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Bibliography on: Microbiome

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 15 Jan 2021 at 01:45 Created: 

Microbiome

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®)

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RevDate: 2021-01-14

Saha S, Mara K, Pardi DS, et al (2021)

Long-term Safety of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection.

Gastroenterology pii:S0016-5085(21)00069-X [Epub ahead of print].

BACKGROUND: Fecal microbiota transplantation (FMT) is highly effective for treating recurrent Clostridioides difficile infection (CDI), with emerging data on intermediate and long-term safety.

METHODS: A prospective survey-based study was conducted (9/2012-6/2018) in patients undergoing FMT for recurrent CDI. Data on demographics and comorbidities were abstracted from medical records. Patients were contacted at 1 week, 1 month, 6 months, 1 year (short-term), ≥2 years post-FMT (long-term). Symptoms and new medical diagnoses were recorded at each time point. Data were weighted to account for survey non-response bias. Multivariate logistic regression models for adverse events were built using age (per 10-year increment), sex, time of survey and comorbidities. P<0.05 was considered statistically significant.

RESULTS: Overall, 609 patients underwent FMT; median age 56 years (range, 18-94), 64.8% were female, 22.8% had inflammatory bowel disease (IBD). At short-term follow up (n=609), >60% patients had diarrhea, <33% had constipation. At 1 year, 9.5% reported additional CDI episodes. On multivariable analysis, patients with IBD, dialysis dependent kidney disease and multiple FMTs had higher risk of diarrhea; risk of constipation was higher in females and lower in IBD (all p<0.05). For long-term follow up (n=447), median time of follow up was 3.7 years (range, 2.0-6.8). Overall, 73 new diagnoses were reported- 13% gastrointestinal, 10% weight gain, 11.8% new infections (all deemed unrelated to FMT). Median time to infections was 29 months (range, 0-73) post-FMT.

CONCLUSION: FMT appears safe with low risk of transmission of infections. Several new diagnoses were reported, which should be explored in future studies.

RevDate: 2021-01-14

Kerkhof LJ (2021)

Is oxford nanopore sequencing ready for analyzing complex microbiomes?.

FEMS microbiology ecology pii:6098400 [Epub ahead of print].

This minireview will discuss the improvements in Oxford Nanopore sequencing technology which make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65-96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis, and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.

RevDate: 2021-01-14

McKinney CA, Bedenice D, Pacheco AP, et al (2021)

Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea.

PloS one, 16(1):e0244381 pii:PONE-D-20-23537.

BACKGROUND AND AIMS: Fecal microbial transplantation (FMT) is empirically implemented in horses with colitis to facilitate resolution of diarrhea. The purpose of this study was to assess FMT as a clinical treatment and modulator of fecal microbiota in hospitalized horses with colitis.

METHODS: A total of 22 horses with moderate to severe diarrhea, consistent with a diagnosis of colitis, were enrolled at two referral hospitals (L1: n = 12; L2: n = 10). FMT was performed in all 12 patients on 3 consecutive days at L1, while treatment at L2 consisted of standard care without FMT. Manure was collected once daily for 4 days from the rectum in all colitis horses, prior to FMT for horses at L1, and from each manure sample used for FMT. Fecal samples from 10 clinically healthy control horses housed at L2, and 30 healthy horses located at 5 barns in regional proximity to L1 were also obtained to characterize the regional healthy equine microbiome. All fecal microbiota were analyzed using 16S amplicon sequencing.

RESULTS AND CONCLUSIONS: As expected, healthy horses at both locations showed a greater α-diversity and lower β-diversity compared to horses with colitis. The fecal microbiome of healthy horses clustered by location, with L1 horses showing a higher prevalence of Kiritimatiellaeota. Improved manure consistency (lower diarrhea score) was associated with a greater α-diversity in horses with colitis at both locations (L1: r = -0.385, P = 0.006; L2: r = -0.479, P = 0.002). Fecal transplant recipients demonstrated a greater overall reduction in diarrhea score (median: 4±3 grades), compared to untreated horses (median: 1.5±3 grades, P = 0.021), with a higher incidence in day-over-day improvement in diarrhea (22/36 (61%) vs. 10/28 (36%) instances, P = 0.011). When comparing microbiota of diseased horses at study conclusion to that of healthy controls, FMT-treated horses showed a lower mean UniFrac distance (0.53±0.27) than untreated horses (0.62±0.26, P<0.001), indicating greater normalization of the microbiome in FMT-treated patients.

RevDate: 2021-01-14

Wang M, Zhao H, Wen X, et al (2021)

Citrus flavonoids and the intestinal barrier: Interactions and effects.

Comprehensive reviews in food science and food safety, 20(1):225-251.

The intestinal barrier plays a central role in sustaining gut homeostasis and, when dysfunctional, may contribute to diseases. Dietary flavonoids derived from Citrus genus represent one of the main naturally occurring phytochemicals with multiple potential benefits for the intestinal barrier function. In the intestine, citrus flavonoids (CFs) undergo ingestion from the lumen, biotransformation in the epithelial cells and/or crosstalk with luminal microbiota to afford various metabolites that may in turn exert protective actions on gut barrier along with their parental compounds. Specifically, the health-promoting properties of CFs and their metabolic bioactives for the intestinal barrier include their capacity to (a) modulate barrier permeability; (b) protect mucus layer; (c) regulate intestinal immune system; (d) fight against oxidative stress; and (e) positively shape microbiome and metabolome. Notably, local effects of CFs can also generate systemic benefits, for instance, improvement of gut microbial dysbiosis helpful to orchestrate gut homeostasis and leading to alleviation of systemic dysmetabolism. Given the important role of the intestinal barrier in overall health, further understanding of underlying action mechanisms and ultimate health effects of CFs as well as their metabolites on the intestine is of great significance to future application of citrus plants and their bioactives as dietary supplements and/or functional ingredients in medical foods.

RevDate: 2021-01-14

Hens K (2020)

[You should exercise a bit more - The ethics of lifestyle and mental health].

Tijdschrift voor psychiatrie, 62(11):976-980.

BACKGROUND: The fact that environmental factors and lifestyle play a role in mental health is well known. In the last decades more research has gone into the link between environment and genetics: epigenetics has shown us the molecular link between these two, and the influence of the microbiome on mental health has demonstrated the importance of food. Still, ethical questions remain about how lifestyle advice can be integrated in clinical practice in an ethical way. AIM: To describe the normative import of our view on biology and individual responsibility and the place of lifestyle in the debate. METHOD: A consideration of ethical aspects of lifestyle and lifestyle advice. RESULTS: The normative import of our view on biology and individual responsibility and the place of lifestyle in the debate is described. It is argued that lifestyle has a unique place between biological and psychosocial concepts. Finally, the pitfalls and opportunities of introducing lifestyle in clinical practice are shown. CONCLUSION: Lifestyle is conceptually situated between the biological and the psychosocial, and sheds new light on the importance of certain explanations for recovery, and the relation with specific treatments. Lifestyle advice can only be used optimally in therapy if mental health care professionals also include a dialogue about assumptions and expectations.

RevDate: 2021-01-14

Yang H, Zhang Y, Chuang S, et al (2021)

Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community.

Ecotoxicology (London, England) [Epub ahead of print].

Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the exogenous inoculum, soil environment, and indigenous microbial microbiome, remain largely unknown. Acetamiprid is a widely used neonicotinoid insecticide which has caused environmental contaminations. Here, we used an acetamiprid-degrading strain, Pigmentiphaga sp. D-2, as inoculum to investigate the effects of bioaugmentation on the soil microbial community and the process of microbiome reassembly. The bioaugmentation treatment removed 94.8 and 92.5% of acetamiprid within 40 days from soils contaminated with 50 and 200 mg/kg acetamiprid, respectively. A decrease in bacterial richness and diversity was detected in bioaugmentation treatments, which later recovered with the removal of acetamiprid from soil. Moreover, the bioaugmentation treatment significantly influenced the bacterial community structure, whereas application of acetamiprid alone had little influence on the soil microbial community. Furthermore, the bioaugmentation treatment improved the growth of bacteria associated with acetamiprid degradation, and the inoculated and recruited taxa significantly influenced the keystone taxa of the indigenous microbiome, resulting in reassembly of the bacterial community yielding higher acetamiprid-degrading efficiency than that of the indigenous and acetamiprid-treated communities. Our results provide valuable insights into the mechanisms of microbiome engineering for bioaugmentation of acetamiprid-contaminated soils.

RevDate: 2021-01-14

Wang Q, Kim SY, Matsushita H, et al (2021)

Oral administration of PEGylated TLR7 ligand ameliorates alcohol-associated liver disease via the induction of IL-22.

Proceedings of the National Academy of Sciences of the United States of America, 118(1):.

Effective therapies for alcohol-associated liver disease (ALD) are limited; therefore, the discovery of new therapeutic agents is greatly warranted. Toll-like receptor 7 (TLR7) is a pattern recognition receptor for single-stranded RNA, and its activation prevents liver fibrosis. We examined liver and intestinal damage in Tlr7-/- mice to determine the role of TLR7 in ALD pathogenesis. In an alcoholic hepatitis (AH) mouse model, hepatic steatosis, injury, and inflammation were induced by chronic binge ethanol feeding in mice, and Tlr7 deficiency exacerbated these effects. Because these results demonstrated that endogenous TLR7 signaling activation is protective in the AH mouse model, we hypothesized that TLR7 activation may be an effective therapeutic strategy for ALD. Therefore, we investigated the therapeutic effect of TLR7 agonistic agent, 1Z1, in the AH mouse model. Oral administration of 1Z1 was well tolerated and prevented intestinal barrier disruption and bacterial translocation, which thus suppressed ethanol-induced hepatic injury, steatosis, and inflammation. Furthermore, 1Z1 treatment up-regulated the expression of antimicrobial peptides, Reg3b and Reg3g, in the intestinal epithelium, which modulated the microbiome by decreasing and increasing the amount of Bacteroides and Lactobacillus, respectively. Additionally, 1Z1 up-regulated intestinal interleukin (IL)-22 expression. IL-22 deficiency abolished the protective effects of 1Z1 in ethanol-induced liver and intestinal damage, suggesting intestinal IL-22 as a crucial mediator for 1Z1-mediated protection in the AH mouse model. Collectively, our results indicate that TLR7 signaling exerts protective effects in the AH mouse model and that a TLR7 ligand, 1Z1, holds therapeutic potential for the treatment of AH.

RevDate: 2021-01-14

Mutnale MC, Reddy GS, K Vasudevan (2021)

Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection.

Microbial ecology [Epub ahead of print].

Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.

RevDate: 2021-01-14

Romano-Keeler J, Fiszbein D, Zhang J, et al (2021)

Center-Based Experiences Implementing Strategies to Reduce Risk of Horizontal Transmission of SARS-Cov-2: Potential for Compromise of Neonatal Microbiome Assemblage.

medRxiv : the preprint server for health sciences.

Perinatal transmission of COVID-19 is poorly understood and many neonatal intensive care units' (NICU) policies minimize mother-infant contact to prevent transmission. We present our unit's approach and ways it may impact neonatal microbiome acquisition. We attended COVID-19 positive mothers' deliveries from March-August 2020. Delayed cord clamping and skin-to-skin were avoided and infants were admitted to the NICU. No parents' visits were allowed and discharge was arranged with COVID-19 negative family members. Maternal breast milk was restricted in the NICU. All twenty-one infants tested negative at 24 and 48 hours and had average hospital stays of nine days. 40% of mothers expressed breastmilk and 30% of infants were discharged with COVID-19 negative caregivers. Extended hospital stays, no skin-to-skin contact, limited maternal milk use, and discharge to caregivers outside primary residences, potentially affect the neonatal microbiome. Future studies are warranted to explore how ours and other centers' similar policies influence this outcome.

RevDate: 2021-01-14

Nie S, Wang A, Y Yuan (2021)

Comparison of clinicopathological parameters, prognosis, micro-ecological environment and metabolic function of Gastric Cancer with or without Fusobacterium sp. Infection.

Journal of Cancer, 12(4):1023-1032 pii:jcav12p1023.

Background: Fusobacterium sp. plays a crucial role in the tumorigenesis and development of gastrointestinal tumors. Our research group previously disclosed that Fusobacterium sp. was more abundant in gastric cancer (GC) tissues than adjacent non-cancerous (NC) tissues. However, Fusobacterium sp. did not exist in all GC tissues and the differentiated features of GC with or without Fusobacterium sp. infection is not clear. Methods: The expression data of 61 GC tissues came from 16S rRNA gene sequencing. Comparison groups were defined based on sOTU at the genus level of Fusobacterium sp., which was performed by the Qiime2 microbiome bioinformatics platform. We used Chi-square and Fisher's exact test to compare clinicopathological parameters, and used Kaplan-Meier analysis, Cox univariate and multivariate analysis to compare prognosis. Micro-ecological environment comparison was characterized by 16S rRNA gene sequencing, and the metabolic function prediction was applied by PICRUSt2. Results of microbial diversity, differential enrichment genus and metabolic function in GC with or without Fusobacterium sp. infection was validated with 229 GC tissues downloaded from an independent cohort in ENA database (PRJNA428883). Results: The infection rate of Fusobacterium sp. in 61 GC tissues was 52.46% and elderly GC patients were more prone to Fusobacterium sp. infection. GC patients infected with Fusobacterium sp. were more likely to have tumor-infiltrating lymphocytes and p53 expression. The microbial diversity and microbial structure showed significant differences between two GC tissue groups with 42 differential enrichment genera. The metabolic function of Fusobacterium sp.-positive GC tissues was related to the biosynthesis of lysine, peptidoglycan, and tRNA. The differences in microbial structure, the existence of some differential enrichment genera and the metabolic function of Fusobacterium sp.-positive GC tissues, were then validated by 229 GC tissues of an independent cohort. Conclusions: Fusobacterium sp. infection can affect the phenotypic characteristics, micro-ecological environment, and metabolic functions of GC, which may provide a basis for further exploring the relationship between Fusobacterium sp. infection and carcinogenesis of GC.

RevDate: 2021-01-14

Xu H, Cao J, Li X, et al (2020)

Regional Differences in the Gut Microbiota and Gut-Associated Immunologic Factors in the Ileum and Cecum of Rats With Collagen-Induced Arthritis.

Frontiers in pharmacology, 11:587534 pii:587534.

Rheumatoid arthritis (RA) is a common autoimmune disease characterized by chronic inflammation and a multifactorial etiology. We previously showed that gut microbiota dysbiosis in the rat ileum is involved in the development of collagen-induced arthritis (CIA). The gut microbiota in the distinct gastrointestinal tract (GIT) plays region-specific roles, but information on the different roles of the microbiota in distinct GIT compartments of CIA rats is limited. This study aimed to evaluate the region-specific differences in the gut microbial communities and certain gut-associated immunologic factors in the ileum and cecum of CIA rats. Ileal and cecal digesta were collected from CIA and control rats for microbiome analysis. We determined the microbial richness, diversity and taxa as well as the expression of interleukin (IL)-1β and IL-17A in the epithelium and lamina propria of the ileum and cecum mucosal layers. The CIA-induced microbiota alterations in the ileum differed from those in the cecum. The ileal microbiota were more markedly influenced in CIA, as revealed by sharp reductions in the abundances of the families Enterococcaceae, Lactobacillaceae and Streptococcaceae and the genera Lactobacillus and Lactococcus. Moreover, significant increases in IL-1β, and IL-17A mRNA expression were detected in only the ileal epithelium and lamina propria of the mucosal layer. Therefore, the microbial characteristics in the ileum were consistent with the immune-mediated inflammatory features of CIA, suggesting that the ileal microbiota might better represent the CIA-induced inflammatory responses than the cecal microbiota and that these responses might partially impact the progression of RA by regulating intestinal mucosal immunity.

