monomethyl ether, and altersetin. The tendency of these mycotoxins to accumulate within bacterial pellets, especially in those of Gram-negative strains, was found to be directly related to their lipophilicity.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

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Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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