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Bibliography on: Microbiome

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ESP: PubMed Auto Bibliography 27 May 2022 at 01:47 Created: 


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

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

Citations The Papers (from PubMed®)


RevDate: 2022-05-26

Sun Y, Zhang M, Ou Z, et al (2022)

Indoor microbiome, microbial and plant metabolites, chemical compounds and asthma symptoms in junior high school students: a multicentre association study in Malaysia.

The European respiratory journal pii:13993003.00260-2022 [Epub ahead of print].

Indoor microbial exposure is associated with asthma, but the health effects of indoor metabolites and chemicals are not comprehensively assessed. Here, we collected classroom dust from 24 junior high schools in three geographically distanced areas in Malaysia, including Johor Bahru, Terengganu, and Penang, and conducted culture-independent high-throughput microbiome and untargeted metabolomics/chemical profilings. 1290 students were surveyed for asthma symptoms (wheeze). In each center, we found significant variation in the prevalence of wheeze among schools, which cannot be explained by personal characteristics and air pollutants. Large-scale microbial variations were observed between three centers; the potential protective bacteria were mainly from phylum Actinobacteria in Johor Bahru, Cyanobacteria in Terengganu, and Proteobacteria in Penang. In total, 2633 metabolites and chemicals were characterized. Many metabolites were enriched in low wheeze schools, including plant secondary metabolites flavonoids/isoflavonoids (isoliquiritigenin, formononetin, astragalin), indole and derivatives (indole, serotonin, 1H-indole-3-carboxaldehyde), and others (biotin, chavicol). A neural-network analysis showed that the indole derivatives were co-occurring with the potential protective microbial taxa, including Actinomycetospora, Fischerella and Truepera, suggesting these microorganisms may pose health effects by releasing indole metabolites. A few synthetic chemicals were enriched in high wheeze schools, including pesticide (2(3H)-benzothiazolethione), fragrance (2-aminobenzoic acid, isovaleric acid), detergent and plastic (phthalic acid), and industrial material (4,4-sulfonyldiphenol). This is the first association study between high-throughput indoor chemical profiling and asthma symptoms. The consistent results from three centers indicate that indoor metabolites/chemicals could be a better indicator than indoor microbiome for environmental and health assessments, providing new insights for asthma prediction, prevention, and control.

RevDate: 2022-05-26

Huang G, Qu Q, Wang M, et al (2022)

Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates.

The Science of the total environment pii:S0048-9697(22)03275-2 [Epub ahead of print].

Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.

RevDate: 2022-05-26

Fitzpatrick F, Safdar N, van Prehn J, et al (2022)

How can patients with Clostridioides difficile infection on concomitant antibiotic treatment be best managed?.

The Lancet. Infectious diseases pii:S1473-3099(22)00274-2 [Epub ahead of print].

Antibiotics are modifiable risk factors for Clostridioides difficile infection (CDI), driving pathogenesis via gut microbiome disruption. The management of patients with CDI prescribed concomitant non-CDI antibiotics is problematic and influences CDI outcome and recurrence risk. Though an assessment of the ongoing requirement for concomitant antibiotics is essential, discontinuation is often not possible. Antibiotics for other reasons might also need to be commenced during CDI therapy. Attempts to minimise the number and duration of antibiotics with a change to a low-risk class are recommended. Fidaxomicin might be preferable to vancomycin due to it having less effect on the gut microbiome; however, vancomycin is also acceptable. Metronidazole should be avoided and proton pump inhibitors discontinued. Access to fidaxomicin might be limited; hence, it should be prioritised for patients at high risk of recurrence. There is insufficient evidence to support extending anti-CDI therapy duration and concerns regarding microbiome effect remain. The addition of bezlotoxumab might be considered if multiple additional risk factors for recurrent CDI exist, though the amount of evidence is low. Investigational approaches to reduce the effect of concomitant antibiotics on the gut microbiome could further optimise CDI treatment in the presence of concomitant antibiotic use in the future.

RevDate: 2022-05-26

Xiong C, Calatayud M, van de Wiele T, et al (2022)

Gut microbiota metabolize arsenolipids in a donor dependent way.

Ecotoxicology and environmental safety, 239:113662 pii:S0147-6513(22)00502-4 [Epub ahead of print].

Understanding the interplay between the gut microbiome and arsenolipids can help us manage the potential health risk of consuming seafood, but little is known about the bioconversion fate of arsenolipids in the gastrointestinal tract. We use an in vitro mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) to mimic the digestive tract of four healthy donors during exposure to two arsenolipids (an arsenic fatty acid AsFA 362 or an arsenic hydrocarbon AsHC 332). The metabolites were analyzed by HPLC-mass spectrometry. The human gut bacteria accumulated arsenolipids in a donor-dependent way, with higher retention of AsHC 332. Colonic microbiota partly transformed both arsenolipids to their thioxo analogs, while AsFA 362 was additionally transformed into arsenic-containing fatty esters, arsenic-containing fatty alcohols, and arsenic-containing sterols. There was no significant difference in water-soluble arsenicals between arsenolipid treatments. The study shows that arsenolipids can be quickly biotransformed into several lipid-soluble arsenicals of unknown toxicity, which cannot be excluded when considering potential implications on human health.

RevDate: 2022-05-26

Brodin P (2022)

Immune-microbe interactions early in life: A determinant of health and disease long term.

Science (New York, N.Y.), 376(6596):945-950.

Research on newborn immunity has revealed the importance of cell ontogeny, feto-maternal tolerance, and the transfer of maternal antibodies. Less is known about postnatal adaptation to environmental exposures. The microbiome and its importance for health have been extensively studied, but it remains unclear how mutually beneficial relationships between commensal microbes and human cells first arise and are maintained throughout life. Such immune-microbe mutualism, and perturbations thereof, is most likely a root cause of increasing incidences of immune-mediated disorders such as allergies and autoimmunity across many industrialized nations during the past century. In this Review, I discuss our current understanding of immune development and propose that mismatches among ancestral, early-life, and adult environments can explain perturbations to immune-microbe interactions, immune dysregulation, and increased risks of immune-mediated diseases.

RevDate: 2022-05-26

Jensen EA, Young JA, Jackson Z, et al (2022)

Excess growth hormone alters the male mouse gut microbiome in an age-dependent manner.

Endocrinology pii:6591911 [Epub ahead of print].

The gut microbiome has an important role in host development, metabolism, growth, and aging. Recent research points toward potential crosstalk between the gut microbiota and the growth hormone (GH)/insulin-like growth factor-1 (IGF-1) axis. Our laboratory previously showed that GH excess and deficiency are associated with an altered gut microbial composition in adult mice. Yet, no study to date has examined the influence of GH on the gut microbiome over time. Our study thus tracked the impact of excess GH action on the longitudinal changes in the gut microbial profile (i.e. abundance, diversity/maturity, predictive metabolic function, and short chain fatty acid [SCFAs] levels) of bovine GH (bGH) transgenic mice at 3, 6, and 12 months of age compared to littermate controls in the context of metabolism, intestinal phenotype, and premature aging. The bGH mice displayed age-dependent changes in microbial abundance, richness, and evenness. Microbial maturity was significantly explained by genotype and age. Moreover, several bacteria (i.e. Lactobacillus, Lachnospiraceae, Bifidobacterium, and Faecalibaculum), predictive metabolic pathways (such as SCFA, vitamin B12, folate, menaquinol, peptidoglycan, and heme B biosynthesis), and SCFA levels (acetate, butyrate, lactate, and propionate) were consistently altered across all three timepoints, differentiating the longitudinal bGH microbiome from controls. Of note, the bGH mice also had significantly impaired intestinal fat absorption with increased fecal output. Collectively, these findings suggest that excess GH alters the gut microbiome in an age-dependent manner with distinct longitudinal microbial and predicted metabolic pathway signatures.

RevDate: 2022-05-26

Chang YH, Yeh KW, Huang JL, et al (2022)

Metabolomics analysis reveals molecular linkages for the impact of vitamin D on childhood allergic airway diseases.

Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology, 33(5):e13785.

BACKGROUND: Several studies have reported the relevance between serum vitamin D and allergic immunoglobulin E (IgE) responses and atopic diseases. However, a metabolomics-based approach to the impacts of vitamin D on allergic reactions remains unclear.

METHODS: A total of 111 children completed a 3-year follow-up were enrolled and classified based on longitudinal vitamin D status (≥ 30 ng/ml, n = 54; 20-29.9 ng/ml, n = 41; <20 ng/ml, n = 16). Urinary metabolomic profiling was performed using 1 H-Nuclear magnetic resonance (NMR) spectroscopy at age 3. Integrative analyses of their associations related to vitamin D levels, atopic indices, and allergies were performed, and their roles in functional metabolic pathways were also assessed.

RESULTS: Six and five metabolites were identified to be significantly associated with vitamin D status and atopic diseases, respectively (FDR-adjusted p-value <.05). A further correlation analysis revealed that vitamin D-associated 3-hydroxyisobutyric acid and glutamine were positively correlated with atopic disease-associated succinic acid and alanine, respectively. Furthermore, hippuric acid was negatively correlated with atopic disease-associated formic acid, which was positively correlated with vitamin D level (p < .01). Absolute eosinophil count (AEC) was positively correlated with serum D. pteronyssinus- and D. farinae-specific IgE level (p < .01) but negatively correlated with vitamin D level (p < .05). Amino acid metabolisms were significantly associated with vitamin D related to childhood allergies.

CONCLUSION: Integrative metabolomic analysis provides the link of vitamin D-associated metabolites with the gut microbiome and immunoallergic reactions related to childhood allergies.

RevDate: 2022-05-26

Hasan R, Bose S, Roy R, et al (2022)

Tumor tissue-specific bacterial biomarker panel for colorectal cancer: Bacteroides massiliensis, Alistipes species, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, Corynebacterium appendicis.

Archives of microbiology, 204(6):348.

Human microbiome studies have shown diversity to exist among different ethnic populations. However, studies pertaining to the microbial composition of CRC among the Indian population have not been well explored. We aimed to decipher the microbial signature in tumor tissues from North Indian CRC patients. Next-generation sequencing of tumor and adjacent tissue-derived bacterial 16S rRNA V3-V4 hypervariable regions was performed to investigate the abundance of specific microbes. The expression profile analysis deciphered a decreased diversity among the tumor-associated microbial communities. At the phyla level, Proteobacteria was differentially expressed in CRC tissues than adjacent normal. Further, DeSeq2 normalization identified 4 out of 79 distinct species (p < 0.005) only in CRC, Bacteroides massiliensis, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, and Corynebacterium appendicis. Thus, the findings suggest that microbial signatures can be used as putative biomarkers in diagnosis, prognosis and treatment management of CRC.