RevDate: 2021-01-14

Stower H (2021)

Microbiome transplant-induced response to immunotherapy.

Nature medicine, 27(1):21.

RevDate: 2021-01-14

Gopinath D, Menon RK, Wie CC, et al (2021)

Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer.

Scientific reports, 11(1):1181.

Microbial dysbiosis has been implicated in the pathogenesis of oral cancer. We analyzed the compositional and metabolic profile of the bacteriome in three specific niches in oral cancer patients along with controls using 16SrRNA sequencing (Illumina Miseq) and DADA2 software. We found major differences between patients and control subjects. Bacterial communities associated with the tumor surface and deep paired tumor tissue differed significantly. Tumor surfaces carried elevated abundances of taxa belonging to genera Porphyromonas, Enterobacteriae, Neisseria, Streptococcus and Fusobacteria, whereas Prevotella, Treponema, Sphingomonas, Meiothermus and Mycoplasma genera were significantly more abundant in deep tissue. The most abundant microbial metabolic pathways were those related to fatty-acid biosynthesis, carbon metabolism and amino-acid metabolism on the tumor surface: carbohydrate metabolism and organic polymer degradation were elevated in tumor tissues. The bacteriome of saliva from patients with oral cancer differed significantly from paired tumor tissue in terms of community structure, however remained similar at taxonomic and metabolic levels except for elevated abundances of Streptococcus, Lactobacillus and Bacteroides, and acetoin-biosynthesis, respectively. These shifts to a pro-inflammatory profile are consistent with other studies suggesting oncogenic properties. Importantly, selection of the principal source of microbial DNA is key to ensure reliable, reproducible and comparable results in microbiome studies.

RevDate: 2021-01-14

Al Kawas S, Al-Marzooq F, Rahman B, et al (2021)

The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study.

Scientific reports, 11(1):1113.

Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect of other tobacco types on the oral microbiome. This study investigates subgingival microbiome composition in smokers of different tobacco types and their effect on periodontal health. Subgingival plaques were collected from 40 individuals, including smokers of either cigarettes, medwakh, or shisha, and non-smokers seeking dental treatment at the University Dental Hospital in Sharjah, United Arab Emirates. The entire (~ 1500 bp) 16S rRNA bacterial gene was fully amplified and sequenced using Oxford Nanopore technology. Subjects were compared for the relative abundance and diversity of subgingival microbiota, considering smoking and periodontal condition. The relative abundances of several pathogens were significantly higher among smokers, such as Prevotella denticola and Treponema sp. OMZ 838 in medwakh smokers, Streptococcus mutans and Veillonella dispar in cigarette smokers, Streptococcus sanguinis and Tannerella forsythia in shisha smokers. Subgingival microbiome of smokers was altered even in subjects with no or mild periodontitis, probably making them more prone to severe periodontal diseases. Microbiome profiling can be a useful tool for periodontal risk assessment. Further studies are recommended to investigate the impact of tobacco cessation on periodontal disease progression and oral microbiome.

RevDate: 2021-01-14

Góngora E, Elliott KH, L Whyte (2021)

Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia).

Scientific reports, 11(1):1200.

The role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.

RevDate: 2021-01-14

Zarantoniello M, Randazzo B, Nozzi V, et al (2021)

Physiological responses of Siberian sturgeon (Acipenser baerii) juveniles fed on full-fat insect-based diet in an aquaponic system.

Scientific reports, 11(1):1057.

Over the last years, the potential use of Black Soldier Fly meal (BSF) as a new and sustainable aquafeed ingredient has been largely explored in several fish species. However, only fragmentary information is available about the use of BSF meal-based diets in sturgeon nutrition. In consideration of a circular economy concept and a more sustainable aquaculture development, the present research represents the first comprehensive multidisciplinary study on the physiological effects of a BSF diet during sturgeon culture in an aquaponic system. Siberian sturgeon (Acipenser baerii) juveniles were fed over a 60-days feeding trial on a control diet (Hi0) and a diet containing 50% of full-fat BSF meal respect to fish meal (Hi50). Physiological responses of fish were investigated using several analytical approaches, such as gas chromatography-mass spectrometry, histology, Fourier Transformed Infrared Spectroscopy (FTIR), microbiome sequencing and Real-time PCR. While aquaponic systems performed optimally during the trial, Hi50 group fish showed lower diet acceptance that resulted in growth and survival reduction, a decrease in hepatic lipids and glycogen content (FTIR), a higher hepatic hsp70.1 gene expression and a worsening in gut histological morphometric parameters. The low feed acceptance showed by Hi50 group sturgeon highlighted the necessity to improve the palatability of BSF-based diet designed for sturgeon culture.

RevDate: 2021-01-14

Imahashi M, Ode H, Kobayashi A, et al (2021)

Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients.

Scientific reports, 11(1):960.

In HIV-1-infected patients, antiretroviral therapy (ART) is a key factor that may impact commensal microbiota and cause the emergence of side effects. However, it is not fully understood how long-term ART regimens have diverse impacts on the microbial compositions over time. Here, we performed 16S ribosomal RNA gene sequencing of the fecal and salivary microbiomes in patients under different long-term ART. We found that ART, especially conventional nucleotide/nucleoside reverse transcriptase inhibitor (NRTI)-based ART, has remarkable impacts on fecal microbial diversity: decreased α-diversity and increased ß-diversity over time. In contrast, dynamic diversity changes in the salivary microbiome were not observed. Comparative analysis of bacterial genus compositions showed a propensity for Prevotella-enriched and Bacteroides-poor gut microbiotas in patients with ART over time. In addition, we observed a gradual reduction in Bacteroides but drastic increases in Succinivibrio and/or Megasphaera under conventional ART. These results suggest that ART, especially NRTI-based ART, has more suppressive impacts on microbiota composition and diversity in the gut than in the mouth, which potentially causes intestinal dysbiosis in patients. Therefore, NRTI-sparing ART, especially integrase strand transfer inhibitor (INSTI)- and/or non-nucleotide reverse transcriptase inhibitor (NNRTI)-containing regimens, might alleviate the burden of intestinal dysbiosis in HIV-1-infected patients under long-term ART.

RevDate: 2021-01-14

Relvas M, Regueira-Iglesias A, Balsa-Castro C, et al (2021)

Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models.

Scientific reports, 11(1):929.

The present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota's abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.

RevDate: 2021-01-14

Jo R, Yama K, Aita Y, et al (2021)

Comparison of oral microbiome profiles in 18-month-old infants and their parents.

Scientific reports, 11(1):861.

The onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.

RevDate: 2021-01-14

Fishbein SRS, Hink T, Reske KA, et al (2021)

Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.

mSphere, 6(1):.

Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin (n = 8) or placebo (n = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity (P = 0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes (P = 0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile, and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.)IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile, perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile/ARO-related outcomes and transmission.

RevDate: 2021-01-14

Yoshimatsu Y, Mikami Y, T Kanai (2021)

Bacteriotherapy for inflammatory bowel disease.

Inflammation and regeneration, 41(1):3.

The number of patients with inflammatory bowel disease is rapidly increasing in developed countries. The main cause of this increase is thought not to be genetic, but secondary to rapidly modernized environmental change. Changes in the environment have been detrimental to enteric probiotics useful for fermentation, inducing an increase in pathobionts that survive by means other than fermentation. This dysregulated microbiota composition, the so-called dysbiosis, is believed to have increased the incidence of inflammatory bowel disease. Bacteriotherapy, a treatment that prophylactically and therapeutically corrects the composition of disturbed intestinal microbiota, is a promising recent development. In fact, fecal microbiome transplantation for recurrent Clostridioides difficile infection in 2013 was a significant contribution for bacteriotherapy. In this paper, we comprehensively review bacteriotherapy in an easy-to-understand format.

RevDate: 2021-01-13

Maghfour J, Olson J, Conic RRZ, et al (2021)

The Association between Alopecia and Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.

IMPORTANCE: The link between autoimmune gut disorders and different types of hair loss conditions has been recently investigated with an increased interest. With acknowledgement of the connection between immune dysregulation and the gut microbiome, this pathway is now becoming recognized as playing an important role in hair growth. The inflammatory cascade that results from the disruption of gut integrity such as seen in inflammatory bowel diseases (IBD) has been associated with certain types of alopecia.

OBJECTIVE: The aim of this work was to evaluate the association between alopecia and IBD.

EVIDENCE REVIEW: A primary literature search was conducted using the PubMed, Embase, and Web of Science databases to identify articles on co-occurring alopecia and IBD from 1967 to 2020. A total of 79 studies were included in the review. A one-way proportional meta-analysis was performed on 19 of the studies to generate the pooled prevalence of alopecia and IBD.

FINDING: The pooled prevalence of non-scarring alopecia among IBD patients was 1.12% (k = 7, I2 = 98.6%, 95% CI 3.1-39.9); the prevalence of IBD among scarring and non-scarring alopecia was 1.99% (k = 12; I2 = 99%, 95% CI 6.2-34). The prevalence of non-scarring alopecia areata (AA) among IBD was compared to the prevalence of AA in the general population (0.63 vs. 0.1%; p < 0.0001). Similarly, the prevalence of IBD among the scarring and non-scarring alopecia groups was compared to the prevalence of IBD in the general population (1.99 vs. 0.396%; p = 0.0004).

CONCLUSION: IBD and alopecia, particularly AA, appear to be strongly associated. Dermatology patients with alopecia may benefit from screening for IBD.

RevDate: 2021-01-13

Nayak RR, Alexander M, Deshpande I, et al (2021)

Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.

Cell host & microbe pii:S1931-3128(20)30670-3 [Epub ahead of print].

Immunomodulatory drugs can inhibit bacterial growth, yet their mechanism of action, spectrum, and clinical relevance remain unknown. Methotrexate (MTX), a first-line rheumatoid arthritis (RA) treatment, inhibits mammalian dihydrofolate reductase (DHFR), but whether it directly impacts gut bacteria is unclear. We show that MTX broadly alters the human gut microbiota. Drug sensitivity varied across strains, but the mechanism of action against DHFR appears conserved between mammalian and bacterial cells. RA patient microbiotas were sensitive to MTX, and changes in gut bacterial taxa and gene family abundance were distinct between responders and non-responders. Transplantation of post-treatment samples into germ-free mice given an inflammatory trigger led to reduced immune activation relative to pre-treatment controls, enabling identification of MTX-modulated bacterial taxa associated with intestinal and splenic immune cells. Thus, conservation in cellular pathways across domains of life can result in broad off-target drug effects on the human gut microbiota with consequences for immune function.

RevDate: 2021-01-13

Tanes C, Bittinger K, Gao Y, et al (2021)

Role of dietary fiber in the recovery of the human gut microbiome and its metabolome.

Cell host & microbe pii:S1931-3128(20)30674-0 [Epub ahead of print].

Gut microbiota metabolites may be important for host health, yet few studies investigate the correlation between human gut microbiome and production of fecal metabolites and their impact on the plasma metabolome. Since gut microbiota metabolites are influenced by diet, we performed a longitudinal analysis of the impact of three divergent diets, vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber, on the human gut microbiome and its metabolome, including after a microbiota depletion intervention. Omnivore and vegan, but not EEN, diets altered fecal amino acid levels by supporting the growth of Firmicutes capable of amino acid metabolism. This correlated with relative abundance of a sizable number of fecal amino acid metabolites, some not previously associated with the gut microbiota. The effect on the plasma metabolome, in contrast, were modest. The impact of diet, particularly fiber, on the human microbiome influences broad classes of metabolites that may modify health.

RevDate: 2021-01-13

Fabusoro OK, LA Mejia (2021)

Nutrition in HIV-Infected Infants and Children: Current Knowledge, Existing Challenges, and New Dietary Management Opportunities.

Advances in nutrition (Bethesda, Md.) pii:6095741 [Epub ahead of print].

HIV infection and undernutrition remain significant public health concerns for infants and children. In infants and children under these conditions, undernutrition is one of the leading causes of death. Proper management of nutrition and related nutrition complications in these groups with increased nutrition needs are prominent challenges, particularly in HIV-prevalent poor-resource environments. Several studies support the complexity of the relation between HIV infection, nutrition, and the immune system. These elements interact and create a vicious circle of poor health outcomes. Recent studies on the use of probiotics as a novel approach to manage microbiome imbalance and gut-mucosal impairment in HIV infection are gaining attention. This new strategy could help to manage dysbiosis and gut-mucosal impairment by reducing immune activation, thereby potentially forestalling unwanted health outcomes in children with HIV. However, existing trials on HIV-infected children are still insufficient. There are also conflicting reports on the dosage and effectiveness of single or multiple micronutrient supplementation in the survival of HIV-infected children with severe acute malnutrition. The WHO has published guidelines that include time of initiation of antiretroviral therapy for HIV-pregnant mothers and their HIV-exposed or HIV-infected children, micronutrient supplementation, dietary formulations, prevention, and management of HIV therapy. However, such guidelines need to be reviewed owing to recent advances in the field of nutrition. There is a need for new intervention studies, practical strategies, and evidence-based guidelines to reduce the disease burden, improve adherence to treatment regimen, and enhance the nutrition, health, and well-being of HIV-infected infants and children. This review provides up-to-date scientific information on current knowledge and existing challenges for nutrition therapy in HIV-infected infants and children. Moreover, it presents new research findings that could be incorporated into current guidelines.

RevDate: 2021-01-13

Lee YT, Mohd Ismail NI, LK Wei (2021)

Microbiome and ischemic stroke: A systematic review.

PloS one, 16(1):e0245038 pii:PONE-D-20-13573.

BACKGROUND: Ischemic stroke is one of the non-communicable diseases that contribute to the significant number of deaths worldwide. However, the relationship between microbiome and ischemic stroke remained unknown. Hence, the objective of this study was to perform systematic review on the relationship between human microbiome and ischemic stroke.

METHODS: A systematic review on ischemic stroke was carried out for all articles obtained from databases until 22nd October 2020. Main findings were extracted from all the eligible studies.

RESULTS: Eighteen eligible studies were included in the systematic review. These studies suggested that aging, inflammation, and different microbial compositions could contribute to ischemic stroke. Phyla Firmicutes and Bacteroidetes also appeared to manipulate post-stroke outcome. The important role of microbiota-derived short-chain fatty acids and trimethylamine N-oxide in ischemic stroke were also highlighted.

CONCLUSIONS: This is the first systematic review that investigates the relationship between microbiome and ischemic stroke. Aging and inflammation contribute to differential microbial compositions and predispose individuals to ischemic stroke.

RevDate: 2021-01-13

Hilgarth M, Redwitz J, Ehrmann MA, et al (2021)

Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera.

International journal of systematic and evolutionary microbiology [Epub ahead of print].

As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella. Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella, for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).

RevDate: 2021-01-13

Manandhar I, Alimadadi A, Aryal S, et al (2021)

Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases.

American journal of physiology. Gastrointestinal and liver physiology [Epub ahead of print].

Despite the availability of various diagnostic tests for inflammatory bowel diseases (IBD), misdiagnosis of IBD occurs frequently, and thus there is a clinical need to further improve the diagnosis of IBD. As gut dysbiosis is reported in IBD patients, we hypothesized that supervised machine learning (ML) could be used to analyze gut microbiome data for predictive diagnostics of IBD. To test our hypothesis, fecal 16S metagenomic data of 729 IBD and 700 non-IBD subjects from the American Gut Project were analyzed using five different ML algorithms. Fifty differential bacterial taxa were identified (LEfSe: LDA > 3) between the IBD and non-IBD groups, and ML classifications trained with these taxonomic features using random forest (RF) achieved a testing AUC of ~0.80. Next, we tested if operational taxonomic units (OTUs), instead of bacterial taxa, could be used as ML features for diagnostic classification of IBD. Top 500 high-variance OTUs were used for ML training and an improved testing AUC of ~0.82 (RF) was achieved. Lastly, we tested if supervised ML could be used for differentiating Crohn's disease (CD) and ulcerative colitis (UC). Using 331 CD and 141 UC samples, 117 differential bacterial taxa (LEfSe: LDA > 3) were identified, and the RF model trained with differential taxonomic features or high-variance OTU features achieved a testing AUC > 0.90. In summary, our study demonstrates the promising potential of artificial intelligence via supervised ML modeling for predictive diagnostics of IBD using gut microbiome data.

RevDate: 2021-01-13

Cuna AC, Morowitz MJ, Ahmed I, et al (2021)

Dynamics of the Preterm Gut Microbiome in Health and Disease.

American journal of physiology. Gastrointestinal and liver physiology [Epub ahead of print].

Advances in metagenomics have allowed a detailed study of the gut microbiome, and its role in human health and disease. Infants born prematurely possess a fragile gut microbial ecosystem that is vulnerable to perturbation. Alterations in the developing gut microbiome in preterm infants are linked to life-threatening diseases such as necrotizing enterocolitis (NEC) and late onset sepsis; and may impact future risk of asthma, atopy, obesity, and psychosocial disease. In this mini review, we summarize recent literature on the origins and patterns of development of the preterm gut microbiome in the perinatal period. The host-microbiome-environmental factors that portend development of dysbiotic intestinal microbial patterns associated with NEC and sepsis are reviewed. Strategies to manipulate the microbiome and mitigate dysbiosis, including the use of probiotics and prebiotics will also be discussed. Finally, we explore the challenges and future directions of gut microbiome research in preterm infants.

RevDate: 2021-01-13

Kollef MH, Torres A, Shorr AF, et al (2021)

Nosocomial Infection.

Critical care medicine, 49(2):169-187.

OBJECTIVE: The first 70 years of critical care can be considered a period of "industrial revolution-like" advancement in terms of progressing the understanding and care of critical illness. Unfortunately, like the industrial revolution's impact on the environment, advancing ICU care of increasingly elderly, immunosuppressed, and debilitated individuals has resulted in a greater overall burden and complexity of nosocomial infections within modern ICUs. Given the rapid evolution of nosocomial infections, the authors provide an updated review.

We searched PubMed and OVID for peer-reviewed literature dealing with nosocomial infections in the critically ill, as well as the websites of government agencies involved with the reporting and prevention of nosocomial infections. Search terms included nosocomial infection, antibiotic resistance, microbiome, antibiotics, and intensive care.

Nosocomial infections in the ICU setting are evolving in multiple domains including etiologic pathogens plus novel or emerging pathogens, prevalence, host risk factors, antimicrobial resistance, interactions of the host microbiome with nosocomial infection occurrence, and understanding of pathogenesis and prevention strategies. Increasing virulence and antimicrobial resistance of nosocomial infections mandate increasing efforts toward their prevention.

CONCLUSIONS: Nosocomial infections are an important determinant of outcome for patients in the ICU setting. Systematic research aimed at improving the prevention and treatment of nosocomial infections is still needed.

RevDate: 2021-01-13

Peters BA, Xue X, Wang Z, et al (2021)

Menopausal status and observed differences in the gut microbiome in women with and without HIV infection.

Menopause (New York, N.Y.), Publish Ahead of Print: pii:00042192-900000000-97021 [Epub ahead of print].

OBJECTIVE: Gut microbiota respond to host physiological phenomena, yet little is known regarding shifts in the gut microbiome due to menopausal hormonal and metabolic changes in women. HIV infection impacts menopause and may also cause gut dysbiosis. We therefore sought to determine the association between menopausal status and gut microbiome composition in women with and without HIV.

METHODS: Gut microbiome composition was assessed in stool from 432 women (99 premenopausal HIV+, 71 premenopausal HIV-, 182 postmenopausal HIV+, 80 postmenopausal HIV-) via 16S rRNA gene sequencing. We examined cross-sectional associations of menopause with gut microbiota overall diversity and composition, and taxon and inferred metagenomic pathway abundance. Models were stratified by HIV serostatus and adjusted for age, HIV-related variables, and other potential confounders.

RESULTS: Menopause, ie post- versus premenopausal status, was associated with overall microbial composition only in women with HIV (permutational MANOVA of Jensen Shannon Divergence: P = 0.01). In women with HIV, menopause was associated with enrichment of gram-negative order Enterobacteriales, depletion of highly abundant taxa within Prevotella copri, and alterations in other low-abundance taxa. Additionally, menopause in women with HIV was associated with enrichment of metagenomic pathways related to Enterobacteriales, including degradation of amino acids and phenolic compounds, biosynthesis of enterobactin, and energy metabolism pathways. Menopause-related differences in some low-abundance taxa were also observed in women without HIV.

CONCLUSIONS: A changing gut microbiome may be an overlooked phenomenon of reproductive aging in women with HIV. Longitudinal assessments across all reproductive stages are necessary to confirm these findings and identify health implications.

RevDate: 2021-01-13

Le Poole IC (2021)

Myron Gordon Award paper: Microbes, T-cell diversity and pigmentation.

Pigment cell & melanoma research [Epub ahead of print].

Melanocytes are static, minimally proliferative cells. This leaves them vulnerable in vitiligo. Yet upon malignant transformation, they form vicious tumors. This profound switch in physiology is accompanied by genetic change, and is driven by environmental factors. If UV exposure in younger years supports malignant transformation and melanoma formation, it can likewise impart mutations on melanocytes that reduce their viability, to initiate vitiligo. A wide variety of microbes can influence these diametrically opposed outcomes before either disease takes hold. These microbes are vehicles of change that we are only beginning to study. Once a genetic modification occurs, there is a wide variety of immune cells ready to respond. Though it does not act alone, the T cell is among the most decisive responders in this process. The same biochemical process that offered the skin protection by producing melanin can become an Achilles heel for the cell when the T cells target melanosomal enzymes or, on occasion, neoantigens. T cells are precise, determined and consequential when they strike. Here we probe the relationship between the microbiome and its metabolites, epithelial integrity, and the activation of T cells that target benign and malignant melanocytes in vitiligo and melanoma.

RevDate: 2021-01-13

Cook KA, Domissy A, Simon RA, et al (2021)

Dysbiosis in aspirin-exacerbated respiratory disease.

International forum of allergy & rhinology [Epub ahead of print].

RevDate: 2021-01-13

Corniello A, Guida M, Stellato L, et al (2021)

Hydrochemical, isotopic and microbiota characterization of telese mineral waters (Southern Italy).

Environmental geochemistry and health [Epub ahead of print].

The study deals with the analyses of springs and wells at the base of Montepugliano Hill that represents the SE edge of the wide carbonate Matese massif (Campania, southern Italy). At the base of the hill, from west to east and for almost one kilometre, cold springs HCO3-Ca type (Grassano springs, ~ 4.5 m3/s; TDS: about 0.45 g/L) pass to hypothermal, HCO3-Ca type, sulphurous and CO2-rich springs (~ 1 m3/s with TDS > 1 g/L). Some of the latter are widely used in Telese Spa and Centro Relax Spa. Chemical and isotopic analyses carried out for this study support the hypothesis that all these waters (mineral and non-mineral) have the same catchment area, which is located in the Matese massif. As regards the sulphurous springs, they receive both meteoric waters infiltration and uprising of deeper waters rich in endogenous CO2 and H2S gases through important faults systems. Far from these faults, the chemistry of groundwater is scarcely (or not at all) affected by these deep fluid enrichment processes. This scheme is very significant; in fact, when very important groundwater resources are present, it is possible to use both mineral waters in Spa and, in areas far from the faults, those not yet mineralized. Finally, at Montepugliano Hill, in the final stage of the flow path, groundwater is also affected by change in the microbiome: this could provide a basis for comparison between various mineral waters.

RevDate: 2021-01-13

Shen J, Wyness AJ, Claire MW, et al (2021)

Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert.

Microbial ecology [Epub ahead of print].

Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.

RevDate: 2021-01-13

Lim MY, Hong S, Kim JH, et al (2021)

Association between Gut Microbiome and Frailty in the Older Adult Population in Korea.

The journals of gerontology. Series A, Biological sciences and medical sciences pii:6092412 [Epub ahead of print].

Frailty is a common geriatric syndrome associated with the risk of adverse health outcomes. Recently, two key pathophysiological characteristics of frailty, altered energy metabolism and dysregulated immunity, have been reported to be associated with gut microbiome dysbiosis, indicating that the gut microbiome plays a role in frailty. However, few studies have directly examined the relationship between the gut microbiome and frailty. Here, we investigated the association of frailty measures with the gut microbiome using 16S rRNA gene sequencing data obtained from the fecal samples of 176 Korean older adults. Overall frailty was scored using the Korean Frailty Index (FI). Grip strength and Geriatric Depression Scale (GDS) scores were used as physical and mental frailty measures, respectively. In contrast to age, metabolic, and inflammatory biomarkers, the frailty measures were associated with inter-individual variations in microbial composition (false discovery rate [FDR] < 0.2). Both FI and GDS scores were negatively associated with microbial diversity (FDR < 0.2). Frailty measures showed distinct associations with specific microbial taxa and metabolic functions. Particularly, the Bacteroides enterotype was found only in subjects categorized in the frail group. Moreover, we observed that the abundance of beneficial taxa, such as Prevotella copri and Coprococcus eutactus, was reduced in frailer individuals, whereas that of detrimental taxa, such as Bacteroides fragilis and Clostridium hathewayi, was increased (FDR < 0.2). Our findings suggest that the gut microbiome can be used an indicator of an increased risk of frailty or a target for improving health in frail older adults.

RevDate: 2021-01-13

Pabbathi NPP, Velidandi A, Tavarna T, et al (2021)

Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review.

Biomass conversion and biorefinery pii:1186 [Epub ahead of print].

As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.

RevDate: 2021-01-13

Kuthyar S, Kowalewski MM, Roellig DM, et al (2021)

Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria.

Ecology and evolution, 11(1):45-57 pii:ECE36910.

Habitat disturbance, a common consequence of anthropogenic land use practices, creates human-animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host-microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host-microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.

RevDate: 2021-01-13

Siwicka-Gieroba D, K Czarko-Wicha (2020)

Lung microbiome - a modern knowledge.

Central-European journal of immunology, 45(3):342-345.

Recent studies have reported that commensal microorganisms are not just "passive occupants" but may play a crucial role in the immune system activation. It is well-known that in critically ill patients, the microbiome is modified and may be associated with the development of immunosuppression in sepsis, contributing to the development of acute renal injury, cardiovascular diseases, or more importantly, respiratory system disturbances. The conviction of lung sterility has gone down in history. The presence of characteristic gut microbiome, such as Bacteroidetes and Enterobacteriaceae, was demonstrated in lungs of critically ill patients. This bacteria's translocation, especially in ischemia-reperfusion injury, results in increased concentration of inflammation response markers and may play a pivotal role in the pathogenesis of respiratory system disturbances, including acute respiratory distress syndrome. Recent studies have shown that ischemia-reperfusion injury is often observed in intensive care units (ICUs) and predispose to microbiome disturbances that are strictly connected with immune system activation and epithelial damage. Potential effects of dysbiosis treatment are under highly activated investigation. Therefore, it is possible that microbiota-targeted therapy may constitute the future therapeutic path in ICUs.

RevDate: 2021-01-13

de Sousa Lopes L, Mendes LW, Antunes JEL, et al (2021)

Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil.

Scientific reports, 11(1):831.

Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.

RevDate: 2021-01-13

Funosas G, Triadó-Margarit X, Castro F, et al (2021)

Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus).

Scientific reports, 11(1):766.

Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.

RevDate: 2021-01-13

Moustafa MAM, Chel HM, Thu MJ, et al (2021)

Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments.

Scientific reports, 11(1):741.

Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.

RevDate: 2021-01-13

Likhitrattanapisal S, Siriarchawatana P, Seesang M, et al (2021)

Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries.

Scientific reports, 11(1):582.

Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.

RevDate: 2021-01-13

Stinson LF, Ma J, Rea A, et al (2021)

Centrifugation does not remove bacteria from the fat fraction of human milk.

Scientific reports, 11(1):572.

Analysis of the human milk microbiome is complicated by the presence of a variable quantity of fat. The fat fraction of human milk is typically discarded prior to analysis. It is assumed that all cells are pelleted out of human milk by high speed centrifugation; however, studies of bovine milk have reported that bacteria may remain trapped within the fat fraction. Here, the bacterial DNA profiles of the fat fraction and cell pellet of human milk (n = 10) were analysed. Human and bacterial DNA was consistently recovered from the fat fraction of human milk (average of 12.4% and 32.7%, respectively). Staphylococcus epidermidis was significantly more abundant in the cell pellet compared to the fat fraction (P = 0.038), and three low-abundance species (< 5% relative abundance) were recovered from one fraction only. However, inclusion of fat reduced the efficiency of DNA extraction by 39%. Culture-based methods were used to quantify the distribution of an exogenously added strain of Staphylococcus aureus in human milk fractions. S. aureus was consistently recovered from the fat fraction (average 28.9%). Bacterial DNA profiles generated from skim milk or cell pellets are not representative of the entire human milk microbiome. These data have critical implications for the design of future work in this field.

RevDate: 2021-01-13

Panpetch W, Kullapanich C, Dang CP, et al (2021)

Candida Administration Worsens Uremia-Induced Gut Leakage in Bilateral Nephrectomy Mice, an Impact of Gut Fungi and Organismal Molecules in Uremia.

mSystems, 6(1):.