RevDate: 2022-05-26

Johny TK, Puthusseri RM, Saidumohamed BE, et al (2022)

Correction to: Appraisal of cytotoxicity and acrylamide mitigation potential of L-asparaginase SlpA from fish gut microbiome.

RevDate: 2022-05-26

Kullberg RFJ, de Brabander J, Boers LS, et al (2022)

Lung Microbiota of Critically Ill COVID-19 Patients are Associated with Non-Resolving Acute Respiratory Distress Syndrome.

American journal of respiratory and critical care medicine [Epub ahead of print].

RATIONALE: Bacterial lung microbiota are correlated with lung inflammation and acute respiratory distress syndrome (ARDS), and altered in severe COVID-19. However, the association between lung microbiota (including fungi) and resolution of ARDS in COVID-19 remains unclear. We hypothesized that increased lung bacterial and fungal burdens are related to non-resolving ARDS and mortality in COVID-19.

OBJECTIVES: To determine the relation between lung microbiota and clinical outcomes of COVID-19-related ARDS.

METHODS: This observational cohort study enrolled mechanically ventilated COVID-19 patients. All patients had ARDS and underwent bronchoscopy with bronchoalveolar lavage (BAL). Lung microbiota were profiled using 16S rRNA gene sequencing and qPCR targeting the 16S and 18S rRNA genes. Key features of lung microbiota (bacterial and fungal burden, α-diversity and community composition) served as predictors. Our primary outcome was successful extubation adjudicated 60 days after intubation, analyzed using a competing risk regression model with mortality as competing risk.

MEASUREMENTS AND MAIN RESULTS: BAL samples of 114 unique COVID-19 patients were analyzed. Patients with increased lung bacterial and fungal burden were less likely to be extubated (subdistribution hazard ratio 0.64 [95% CI 0.42-0.97], p=0.034 and 0.59 [95% CI 0.42-0.83], p=0.0027 per log10 increase in bacterial and fungal burden, respectively) and had higher mortality (bacterial burden p=0.012, fungal burden p=0.0498). Lung microbiota composition was associated with successful extubation (p=0.0045). Proinflammatory cytokines (e.g. tumor necrosis factor-α) were associated with the microbial burdens.

CONCLUSIONS: Bacterial and fungal lung microbiota are related to non-resolving ARDS in COVID-19, and represent an important contributor to heterogeneity in COVID-19-related ARDS. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (

RevDate: 2022-05-26

Li G, Li Y, K Chen (2022)

It's all relative: Regression analysis with compositional predictors.

Biometrics [Epub ahead of print].

Compositional data reside in a simplex and measure fractions or proportions of parts to a whole. Most existing regression methods for such data rely on log-ratio transformations that are inadequate or inappropriate in modeling high dimensional data with excessive zeros and hierarchical structures. Moreover, such models usually lack a straightforward interpretation due to the interrelation between parts of a composition. We develop a novel relative-shift regression framework that directly uses proportions as predictors. The new framework provides a paradigm shift for regression analysis with compositional predictors and offers a superior interpretation of how shifting concentration between parts affects the response. New equi-sparsity and tree-guided regularization methods and an efficient smoothing proximal gradient algorithm are developed to facilitate feature aggregation and dimension reduction in regression. A unified finite-sample prediction error bound is derived for the proposed regularized estimators. We demonstrate the efficacy of the proposed methods in extensive simulation studies and a real gut microbiome study. Guided by the taxonomy of the microbiome data, the framework identifies important taxa at different taxonomic levels associated with the neurodevelopment of preterm infants. This article is protected by copyright. All rights reserved.

RevDate: 2022-05-26

Bae SS, Dong TS, Wang J, et al (2022)

Altered Gut Microbiome in Patients With Dermatomyositis.

ACR open rheumatology [Epub ahead of print].

OBJECTIVE: The study objective was to compare the microbial composition of patients with dermatomyositis (DM) and healthy controls (HCs) and determine whether microbial alterations are associated with clinical manifestations of DM.

METHODS: The 16S ribosomal RNA gene sequencing was performed on fecal samples from patients with DM and HCs. Microbial composition and diversity were compared between subjects with DM and HCs and in association with several DM-specific clinical variables, including myositis-specific autoantibodies (MSAs). Differentially abundant microbial taxa and genes associated with clinical characteristics were identified, and functional analysis was performed using predicted metagenomics. Dietary intake was assessed using a 24-hour dietary recall.

RESULTS: The fecal microbiome of 36 patients with DM and 26 HCs were analyzed. Patients with DM trended toward lower microbial diversity compared with HCs. The higher physician global damage score was significantly correlated with the lower microbial diversity in patients with DM. Patients with interstitial lung disease (ILD)-associated MSA (antisynthetase antibody (ab), anti-melanoma differentiation-associated protein 5 ab, n = 12) had significant differences in microbial composition and lower microbial diversity compared with HCs. Differential abundance testing demonstrated a unique taxonomic signature in the ILD-MSA subgroup, and predictive metagenomics identified functional alterations in a number of metabolic pathways. A significant increase in the relative abundance of Proteobacteria was positively correlated with multiple pathways involved in lipopolysaccharide synthesis and transport in the ILD-MSA group.

CONCLUSION: Patients with DM, particularly with ILD-associated MSAs, have lower microbial diversity and a distinct taxonomic composition compared with HCs. Further studies are needed to validate our findings and elucidate specific pathogenetic mechanisms that link the gut microbiome to clinical and pathological features of DM.

RevDate: 2022-05-26

Lu W, Wang Y, Fang Z, et al (2022)

Bifidobacterium longum CCFM752 prevented hypertension and aortic lesion, improved antioxidative ability, and regulated the gut microbiome in spontaneously hypertensive rats.

Food & function [Epub ahead of print].

Oxidative stress and gut dysbiosis are important risk factors for hypertension. In this study, the preventive effect of Bifidobacterium longum CCFM752 (CCFM752) on hypertension was evaluated. 5-week-old spontaneously hypertensive rats (SHR) were treated with vehicle or CCFM752 (1.0 × 109 CFU day-1) for 12 weeks. The increase in systolic blood pressure and diastolic blood pressure was significantly prevented by CCFM752 treatment. Simultaneously, CCFM752 prevented aortic fibrosis and hypertrophy and increased aortic endothelial nitric oxide synthase (eNOS) activity. CCFM752 presented an antioxidative effect by inhibiting aortic NADPH oxidase activation and increasing aortic and serum catalase activity, and reducing aortic reactive oxygen species (ROS). The gut dysbiosis of SHR, including the increased Firmicutes/Bacteroidetes ratio, decreased Actinobacteria as well as reduced α-diversity, were restored by CCFM752. CCFM752 also increased the prevalence of Bifidobacterium and Lactobacillus, while decreasing Turicibacter at the genus level. Furthermore, serum metabolomic analysis revealed that CCFM752 up-regulated serum proline and pyridoxamine 5'-phosphate, both of which were negatively correlated with blood pressure. In conclusion, the positive impact of CCFM752 on the gut microbiota may contribute to the antioxidative effect as well as its preventive effect on hypertension.

RevDate: 2022-05-26

Shao M, Kuang Z, Wang W, et al (2022)

Aucubin Exerts Anticancer Activity in Breast Cancer and Regulates Intestinal Microbiota.

Evidence-based complementary and alternative medicine : eCAM, 2022:4534411.

Aucubin, a natural compound isolated from herbal medicine, has been reported to possess multiple beneficial properties. In this study, we aimed to verify the anticancer effect of aucubin on breast cancer and investigate the effect of cancer on the intestinal flora and whether aucubin has a therapeutic effect on intestinal problems caused by cancer. We established the breast cancer model with mouse 4T1 cell line and BALB/c mice. Aucubin was given once a day by gavage for 14 days. The results showed that aucubin suppress the growth of tumor in vivo by inducing tumor cell apoptosis. The tumor suppression rate of aucubin could reach 51.31 ± 4.07%. Organ histopathology was evaluated by tissue staining, which demonstrated that aucubin could alleviate the organ inflammatory damage caused by breast cancer without visible side effects. Moreover, aucubin could increase the expression of colonic tight junction protein occluding and adjust the gut microbiome to normal level according to 16S rDNA high-throughput sequencing. Herein, our results provide evidence for developing aucubin as an alternative and safe therapeutic for breast cancer treatment.

RevDate: 2022-05-26

Bharanidharan R, Thirugnanasambantham K, Ibidhi R, et al (2022)

Metabolite Profile, Ruminal Methane Reduction, and Microbiome Modulating Potential of Seeds of Pharbitis nil.

Frontiers in microbiology, 13:892605.

We identified metabolites in the seeds of Pharbitis nil (PA) and evaluated their effects on rumen methanogenesis, fiber digestibility, and the rumen microbiome in vitro and in sacco. Four rumen-cannulated Holstein steers (mean body weight 507 ± 32 kg) were used as inoculum donor for in vitro trial and live continuous culture system for in sacco trial. PA was tested in vitro at doses ranging from 4.5 to 45.2% dry matter (DM) substrate. The in sacco trial was divided into three phases: a control phase of 10 days without nylon bags containing PA in the rumen, a treatment phase of 11 days in which nylon bags containing PA (180 g) were placed in the rumen, and a recovery phase of 10 days after removing the PA-containing bags from the rumen. Rumen headspace gas and rumen fluid samples were collected directly from the rumen. PA is enriched in polyunsaturated fatty acids dominated by linoleic acid (C18:2) and flavonoids such as chlorogenate, quercetin, quercetin-3-O-glucoside, and quinic acid derivatives. PA decreased (p < 0.001) methane (CH4) production linearly in vitro with a reduction of 24% at doses as low as 4.5% DM substrate. A quadratic increase (p = 0.078) in neutral detergent fiber digestibility was also noted, demonstrating that doses < 9% DM were optimal for simultaneously enhancing digestibility and CH4 reduction. In sacco, a 50% decrease (p = 0.087) in CH4 coupled with an increase in propionate suggested increased biohydrogenation in the treatment phase. A decrease (p < 0.005) in ruminal ammonia nitrogen (NH3-N) was also noted with PA in the rumen. Analysis of the rumen microbiome revealed a decrease (p < 0.001) in the Bacteroidetes-to-Firmicutes ratio, suggesting PA to have antiprotozoal potential. At the genus level, a 78% decrease in Prevotella spp. and a moderate increase in fibrolytic Ruminococcus spp. were noted in the treatment phase. In silico binding of PA metabolites to cyclic GMP-dependent protein kinase of Entodinium caudatum supported the antiprotozoal effect of PA. Overall, based on its high nutrient value and antiprotozoal activity, PA could probably replace the ionophores used for CH4 abatement in the livestock industry.