The impact of gut fungi and (1→3)-β-d-glucan (BG), a major fungal cell wall component, on uremia was explored by Candida albicans oral administration in bilateral nephrectomy (BiNx) mice because of the prominence of C. albicans in the human intestine but not in mice. As such, BiNx with Candida administration (BiNx-Candida) enhanced intestinal injury (colon cytokines and apoptosis), gut leakage (fluorescein isothiocyanate [FITC]-dextran assay, endotoxemia, serum BG, and bacteremia), systemic inflammation, and liver injury at 48 h postsurgery compared with non-Candida BiNx mice. Interestingly, uremia-induced enterocyte apoptosis was severe enough for gut translocation of viable bacteria, as indicated by culture positivity for bacteria in blood, mesenteric lymph nodes (MLNs), and other organs, which was more severe in BiNx-Candida than in non-Candida BiNx mice. Candida induced alterations in the gut microbiota of BiNx mice as indicated by (i) the higher fungal burdens in the feces of BiNx-Candida mice than in sham-Candida mice by culture methods and (ii) increased Bacteroides with decreased Firmicutes and reduced bacterial diversity in the feces of BiNx-Candida mice compared with non-Candida BiNx mice by fecal microbiome analysis. In addition, lipopolysaccharide plus BG (LPS+BG), compared with each molecule alone, induced high supernatant cytokine levels, which were enhanced by uremic mouse serum in both hepatocytes (HepG2 cells) and macrophages (RAW264.7 cells). Moreover, LPS+BG, but not each molecule alone, reduced the glycolysis capacity and mitochondrial function in HepG2 cells as determined by extracellular flux analysis. Additionally, a probiotic, Lactobacillus rhamnosus L34 (L34), attenuated disease severity only in BiNx-Candida mice but not in non-Candida BiNx mice, as indicated by liver injury and serum cytokines through the attenuation of gut leakage, the fecal abundance of fungi, and fecal bacterial diversity but not fecal Gram-negative bacteria. In conclusion, Candida enhanced BiNx severity through the worsening of gut leakage and microbiota alterations that resulted in bacteremia, endotoxemia, and glucanemia.IMPORTANCE The impact of fungi in the intestine on acute uremia was demonstrated by the oral administration of Candida albicans in mice with the removal of both kidneys. Because fungi in the mouse intestine are less abundant than in humans, a Candida-administered mouse model has more resemblance to patient conditions. Accordingly, acute uremia, without Candida, induced intestinal mucosal injury, which resulted in the translocation of endotoxin, a major molecule of gut bacteria, from the intestine into blood circulation. In acute uremia with Candida, intestinal injury was more severe due to fungi and the alteration in intestinal bacteria (increased Bacteroides with decreased Firmicutes), leading to the gut translocation of both endotoxin from gut bacteria and (1→3)-β-d-glucan from Candida, which synergistically enhanced systemic inflammation in acute uremia. Both pathogen-associated molecules were delivered to the liver and induced hepatocyte inflammatory responses with a reduced energy production capacity, resulting in acute uremia-induced liver injury. In addition, Lactobacillus rhamnosus attenuated intestinal injury through reduced gut Candida and improved intestinal bacterial conditions.

RevDate: 2021-01-13

Tláskal V, Brabcová V, Větrovský T, et al (2021)

Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition.

mSystems, 6(1):.

Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils.IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.

RevDate: 2021-01-13

Fagorzi C, Bacci G, Huang R, et al (2021)

Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis.

mSystems, 6(1):.

Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.

RevDate: 2021-01-13

He JW, Zhou XJ, Li YF, et al (2021)

Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy.

mSystems, 6(1):.

The gut microbiota has been implicated in immunoglobin A nephropathy (IgAN) because the intestinal immune response is assumed to be one of the disease triggers. Since the microbial composition is heritable, we hypothesize that genetic variants controlling gut microbiota composition may be associated with susceptibility to IgAN or clinical phenotypes. A total of 175 gut-microbiome-associated genetic variants were retrieved from the Genome-Wide Association Study (GWAS) Catalog. Genetic associations were examined in 1,511 patients with IgAN and 4,469 controls. Subphenotype associations and microbiome annotations were undertaken for a better understanding of how genes shaped phenotypes. Likely candidate microbes suggested in genetic associations were validated using 16S rRNA gene sequencing in two independent data sets with 119 patients with IgAN and 45 controls in total. Nine genetic variants were associated with susceptibility to IgAN. Risk genotypes of LYZL1 were associated with higher serum levels of galactose-deficient IgA1 (Gd-IgA1). Other significant findings included the associations between the risk genotype of SIPA1L3 and early age at onset, PLTP and worse kidney function, and AL365503.1 and more severe hematuria. Besides, risk genotypes of LYZL1 and SIPA1L3 were associated with decreased abundances of Dialister and Bacilli, respectively. Risk genotypes of PLTP and AL365503.1 were associated with increased abundances of Erysipelotrichaceae and Lachnobacterium, respectively. 16S data validated a decreased tendency for Dialister and an increased tendency for Erysipelotrichaceae in IgAN. In this pilot study, our results provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics and shed new light on candidate bacteria for future pathogenesis studies.IMPORTANCE The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]). The relationship between host genetics and the microbiota and the role of the microbiota in IgAN are unclear. We retrieved the GWAS Catalog and associated microbiome QTL in IgAN, observing that nine genetic variants were associated with IgAN susceptibility and some clinical phenotypes. In a consistent way, the decreased abundance of Dialister was associated with higher serum levels of Gd-IgA1, and 16S rRNA gene analysis confirmed the decreased abundance of Dialister in IgAN. These data provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics, which is a new strategy for future pathogenesis and intervention studies.

RevDate: 2021-01-13

Griesenauer B, González-Beiras C, Fortney KR, et al (2021)

Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island.

mBio, 12(1):.

Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases are idiopathic (IU). Using mass drug administration (MDA) of azithromycin, a yaws eradication campaign on Lihir Island in Papua New Guinea reduced but failed to eradicate yaws; IU rates remained constant throughout the campaign. To identify potential etiologies of IU, we obtained swabs of CU lesions (n = 279) and of the skin of asymptomatic controls (AC; n = 233) from the Lihir Island cohort and characterized their microbiomes using a metagenomics approach. CU bacterial communities were less diverse than those of the AC. Using real-time multiplex PCR with pathogen-specific primers, we separated CU specimens into HD-positive (HD+), TP+, HD+TP+, and IU groups. Each CU subgroup formed a distinct bacterial community, defined by the species detected and/or the relative abundances of species within each group. Streptococcus pyogenes was the most abundant organism in IU (22.65%) and was enriched in IU compared to other ulcer groups. Follow-up samples (n = 31) were obtained from nonhealed ulcers; the average relative abundance of S. pyogenes was 30.11% in not improved ulcers and 0.88% in improved ulcers, suggesting that S. pyogenes in the not improved ulcers may be azithromycin resistant. Catonella morbi was enriched in IU that lacked S. pyogenes As some S. pyogenes and TP strains are macrolide resistant, penicillin may be the drug of choice for CU azithromycin treatment failures. Our study will aid in the design of diagnostic tests and selective therapies for CU.IMPORTANCE Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi, the cause(s) of the remaining one-third is unknown. Given the failure of mass drug administration of azithromycin to eradicate CU, the World Health Organization recently proposed an integrated disease management strategy to control CU. Success of this strategy requires determining the unknown cause(s) of CU. By using 16S rRNA gene sequencing of swabs obtained from CU and the skin of asymptomatic children, we identified another possible cause of skin ulcers, Streptococcus pyogenes Although S. pyogenes is known to cause impetigo and cellulitis, this is the first report implicating the organism as a causal agent of CU. Inclusion of S. pyogenes into the integrated disease management plan will improve diagnostic testing and treatment of this painful and debilitating disease of children and strengthen elimination efforts.

RevDate: 2021-01-13

Amenyogbe N, Dimitriu P, Smolen KK, et al (2021)

Biogeography of the Relationship between the Child Gut Microbiome and Innate Immune System.

mBio, 12(1):.

The gut microbiome is a well-recognized modulator of host immunity, and its compositions differ between geographically separated human populations. Systemic innate immune responses to microbial derivatives also differ between geographically distinct human populations. However, the potential role of the microbiome in mediating geographically varied immune responses is unexplored. We here applied 16S amplicon sequencing to profile the stool microbiome and, in parallel, measured whole-blood innate immune cytokine responses to several pattern recognition receptor (PRR) agonists among 2-year-old children across biogeographically diverse settings. Microbiomes differed mainly between high- and low-resource environments and were not strongly associated with other demographic factors. We found strong correlations between responses to Toll-like receptor 2 (TLR2) and relative abundances of Bacteroides and Prevotella populations, shared among Canadian and Ecuadorean children. Additional correlations between responses to TLR2 and bacterial populations were specific to individual geographic cohorts. As a proof of concept, we gavaged germfree mice with human donor stools and found murine splenocyte responses to TLR stimulation were consistent with responses of the corresponding human donor populations. This study identified differences in immune responses correlating to gut microbiomes across biogeographically diverse settings and evaluated biological plausibility using a mouse model. This insight paves the way to guide optimization of population-specific interventions aimed to improve child health outcomes.IMPORTANCE Both the gut microbiome and innate immunity are known to differ across biogeographically diverse human populations. The gut microbiome has been shown to directly influence systemic immunity in animal models. With this, modulation of the gut microbiome represents an attractive avenue to improve child health outcomes associated with altered immunity using population-specific approaches. However, there are very scarce data available to determine which members of the gut microbiome are associated with specific immune responses and how these differ around the world, creating a substantial barrier to rationally designing such interventions. This study addressed this knowledge gap by identifying relationships between distinct bacterial taxa and cytokine responses to specific microbial agonists across highly diverse settings. Furthermore, we provide evidence that immunomodulatory effects of region-specific stool microbiomes can be partially recapitulated in germfree mice. This is an important contribution toward improving global child health by targeting the gut microbiome.

RevDate: 2021-01-13

Hussein AA, Elsayed AS, Durrani M, et al (2021)

Investigating the association between the urinary microbiome and bladder cancer: An exploratory study.

Urologic oncology pii:S1078-1439(20)30641-4 [Epub ahead of print].

INTRODUCTION: We sought to investigate the association between the urinary microbiome and bladder cancer, including the difference between nonmuscle-invasive (NMIBC) and muscle-invasive (MIBC) bladder cancer, and Bacillus Calmette Guerin (BCG) responsive vs. BCG-refractory NMIBC.

METHODS: Urine specimens were collected from consecutive patients with bladder cancer and healthy volunteers. Urine samples were analyzed using 16S rRNA sequencing to identify and compare any present bacteria. Alteration in the urinary microbiome was described in terms of alpha (diversity of populations within a sample) and beta diversities (differences between populations among different samples). Analyses were corrected for age, sex, method of sample preservation, and method of collection (mid-stream catch vs. catheterized urine).

RESULTS: Fifty-three samples (43 patients with bladder cancer, and 10 controls) were included. For bladder cancer patients, mean age was 70 years, 7 (16%) were females; and 29 (67%) had NMIBC. Among patients with NMIBC, 11 (38%) patients received BCG, 6 of which had recurrence or progression after a median follow up of 13 months. Comparing the microbiome of bladder cancer patients vs. healthy controls, beta-diversity was significantly different, with Actinomyces, Achromobacter, Brevibacterium, and Brucella significantly more abundant in urine samples of bladder cancer patients. Comparing NMIBC and MIBC, Hemophilus and Veillonella were significantly more abundant in urine of MIBC patients, while Cupriavidus was significantly more abundant in NMIBC patients. Among NMIBC patients, Serratia and Brochothrix, Negativicoccus, Escherichia-Shigella, and Pseudomonas were significantly more abundant in patients who responded to BCG in comparison to those who did not.

CONCLUSION: Urinary microbiome varied between patients with bladder cancer and healthy controls. Moreover, urinary microbial profiles differed among patient with NMIBC vs. MIBC, and among BCG responsive vs. BCG refractory NMIBC.

RevDate: 2021-01-13

Elshahed MS, Miron A, Aprotosoaie AC, et al (2021)

Pectin in diet: Interactions with the human microbiome, role in gut homeostasis, and nutrient-drug interactions.

Carbohydrate polymers, 255:117388.

Pectins are a part of daily diet as well as food additives that are indigestible polysaccharides by human enzymes, however, they can be easily degraded by gut bacteria with the production of short chain fatty acids (SCFAs). Knowledge of pectin gut homeostasis and further how pectin affect gut bacterial communities is insufficient and limited. This review focuses on providing the whole story of how pectin functions as prebiotics in the gut. Understanding the interplay between functional and immunological responses inside animal or human gut as influenced by pectin in diets is provided. The interaction between pectin and gut microbiota is presented from both sides, in terms of how pectin affects gut microbiome and or the fermentation products produced in response by gut bacteria. This knowledge can be used to define preferred dietary pectins, targeting beneficial bacteria, and favoring balanced microbiota communities in the gut to maximize pectins' health benefits.

RevDate: 2021-01-13

Hövels M, Kosciow K, U Deppenmeier (2021)

Characterization of a novel endo-levanase from Azotobacter chroococcum DSM 2286 and its application for the production of prebiotic fructooligosaccharides.

Carbohydrate polymers, 255:117384.

Prebiotics are known for their ability to modulate the composition of the human microbiome and mediate health-promoting benefits. Endo-levanases, which hydrolyze levan into short-chain FOS, could be used for the production of levan-based prebiotics. The novel endo-levanase (LevB2286) from Azotobacter chroococcum DSM 2286, combines an exceptionally high specific activity with advantageous hydrolytic properties. Starting from levan isolated from Timothy grass, LevB2286 produced FOS ranging from DP 2 - 8. In contrast to endo-levanases described in the literature, LevB2286 formed minor amounts of fructose and levanbiose, even with greatly extended incubation. The combined activity of LevB2286 and the levansucrase LevS1417 from Gluconobacter japonicus LMG 1417 led to a one-step synthesis of levan-type FOS from sucrose. 387.4 ± 17.3 g L-1 FOS were produced within 48 h by the production strategy based on crude cell extract of recombinant Escherichia coli expressing levS1417 and levB2286 simultaneously.

RevDate: 2021-01-13

Yan Z, He F, Xiao F, et al (2021)

A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis.

Microbiome, 9(1):12.

BACKGROUND: Proteolysis regulation allows gut microbes to respond rapidly to dynamic intestinal environments by fast degradation of misfolded proteins and activation of regulatory proteins. However, alterations of gut microbial proteolytic signatures under complex disease status such as inflammatory bowel disease (IBD, including Crohn's disease (CD) and ulcerative colitis (UC)), have not been investigated. Metaproteomics holds the potential to investigate gut microbial proteolysis because semi-tryptic peptides mainly derive from endogenous proteolysis.

RESULTS: We have developed a semi-tryptic peptide centric metaproteomic mining approach to obtain a snapshot of human gut microbial proteolysis signatures. This approach employed a comprehensive meta-database, two-step multiengine database search, and datasets with high-resolution fragmentation spectra to increase the confidence of semi-tryptic peptide identification. The approach was validated by discovering altered proteolysis signatures of Escherichia coli heat shock response. Utilizing two published large-scale metaproteomics datasets containing 623 metaproteomes from 447 fecal and 176 mucosal luminal interface (MLI) samples from IBD patients and healthy individuals, we obtain potential signatures of altered gut microbial proteolysis at taxonomic, functional, and cleavage site motif levels. The functional alterations mainly involved microbial carbohydrate transport and metabolism, oxidative stress, cell motility, protein synthesis, and maturation. Altered microbial proteolysis signatures of CD and UC mainly occurred in terminal ileum and descending colon, respectively. Microbial proteolysis patterns exhibited low correlations with β-diversity and moderate correlations with microbial protease and chaperones levels, respectively. Human protease inhibitors and immunoglobulins were mainly negatively associated with microbial proteolysis patterns, probably because of the inhibitory effects of these host factors on gut microbial proteolysis events.

CONCLUSIONS: This semi-tryptic peptide centric mining strategy offers a label-free approach to discover signatures of in vivo gut microbial proteolysis events if experimental conditions are well controlled. It can also capture in vitro proteolysis signatures to facilitate the evaluation and optimization of experimental conditions. Our findings highlight the complex and diverse proteolytic events of gut microbiome, providing a unique layer of information beyond taxonomic and proteomic abundance. Video abstract.

RevDate: 2021-01-13

Silverstein RB, IU Mysorekar (2021)

Group therapy on in utero colonization: seeking common truths and a way forward.

Microbiome, 9(1):7.

The human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers of human fate almost at par with our genome and epigenome. It is now well accepted after decades of disbelief that a broad understanding of human development, health, physiology, and disease requires understanding of the microbiome along with the genome and epigenome. We are learning daily of the interdependent relationships between microbiome/microbiota and immune responses, mood, cancer progression, response to therapies, aging, obesity, antibiotic usage, and overusage and much more. The next frontier in microbiome field is understanding when does this influence begin? Does the human microbiome initiate at the time of birth or are developing human fetuses already primed with microbes and their products in utero. In this commentary, we reflect on evidence gathered thus far on this question and identify the unknown common truths. We present a way forward to continue understanding our microbial colleagues and our interwoven fates.

RevDate: 2021-01-13

de Goffau MC, Charnock-Jones DS, Smith GCS, et al (2021)

Batch effects account for the main findings of an in utero human intestinal bacterial colonization study.

Microbiome, 9(1):6.

A recent study by Rackaityte et al. reported evidence for a low level of bacterial colonization, specifically of Micrococcus luteus, in the intestine of second trimester human fetuses. We have re-analyzed their sequence data and identified a batch effect which violates the underlying assumptions of the bioinformatic method used for contamination removal. This batch effect resulted in Micrococcus not being identified as a contaminant in the original work and being falsely assigned to the fetal samples. We further provide evidence that the micrographs presented by Rackaityte et al. are unlikely to show Micrococci or other bacteria as the size of the particles shown exceeds that of related bacterial cells. Finally, phylogenetic analysis showed that the microbes cultured from the fetal samples differed significantly from those detected by sequencing. Overall, our findings show that the presence of Micrococcus in the fetal gut is not supported by the primary sequence data. Our findings underline important aspects of the nature of contamination for both sequencing and culture approaches in microbiome studies and the appropriate use of automated contamination identification tools.

RevDate: 2021-01-13

Blaser MJ, Devkota S, McCoy KD, et al (2021)

Lessons learned from the prenatal microbiome controversy.

Microbiome, 9(1):8.

For more than a century, the prenatal environment was considered sterile. Over the last few years, findings obtained with next-generation sequencing approaches from samples of the placenta, the amniotic fluid, meconium, and even fetal tissues have challenged the dogma of a sterile womb, and additional reports have emerged that used culture, microscopy, and quantitative PCR to support the presence of a low-biomass microbial community at prenatal sites. Given the substantial implications of prenatal exposure to microbes for the development and health of the host, the findings have gathered substantial interest from academics, high impact journals, the public press, and funding agencies. However, an increasing number of studies have challenged the prenatal microbiome identifying contamination as a major issue, and scientists that remained skeptical have pointed to inconsistencies with in utero colonization, the impact of c-sections on early microbiome assembly, and the ability to generate germ-free mammals. A lively academic controversy has emerged on the existence of the wider importance of prenatal microbial communities. Microbiome has asked experts to discuss these issues and provide their thoughts on the implications. To allow for a broader perspective of this discussion, we have specifically selected scientists, who have a long-standing expertise in microbiome sciences but who have not directly been involved in the debate so far.

RevDate: 2021-01-13

Walter J, MW Hornef (2021)

A philosophical perspective on the prenatal in utero microbiome debate.

Microbiome, 9(1):5.

Within the last 6 years, a research field has emerged that focuses on the characterization of microbial communities in the prenatal intrauterine environment of humans and their putative role in human health. However, there is considerable controversy around the existence of such microbial populations. The often contentious debate is primarily focused on technical aspects of the research, such as difficulties to assure aseptic sampling and to differentiate legitimate signals in the data from contamination. Although such discussions are clearly important, we feel that the problems with the prenatal microbiome field go deeper. In this commentary, we apply a philosophical framework to evaluate the foundations, experimental approaches, and interpretations used by scientists on both sides of the debate. We argue that the evidence for a "sterile womb" is based on a scientific approach that aligns well with important principles of the philosophy of science as genuine tests of the hypothesis and multiple angles of explanatory considerations were applied. In contrast, research in support of the "in utero colonization hypothesis" is solely based on descriptive verifications that do not provide explanatory insight, which weakens the evidence for a prenatal intrauterine microbiome. We propose that a reflection on philosophical principles can inform not only the debate on the prenatal intrauterine microbiome but also other disciplines that attempt to study low-biomass microbial communities.

RevDate: 2021-01-13

Fricke WF, J Ravel (2021)

Microbiome or no microbiome: are we looking at the prenatal environment through the right lens?.

Microbiome, 9(1):9.

RevDate: 2021-01-13

Wang Y, Wan X, Wu X, et al (2021)

Eubacterium rectale contributes to colorectal cancer initiation via promoting colitis.

Gut pathogens, 13(1):2.

BACKGROUND: Inflammatory bowel disease caused by microbial dysbiosis is an important factor contributing to colorectal cancer (CRC) initiation. The 'driver-passenger' model in human gut microbial dysbiosis suggests that 'driver' bacteria may colonize with low relative abundance on tumor site but persistently induce chronic change in normal intestinal epithelium and initiate CRC. They are gradually replaced by 'passenger' bacteria later on, due to their low adaptability to the on-tumor site niche.

RESULTS: To reveal site-specific bacterial taxon markers in CRC patients, we analyzed the gut mucosal microbiome of 75 paired samples of on-tumor and tumor-adjacent sites, 75 off-tumor sites, and 26 healthy controls. Linear discriminant analysis of relative abundance profiles revealed unique bacterial taxon distribution correlated with specific tumor sites, with Eubacterium having the distribution characteristic of potential driver bacteria. We further show that Eubacterium rectale endotoxin activates the transcription factor NF-κΒ, which regulates multiple aspects of innate and adaptive immune responses in normal colon epithelial cells. Unlike the 'passenger' bacterium Fusobacterium nucleatum, E. rectale promotes dextran sodium sulfate-induced colitis in Balb/c mice.

CONCLUSIONS: Our findings reveal that E. rectale functions as a 'driver' bacterium and contributes to cancer initiation via promoting inflammation.

RevDate: 2021-01-13

Yeung M, Saingam P, Xu Y, et al (2021)

Low-dosage ozonation in gas-phase biofilter promotes community diversity and robustness.

Microbiome, 9(1):14.

BACKGROUND: The ozonation of biofilters is known to alleviate clogging and pressure drop issues while maintaining removal performances in biofiltration systems treating gaseous volatile organic compounds (VOCs). The effects of ozone on the biofilter microbiome in terms of biodiversity, community structure, metabolic abilities, and dominant taxa correlated with performance remain largely unknown.

METHODS: This study investigated two biofilters treating high-concentration toluene operating in parallel, with one acting as control and the other exposed to low-dosage (200 mg/m3) ozonation. The microbial community diversity, metabolic rates of different carbon sources, functional predictions, and microbial co-occurrence networks of both communities were examined.

RESULTS: Consistently higher biodiversity of over 30% was observed in the microbiome after ozonation, with increased overall metabolic abilities for amino acids and carboxylic acids. The relative abundance of species with reported stress-tolerant and biofilm-forming abilities significantly increased, with a consortium of changes in predicted biological pathways, including shifts in degradation pathways of intermediate compounds, while the correlation of top ASVs and genus with performance indicators showed diversifications in microbiota responsible for toluene degradation. A co-occurrence network of the community showed a decrease in average path distance and average betweenness with ozonation.

CONCLUSION: Major degrading species highly correlated with performance shifted after ozonation. Increases in microbial biodiversity, coupled with improvements in metabolizing performances of multiple carbon sources including organic acids could explain the consistent performance commonly seen in the ozonation of biofilters despite the decrease in biomass, while avoiding acid buildup in long-term operation. The increased presence of stress-tolerant microbes in the microbiome coupled with the decentralization of the co-occurrence network suggest that ozonation could not only ameliorate clogging issues but also provide a microbiome more robust to loading shock seen in full-scale biofilters. Video abstract.

RevDate: 2021-01-13

Chen C, Niu M, Pan J, et al (2021)

Bacteroides, butyric acid and t10,c12-CLA changes in colorectal adenomatous polyp patients.

Gut pathogens, 13(1):1.

BACKGROUND: Colorectal adenomatous polyps (CAPs) are considered precancerous lesions of colorectal cancer (CRC). The gut microbiota participates in the process of digestion and, in the process, produces metabolites, mainly short-chain fatty acids (SCFAs), secondary bile acids and conjugated linoleic acid (CLA). This study aimed to investigate the gut microbiota constituents and metabolites in the faeces of CAP patients to identify microbiota or metabolites that can be used as sensitive biological predictors and to provide a theoretical basis for the clinical treatment of CAPs.

METHODS: 16S rRNA sequence analysis was used to detect microbial changes in the faeces of CAP patients. qPCR analysis was used to evaluate the ability of the microbiota to produce metabolites, and the contents of metabolites in faeces were detected by ion chromatography and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS).

RESULTS: Based on the detection of the gut microbiota, patients with CAPs had increased abundances of Bacteroides and Citrobacter, and the abundances of Weissella and Lactobacillus were decreased. We also explored gene expression, and the abundance of butyrate-producing bacterial genes was significantly increased in the faeces of CAP patients, but those of secondary bile acid-producing and CLA-producing bacterial genes showed no differences in faecal samples. The acetic acid and butyric acid contents were increased in the faeces of the CAP group, and the healthy control group had higher t10,c12-CLA contents.

CONCLUSION: The gut microbiota analysis results, assessed in faeces, showed that Bacteroides and Citrobacter were positively correlated with CAPs, which indicated that changes in specific genera might be detrimental to intestinal health. In addition, t10,c12-CLA played an important role in protecting the intestine.

RevDate: 2021-01-13

Liu J, Liu C, J Yue (2021)

Radiotherapy and the gut microbiome: facts and fiction.

Radiation oncology (London, England), 16(1):9.

An ever-growing body of evidence has linked the gut microbiome with both the effectiveness and the toxicity of cancer therapies. Radiotherapy is an effective way to treat tumors, although large variations exist among patients in tumor radio-responsiveness and in the incidence and severity of radiotherapy-induced side effects. Relatively little is known about whether and how the microbiome regulates the response to radiotherapy. Gut microbiota may be an important player in modulating "hot" versus "cold" tumor microenvironment, ultimately affecting treatment efficacy. The interaction of the gut microbiome and radiotherapy is a bidirectional function, in that radiotherapy can disrupt the microbiome and those disruptions can influence the effectiveness of the anticancer treatments. Limited data have shown that interactions between the radiation and the microbiome can have positive effects on oncotherapy. On the other hand, exposure to ionizing radiation leads to changes in the gut microbiome that contribute to radiation enteropathy. The gut microbiome can influence radiation-induced gastrointestinal mucositis through two mechanisms including translocation and dysbiosis. We propose that the gut microbiome can be modified to maximize the response to treatment and minimize adverse effects through the use of personalized probiotics, prebiotics, or fecal microbial transplantation. 16S rRNA sequencing is the most commonly used approach to investigate distribution and diversity of gut microbiome between individuals though it only identifies bacteria level other than strain level. The functional gut microbiome can be studied using methods involving metagenomics, metatranscriptomics, metaproteomics, as well as metabolomics. Multiple '-omic' approaches can be applied simultaneously to the same sample to obtain integrated results. That said, challenges and remaining unknowns in the future that persist at this time include the mechanisms by which the gut microbiome affects radiosensitivity, interactions between the gut microbiome and combination treatments, the role of the gut microbiome with regard to predictive and prognostic biomarkers, the need for multi "-omic" approach for in-depth exploration of functional changes and their effects on host-microbiome interactions, and interactions between gut microbiome, microbial metabolites and immune microenvironment.

RevDate: 2021-01-13

Butler ÉM, Reynolds AJ, Derraik JGB, et al (2021)

The views of pregnant women in New Zealand on vaginal seeding: a mixed-methods study.

BMC pregnancy and childbirth, 21(1):49.

BACKGROUND: Vaginal seeding is the administration of maternal vaginal bacteria to babies following birth by caesarean section (CS), intended to mimic the microbial exposure that occurs during vaginal birth. Appropriate development of the infant gut microbiome assists early immune development and might help reduce the risk of certain health conditions later in life, such as obesity and asthma. We aimed to explore the views of pregnant women on this practice.

METHODS: We conducted a sequential mixed-methods study on the views of pregnant women in New Zealand (NZ) on vaginal seeding. Phase one: brief semi-structured interviews with pregnant women participating in a clinical trial of vaginal seeding (n = 15); and phase two: online questionnaire of pregnant women throughout NZ (not in the trial) (n = 264). Reflexive thematic analysis was applied to interview and open-ended questionnaire data. Closed-ended questionnaire responses were analysed using descriptive statistics.

RESULTS: Six themes were produced through analysis of the open-ended data: "seeding replicates a natural process", "microbiome is in the media", "seeding may have potential benefits", "seeking validation by a maternity caregiver", "seeding could help reduce CS guilt", and "the unknowns of seeding". The idea that vaginal seeding replicates a natural process was suggested by some as an explanation to help overcome any initial negative perceptions of it. Many considered vaginal seeding to have potential benefit for the gut microbiome, while comparatively fewer considered it to be potentially beneficial for specific conditions such as obesity. Just under 30% of questionnaire respondents (n = 78; 29.5%) had prior knowledge of vaginal seeding, while most (n = 133; 82.6%) had an initially positive or neutral reaction to it. Few respondents changed their initial views on the practice after reading provided evidence-based information (n = 60; 22.7%), but of those who did, most became more positive (n = 51; 86.4%).

CONCLUSIONS: Given its apparent acceptability, and if shown to be safe and effective for the prevention of early childhood obesity, vaginal seeding could be a non-stigmatising approach to prevention of this condition among children born by CS. Our findings also highlight the importance of lead maternity carers in NZ remaining current in their knowledge of vaginal seeding research.

RevDate: 2021-01-13

Sanders D, Grunden A, RR Dunn (2021)

A review of clothing microbiology: the history of clothing and the role of microbes in textiles.

Biology letters, 17(1):20200700.

Humans have worn clothing for thousands of years, and since its invention, clothing has evolved from its simple utilitarian function for survival to become an integral part of society. While much consideration has been given to the broad environmental impacts of the textile and laundering industries, little is known about the impact wearing clothing has had on the human microbiome, particularly that of the skin, despite our long history with clothing. This review discusses the history of clothing and the evolution of textiles, what is and is not known about microbial persistence on and degradation of various fibres, and what opportunities for the industrial and environmental application of clothing microbiology exist for the future.

RevDate: 2021-01-13

Landlinger C, Tisakova L, Oberbauer V, et al (2021)

Engineered Phage Endolysin Eliminates Gardnerella Biofilm without Damaging Beneficial Bacteria in Bacterial Vaginosis Ex Vivo.

Pathogens (Basel, Switzerland), 10(1): pii:pathogens10010054.

Bacterial vaginosis is characterized by an imbalance of the vaginal microbiome and a characteristic biofilm formed on the vaginal epithelium, which is initiated and dominated by Gardnerella bacteria, and is frequently refractory to antibiotic treatment. We investigated endolysins of the type 1,4-beta-N-acetylmuramidase encoded on Gardnerella prophages as an alternative treatment. When recombinantly expressed, these proteins demonstrated strong bactericidal activity against four different Gardnerella species. By domain shuffling, we generated several engineered endolysins with 10-fold higher bactericidal activity than any wild-type enzyme. When tested against a panel of 20 Gardnerella strains, the most active endolysin, called PM-477, showed minimum inhibitory concentrations of 0.13-8 µg/mL. PM-477 had no effect on beneficial lactobacilli or other species of vaginal bacteria. Furthermore, the efficacy of PM-477 was tested by fluorescence in situ hybridization on vaginal samples of fifteen patients with either first time or recurring bacterial vaginosis. In thirteen cases, PM-477 killed the Gardnerella bacteria and physically dissolved the biofilms without affecting the remaining vaginal microbiome. The high selectivity and effectiveness in eliminating Gardnerella, both in cultures of isolated strains as well as in clinically derived samples of natural polymicrobial biofilms, makes PM-477 a promising alternative to antibiotics for the treatment of bacterial vaginosis, especially in patients with frequent recurrence.