RevDate: 2022-05-26

Reyes G, Betancourt I, Andrade B, et al (2022)

Microbiome of Penaeus vannamei Larvae and Potential Biomarkers Associated With High and Low Survival in Shrimp Hatchery Tanks Affected by Acute Hepatopancreatic Necrosis Disease.

Frontiers in microbiology, 13:838640.

Acute hepatopancreatic necrosis disease (AHPND) is an emerging bacterial disease of cultured shrimp caused mainly by Vibrio parahaemolyticus, which harbors the lethal PirAB toxin genes. Although Penaeus vannamei (P. vannamei) postlarvae are susceptible to AHPND, the changes in the bacterial communities through the larval stages affected by the disease are unknown. We characterized, through high-throughput sequencing, the microbiome of P. vannamei larvae infected with AHPND-causing bacteria through the larval stages and compared the microbiome of larvae collected from high- and low-survival tanks. A total of 64 tanks from a commercial hatchery were sampled at mysis 3, postlarvae 4, postlarvae 7, and postlarvae 10 stages. PirAB toxin genes were detected by PCR and confirmed by histopathology analysis in 58 tanks. Seven from the 58 AHPND-positive tanks exhibited a survival rate higher than 60% at harvest, despite the AHPND affectation, being selected for further analysis, whereas 51 tanks exhibited survival rates lower than 60%. A random sample of 7 out of these 51 AHPND-positive tanks was also selected. Samples collected from the selected tanks were processed for the microbiome analysis. The V3-V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene of the samples collected from both the groups were sequenced. The Shannon diversity index was significantly lower at the low-survival tanks. The microbiomes were significantly different between high- and low-survival tanks at M3, PL4, PL7, but not at PL10. Differential abundance analysis determined that biomarkers associated with high and low survival in shrimp hatchery tanks affected with AHPND. The genera Bacillus, Vibrio, Yangia, Roseobacter, Tenacibaculum, Bdellovibrio, Mameliella, and Cognatishimia, among others, were enriched in the high-survival tanks. On the other hand, Gilvibacter, Marinibacterium, Spongiimonas, Catenococcus, and Sneathiella, among others, were enriched in the low-survival tanks. The results can be used to develop applications to prevent losses in shrimp hatchery tanks affected by AHPND.

RevDate: 2022-05-26

Cao D, Pang M, Wu D, et al (2022)

Alterations in the Gut Microbiota of Tibetan Patients With Echinococcosis.

Frontiers in microbiology, 13:860909.

There are two main types of echinococcosis, namely alveolar echinococcosis (AE) and cystic echinococcosis (CE). They are zoonotic parasitic diseases caused by the metacestodes of Echinococcus multilocularis and Echinococcus granulosus. In order to explore the gut microbiome composition of patients with echinococcosis, we analyzed fecal samples of seven patients with AE, six patients with CE, and 13 healthy individuals from the Qinghai-Tibetan Plateau, China. Using metagenomic next-generation sequencing, we identified fecal bacteria in the patients with AE and CE. The gut microbiota was analyzed by next-generation metagenomic sequencing (mNGS) to compare patients with either AE or CE against healthy individuals. We found there were some differences between them in abundant bacteria. Our results led to five findings: (1) Between patients with echinococcosis and healthy individuals, the differential bacteria were from four phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria. (2) Rothia mucilaginosa, Veillonella dispar, Veillonella atypica, Streptococcus parasanguinis, Streptococcus salivarius, and Alistipes finegoldii were abundant in the feces of patients with AE. (3) Bacteroides dorei, Parabacteroides distasonis, Escherichia sp_E4742, and Methanobrevibacter smithii were abundant in the feces of the patients with CE. (4) At the phylum and class level, compared to the AE group, the healthy group was characterized by higher numbers of Actinobacteria. (5) At the family level, Lachnospiraceae and Eubacteriaceae were more abundant in the feces of healthy individuals than in AE patients. The genera Coprococcus, Eubacterium, and Bilophia were more abundant in the healthy group, while the genus Rothia was more abundant in the AE group. The results of this study enrich our understanding of the gut microbiome composition of patients with AE and CE in the Qinghai-Tibetan Plateau.

RevDate: 2022-05-26

Ganesan R, Jeong JJ, Kim DJ, et al (2022)

Recent Trends of Microbiota-Based Microbial Metabolites Metabolism in Liver Disease.

Frontiers in medicine, 9:841281.

The gut microbiome and microbial metabolomic influences on liver diseases and their diagnosis, prognosis, and treatment are still controversial. Research studies have provocatively claimed that the gut microbiome, metabolomics understanding, and microbial metabolite screening are key approaches to understanding liver cancer and liver diseases. An advance of logical innovations in metabolomics profiling, the metabolome inclusion, challenges, and the reproducibility of the investigations at every stage are devoted to this domain to link the common molecules across multiple liver diseases, such as fatty liver, hepatitis, and cirrhosis. These molecules are not immediately recognizable because of the huge underlying and synthetic variety present inside the liver cellular metabolome. This review focuses on microenvironmental metabolic stimuli in the gut-liver axis. Microbial small-molecule profiling (i.e., semiquantitative monitoring, metabolic discrimination, target profiling, and untargeted profiling) in biological fluids has been incompletely addressed. Here, we have reviewed the differential expression of the metabolome of short-chain fatty acids (SCFAs), tryptophan, one-carbon metabolism and bile acid, and the gut microbiota effects are summarized and discussed. We further present proof-of-evidence for gut microbiota-based metabolomics that manipulates the host's gut or liver microbes, mechanosensitive metabolite reactions and potential metabolic pathways. We conclude with a forward-looking perspective on future attention to the "dark matter" of the gut microbiota and microbial metabolomics.

RevDate: 2022-05-25

Álvarez-Barragán J, Cravo-Laureau C, R Duran (2022)

Fungal-bacterial network in PAH-contaminated coastal marine sediment.

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

Fungal microbiome interacts with the other biotic components in coastal sediment playing a key role in the overall coordination of the whole microbial community. These interactions are affected by human activities, such as the constant affluence of polycyclic aromatic hydrocarbons (PAHs). Although fungi and bacteria interactions have been found to play a key role in PAH bioremediation in soil, the effect of PAHs on fungal diversity and their specific interactions with bacteria in coastal sediments are yet to be investigated. The understanding of fungal bacterial interactions under PAH contamination is critical for further bioremediation regarding the important fungal diversity observed in coastal sediment. Here, we investigated the fungal bacterial co-occurrence in PAH-contaminated sediments. The co-occurrence network, constructed with sequencing data (bacterial 16S and fungal 18S rRNA genes barcoding) from 51 PAH-contaminated samples, revealed modules dominated by either fungi or bacteria, reflecting probably the different types of interaction possible between fungi and bacteria. Then, a network constructed from non-contaminated sample data was compared with a network built from the corresponding PAH-contaminated samples issued from a mesocosm experiment. The comparison revealed the effect of PAHs in fungi and bacteria interactions, characterized by a PAH-contaminated network exhibiting less abundant and diverse fungal and bacterial ASVs than the non-contaminated network. However, the links between the remaining ASVs in the PAH-contaminated network showed stronger correlations. Noteworthy, an ASV affiliated to Chrytridiomycota phylum was identified as a keystone fungal ASV forming a module in association with facultative anaerobic and anaerobic bacteria affiliated to the families Prolixibacteraceae, Fusobacteriaceae, and Desulfobulbaceae. These results suggest that fungi promote bacterial anaerobic metabolisms, which are important to cope with the presence of PAHs in sediments. Our study reveals the importance of fungal bacterial interactions in coastal sediments paving the way for future studies to fully understand fungal role in coastal sediment.

RevDate: 2022-05-25

Zhang Y, Bhosle A, Bae S, et al (2022)

Discovery of bioactive microbial gene products in inflammatory bowel disease.

Nature [Epub ahead of print].

Microbial communities and their associated bioactive compounds1-3 are often disrupted in conditions such as the inflammatory bowel diseases (IBD)4. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive5-7. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.

RevDate: 2022-05-25

Iwańska O, Latoch P, Suchora M, et al (2022)

Lake microbiome and trophy fluctuations of the ancient hemp rettery.

Scientific reports, 12(1):8846.

Lake sediments not only store the long-term ecological information including pollen and microfossils but are also a source of sedimentary DNA (sedDNA). Here, by the combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedDNA we were able to paint a comprehensive picture of the fluctuations in trophy and bacterial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of the Roman and Early Medieval periods and correlated these to the increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply-hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest the employment of the fibre count analysis as an additional and independent proxy.

RevDate: 2022-05-25

Hedin KA, Rees VE, Zhang H, et al (2022)

Effects of broad-spectrum antibiotics on the colonisation of probiotic yeast Saccharomyces boulardii in the murine gastrointestinal tract.

Scientific reports, 12(1):8862.

Mouse models are commonly used to study the colonisation profiles of microorganisms introduced to the gastrointestinal tract. Three commonly used mouse models include conventional, germ-free, and antibiotic-treated mice. However, colonisation resistance in conventional mice and specialised equipment for germ-free mice are usually limiting factors in their applications. In this study, we sought to establish a robust colonisation model for Saccharomyces boulardii, a probiotic yeast that has caught attention in the field of probiotics and advanced microbiome therapeutics. We characterised the colonisation of S. boulardii in conventional mice and mice treated with a cocktail of broad-spectrum antibiotics, including ampicillin, kanamycin, metronidazole and vancomycin. We found colonisation levels increased up to 10,000-fold in the antibiotic-treated mice compared to nonantibiotic-treated mice. Furthermore, S. boulardii was detected continuously in more than 75% of mice for 10 days after the last administration in antibiotic-treated mice, in contrast to in nonantibiotic-treated mice where S. boulardii was undetectable in less than 2 days. Finally, we demonstrated that this antibiotic cocktail can be used in two commonly used mouse strains, C57BL/6 and ob/ob mice, both achieving ~ 108 CFU/g of S. boulardii in faeces. These findings highlight that the antibiotic cocktail used in this study is an advantageous tool to study S. boulardii based probiotic and advanced microbiome therapeutics.

RevDate: 2022-05-25

Pailhoriès H, Herrmann JL, Velo-Suarez L, et al (2022)

Antibiotic resistance in chronic respiratory diseases: from susceptibility testing to the resistome.

European respiratory review : an official journal of the European Respiratory Society, 31(164): pii:31/164/210259.

The development of resistome analysis, i.e. the comprehensive analysis of antibiotic-resistance genes (ARGs), is enabling a better understanding of the mechanisms of antibiotic-resistance emergence. The respiratory microbiome is a dynamic and interactive network of bacteria, with a set of ARGs that could influence the response to antibiotics. Viruses such as bacteriophages, potential carriers of ARGs, may also form part of this respiratory resistome. Chronic respiratory diseases (CRDs) such as cystic fibrosis, severe asthma, chronic obstructive pulmonary disease and bronchiectasis, managed with long-term antibiotic therapies, lead to multidrug resistance. Antibiotic susceptibility testing provides a partial view of the bacterial response to antibiotics in the complex lung environment. Assessing the ARG network would allow personalised, targeted therapeutic strategies and suitable antibiotic stewardship in CRDs, depending on individual resistome and microbiome signatures. This review summarises the influence of pulmonary antibiotic protocols on the respiratory microbiome, detailing the variable consequences according to antibiotic class and duration of treatment. The different resistome-profiling methods are explained to clarify their respective place in antibiotic-resistance analysis in the lungs. Finally, this review details current knowledge on the respiratory resistome related to therapeutic strategies and provides insight into the application of resistome analysis to counter the emergence of multidrug-resistant respiratory pathogens.

RevDate: 2022-05-25

Guo P, Xue M, Teng X, et al (2022)

Antarctic Krill Oil ameliorates liver injury in rats exposed to alcohol by regulating bile acids metabolism and gut microbiota.

The Journal of nutritional biochemistry pii:S0955-2863(22)00132-2 [Epub ahead of print].

Bile acids (BAs) metabolism plays an important role in alcohol liver disease (ALD) through the gut microflora-bile acids-liver axis. Antarctic Krill Oil (AKO) has protective effects on the liver, while whether AKO can protect against liver injury caused by alcohol is unclear. This study investigated the effects of AKO on BAs metabolism and intestinal microbiota in a rat model of alcohol-induced liver disease. Sprague-Dawley (SD) rats were randomly divided into five groups: control group, model group, low-dose AKO-treatment group (100 mg/kg/d), high-dose AKO-treatment group (200 mg/kg/d), and AKO control group (200 mg/kg/d). Administration of alcohol (8 to 10 mL/kg/ d) for 16 weeks induced liver injury in rats. We found that AKO supplementation significantly protected the liver against alcohol-induced injury, evidenced by allayed hepatic histopathological changes, and inhibited the alcohol-induced elevation of serum biochemical indices. Furthermore, AKO could regulate BAs metabolism by activating the intestinal-hepatic FXR-FGF15-FGFR4 signaling axis with subsequently decreased cholesterol 7α-hydroxylase (CYP7A1) and sterol 12α-hydroxylase (CYP8B1) levels, reduced hepatic BAs production, decreased serum BAs level and increased fecal excretion of BAs. Additionally, 16S rDNA sequencing revealed that the gut microbiome richness and composition were altered in alcohol-treated rats in comparison to the control and AKO-administrated rats. Spearman's correlation analysis showed that differential gut bacterial genera correlated with the levels of BAs profiles in the serum, liver, and feces. These findings suggested that AKO dietary supplementation may protect against alcohol-induced liver injury through modulating BAs metabolism and altering the gut microbiome.

RevDate: 2022-05-25

Wu JT, Sun CL, Lai TT, et al (2022)

Oral short-chain fatty acids administration regulates innate anxiety in adult microbiome-depleted mice.

Neuropharmacology pii:S0028-3908(22)00199-X [Epub ahead of print].

Anxiety is characterized by tension feelings and worried thoughts even in the absence of threatening stimulus. Pathological condition of anxiety elicits defensive behavior and aversive reaction ultimately impacting individuals and society. The gut microbiota has been shown to contribute to the modulation of anxiety-like behavior in rodents through the gut-brain axis. Several studies observed that germ-free (GF) and the broad spectrum of antibiotic cocktail (ABX)-treated rodents display lowered anxiety-like behavior. We speculate that gut microbial short-chain fatty acids (SCFA) modulate the innate anxiety response. Herein, we administered SCFA in the drinking water in adult mice treated with ABX to deplete the microbiota and tested their anxiety-like behaviors. To further augment the innate fear response, we enhanced the aversive stimulus of the anxiety-related behavior tests. Strikingly, we found that the anxiety-like behavior in ABX mice was not altered when enhanced aversive stimulus, while control and ABX mice supplemented with SCFA displayed increased anxiety-like behavior. Vagus nerve serves as a promising signaling pathway in the gut-brain axis. We determined the role of vagus nerve by subdiaphragmatic vagotomy (SDV) in ABX mice supplemented with SCFA. The restored anxiety-like behavior in ABX mice by SCFA was unaffected by SDV. These findings suggest that gut microbiota can regulate anxiety-like behavior through their fermentation products SCFA.

RevDate: 2022-05-25

Khalikov AA, Kildyushov EM, Kuznetsov KO, et al (2022)

[Estimation of time since death with the postmortem microbiome: a modern view and approaches to solving the problem].

Sudebno-meditsinskaia ekspertiza, 65(3):49-53.

The aim of the review is to summarize and update the data of modern studies devoted to determining the post-mortem interval (PMI) with the use of microorganisms, as well as disclosing prospects for further study in the presented direction. Estimating the time elapsed since death based on the postmortem microbiome has great potential for accurate determination of PMI, but all methods currently used have their limitations. The dynamics of changes in microbial communities due to the influence of many external and internal factors significantly complicates the process of interpreting the results. The change of microbial communities in the human corpse has shown promising results for the assessment of PMI, but to date there is no evidence of the repeatability of such a continuity in various geographic and ecological conditions. The question of conducting new, large-scale studies, taking in all the factors that could affect the posthumous microbiome, is becoming urgent.

RevDate: 2022-05-25

Luo T, Guo Z, Liu D, et al (2022)

Deficiency of PSRC1 accelerates atherosclerosis by increasing TMAO production via manipulating gut microbiota and flavin monooxygenase 3.

Gut microbes, 14(1):2077602.

Maladaptive inflammatory and immune responses are responsible for intestinal barrier integrity and function dysregulation. Proline/serine-rich coiled-coil protein 1 (PSRC1) critically contributes to the immune system, but direct data on the gut microbiota and the microbial metabolite trimethylamine N-oxide (TMAO) are lacking. Here, we investigated the impact of PSRC1 deletion on TMAO generation and atherosclerosis. We first found that PSRC1 deletion in apoE-/- mice accelerated atherosclerotic plaque formation, and then the gut microbiota and metabolites were detected using metagenomics and untargeted metabolomics. Our results showed that PSRC1 deficiency enriched trimethylamine (TMA)-producing bacteria and functional potential for TMA synthesis and accordingly enhanced plasma betaine and TMAO production. Furthermore, PSRC1 deficiency resulted in a proinflammatory colonic phenotype that was significantly associated with the dysregulated bacteria. Unexpectedly, hepatic RNA-seq indicated upregulated flavin monooxygenase 3 (FMO3) expression following PSRC1 knockout. Mechanistically, PSRC1 overexpression inhibited FMO3 expression in vitro, while an ERα inhibitor rescued the downregulation. Consistently, PSRC1-knockout mice exhibited higher plasma TMAO levels with a choline-supplemented diet, which was gut microbiota dependent, as evidenced by antibiotic treatment. To investigate the role of dysbiosis induced by PSRC1 deletion in atherogenesis, apoE-/- mice were transplanted with the fecal microbiota from either apoE-/- or PSRC1-/-apoE-/- donor mice. Mice that received PSRC1-knockout mouse feces showed an elevation in TMAO levels, as well as plaque lipid deposition and macrophage accumulation, which were accompanied by increased plasma lipid levels and impaired hepatic cholesterol transport. Overall, we identified PSRC1 as an atherosclerosis-protective factor, at least in part, attributable to its regulation of TMAO generation via a multistep pathway. Thus, PSRC1 holds great potential for manipulating the gut microbiome and alleviating atherosclerosis.

RevDate: 2022-05-25

Andrlová H, Miltiadous O, Kousa AI, et al (2022)

MAIT and Vδ2 unconventional T cells are supported by a diverse intestinal microbiome and correlate with favorable patient outcome after allogeneic HCT.

Science translational medicine, 14(646):eabj2829.

Microbial diversity is associated with improved outcomes in recipients of allogeneic hematopoietic cell transplantation (allo-HCT), but the mechanism underlying this observation is unclear. In a cohort of 174 patients who underwent allo-HCT, we demonstrate that a diverse intestinal microbiome early after allo-HCT is associated with an increased number of innate-like mucosal-associated invariant T (MAIT) cells, which are in turn associated with improved overall survival and less acute graft-versus-host disease (aGVHD). Immune profiling of conventional and unconventional immune cell subsets revealed that the prevalence of Vδ2 cells, the major circulating subpopulation of γδ T cells, closely correlated with the frequency of MAIT cells and was associated with less aGVHD. Analysis of these populations using both single-cell transcriptomics and flow cytometry suggested a shift toward activated phenotypes and a gain of cytotoxic and effector functions after transplantation. A diverse intestinal microbiome with the capacity to produce activating ligands for MAIT and Vδ2 cells appeared to be necessary for the maintenance of these populations after allo-HCT. These data suggest an immunological link between intestinal microbial diversity, microbe-derived ligands, and maintenance of unconventional T cells.

RevDate: 2022-05-25

Furlaneto F, Ishikawa KH, Messora MR, et al (2022)

Probiotics During the Therapeutic Management of Periodontitis.

Advances in experimental medicine and biology, 1373:353-375.

Scaling and root planing is the gold standard for the treatment of periodontitis, but administration of systemic antibiotics may be needed especially for sites with deep probing depths, or in the presence of comorbidities. However, treated sites are subject to recolonization with a microbiota similar to that present before therapy, and supportive periodontal therapy is employed after the treatment of active disease. The use of beneficial organisms, known as probiotics, seems an attractive proposal to promote a healthy associated subgingival microbiome and to control inflammation for the management of periodontitis. The mechanisms underlying the benefits promoted by probiotics involve interference on periodontopathogens, modulation of the exacerbated immune host response and the ability to restore the integrity of the epithelial barrier on mucosa surfaces. This review examines the scientific data related to the effects of probiotics on the treatment of periodontal diseases and addresses the future approaches necessary for their implementation.

RevDate: 2022-05-25

Prado MM, Figueiredo N, Pimenta AL, et al (2022)

Recent Updates on Microbial Biofilms in Periodontitis: An Analysis of In Vitro Biofilm Models.