RevDate: 2021-01-13

Juste Contin Gomes M, Stampini Duarte Martino H, E Tako (2021)

Effects of Iron and Zinc Biofortified Foods on Gut Microbiota In Vivo (Gallus gallus): A Systematic Review.

Nutrients, 13(1): pii:nu13010189.

Dietary iron and zinc deficiencies are a global health concern. Bacteria that colonize the gastrointestinal tract depend on minerals to maintain their activities; thus, recent evidence suggests that biofortified foods can modulate the host's beneficial bacterial taxa. The current review analyzed the research data that linked between iron and zinc biofortified foods and gut microbiota modulation. The data analysis was based on the PRISMA guidelines and the data search was performed at PubMed, Web of Science, Science Direct, and Scopus databases for experimental studies published from January 2010 until December 2020. The five selected studies were conducted in an experimental in vivo model (Gallus gallus). The identified and discussed research showed positive effects of biofortified foods on the composition and function of the gut microbiota. Further, an increase in short chain fatty acids producing bacterial populations as Lactobacillus and Ruminococcus, and a decrease in potentially pathogenic bacteria as Streptococcus, Escherichia, and Enterobacter was identified due to the consumption of biofortified foods. In conclusion, biofortified foods may contribute to improved gut health without increasing the colonization of pathogenic bacteria. The dietary inclusion of approximately 50% of iron/zinc biofortified foods has a significant beneficial effect on the gut microbiota. Additional studies in humans and animal models are warranted to further establish the suggested effects on the intestinal microbiome. PROSPERO (CRD42020184221).

RevDate: 2021-01-13

Mahapatro M, Erkert L, C Becker (2021)

Cytokine-Mediated Crosstalk between Immune Cells and Epithelial Cells in the Gut.

Cells, 10(1): pii:cells10010111.

Cytokines are small proteins that are secreted by a vast majority of cell types in the gut. They not only establish cell-to-cell interactions and facilitate cellular signaling, but also regulate both innate and adaptive immune responses, thereby playing a central role in genetic, inflammatory, and infectious diseases of the gut. Both, immune cells and gut epithelial cells, play important roles in intestinal disease development. The epithelium is located in between the mucosal immune system and the gut microbiome. It not only establishes an efficient barrier against gut microbes, but it also signals information from the gut lumen and its composition to the immune cell compartment. Communication across the epithelial cell layer also occurs in the other direction. Intestinal epithelial cells respond to immune cell cytokines and their response influences and shapes the microbial community within the gut lumen. Thus, the epithelium should be seen as a translator or a moderator between the microbiota and the mucosal immune system. Proper communication across the epithelium seems to be a key to gut homeostasis. Indeed, current genome-wide association studies for intestinal disorders have identified several disease susceptibility loci, which map cytokine signatures and their related signaling genes. A thorough understanding of this tightly regulated cytokine signaling network is crucial. The main objective of this review was to shed light on how cytokines can orchestrate epithelial functions such as proliferation, cell death, permeability, microbe interaction, and barrier maintenance, thereby safeguarding host health. In addition, cytokine-mediated therapy for inflammation and cancer are discussed.

RevDate: 2021-01-13

Mannaa M, YS Seo (2021)

Plants under the Attack of Allies: Moving towards the Plant Pathobiome Paradigm.

Plants (Basel, Switzerland), 10(1): pii:plants10010125.

Plants are functional macrobes living in a close association with diverse communities of microbes and viruses as complex systems that continuously interact with the surrounding environment. The microbiota within the plant holobiont serves various essential and beneficial roles, such as in plant growth at different stages, starting from seed germination. Meanwhile, pathogenic microbes-differentiated from the rest of the plant microbiome based on their ability to damage the plant tissues through transient blooming under specific conditions-are also a part of the plant microbiome. Recent advances in multi-omics have furthered our understanding of the structure and functions of plant-associated microbes, and a pathobiome paradigm has emerged as a set of organisms (i.e., complex eukaryotic, microbial, and viral communities) within the plant's biotic environment which interact with the host to deteriorate its health status. Recent studies have demonstrated that the one pathogen-one disease hypothesis is insufficient to describe the disease process in many cases, particularly when complex organismic communities are involved. The present review discusses the plant holobiont and covers the steady transition of plant pathology from the one pathogen-one disease hypothesis to the pathobiome paradigm. Moreover, previous reports on model plant diseases, in which more than one pathogen or co-operative interaction amongst pathogenic microbes is implicated, are reviewed and discussed.

RevDate: 2021-01-12

Chaudhari SN, Luo JN, Harris DA, et al (2020)

A microbial metabolite remodels the gut-liver axis following bariatric surgery.

Cell host & microbe pii:S1931-3128(20)30666-1 [Epub ahead of print].

Bariatric surgery is the most effective treatment for type 2 diabetes and is associated with changes in gut metabolites. Previous work uncovered a gut-restricted TGR5 agonist with anti-diabetic properties-cholic acid-7-sulfate (CA7S)-that is elevated following sleeve gastrectomy (SG). Here, we elucidate a microbiome-dependent pathway by which SG increases CA7S production. We show that a microbial metabolite, lithocholic acid (LCA), is increased in murine portal veins post-SG and by activating the vitamin D receptor, induces hepatic mSult2A1/hSULT2A expression to drive CA7S production. An SG-induced shift in the microbiome increases gut expression of the bile acid transporters Asbt and Ostα, which in turn facilitate selective transport of LCA across the gut epithelium. Cecal microbiota transplant from SG animals is sufficient to recreate the pathway in germ-free (GF) animals. Activation of this gut-liver pathway leads to CA7S synthesis and GLP-1 secretion, causally connecting a microbial metabolite with the improvement of diabetic phenotypes.

RevDate: 2021-01-12

Seguin-Orlando A, Donat R, Der Sarkissian C, et al (2021)

Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.

Current biology : CB pii:S0960-9822(20)31835-2 [Epub ahead of print].

The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.

RevDate: 2021-01-12

O'Brien AM, Jack CN, Friesen ML, et al (2021)

Whose trait is it anyways? Coevolution of joint phenotypes and genetic architecture in mutualisms.

Proceedings. Biological sciences, 288(1942):20202483.

Evolutionary biologists typically envision a trait's genetic basis and fitness effects occurring within a single species. However, traits can be determined by and have fitness consequences for interacting species, thus evolving in multiple genomes. This is especially likely in mutualisms, where species exchange fitness benefits and can associate over long periods of time. Partners may experience evolutionary conflict over the value of a multi-genomic trait, but such conflicts may be ameliorated by mutualism's positive fitness feedbacks. Here, we develop a simulation model of a host-microbe mutualism to explore the evolution of a multi-genomic trait. Coevolutionary outcomes depend on whether hosts and microbes have similar or different optimal trait values, strengths of selection and fitness feedbacks. We show that genome-wide association studies can map joint traits to loci in multiple genomes and describe how fitness conflict and fitness feedback generate different multi-genomic architectures with distinct signals around segregating loci. Partner fitnesses can be positively correlated even when partners are in conflict over the value of a multi-genomic trait, and conflict can generate strong mutualistic dependency. While fitness alignment facilitates rapid adaptation to a new optimum, conflict maintains genetic variation and evolvability, with implications for applied microbiome science.

RevDate: 2021-01-12

Onwuliri V, Agbakoba NR, KC Anukam (2021)

Topical cream containing live lactobacilli decreases malodour-producing bacteria and downregulates genes encoding PLP-dependent enzymes on the axillary skin microbiome of healthy adult Nigerians.

Journal of cosmetic dermatology [Epub ahead of print].

BACKGROUND: Clinical data exist that supports the utility of topical probiotics for certain dermatological diseases such as atopic dermatitis, acne, and psoriasis. However, there is paucity of data on the use of live lactobacilli to control axillary malodour. The objective of this study was to determine whether application of topical oil-based cream containing live Lactobacilli could decrease malodour-producing bacteria in the axilla of healthy subjects.

METHODS: Twenty-five adult volunteers comprising 12 males and 13 females provided informed consent. Axillary skin swabs were collected before and after 14 days application of topical cream containing live Lactobacillus pentosus KCA1. Bacterial DNA was extracted and V4 region of the 16S rRNA were amplified and sequenced in a pair-end configuration on the Illumina MiSeq platform rendering 2 x 150 bp sequences. Microbial taxonomy to species level was generated using the Greengenes database. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify biologically and statistically significant differences in relative abundance.

RESULTS: Actinobacteria decreased from 70% to 24%, Firmicutes increased from 26.6% to 73.9% among the female participants. In males, Actinobacteria decreased from 65% to 38%, while Firmicutes increased from 24% to 57%. Corynebacterium decreased from 62.91% to 36.63%, while Lactobacillus increased from 0.06% to 23.11%. In males, unliked females, there were reduction of Staphylococcus species associated with malodour, notably Staphylococcus hominis, Staphylococcus haemolyticus, and Staphylococcus lugdunensis. Bacterial functional gene- Pyridoxal protein dependent enzymes involved in biotransformation of malodor precursor to volatile thioalcohols were down-regulated.

CONCLUSIONS: Application of Lactobacillus pentosus KCA1 cream led to a significant decrease in the relative abundance of odour-producing Corynebacterium species in both female and male subjects. Some species associated with malodour especially Corynebacterium striatum, Corynebacterium jeikeium, Corynebacterium tuberculostearicum, Staphylococcus hominis decreased by 96%, 73%, 7% and 20.8% respectively in males.

RevDate: 2021-01-12

Garber JM, Hennet T, CM Szymanski (2021)

Significance of fucose in intestinal health and disease.

Molecular microbiology [Epub ahead of print].

The deoxy hexose sugar L-fucose is important for many biological processes within the human body and the associated microbiota. This carbohydrate is abundant in host gut mucosal surfaces, numerous microbial cell surface structures, and some dietary carbohydrates. Fucosylated oligosaccharides facilitate the establishment of a healthy microbiota and provide protection from infection. However, there are instances where pathogens can also exploit these fucosylated structures to cause infection. Furthermore, deficiencies in host fucosylation are associated with specific disease outcomes. This review focuses on our current understanding of the impact of fucosylation within the mucosal environment of the gastrointestinal tract with a specific emphasis on the mediatory effects in host-microbe interactions.

RevDate: 2021-01-12

Costa CPS, Silva MA, Neto LGL, et al (2021)

Is there bacterial infection in intact crowns teeth and pulp necrosis of sickle-cell anaemia patients? A case series study nested in a cohort.

International endodontic journal [Epub ahead of print].

AIM: To evaluate the presence of bacteria in permanent teeth with intact crowns (without caries, periodontal disease, or dental trauma) in sickle cell anaemia patients (HbSS genotype) by analyzing their clinical, imaging, and microbiological parameters.

METHODOLOGY: This is a case series study nested in a cohort. In the first follow-up of this cohort study (Costa et al. 2013), ten HbSS patients with at least one tooth with intact crown and clinically diagnosed with pulp necrosis, by pulse oximetry adapted for dentistry and a cold sensitivity test (n = 27 teeth), were selected. Changes in the pulp chamber, root, and periodontal ligament were identified in the tomographic analysis. Bacterial culture, staining for live and dead bacteria, and real-time polymerase chain reaction with 16S rRNA primers were used to identify the presence of bacteria. Culture sample collection was performed immediately after access to the pulp chamber. The microbiome was analyzed with a MiSeq sequencer (Illumina, San Diego, CA).

RESULTS: The diagnosis of pulp necrosis was clinically confirmed in 82% (22/27) of the teeth. The amount of bacterial load identified was less than 100 copies/μL in 23% (5/22) of the teeth with intact crowns and pulp necrosis. Thirteen bacterial species were identified that are commonly found in urinary tract infection, septicemia, and infective endocarditis. Only one of these species, Granulicatella adjacens, has also be found in primary endodontic infections.

CONCLUSION: Prospective clinical, imaging and microbiological analyses suggest that pulp necrosis of teeth with intact crowns from HbSS patients is not caused by the presence of bacteria.

RevDate: 2021-01-13

Brandon AM, Garcia AM, Khlystov NA, et al (2021)

Enhanced Bioavailability and Microbial Biodegradation of Polystyrene in an Enrichment Derived from the Gut Microbiome of Tenebrio molitor (Mealworm Larvae).

Environmental science & technology [Epub ahead of print].

As the global threat of plastic pollution has grown in scale and urgency, so have efforts to find sustainable and efficient solutions. Research conducted over the past few years has identified gut environments within insect larvae, including Tenebrio molitor (yellow mealworms), as microenvironments uniquely suited to rapid plastic biodegradation. However, there is currently limited understanding of how the insect host and its gut microbiome collaborate to create an environment conducive to plastic biodegradation. In this work, we provide evidence that T. molitor secretes one or more emulsifying factor(s) (30-100 kDa) that mediate plastic bioavailability. We also demonstrate that the insect gut microbiome secretes factor(s) (<30 kDa) that enhance respiration on polystyrene (PS). We apply these insights to culture PS-fed gut microbiome enrichments, with elevated rates of respiration and degradation compared to the unenriched gut microbiome. Within the enrichment, we identified eight unique gut microorganisms associated with PS biodegradation including Citrobacter freundii, Serratia marcescens, and Klebsiella aerogenes. Our results demonstrate that both the mealworm itself and its gut microbiome contribute to accelerated plastic biodegradation. This work provides new insights into insect-mediated mechanisms of plastic degradation and potential strategies for cultivation of plastic-degrading microorganisms in future investigations and scale-up.

RevDate: 2021-01-13

Chatkin J, Correa L, U Santos (2021)

External Environmental Pollution as a Risk Factor for Asthma.

Clinical reviews in allergy & immunology [Epub ahead of print].

Air pollution is a worrisome risk factor for global morbidity and mortality and plays a special role in many respiratory conditions. It contributes to around 8 million deaths/year, with outdoor exposure being responsible for more than 4.2 million deaths throughout the world, while more than 3.8 million die from situations related to indoor pollution. Pollutant agents induce several respiratory symptoms. In addition, there is a clear interference in numerous asthma outcomes, such as incidence, prevalence, hospital admission, visits to emergency departments, mortality, and asthma attacks, among others. The particulate matter group of pollutants includes coarse particles/PM10, fine particles/PM2.5, and ultrafine particles/PM0.1. The gaseous components include ground-level ozone, nitrogen dioxide, sulfur dioxide, and carbon monoxide. The timing, load, and route of allergen exposure are other items affecting allergic disease phenotypes. The complex interaction between pollutant exposures and human host factors has an implication in the development and rise of asthma as a public health problem. However, there are hiatuses in the understanding of the pathways in this disease. The routes through which pollutants induce asthma are multiple, and include the epigenetic changes that occur in the respiratory tract microbiome, oxidative stress, and immune dysregulation. In addition, the expansion of the modern Westernized lifestyle, which is characterized by intense urbanization and more time spent indoors, resulted in greater exposure to polluted air. Another point to consider is the different role of the environment according to age groups. Children growing up in economically disadvantaged neighborhoods suffer more important negative health impacts. This narrative review highlights the principal polluting agents, their sources of emission, epidemiological findings, and mechanistic evidence that links environmental exposures to asthma.

RevDate: 2021-01-12

Chan AP, Namjoshi SS, Jardack PM, et al (2021)

Long-Term Dietary Changes in Subjects with Glucose Galactose Malabsorption Secondary to Biallelic Mutations of SLC5A1.