Advances in experimental medicine and biology, 1373:159-174.

The development of oral biofilm models has been extremely important to study the specific role of most microbial species at the early stages of periodontitis. The current knowledge on monospecies or multispecies biofilms originates mainly from the observation of in vitro dynamic or static biofilm model systems, which were engineered to mimic clinical oral conditions. In the last few decades, mounting evidence has confirmed that biofilms are the major form of bacterial lifestyle, and more importantly, that microorganisms dwelling in sessile mixed-species aggregates display completely different phenotypes and physiological characteristics than when living in planktonic pure cultures. Interspecies interactions within these communities, mediated by chemical communication systems, have been shown to affect biofilm physiology and increase antimicrobial resistance by up to 1000 fold. These aspects reinforce the importance of developing multispecies biofilm models to better understand and control biofilms. Literature reports demonstrate that while monospecies models are still most commonly used in caries research, authors have used different multispecies models to study periodontal diseases. Periodontitis is a polymicrobial biofilm-dependent disease mainly associated with Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. Interestingly, these species hardly adhere to substrates commonly used for biofilm formation, which makes multispecies models essential for an accurate analysis of periodontitis-related biofilms. The multispecies models currently available are generally composed of 6-10 species, but a more recent 34-species model was developed to better examine the dynamics within oral biofilms. The complexity of such polymicrobial biofilm models mimics more consistently the oral microbiome and different aspects of the oral environment. Collectively, the evidence on multispecies biofilm models described herein may support future studies on the use of antimicrobials for biofilm control as well as provide research opportunities to expand the current knowledge on interspecies interactions. The present manuscript reviews the most recent updates on in vitro biofilm model systems for periodontitis.

RevDate: 2022-05-25

Karkowska-Kuleta J, Satala D, Smolarz M, et al (2022)

Fungi-A Component of the Oral Microbiome Involved in Periodontal Diseases.

Advances in experimental medicine and biology, 1373:113-138.

The human oral cavity is a diverse ecological niche favorable for colonization by hundreds of different species of microorganisms. They include not only bacteria but also numerous species of fungi, many of which are able to cause opportunistic infections when the host's immunity is impaired, predominantly by systemic and chronic diseases like diabetes, pulmonary diseases, renal disorders, or acquired immunodeficiency syndrome. Within the dental biofilm and subgingival sites, fungi of the genus Candida are often found, also in individuals affected with periodontitis. Moreover, fungal species of other genera, including Malassezia, Aspergillus, Penicillium, and Rhodotorula were identified in the oral cavity as well. The wide range of various virulence factors and mechanisms displayed by fungal pathogens allows them effectively invading host tissues during periodontal infections. These pathogenicity-related mechanisms include firstly the fungal ability to adhere successfully to the host tissues closely related to the formation of hyphae, the increase in the surface hydrophobicity, and the surface display of a wide variety of adhesins. Further mechanisms include biofilm formation and secretion of an armory of hydrolytic enzymes and toxins enabling the attack on host cells, modulation of the local inflammatory state, and evading the host immune system. In the pathogenesis of periodontitis, the significant role of fungal co-existence with key bacterial periodontopathogens has been demonstrated, and such interactions were primarily confirmed for Candida albicans and Porphyromonas gingivalis, where the presence of fungi ensured the survival of strictly anaerobic bacteria under unfavorable aerobic conditions. However, several other mechanisms, including those related to the production of quorum sensing molecules, might also be indicated as particularly important for synergistic or antagonistic interactions with a variety of bacterial species within mixed biofilms. These interactions constitute an extraordinary challenge for applying effective methods of combating biofilm-related infections in the periodontium without the risk of the development of drug resistance, the recurrence of disease symptoms, and the progress of life-threating systemic complications.

RevDate: 2022-05-25

Fong SB, Boyer E, Bonnaure-Mallet M, et al (2022)

Microbiota in Periodontitis: Advances in the Omic Era.

Advances in experimental medicine and biology, 1373:19-43.

The complexity of the oral microbiome continues to astound researchers even with the advancement of multi-disciplinary strategies being used to study these microorganisms in relation to the human body. There is extensive literature available that explains how oral bacterial communities exist within the biofilm and maintains a balance with the host immune system, but when this balance is tipped disease can occur. The purpose of this review is to highlight the subgingival microbial compositions during health and periodontal disease using next generation sequencing techniques, as well as determining the types of functional activities that partake during these states. The subgingival microbiota is a fluid structure that can adapt accordingly to the environment and the identification of signature biomarkers may aid in the assessment of risk and disease severity in an individual to complement clinical diagnosis in the future.

RevDate: 2022-05-25

Simopoulos CMA, Figeys D, M Lavallée-Adam (2022)

Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies.

Methods in molecular biology (Clifton, N.J.), 2456:319-338.

Constant improvements in mass spectrometry technologies and laboratory workflows have enabled the proteomics investigation of biological samples of growing complexity. Microbiomes represent such complex samples for which metaproteomics analyses are becoming increasingly popular. Metaproteomics experimental procedures create large amounts of data from which biologically relevant signal must be efficiently extracted to draw meaningful conclusions. Such a data processing requires appropriate bioinformatics tools specifically developed for, or capable of handling metaproteomics data. In this chapter, we outline current and novel tools that can perform the most commonly used steps in the analysis of cutting-edge metaproteomics data, such as peptide and protein identification and quantification, as well as data normalization, imputation, mining, and visualization. We also provide details about the experimental setups in which these tools should be used.

RevDate: 2022-05-25

Lacey KA, Gonzalez S, Yeung F, et al (2022)

Microbiome-Independent Effects of Antibiotics in a Murine Model of Nosocomial Infections.

mBio [Epub ahead of print].

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common causes of hospital-acquired pneumonia. To better manage patients with MRSA pneumonia, we require a greater understanding of the host-pathogen interactions during infection. MRSA research focuses on highly virulent and cytotoxic strains, which demonstrate robust phenotypes in animal models of infection. However, nosocomial infections are often caused by hospital-acquired MRSA (HA-MRSA) isolates that exhibit low cytotoxicity and few or no phenotypes in mice, thereby confounding mechanistic studies of pathogenesis. Consequently, virulence pathways utilized by HA-MRSA in nosocomial pneumonia are largely unknown. Here, we report that conditioning mice with broad-spectrum antibiotics lowers the barrier to pneumonia, thereby transforming otherwise avirulent HA-MRSA isolates into lethal pathogens. HA-MRSA isolates are avirulent in gnotobiotic mice, mimicking results in conventional animals. Thus, the observed enhanced susceptibility to infection in antibiotic-treated mice is not due to depletion of the microbiota. More generally, we found that antibiotic conditioning leads to increased susceptibility to infection by diverse antimicrobial-resistant (AMR) pathogens of low virulence. Treatment with antibiotics leads to dehydration and malnutrition, suggesting a potential role for these clinically relevant and reducible hospital complications in susceptibility to pathogens. In sum, the model described here mitigates the impact of low virulence in immunocompetent mice, providing a convenient model to gain fundamental insight into the pathogenesis of nosocomial pathogens. IMPORTANCE Antimicrobial-resistant (AMR) pathogens are responsible for over 2.8 million infections and over 35,000 deaths per year in the United States. To study these microbes, animal models that are susceptible to these pathogens are required. However, many of these pathogens exhibit low virulence in conventional mice, which has negatively impacted mechanistic studies. Here, we show that mice treated with antibiotics in their drinking water become exquisitely susceptible to low-virulence AMR pathogens. Surprisingly, the increased susceptibility was independent of the impact of antibiotics on the microbiome and seems to be due to an unintended consequence of antibiotic treatment: weight loss due to dehydration and caloric restriction. Unlike other models used to sensitize mice to low-virulence pathogens, our model does not reduce phagocyte numbers. Thus, here, we describe an immunocompetent mouse model to facilitate the identification of novel targets and accelerate the development of preventives and therapeutics to combat infections by AMR pathogens.

RevDate: 2022-05-25

Duan Y, Wei Y, Xing M, et al (2022)

Anaerobic Hydroxyproline Degradation Involving C-N Cleavage by a Glycyl Radical Enzyme.

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

Hydroxyprolines are highly abundant in nature as they are components of many structural proteins and osmolytes. Anaerobic degradation of trans-4-hydroxy-l-proline (t4L-HP) was previously found to involve the glycyl radical enzyme (GRE) t4L-HP dehydratase (HypD). Here, we report a pathway for anaerobic hydroxyproline degradation that involves a new GRE, trans-4-hydroxy-d-proline (t4D-HP) C-N-lyase (HplG). In this pathway, cis-4-hydroxy-l-proline (c4L-HP) is first isomerized to t4D-HP, followed by radical-mediated ring opening by HplG to give 2-amino-4-ketopentanoate (AKP), the first example of a ring opening reaction catalyzed by a GRE 1,2-eliminase. Subsequent cleavage by AKP thiolase (OrtAB) yields acetyl-CoA and d-alanine. We report a crystal structure of HplG in complex with t4D-HP at a resolution of 2.7 Å, providing insights into its catalytic mechanism. Different from HypD commonly identified in proline-reducing Clostridia, HplG is present in other types of fermenting bacteria, including propionate-producing bacteria, underscoring the diversity of enzymatic radical chemistry in the anaerobic microbiome.

RevDate: 2022-05-25

Romo-Vaquero M, Fernández-Villalba E, Gil-Martinez AL, et al (2022)

Urolithins: potential biomarkers of gut dysbiosis and disease stage in Parkinson's patients.

Food & function [Epub ahead of print].

Gut microbiota alteration (gut dysbiosis) occurs during the onset and progression of Parkinson's disease. Gut dysbiosis biomarkers could be relevant to prodromal disease. Urolithins, anti-inflammatory metabolites produced from some dietary polyphenols by specific gut microbial ecologies (urolithin metabotypes), have been proposed as biomarkers of gut microbiota composition and functionality. However, this has not been explored in Parkinson's disease patients. The current study aimed to assess associations between urolithin metabotypes, gut dysbiosis and disease severity in Parkinson's disease patients. Participants (52 patients and 117 healthy controls) provided stool samples for microbiota sequencing and urine samples for urolithin profiling before and after consuming 30 g of walnuts for three days. Data on demographics, medication, disease duration and Hoehn and Yahr disease stage were collected. We observed a significant gradual increase of urolithin non-producers (metabotype-0) as the disease severity increased. The gut microbiome of metabotype-0 patients and patients with the greatest severity was characterized by a more altered bacterial composition, i.e., increased pro-inflammatory Enterobacteriaceae and reduced protective bacteria against autoimmune and inflammatory processes, including butyrate and urolithin-producing bacteria (Lachnospiraceae members and Gordonibacter). Besides, their microbiome was characterized by predictive functions of lipopolysaccharide biosynthesis and metabolism of glutathione, cysteine and methionine that could indirectly reflect the gut pro-inflammatory status. Urolithin detection in urine is a feasible, non-invasive and fast approach that can reflect gut microbiome dysbiosis and intestinal inflammation in Parkinson's disease patients. Our current study could provide novel strategies for improving diagnostics, and for preventing and treating disease progression in microbiota-based interventions.

RevDate: 2022-05-25

Evans SE, Zandonà E, Amaral JR, et al (2022)

Shifts in gut microbiome across five decades of repeated guppy translocations in Trinidadian streams.

Proceedings. Biological sciences, 289(1975):20211955.

An organism's gut microbiome can alter its fitness, yet we do not know how gut microbiomes change as their hosts evolve in the wild. We took advantage of a five-decade 'chronosequence' of translocated fish populations to examine associated changes in the gut microbiome. Populations of Trinidadian guppies have displayed parallel phenotypic convergence six times when moved from high predation (HP) to low predation (LP) environments. Across four drainages, we found microbiomes of fish translocated 5-6 years prior to sampling were already distinct from the microbiomes of their HP source populations. Changes in environmental conditions were most important in driving this shift, followed by phenotypic shifts in gut morphology. After 30-60 years in LP environments, microbiome composition was still distinct from native LP populations, but microbiome function was not. We found some evidence that nitrogen fixation enhanced gut nutrient absorption, but most functional shifts were not parallel across drainages. Stream-and drainage-specific signatures were present for both composition and function, despite our overall finding of consistent microbiome change across drainages. As we unravel the complexities of host-microbiome evolution in the wild, studies should consider environmental microbial colonization, host phenotypic plasticity in nature, and more realistic environmental conditions excluded from laboratory studies.

RevDate: 2022-05-25

Jaber M, Altamimi M, Altamimi A, et al (2022)

Mediterranean diet diminishes the effects of Crohn's disease and improves its parameters: A systematic review.

Nutrition and health [Epub ahead of print].

BACKGROUND: The pathogenesis and clinical course of Crohn's disease (CD) is influenced by diet. Mediterranean Diet (MD) helps Crohn's patients through many mechanisms.

AIMS: This study aimed to evaluate the effect of the MD on CD patients and to evaluate such effect on body parameters.

METHODS: PubMed, Science Direct, Web of Science, MEDLINE and Cochrane central library were searched for MD and CD from 2010 to 2020. Included studies met the following criteria: (1) male and female adults (18-75 years) with a confirmed diagnosis of CD; (2) MD as an intervention; (3) original interventional Trial, Cross-Sectional Analysis, or Prospective Cohort Studies.

RESULTS: Five studies were included, involving 83,564 participants. A small number of patients with CD fulfilled the P-MDS criteria, the overall scores were low, 4.7 and 4.5 for females and males respectively. Patients with an inactive disease whose adherence to MD was greater, the MD score was negatively correlated with disease activity (p <0.001) and positively with IBDQ (p = 0.008). Twenty-seven percent had a prevalence of impaired adherence to a MD (mMED score = 0-2), giving such a population a risk attributed to 12% for the later CD. Seventy-point reduction in CDAI + decreased fecal CRP / calprotectin, calprotectin <250 mcg/gm or >50% decrease from baseline and hsCRP < 5 mg/L or >50% from baseline.

CONCLUSIONS: MD showed anti-inflammatory properties. Adherence to MD was associated with improvement in CD patients and negatively correlated with the disease activity, in addition to a lower risk of developing CD later in life.

RevDate: 2022-05-25

Gulliver EL, Young RB, Chonwerawong M, et al (2022)

Review article: the future of microbiome-based therapeutics.

Alimentary pharmacology & therapeutics [Epub ahead of print].

BACKGROUND: From consumption of fermented foods and probiotics to emerging applications of faecal microbiota transplantation, the health benefit of manipulating the human microbiota has been exploited for millennia. Despite this history, recent technological advances are unlocking the capacity for targeted microbial manipulation as a novel therapeutic.

AIM: This review summarises the current developments in microbiome-based medicines and provides insight into the next steps required for therapeutic development.

METHODS: Here we review current and emerging approaches and assess the capabilities and weaknesses of these technologies to provide safe and effective clinical interventions. Key literature was identified through Pubmed searches with the following key words, 'microbiome', 'microbiome biomarkers', 'probiotics', 'prebiotics', 'synbiotics', 'faecal microbiota transplant', 'live biotherapeutics', 'microbiome mimetics' and 'postbiotics'.

RESULTS: Improved understanding of the human microbiome and recent technological advances provide an opportunity to develop a new generation of therapies. These therapies will range from dietary interventions, prebiotic supplementations, single probiotic bacterial strains, human donor-derived faecal microbiota transplants, rationally selected combinations of bacterial strains as live biotherapeutics, and the beneficial products or effects produced by bacterial strains, termed microbiome mimetics.

CONCLUSIONS: Although methods to identify and refine these therapeutics are continually advancing, the rapid emergence of these new approaches necessitates accepted technological and ethical frameworks for measurement, testing, laboratory practices and clinical translation.

RevDate: 2022-05-25

Notarbartolo V, Giuffrè M, Montante C, et al (2022)

Composition of Human Breast Milk Microbiota and Its Role in Children's Health.

Pediatric gastroenterology, hepatology & nutrition, 25(3):194-210.

Human milk contains a number of nutritional and bioactive molecules including microorganisms that constitute the so-called "Human Milk Microbiota (HMM)". Recent studies have shown that not only bacterial but also viral, fungal, and archaeal components are present in the HMM. Previous research has established, a "core" microbiome, consisting of Firmicutes (i.e., Streptococcus, Staphylococcus), Proteobacteria (i.e., Serratia, Pseudomonas, Ralstonia, Sphingomonas, Bradyrhizobium), and Actinobacteria (i.e., Propionibacterium, Corynebacterium). This review aims to summarize the main characteristics of HMM and the role it plays in shaping a child's health. We reviewed the most recent literature on the topic (2019-2021), using the PubMed database. The main sources of HMM origin were identified as the retrograde flow and the entero-mammary pathway. Several factors can influence its composition, such as maternal body mass index and diet, use of antibiotics, time and type of delivery, and mode of breastfeeding. The COVID-19 pandemic, by altering the mother-infant dyad and modifying many of our previous habits, has emerged as a new risk factor for the modification of HMM. HMM is an important contributor to gastrointestinal colonization in children and therefore, it is fundamental to avoid any form of perturbation in the HMM that can alter the microbial equilibrium, especially in the first 100 days of life. Microbial dysbiosis can be a trigger point for the development of necrotizing enterocolitis, especially in preterm infants, and for onset of chronic diseases, such as asthma and obesity, later in life.

RevDate: 2022-05-25

Farzan S, Coyle T, Coscia G, et al (2022)

Clinical Characteristics and Management Strategies for Adult Obese Asthma Patients.

Journal of asthma and allergy, 15:673-689 pii:285738.

The rates of asthma and obesity are increasing concurrently in the United States. Epidemiologic studies demonstrate that the incidence of asthma increases with obesity. Furthermore, obese individuals have asthma that is more severe, harder to control, and resistant to standard medications. In fact, specific asthma-obesity phenotypes have been identified. Various pathophysiologic mechanisms, including mechanical, inflammatory, metabolic and microbiome-associated, are at play in promulgating the obese-asthma phenotypes. While standard asthma medications, such as inhaled corticosteroids and biologics, are currently used to treat obese asthmatics, they may have limited effectiveness. Targeting the underlying aberrant processes, such as addressing steroid resistance, microbiome, metabolic and weight loss approaches, may be helpful.

RevDate: 2022-05-25

Ding X, Tang Q, Xu Z, et al (2022)

Challenges and innovations in treating chronic and acute wound infections: from basic science to clinical practice.

Burns & trauma, 10:tkac014 pii:tkac014.

Acute and chronic wound infection has become a major worldwide healthcare burden leading to significantly high morbidity and mortality. The underlying mechanism of infections has been widely investigated by scientist, while standard wound management is routinely been used in general practice. However, strategies for the diagnosis and treatment of wound infections remain a great challenge due to the occurrence of biofilm colonization, delayed healing and drug resistance. In the present review, we summarize the common microorganisms found in acute and chronic wound infections and discuss the challenges from the aspects of clinical diagnosis, non-surgical methods and surgical methods. Moreover, we highlight emerging innovations in the development of antimicrobial peptides, phages, controlled drug delivery, wound dressing materials and herbal medicine, and find that sensitive diagnostics, combined treatment and skin microbiome regulation could be future directions in the treatment of wound infection.

RevDate: 2022-05-25

Yanckello LM, Fanelli B, McCulloch S, et al (2022)

Inulin Supplementation Mitigates Gut Dysbiosis and Brain Impairment Induced by Mild Traumatic Brain Injury during Chronic Phase.

Journal of cellular immunology, 4(2):50-64.

Mild traumatic brain injury (mTBI) has been shown to acutely alter the gut microbiome diversity and composition, known as dysbiosis, which can further exacerbate metabolic and vascular changes in the brain in both humans and rodents. However, it remains unknown how mTBI affects the gut microbiome in the chronic phase recovery (past one week post injury). It is also unknown if injury recovery can be improved by mitigating dysbiosis. The goal of the study is to fill the knowledge gap. First, we aim to understand how mTBI alters the gut microbiome through the chronic period of recovery (3 months post injury). In addition, as the gut microbiome can be modulated by diet, we also investigated if prebiotic inulin, a fermentable fiber that promotes growth of beneficial bacteria and metabolites, would mitigate dysbiosis, improve systemic metabolism, and protect brain structural and vascular integrity when administered after 3 months post closed head injury (CHI). We found that CHI given to male mice at 4 months of age induced gut dysbiosis which peaked at 1.5 months post injury, reduced cerebral blood flow (CBF) and altered brain white matter integrity. Interestingly, we also found that Sham mice had transient dysbiosis, which peaked 24 hours after injury and then normalized. After 8 weeks of inulin feeding, CHI mice had increased abundance of beneficial/anti-inflammatory bacteria, reduced abundance of pathogenic bacteria, enriched levels of short-chain fatty acids, and restored CBF in both hippocampi and left thalamus, compared to the CHI-control fed and Sham groups. Using machine learning, we further identified top bacterial species that separate Sham and CHI mice with and without the diet. Our results indicate that there is an injury- and time-dependent dysbiosis between CHI and Sham mice; inulin is effective to mitigate dysbiosis and improve brain injury recovery in the CHI mice. As there are currently no effective treatments for mTBI, the study may have profound implications for developing therapeutics or preventive interventions in the future.