Digestive diseases and sciences [Epub ahead of print].

BACKGROUND: Glucose galactose malabsorption (GGM) is a congenital diarrheal disorder of intestinal Na+/glucose cotransport (SGLT1/SLC5A1). The required glucose and galactose-restricted diet has been well described in infancy, but long-term nutrition follow-up is limited.

AIM: To perform a comprehensive nutritional assessment on a cohort of patients with GGM to gain insights into the consumption patterns within the population.

METHODS: A cross-sectional study examining dietary intake of a GGM cohort using prospective food records. The calories and nutrients of all foods, beverages, and condiments were analyzed with descriptive statistics and compared to intake patterns of age- and sex-matched NHANES groups.

RESULTS: The six patients were 0.7-26 years old. Whole foods and vegetable fats were major parts of the diet, while dairy and added sweeteners were restricted. Compared to typical US intakes, mean macronutrient distribution was 88th percentile from fat, 18th percentile from carbohydrates, and 78th percentile from protein. Fructose consumption, as a proportion of total sugar intake, decreased with age, from 86.1 to 50.4%. Meanwhile, glucose consumption increased with age, from 13.8 to 48.6% of sugar intake. However, the actual amount of glucose consumed remained low, equivalent to 4th percentile of US consumption level. Galactose intake was marginal throughout life.

CONCLUSIONS: A GGM diet is a high-fat and high-protein/low-carbohydrate diet that is rich in fruits and vegetables but limited in dairy and added sugar. Relatively less fructose but more glucose is incorporated into the diet with age. Future studies should investigate the effects of the GGM diet on gut microbiome and long-term health.

RevDate: 2021-01-12

Jang K, Purvis JM, SW Kim (2021)

Dose-response and functional role of whey permeate as a source of lactose and milk oligosaccharides on intestinal health and growth of nursery pigs.

Journal of animal science pii:6089171 [Epub ahead of print].

Two experiments were conducted to evaluate dose-response and supplemental effects of whey permeate on growth performance and intestinal health of nursery pigs. In Exp. 1, 1,080 pigs weaned at 6.24 kg body weight (BW) were allotted to 5 treatments (8 pens/treatment) with increasing levels of whey permeate in 3 phases (from 10 to 30%, 3 to 23%, and 0 to 9% for phase 1, 2, and 3, respectively) fed until 11 kg BW and then fed a common phase 4 diet (0% whey permeate) until 25 kg BW in a 48 d feeding trial. Feed intake and BW were measured at the end of each phase. In Exp. 2, 1,200 nursery pigs at 7.50 kg BW were allotted to 6 treatments (10 pens/treatment) with increasing levels of whey permeate from 0 to 18.75% fed until 11 kg BW. Feed intake and BW were measured during 11 d. Six pigs per treatment (1 per pens) were euthanized to collect the jejunum to evaluate tumor necrosis factor alpha, interleukin-8 (IL-8), transforming growth factor beta 1, mucin 2, histomorphology, digestive enzyme activity, crypt cell proliferation rate, and jejunal mucosa-associated microbiota. Data were analyzed using contrasts in the MIXED procedure and a broken-line analysis using the NLIN procedure of SAS. In Exp. 1, increasing whey permeate had quadratic effect (P < 0.05) on feed efficiency (G:F; maximum: 1.35 at 18.3%) in phase 1. Increasing whey permeate linearly increased (P < 0.05) average daily gain (ADG; 292 to 327 g/d) and G:F (0.96 to 1.04) of pigs in phase 2. In Exp. 2, increasing whey permeate linearly increased (P < 0.05) ADG (349 to 414 g/d) and G:F (0.78 to 0.85), and linearly increased (P < 0.05) crypt cell proliferation rate (27.8 to 37.0%). The breakpoint from a broken-line analysis was obtained at 13.6% whey permeate for maximal G:F. Increasing whey permeate tended to change IL-8 (quadratic, P = 0.052; maximum: 223 pg/mg at 10.9%), to decrease Firmicutes:Bacteroidetes (P = 0.073, 1.59 to 1.13), increase (P = 0.089) Bifidobacteriaceae (0.73 to 1.11%), and to decrease Enterobacteriaceae (P = 0.091, 1.04 to 0.52%) and Stretococcaceae (P = 0.094, 1.50 to 0.71%) in the jejunal mucosa. In conclusion, dietary inclusion of whey permeate increased growth of nursery pigs from 7 to 11 kg BW. Pigs grew most efficiently with 13.6% whey permeate. Improvement in growth performance partly attributed from stimulating intestinal immune response and enterocyte proliferation with positive changes in jejunal mucosa-associated microbiota in nursery pigs.

RevDate: 2021-01-13

Almeida AR, Domingues I, I Henriques (2020)

Zebrafish and water microbiome recovery after oxytetracycline exposure.

Environmental pollution (Barking, Essex : 1987), 272:116371 pii:S0269-7491(20)37060-3 [Epub ahead of print].

Oxytetracycline (OTC) is a broad-spectrum antibiotic widely used in aquaculture, resulting in contamination of aquatic environments. In a previous study, we observed significant effects of OTC sublethal concentrations in zebrafish, its microbiome and the water bacterial community. Here we assessed the extent to which these effects are reversible after a recovery period. Zebrafish adults were exposed to OTC (10,000 μg/L) via water exposure. Effects were analyzed at 5 days (5 dE) and 2 months (2 mE) of exposure and recovery was assessed at 5 days (5dPE) and 1 month (1mPE) after exposure Impacts were observed in fish energetic reserves and in fish and water microbiomes structure, being significant even at 5 dE. At energetic reserves level, the effect in cellular energy allocation (CEA) was dependent on the exposure time: initially CEA increased while after 2 mE CEA decreased. At microbiome level, diversity was not affected but the richness of the water microbiome significantly decreased at 2 mE. Regarding the post-exposure period, at CEA level, organisms seem to recover. In water and gut microbiomes OTC effects were also attenuated after exposure ceases, indicating a recovery. Even so, the structure of water exposed community remained significantly different towards the control, while richness of this community significantly increased at 1mPE. During exposure the relative abundance of 11 and 16 genera was significantly affected in the gut and water microbiomes, respectively, though these numbers decreased to 4 and 8 genera in the post-exposure period. At functional level during exposure 12 and 13 pathways were predicted to be affected in zebrafish gut and water microbiomes respectively, while post-exposure few pathways remained significantly affected. Hence, our results suggest a recovery of the fish fitness as well as of the water and intestine microbiomes after exposure ceases. Even so, some of the effects caused by OTC remain significant after this recovery period.

RevDate: 2021-01-12

Chan CWH, Leung TF, Choi KC, et al (2021)

Association of early-life gut microbiome and lifestyle factors in the development of eczema in Hong Kong infants.

Experimental dermatology [Epub ahead of print].

Childhood eczema is common but its prevalence is variable in different regions of the world. In this study, we explore the associations of various risk factors such as the microbiome, environment, lifestyle, diet and maternal stress with the development of eczema among infants in Hong Kong. Upon enrolment in the study, the infants' parents provided demographic data by self-reporting. At enrolment and 1 year after birth, the infants' allergic conditions, lifestyles and dietary factors and the degree of maternal stress were assessed using various questionnaires. The infants' gut microbiomes were analysed by 16S RNA sequencing, and the longitudinal changes in various bacterial strains were compared between control and eczema-affected groups. Multivariate analyses (after adjustment for other significant factors) revealed that the changes in the abundance of Hungatella hathewayi in the gut were significantly associated with the development of eczema (p = 0.005). In conclusion, the increased abundance of Hungatella hathewayi was associated with an increased risk of developing eczema by 1 year of age. This study thus explored the potential risk factors for the development of eczema in Hong Kong infants, and sheds light on the possible association between early-life gut microbiome and other environmental factors.

RevDate: 2021-01-12

Tyagi AM, Darby TM, Hsu E, et al (2021)

The gut microbiota is a transmissible determinant of skeletal maturation.

eLife, 10: pii:64237.

Genetic factors account for the majority of the variance of human bone mass, but the contribution of non-genetic factors remains largely unknown. By utilizing maternal/offspring transmission, cohabitation, or fecal material transplantation (FMT) studies, we investigated the influence of the gut microbiome on skeletal maturation. We show that the gut microbiome is a communicable regulator of bone structure and turnover in mice. In addition, we found that the acquisition of a specific bacterial strain, segmented filamentous bacteria (SFB), a gut microbe that induces intestinal Th17 cell expansion, was sufficient to negatively impact skeletal maturation. These findings have significant translational implications, as the identification of methods or timing of microbiome transfer may lead to the development of bacteriotherapeutic interventions to optimize skeletal maturation in humans. Moreover, the transfer of SFB-like microbes capable of triggering the expansion of human Th17 cells during therapeutic FMT procedures could lead to significant bone loss in fecal material recipients.

RevDate: 2021-01-12

Hariharan R, Mousa A, B de Courten (2021)

Influence of AMY1A copy number variations on obesity and other cardiometabolic risk factors: A review of the evidence.

Obesity reviews : an official journal of the International Association for the Study of Obesity [Epub ahead of print].

The rising incidence of obesity and type 2 diabetes is contributing to the escalating burden of disease globally. These metabolic disorders are closely linked with diet and in particular with carbohydrate consumption; hence, it is important to understand the underlying mechanisms that influence carbohydrate metabolism. Amylase, the enzyme responsible for the digestion of starch, is coded by the genes AMY1A, AMY1B, and AMY1C (salivary amylase) and AMY2A and AMY2B (pancreatic amylase). Previous studies demonstrate wide variations in AMY1A copy numbers, which can be attributed to several genetic, nutritional, and geographical diversities seen in populations globally. Current literature suggests that AMY1A copy number variations are important in obesity and other cardiometabolic disorders through their effects on glucose and lipid homeostasis, inflammatory markers, and the gut microbiome. This review synthesizes the available evidence to improve understanding of the role of AMY1A in obesity and related cardiometabolic risk factors and disorders including insulin resistance and type 2 diabetes, cardiovascular risk and inflammation, and the gut microbiome.

RevDate: 2021-01-12

Camarena-Pozos DA, Flores-Núñez VM, López MG, et al (2021)

Fungal volatiles emitted by members of the microbiome of desert plants are diverse and capable of promoting plant growth.

Environmental microbiology [Epub ahead of print].

Fungi represent a group of eukaryotic microorganisms that are an important part of the plant microbiome. They produce a vast array of metabolites, including fungal volatile organic compounds (fVOCs). However, the diversity and biological activities of fVOCs emitted by the mycobiota of plants native to arid and semi-arid environments remains under-explored. We characterized the chemical diversity of fVOCs produced by 22 representative members of the microbiome of agaves and cacti using SPME-GC-MS. We further tested the effects of pure compounds on the growth and development of Arabidopsis thaliana and host plants. Members of the Sordariomycetes (9 strains), Eurotiomycetes (3), Dothideomycetes (8), Saccharomycetes (1) and Mucoromycetes (1) were included in our study. We identified 94 fungal organic volatiles classified in nine chemical classes. Terpenes showed the greatest chemical diversity, followed by alcohols and aliphatic compounds. We discovered that camphene and benzyl benzoate, together with the widely distributed and already tested benzyl alcohol, 2-phenylethyl alcohol and 3-methyl-1-butanol, improved plant growth and development of A. thaliana, Agave tequilana and Agave salmiana. Our studies on the fungal VOCs from desert plants underscore an untapped chemical diversity with promising biotechnological applications. This article is protected by copyright. All rights reserved.

RevDate: 2021-01-12

Neu AT, Hughes IV, Allen EE, et al (2021)

Decade-scale stability and change in a marine bivalve microbiome.

Molecular ecology [Epub ahead of print].

Predicting how populations and communities of organisms will respond to anthropogenic change is of paramount concern in ecology today. For communities of microorganisms, however, these predictions remain challenging, primarily due to data limitations. Information about long-term dynamics of host-associated microbial communities, in particular, are lacking. In this study, we use well-preserved and freshly collected samples of soft tissue from a marine bivalve host, Donax gouldii, at a single site to quantify the diversity and composition of its microbiome over a decadal timescale. Site-level measurements of temperature, salinity and chlorophyll a allowed us to test how the microbiome of this species responded to two natural experiments - a seasonal increase in temperature and a phytoplankton bloom. Our results show that ethanol-preserved tissue can provide high-resolution information about temporal trends in compositions of host-associated microbial communities. Specifically, we found that the richness of amplicon sequence variants (ASVs) associated with D. gouldii did not change significantly over time despite increases in water temperature (+1.6°C due to seasonal change) and chlorophyll a concentration (more than nine-fold). The phylogenetic composition of the communities, on the other hand, varied significantly between all collection years, with only six ASVs persisting over our sampling period. Overall, these results suggest that the diversity of microbial taxa associated with D. gouldii has remained stable over time and in response to seasonal environmental change over the course of more than a decade, but such stability is underlain by substantial turnover in the composition of the microbiome.

RevDate: 2021-01-12

Yamane K, Nakamura H, Hamasaki M, et al (2021)

Immune complexome analysis reveals the presence of immune complexes and identifies disease-specific immune complex antigens in saliva samples from patients with Sjögren's syndrome.

Clinical and experimental immunology [Epub ahead of print].

Sjögren's syndrome (SS) is a chronic autoimmune disease that mainly damages the salivary and lacrimal glands. Immune complex (IC) formation triggers local inflammation through IC deposition and decreased antigen function. Some ICs can leak from the lesion and into the saliva but no salivary ICs have been reported to date. We used immune complexome analysis to comprehensively identify antigens incorporated into IC (IC-antigens) in saliva samples from patients with SS (n=9) or with xerostomia (n=7). Neutrophil defensin 1 (67%), small proline-rich protein 2D (67%), myeloperoxidase (44%), neutrophil elastase (44%), cathepsin G (33%), nuclear mitotic apparatus 1 (33%) and phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit gamma (33%) were identified as new IC-antigens specifically and frequently detected in the saliva of SS patients. Of these, neutrophil defensin 1, myeloperoxidase, neutrophil elastase and cathepsin G are neutrophil intracellular proteins, which suggests that repeated destruction of neutrophils due to abnormal autoimmunity may be involved in the pathogenesis of SS. We also analyzed serum samples from three SS patients. There was little overlap of IC-antigens between two of the samples (less than 30% of the IC-antigens in the saliva samples), suggesting that many ICs are formed locally and independently of the circulation. In addition, we found that four SS-specific salivary antigens show sequence homology with several proteins of oral microbiomes but no antigen has homology with Epstein-Barr virus proteins. The homology between some IC-antigens and oral microbiome proteins may indicate the impact of oral infection on local autoimmunity through molecular mimicry theory.

RevDate: 2021-01-12

Wood HL, Acharjee A, Pearce H, et al (2021)

Breastfeeding promotes early neonatal regulatory T cell expansion and immune tolerance of non-inherited maternal antigens.

Allergy [Epub ahead of print].

BACKGROUND: Breastfeeding is associated with long-term health benefits, such as a lower incidence of childhood infections, asthma, obesity and autoimmune disorders. However, little is known regarding how the maternal and neonatal immune systems interact after parturition when the neonate receives nutrition from maternal breastmilk.

METHODS: We undertook a comparative analysis of immune repertoire and function at birth and 3 weeks of age in a cohort of 38 term neonates born by caesarean section grouped according to feeding method (breastmilk versus formula). We used flow cytometry to study the immune phenotype in neonatal and maternal blood samples and mixed lymphocyte reactions to establish the proliferation response of neonatal versus maternal lymphocytes and vice versa. The microbiome of neonatal stool samples was also investigated using 16S rRNA sequencing.

RESULTS: We show that the proportion of regulatory T cells (Tregs) increases in this period and is nearly two-fold higher in exclusively breastfed neonates compared to those who received formula milk only. Moreover, breastfed neonates show a specific and Treg-dependent reduction in proliferative T cell responses to non-inherited maternal antigens (NIMA), associated with a reduction in inflammatory cytokine production. We also observed the enrichment of short chain fatty acid producing taxa (Veillonella and Gemella) in stool samples of exclusively breastfed neonates.

CONCLUSIONS: These data indicate that exposure of the neonate to maternal cells through breastfeeding acts to drive the maturation of Tregs and 'tolerizes' the neonate towards NIMA.

RevDate: 2021-01-12

Nunn KL, Witkin SS, Schneider GM, et al (2021)

Changes in the Vaginal Microbiome during the Pregnancy to Postpartum Transition.

Reproductive sciences (Thousand Oaks, Calif.) [Epub ahead of print].

Substantial changes in the composition of the vaginal microbiome occur following the end of pregnancy. To identify potential drivers of microbiome changes in individual women during the pregnancy to postpartum transition, we evaluated vaginal samples from 48 pregnant women during their first and third trimesters and postpartum. We determined the species composition of vaginal communities and the vaginal fluid levels of compounds involved in mediating changes in host physiology and the immune system at each time point. We used linear mixed-effects models to characterize associations. Consistent with previous reports, but with a larger sample size, a US population, and variations in the dominant bacteria, the vaginal microbiome was found to be more diverse during the postpartum period. There was a lower abundance of Lactobacillus and significantly higher proportions of Streptococcus anginosus and Prevotella bivia. Moreover, we uniquely demonstrated that postpartum vaginal secretions were also altered postpartum. There were elevated levels of hyaluronan and Hsp70 and decreased levels of the D- and L-lactic acid isomers. We posit that these variations are consequences of alterations in the vagina after delivery that profoundly alter the host environment and, thus, lead to changes in the capability of different bacterial species to survive and proliferate.

RevDate: 2021-01-13
CmpDate: 2021-01-13

Malakar D, Sarathbabu S, Borah P, et al (2021)

Fish gill microbiome from India's largest Brahmaputra River-a trans-border biodiversity hotspot region.

Environmental monitoring and assessment, 193(2):56 pii:10.1007/s10661-021-08847-z.

In this study, we sequenced the V3-V4 region of 16S rRNA gene amplicon using paired-end Illumina HiSeq to study the bacterial community in the gills of fish from the bank of the trans-border river of Brahmaputra, Northeast India. Metagenome data consisted of 278,784 reads, 248-bp length, and 56.48% GC content with 85% sequence having a Phred score Q = 30. Community metagenomics revealed a total of 631 genera belonging to 22 different phyla, dominated by Proteobacteria (118,222 features), Firmicutes (101,043 features), Actinobacteria (34,189 features), Bacteroidetes (17,977 features), and Cyanobacteria (2730 features). The bacterial community identified was composed of both pathogenic zoonotic and non-harmful groups. The pathway or functional analysis of the fish gill microbiome exhibited 21 different pathways which also included the pathogenic-related functions. Our data detected a wide group of bacterial communities that will be useful in further isolating and characterizing the pathogenic bacteria from the fish and also to understand the bacterial association in highly consumed fish.

RevDate: 2021-01-12

Guo L, Xiao P, Zhang X, et al (2021)

Inulin ameliorates schizophrenia via modulation of the gut microbiota and anti-inflammation in mice.

Food & function [Epub ahead of print].

The microbiome-gut-brain (MGB) axis, which regulates neurological and cognitive functions, plays an essential role in schizophrenia (SCZ) progression. Dietary inulin could be a novel strategy for the treatment of SCZ due to its modulating effects on the gut microbiota. In this study, the effects of inulin on mice with SCZ were studied. As indicated by the behavioural tests, expression of neurotransmitters, inflammatory indicators, and brain morphology, inulin administration ameliorated aberrant behaviours (locomotor hypoactivity, anxiety disorders and depressive behaviours, and impaired learning and spatial recognition memory) and effectively reduced neuroinflammation and neuronal damage. In addition, inulin improved intestinal integrity and permeability, as indicated by the elevated expression of tight junction proteins (p < 0.05). The results of 16S rRNA sequencing and analysis showed that inulin increased the abundance of Lactobacillus and Bifidobacterium, which were negatively correlated with 5-hydroxytryptamine and inflammatory cytokines and positively correlated with brain-derived neurotrophic factor (BDNF). Inulin caused a reduction in Akkermansia that was positively correlated with inflammatory cytokines and negatively correlated with BDNF. These results suggested that dietary inulin modulated the gut microbiota and exerted anti-inflammatory effects in mice though the MGB axis, which further ameliorated SCZ. Therefore, the results of this study provide a potential explanation for inulin intervention in the treatment of SCZ.

RevDate: 2021-01-12

Asnicar F, Berry SE, Valdes AM, et al (2021)

Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.

Nature medicine [Epub ahead of print].

The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.

RevDate: 2021-01-12

Lee SH, Cho SY, Yoon Y, et al (2021)

Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice.

Nature microbiology [Epub ahead of print].

The gut microbiome can influence the development of tumours and the efficacy of cancer therapeutics1-5; however, the multi-omics characteristics of antitumour bacterial strains have not been fully elucidated. In this study, we integrated metagenomics, genomics and transcriptomics of bacteria, and analyses of mouse intestinal transcriptome and serum metabolome data to reveal an additional mechanism by which bacteria determine the efficacy of cancer therapeutics. In gut microbiome analyses of 96 samples from patients with non-small-cell lung cancer, Bifidobacterium bifidum was abundant in patients responsive to therapy. However, when we treated syngeneic mouse tumours with commercial strains of B. bifidum to establish relevance for potential therapeutic uses, only specific B. bifidum strains reduced tumour burden synergistically with PD-1 blockade or oxaliplatin treatment by eliciting an antitumour host immune response. In mice, these strains induced tuning of the immunological background by potentiating the production of interferon-γ, probably through the enhanced biosynthesis of immune-stimulating molecules and metabolites.

RevDate: 2021-01-12

Debesa-Tur G, Pérez-Brocal V, Ruiz-Ruiz S, et al (2021)

Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients.

Scientific reports, 11(1):391.

An increased risk of developing colorectal cancer (CRC) and other types of tumor is associated to Lynch syndrome (LS), an inherited condition caused by germline mutations in mismatch repair genes. We selected a cohort of LS patients that had developed CRC and had undergone surgical resection. Formalin-fixed paraffin embedded (FFPE) tissue blocks from matched colorectal and normal mucosa were used for genomic DNA extraction with a commercial kit and sequenced by high-throughput sequencing. A metagenomic approach enabled the taxonomic and functional identification of the microbial community and associated genes detected in the specimens. Slightly lower taxonomic diversity was observed in the tumor compared to the non-tumor tissue. Furthermore, the most remarkable differences between tumors and healthy tissue was the significant increase in the genus Fusobacterium in the former, in particular the species F. nucleatum, as well as Camplylobacter or Bacteroides fragilis, in accordance with previous studies of CRC. However, unlike prior studies, the present work is not based on directed detection by qPCR but instead uses a metagenomic approach to retrieve the whole bacterial community, and addresses the additional difficulty of using long-term stored FFPE samples.

RevDate: 2021-01-12

Jin X, Zhang Y, Celniker SE, et al (2021)

Gut microbiome partially mediates and coordinates the effects of genetics on anxiety-like behavior in Collaborative Cross mice.

Scientific reports, 11(1):270.

Growing evidence suggests that the gut microbiome (GM) plays a critical role in health and disease. However, the contribution of GM to psychiatric disorders, especially anxiety, remains unclear. We used the Collaborative Cross (CC) mouse population-based model to identify anxiety associated host genetic and GM factors. Anxiety-like behavior of 445 mice across 30 CC strains was measured using the light/dark box assay and documented by video. A custom tracking system was developed to quantify seven anxiety-related phenotypes based on video. Mice were assigned to a low or high anxiety group by consensus clustering using seven anxiety-related phenotypes. Genome-wide association analysis (GWAS) identified 141 genes (264 SNPs) significantly enriched for anxiety and depression related functions. In the same CC cohort, we measured GM composition and identified five families that differ between high and low anxiety mice. Anxiety level was predicted with 79% accuracy and an AUC of 0.81. Mediation analyses revealed that the genetic contribution to anxiety was partially mediated by the GM. Our findings indicate that GM partially mediates and coordinates the effects of genetics on anxiety.

RevDate: 2021-01-12

Murphy KM, Edwards J, Louie KB, et al (2021)

Bioactive diterpenoids impact the composition of the root-associated microbiome in maize (Zea mays).

Scientific reports, 11(1):333.

Plants deploy both primary and species-specific, specialized metabolites to communicate with other organisms and adapt to environmental challenges, including interactions with soil-dwelling microbial communities. However, the role of specialized metabolites in modulating plant-microbiome interactions often remains elusive. In this study, we report that maize (Zea mays) diterpenoid metabolites with known antifungal bioactivities also influence rhizosphere bacterial communities. Metabolite profiling showed that dolabralexins, antibiotic diterpenoids that are highly abundant in roots of some maize varieties, can be exuded from the roots. Comparative 16S rRNA gene sequencing determined the bacterial community composition of the maize mutant Zman2 (anther ear 2), which is deficient in dolabralexins and closely related bioactive kauralexin diterpenoids. The Zman2 rhizosphere microbiome differed significantly from the wild-type sibling with the most significant changes observed for Alphaproteobacteria of the order Sphingomonadales. Metabolomics analyses support that these differences are attributed to the diterpenoid deficiency of the Zman2 mutant, rather than other large-scale metabolome alterations. Together, these findings support physiological functions of maize diterpenoids beyond known chemical defenses, including the assembly of the rhizosphere microbiome.

RevDate: 2021-01-12

Mocking RJT, Naviaux JC, Li K, et al (2021)

Metabolic features of recurrent major depressive disorder in remission, and the risk of future recurrence.

Translational psychiatry, 11(1):37.

Recurrent major depressive disorder (rMDD) is a relapsing-remitting disease with high morbidity and a 5-year risk of recurrence of up to 80%. This was a prospective pilot study to examine the potential diagnostic and prognostic value of targeted plasma metabolomics in the care of patients with rMDD in remission. We used an established LC-MS/MS platform to measure 399 metabolites in 68 subjects with rMDD (n = 45 females and 23 males) in antidepressant-free remission and 59 age- and sex-matched controls (n = 40 females and 19 males). Patients were then followed prospectively for 2.5 years. Metabolomics explained up to 43% of the phenotypic variance. The strongest biomarkers were gender specific. 80% of the metabolic predictors of recurrence in both males and females belonged to 6 pathways: (1) phospholipids, (2) sphingomyelins, (3) glycosphingolipids, (4) eicosanoids, (5) microbiome, and (6) purines. These changes traced to altered mitochondrial regulation of cellular redox, signaling, energy, and lipid metabolism. Metabolomics identified a chemical endophenotype that could be used to stratify rrMDD patients at greatest risk for recurrence with an accuracy over 0.90 (95%CI = 0.69-1.0). Power calculations suggest that a validation study of at least 198 females and 198 males (99 cases and 99 controls each) will be needed to confirm these results. Although a small study, these results are the first to show the potential utility of metabolomics in assisting with the important clinical challenge of prospectively identifying the patients at greatest risk of recurrence of a depressive episode and those who are at lower risk.

RevDate: 2021-01-12

McNamara MP, Singleton JM, Cadney MD, et al (2021)

Early-life effects of juvenile Western diet and exercise on adult gut microbiome composition in mice.

The Journal of experimental biology pii:jeb.239699 [Epub ahead of print].

Alterations to the gut microbiome caused by changes in diet, consumption of antibiotics, etc., can affect host function. Moreover, perturbation of the microbiome during critical developmental periods potentially have long-lasting impacts on hosts. Using four selectively bred High Runner and four non-selected Control lines of mice, we examined the effects of early-life diet and exercise manipulations on the adult microbiome by sequencing the hypervariable Internal Transcribed Spacer region of the bacterial gut community. Mice from High Runner lines run ∼3-fold more on wheels than do Controls, and have several other phenotypic differences (e.g., higher food consumption and body temperature) that could alter the microbiome, either acutely or in terms of coevolution. Males from generation 76 were given wheels and/or Western diet from weaning until sexual maturity at 6 weeks of age, then housed individually without wheels on standard diet until 14 weeks of age, when fecal samples were taken. Juvenile Western diet reduced bacterial richness and diversity after the 8-week washout period (equivalent to ∼6 human years). We also found interactive effects of genetic linetype, juvenile diet, and/or juvenile exercise on microbiome composition and diversity. Microbial community structure clustered significantly in relation to both linetype and diet. Western diet also reduced the relative abundance of Muribaculum intestinale These results constitute one of the first reports of juvenile diet having long-lasting effects on the adult microbiome after a substantial washout period. Moreover, we found interactive effects of diet with early-life exercise exposure, and a dependence of these effects on genetic background.

RevDate: 2021-01-12

Yeoh YK, Zuo T, Lui GC, et al (2021)

Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19.

Gut pii:gutjnl-2020-323020 [Epub ahead of print].

OBJECTIVE: Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus.

METHODS: In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma.

RESULTS: Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase.

CONCLUSION: Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.

RevDate: 2021-01-12

Frey DL, Boutin S, Dittrich SA, et al (2021)

Relationship between airway dysbiosis, inflammation and lung function in adults with cystic fibrosis.

Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society pii:S1569-1993(20)30954-1 [Epub ahead of print].

Airway dysbiosis has been associated with lung disease severity in patients with cystic fibrosis (CF). However, the relationship between dysbiosis, airway inflammation and lung function impairement remains poorly understood. The aim of this study was therefore to determine how the structure of the sputum microbiota, airway inflammation markers and spirometry are related in patients with CF. Sputum samples were collected from 106 CF patients between 12 and 72 years. These were analyzed by 16S rRNA gene amplicon sequencing. Moreover, levels of pro-inflammatory cytokines (IL-1β, IL-8, IL-6 and TNF-α) and Neutrophil elastase (NE) were determined. The relationship between the microbiota, inflammation markers and forced expiratory volume in one second percent predicted (FEV1% predicted) was evaluated by multi-parameter analysis. The microbiota α-diversity correlated inverse with inflammation markers IL-1β, IL-8, TNF-α, NE and positively with FEV1% predicted. Patients could be divided into 7 clusters based on their microbiota structure. The most diverse cluster was defined by oropharyngeal-like flora (OF) while the others were characterized by the dominance of a single pathogen. Patients with the diverse OF microbiota cluster had lower sputum inflammatory markers and higher FEV1% predicted compared to patients with a pathogen-dominated microbiota including Pseudomonas aeruginosa. Our results suggest that the diversity of the airway microbiota is an important biomarker of the severity of airway inflammation linking dysbiosis to lung function decline in patients with CF.

RevDate: 2021-01-12

Jain T, V Dudeja (2021)

Neoadjuvant therapy alters the biliary microbiome in PDAC.

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RJR Experience and Expertise

Researcher

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.

Educator

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.

Administrator

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.

Technologist

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.

Publisher

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.

Speaker

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.

Facilitator

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.

Designer

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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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.

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Curriculum Vitae for R J Robbins

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