RevDate: 2022-05-24

Bi Y, Wang X, Cai Y, et al (2022)

Arbuscular mycorrhizal colonization increases plant above-belowground feedback in a northwest Chinese coal mining-degraded soil by increasing photosynthetic carbon assimilation and allocation to maize.

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

A three-compartment culture system was used to study the mechanism by which the AM fungus Funneliformis mosseae influences host plant growth and soil organic carbon (SOC) content in a northwest China coal mining area. A 13CO2 pulse tracing technique was used to trace the allocation of maize photosynthetic C in shoots, roots, AM fungus, and soil. Carbon accumulation and allocation in mycorrhizal (inoculated with Funneliformis mosseae) and non-mycorrhizal treatments were detected. AM fungal inoculation significantly increased the 13C concentration and content in both above- and below-ground plant parts and also significantly enhanced anti-aging ability by increasing soluble sugars and catalase activity (CAT) in maize leaves while reducing foliar malondialdehyde content (MDA) and leaf temperature and promoted plant growth. AM fungi also increased P uptake to promote maize growth. Soil organic carbon (SOC), glomalin, microbial biomass carbon (MBC), and nitrogen (MBN) contents increased significantly after inoculation. A mutually beneficial system was established involving maize, the AM fungus and the microbiome, and the AM fungus became an important regulator of C flux between the above- and below-ground parts of the system. Inoculation with the AM fungus promoted plant growth, C fixation and allocation belowground to enhance soil quality. A positive above-belowground feedback appeared to be established.

RevDate: 2022-05-24

Okuda S, Hirose Y, Takihara H, et al (2022)

Unveiling microbiome profiles in human inner body fluids and tumor tissues with pancreatic or biliary tract cancer.

Scientific reports, 12(1):8766.

With the discovery of bacterial symbiosis in the tissues of various cancers, the study of the tumor microbiome is attracting a great deal of attention. Anatomically, since the gastrointestinal tract, liver, and pancreas form a continuous ductal structure, the microbiomes in the digestive juices of these organs may influence each other. Here, we report a series of microbiome data in tumor-associated tissues such as tumor, non-tumor, and lymph nodes, and body fluids such as saliva, gastric juice, pancreatic juice, bile, and feces of patients with pancreatic or biliary tract cancers. The results show that the microbiome of tumor-associated tissues has a very similar bacterial composition, but that in body fluids has different bacterial composition which varies by location, where some bacteria localize to specific body fluids. Surprisingly, Akkermansia was only detected in the bile of patients with biliary tract cancer and its presence was significantly associated with the performance of external biliary drainage (P = 0.041). Furthermore, we found that tumor-associated tissues and body fluids in deep inner body are mostly inhabited by unidentified and uncharacterized bacteria, suggesting that such bacteria may be potential targets for precision therapy in the future.

RevDate: 2022-05-24

Sun H, Zhao F, Liu Y, et al (2022)

Probiotics synergized with conventional regimen in managing Parkinson's disease.

NPJ Parkinson's disease, 8(1):62.

Parkinson's disease (PD) is mainly managed by pharmacological therapy (e.g., Benserazide and dopamine agonists). However, prolonged use of these drugs would gradually diminish their dopaminergic effect. Gut dysbiosis was observed in some patients with PD, suggesting close association between the gut microbiome and PD. Probiotics modulate the host's gut microbiota beneficially. A 3-month randomized, double-blind, placebo-controlled clinical trial was conducted to investigate the beneficial effect of probiotic co-administration in patients with PD. Eighty-two PD patients were recruited and randomly divided into probiotic [n = 48; Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8), Benserazide, dopamine agonists] and placebo (n = 34; placebo, Benserazide, dopamine agonists) groups. Finally, 45 and 29 patients from Probio-M8 and placebo groups provided complete fecal and serum samples for further omics analysis, respectively. The results showed that Probio-M8 co-administration conferred added benefits by improving sleep quality, alleviating anxiety, and gastrointestinal symptoms. Metagenomic analysis showed that, after the intervention, there were significantly more species-level genome bins (SGBs) of Bifidobacterium animalis, Ruminococcaceae, and Lachnospira, while less Lactobacillus fermentum and Klebsiella oxytoca in Probio-M8 group (P < 0.05). Interestingly, Lactobacillus fermentum correlated positively with the scores of UPDRS-III, HAMA, HAMD-17, and negatively with MMSE. Klebsiella oxytoca correlated negatively with feces hardness. Moreover, co-administering Probio-M8 increased SGBs involved in tryptophan degradation, gamma-aminobutyric acid, short-chain fatty acids, and secondary bile acid biosynthesis, as well as serum acetic acid and dopamine levels (P < 0.05). Taken together, Probio-M8 synergized with the conventional regimen and strengthened the clinical efficacy in managing PD, accompanied by modifications of the host's gut microbiome, gut microbial metabolic potential, and serum metabolites.

RevDate: 2022-05-24

Hermida LC, Gertz EM, E Ruppin (2022)

Predicting cancer prognosis and drug response from the tumor microbiome.

Nature communications, 13(1):2896.

Tumor gene expression is predictive of patient prognosis in some cancers. However, RNA-seq and whole genome sequencing data contain not only reads from host tumor and normal tissue, but also reads from the tumor microbiome, which can be used to infer the microbial abundances in each tumor. Here, we show that tumor microbial abundances, alone or in combination with tumor gene expression, can predict cancer prognosis and drug response to some extent-microbial abundances are significantly less predictive of prognosis than gene expression, although similarly as predictive of drug response, but in mostly different cancer-drug combinations. Thus, it appears possible to leverage existing sequencing technology, or develop new protocols, to obtain more non-redundant information about prognosis and drug response from RNA-seq and whole genome sequencing experiments than could be obtained from tumor gene expression or genomic data alone.

RevDate: 2022-05-24

Zeyue YU, Liyu H, Zongyuan LI, et al (2022)

Correlation between slow transit constipation and spleen deficiency, and gut microbiota: a pilot study.

Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan, 42(3):353-363.

OBJECTIVE: To investigate the effect of slow transit constipation (STC) and spleen deficiency on gut microbiota, and the mechanism underlying the action that the positive drug Maren Runchang (MR) alleviates STC.

METHODS: STC was induced, using the cathartic method of Senna and the hunger-fullness disorder method, in ICR mice; one group of model mice was treated with MR (6.24 g/kg). The changes in the general condition, fecal parameters, D-xylose content in the serum, intestinal propulsion rate, and histopathology of the colon were assessed after STC induction in the control, model, and MR groups. Fecal microbiota transplantation (FMT) was performed from STC mice into pseudo germ-free mice. Changes in the contents of substance P (SP), vasoactive intestinal peptide (VIP), and gut microbiota in STC mice and pseudo germ-free mice were assessed after FMT.

RESULTS: Compared with the control group, the model mice showed the following results: the time of the first black stool was significantly longer (0.01), the number and weight of black stools were significantly reduced within 6 h (0.05), the D-xylose content in the serum was significantly reduced (< 0.05), the intestinal propulsion rate decreased (< 0.01), the content of VIP in colon tissue significantly increased (< 0.05), and SP content in the colon tissue significantly decreased (< 0.01); moreover, the colon showed significant inflame-mation and injury. Furthermore, the abundance of Firmicutes was increased, the abundance of Bacteroides decreased, and the abundance of decreased, while the abundance of the conditional pathogenic bacteria and Klebsiella increased. However, after treatment with MR, the time of the first black stool decreased (0.01), the number of black stools within 6 h increased, and the intestinal propulsion rate increased (< 0.05). Moreover, the content of D-xylose in the serum and the content of VIP in colon tissue significantly decreased (< 0.05), the content of SP in colon tissue significantly increased (< 0.01), and colon inflammation significantly improved. Additionally, the abundance of Firmicutes decreased, and the abundance of Bacteroides increased. The abundance of increased, and the abundance of decreased. In the model + FMT group, compared with control + FMT group, the content of VIP in colon tissue decreased (< 0.05), the content of SP in colon tissue significantly increased (< 0.01), and the abundance of probiotics, such as , decreased. In the MR + FMT group, compared with the model + FMT group, the content of VIP in colon tissue increased, the content of SP in colon tissue significantly decreased (< 0.01), and the abundance of probiotics increased.

CONCLUSIONS: STC mice with spleen deficiency show a decreased abundance of beneficial bacteria, such as , and an increased abundance of the conditional pathogenic bacteria . Furthermore, the mechanism of action of MR in treating STC may involve the regulation of intestinal movement, reduction of intestinal inflammation, elevation of intestinal absorption, and regulation of gut microbiota.

RevDate: 2022-05-25

Caira-Chuquineyra B, Fernandez-Guzman D, Soriano-Moreno DR, et al (2022)

Fecal Microbiota Transplantation for People Living with Human Immunodeficiency Virus: A Scoping Review.

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

The aim of this scoping review was to determine the characteristics of studies evaluating fecal microbiota transplantation (FMT), as well as its effects and safety as a therapeutic intervention for people living with human immunodeficiency virus (HIV). We conducted a scoping review following the methodology of the Joanna Briggs Institute. We searched the following databases: PubMed, Web of Science, Scopus, Embase, Cochrane Library, and Medline until September 19, 2021. Studies that used FMT in people living with HIV and explored its effects on the health of these people were included. Two randomized and 2 uncontrolled clinical trials with a total of 55 participants were included. Participants were well-controlled HIV-infected people. Regarding microbiota changes, three studies found significant post-FMT increases in Fusobacterium, Prevotella, α-diversity, Chao index, and/or Shannon index, and/or decreases in Bacteroides. Regarding markers of intestinal damage, one study found a decrease in intestinal fatty acid binding protein post-FMT, and another study found an increase in zonulin. Other outcomes evaluated by the studies were as follows: markers of immune and inflammatory activation, markers of immunocompetence (CD4+, and CD8+ T lymphocytes), and HIV viral load; however, none showed significant changes. Clinical outcomes were not evaluated by these studies. Regarding the safety of FMT, only mild adverse events were appreciated. No serious adverse event was reported. The clinical evidence for FMT in people living with HIV is sparse. FMT appears to have good tolerability and, no serious adverse event has been reported so far. Further clinical trials and evaluation of clinically important biomedical outcomes for FMT in people living with HIV are needed.

RevDate: 2022-05-24

Ippolito JR, Piccolo BD, Robeson MS, et al (2022)

Iron deficient diets modify the gut microbiome and reduce the severity of enteric infection in a mouse model of S. Typhimurium-induced enterocolitis.

The Journal of nutritional biochemistry pii:S0955-2863(22)00136-X [Epub ahead of print].

Enteric infections are widespread in infants and children living in low-resource settings. Iron availability in the gastrointestinal tract may modify the gut microbiome and impact the incidence and severity of enteropathy. This study was designed to determine the effect of an iron-deplete compared to an iron-rich environment in the lower intestine on the gut microbiome, and whether iron availability in the lower intestine affects the host immune response and severity of enteric infection in young mice. Weanling C57BL/6 mice were fed an iron deficient (Fe-, <6 ppm iron) or an iron fortified (Fe+, 300 ppm iron) diet for 6 weeks. Mice were pretreated with streptomycin prior to oral inoculation of Salmonella enterica subspecies enterica serovar Typhimurium to induce enteric infection (Sal+) or saline control (Sal-). Cecal iron concentrations were 55-fold greater with Fe+Sal- compared to Fe-Sal-. Microbiome sequencing revealed shifts in gut microbiota with dietary iron and enteric infection. There was ∼30% more S. Typhimurium in the cecum of Fe+Sal+ compared to Fe-Sal+. Plasma hepcidin increased with dietary iron and enteric infection, but was greatest in Fe+Sal+. Plasma lipocalin-2 and spleen size relative to bodyweight were greater in Fe+Sal+ compared to Fe+Sal-, Fe-Sal- and Fe-Sal+, and Fe+Sal+ lost more bodyweight compared to Fe-Sal+. Unabsorbed iron in the lower intestine modifies the gut microbiome and promotes a more severe enteropathy. These findings suggest the need for alternative iron supplementation strategies in areas where iron deficiency and enteric infection are common.

RevDate: 2022-05-24

Hall JA, Jewell DE, E Ephraim (2022)

Feeding cats with chronic kidney disease food supplemented with betaine and prebiotics increases total body mass and reduces uremic toxins.

PloS one, 17(5):e0268624 pii:PONE-D-21-35710.

Cats with chronic kidney disease (CKD) have a decreased ability to maintain body weight. As CKD advances, loss of body weight contributes to morbidity and mortality. The goal of this study was to evaluate the combined effects of feeding betaine and prebiotics on body weight of both CKD and healthy cats. The pre-trial food (control food) was a complete and balanced dry food designed to aid in the management of CKD. Test food was the control food supplemented with betaine (0.500%) and prebiotics: long-chain oat beta-glucan (0.586%) and 0.407% short chain fructooligosaccharides (scFOS). The CKD cats (n = 7) were fed pre-trial food for 28 days and then randomly assigned to control food or test food. Each food was fed for 8 weeks in a cross-over study design. In a second study, healthy cats received control food or test food for 8 weeks (n = 8 each group). Blood, urine, and fecal samples were collected to evaluate concentrations of relevant kidney function biomarkers and metabolites at the end of each feeding period for CKD cats, and blood samples were collected monthly to evaluate concentrations of plasma metabolites for healthy cats. Body weight and composition were measured using dual-energy X-ray absorptiometry (DEXA) scan at baseline and after each feeding period. Total body mass was significantly higher in CKD cats after consuming test food compared with control food (P = 0.004), with no significant difference in food intake while consuming test or control food (P = 0.34). Test food did not affect total body mass or composition of healthy cats. Indole compounds produced by bacterial metabolism were decreased in urine and increased in feces of CKD cats fed test food, and plasma concentrations were negatively correlated with the level of kidney function, indicating a potential benefit of consuming test food. In healthy cats, consuming test food resulted in significantly decreased concentrations of plasma P-cresol sulfate (P = 0.004) and increased concentrations of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA; both P < 0.05), despite the fact that both control and test foods had similar concentrations of these long-chain fatty acids, 0.03% and 0.02%, respectively. These results suggest that the addition of betaine and prebiotics to the control food formula may have increased total body mass in CKD cats by enhancing one-carbon metabolism and by modulating the gut microbiome.

RevDate: 2022-05-24

Mueller MG, Das P, Andy U, et al (2022)

Longitudinal urinary microbiome characteristics in women with urgency urinary incontinence undergoing sacral neuromodulation.

International urogynecology journal [Epub ahead of print].

INTRODUCTION AND HYPOTHESIS: The objective was to evaluate the stability of the urinary microbiome communities in women undergoing sacral neuromodulation (SNM) for urgency urinary incontinence (UUI). We hypothesized that clinical response to SNM therapy would be associated with changes in the urinary microbiome.

METHODS: Women completed the Overactive Bladder Questionnaire Short-Form, the International Consultation on Incontinence Questionnaire Short Form, and the Female Sexual Function Index at baseline and 3 months post-SNM implantation. Transurethral urinary specimens were obtained for microbiome analysis at baseline and 3 months postoperatively. The V4 region of the 16S rRNA gene (515F-806R) was amplified with region-specific primers, and Amplicon Sequence Variants (ASVs) were identified with a closed-reference approach of taxonomic classification. Alpha-diversity was calculated using the phylogenetic (i.e., Faith's phylogenetic diversity) and nonphylogenetic metrics (i.e., Shannon diversity, and Pielou's evenness) using the QIIME2 plugin. Longitudinal paired volatility analysis was performed using the DEICODE and Gemelli plugin to account for host specificity across both time and space.

RESULTS: Nineteen women who underwent SNM and provided both baseline and 3-month urine samples were included in this analysis. Women reported improvement in objective (number of UUI episodes) and subjective (symptom severity and health-related quality of life) measures. Ninety percent of the bacteria were classified as Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. No significant differences were observed in each subject's beta-diversity at 3 months compared with their baseline microbiome.

CONCLUSIONS: Our descriptive pilot study of a cohort of women who had achieved objective and subjective improvements in UUI following SNM therapy demonstrates that the urinary microbiome remains relatively stable, despite variability amongst the cohort.

RevDate: 2022-05-24

Tong X, Yu X, Du Y, et al (2022)

Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.

Microbiology spectrum [Epub ahead of print].

While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19}], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner. IMPORTANCE While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening. Our study revealed the complexity of circulating microbial cfDNA and indicated that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner, especially with regard to geographic patterns and coexistence networks.

RevDate: 2022-05-24

Leng J, Yu L, Dai Y, et al (2022)

Recent advances in research on biocontrol of postharvest fungal decay in apples.

Critical reviews in food science and nutrition [Epub ahead of print].

Apple is the largest fruit crop produced in temperate regions and is a popular fruit worldwide. It is, however, susceptible to a variety of postharvest fungal pathogens, including Penicillium expansum, Botrytis cinerea, Botryosphaeria dothidea, Monilia spp., and Alternaria spp. Decays resulting from fungal infections severely reduce apple quality and marketable yield. Biological control utilizing bacterial and fungal antagonists is an eco-friendly and effective method of managing postharvest decay in horticultural crops. In the current review, research on the pathogenesis of major decay fungi and isolation of antagonists used to manage postharvest decay in apple is presented. The mode of action of postharvest biocontrol agents (BCAs), including recent molecular and genomic studies, is also discussed. Recent research on the apple microbiome and its relationship to disease management is highlighted, and the use of additives and physical treatments to enhance biocontrol efficacy of BCAs is reviewed. Biological control is a critical component of an integrated management system for the sustainable approaches to apple production. Additional research will be required to explore the feasibility of developing beneficial microbial consortia and novel antimicrobial compounds derived from BCAs for postharvest disease management, as well as genetic approaches, such as the use of CRISPR/Cas9 technology.

RevDate: 2022-05-24

Semler AC, Fortney JL, Fulweiler RW, et al (2022)

Cold Seeps on the Passive Northern U.S. Atlantic Margin Host Globally Representative Members of the Seep Microbiome with Locally Dominant Strains of Archaea.

Applied and environmental microbiology [Epub ahead of print].

Marine cold seeps are natural sites of methane emission and harbor distinct microbial communities capable of oxidizing methane. The majority of known cold seeps are on tectonically active continental margins, but recent discoveries have revealed abundant seeps on passive margins as well, including on the U.S. Atlantic Margin (USAM). We sampled in and around four USAM seeps and combined pore water geochemistry measurements with amplicon sequencing of 16S rRNA and mcrA (DNA and RNA) to investigate the microbial communities present, their assembly processes, and how they compare to communities at previously studied sites. We found that the USAM seeps contained communities consistent with the canonical seep microbiome at the class and order levels but differed markedly at the sequence variant level, especially within the anaerobic methanotrophic (ANME) archaea. The ANME populations were highly uneven, with just a few dominant mcrA sequence variants at each seep. Interestingly, the USAM seeps did not form a distinct phylogenetic cluster when compared with other previously described seeps around the world. Consistent with this, we found only a very weak (though statistically significant) distance-decay trend in seep community similarity across a global data set. Ecological assembly indices suggest that the USAM seep communities were assembled primarily deterministically, in contrast to the surrounding nonseep sediments, where stochastic processes dominated. Together, our results suggest that the primary driver of seep microbial community composition is local geochemistry-specifically methane, sulfide, nitrate, acetate, and ammonium concentrations-rather than the geologic context, the composition of nearby seeps, or random events of dispersal. IMPORTANCE Cold seeps are now known to be widespread features of passive continental margins, including the northern U.S. Atlantic Margin (USAM). Methane seepage is expected to intensify at these relatively shallow seeps as bottom waters warm and underlying methane hydrates dissociate. While methanotrophic microbial communities might reduce or prevent methane release, microbial communities on passive margins have rarely been characterized. In this study, we investigated the Bacteria and Archaea at four cold seeps on the northern USAM and found that despite being colocated on the same continental slope, the communities significantly differ by site at the sequence variant level, particularly methane-cycling community members. Differentiation by site was not observed in similarly spaced background sediments, raising interesting questions about the dispersal pathways of cold seep microorganisms. Understanding the genetic makeup of these discrete seafloor ecosystems and how their microbial communities develop will be increasingly important as the climate changes.

RevDate: 2022-05-23

Lawrence K, Myrissa K, Toribio-Mateas M, et al (2022)

Trialling a microbiome-targeted dietary intervention in children with ADHD-the rationale and a non-randomised feasibility study.

Pilot and feasibility studies, 8(1):108.

BACKGROUND: Dietary interventions have been previously explored in children with ADHD. Elimination diets and supplementation can produce beneficial behaviour changes, but little is known about the mechanisms mediating change. We propose that these interventions may work, in part, by causing changes in the gut microbiota. A microbiome-targeted dietary intervention was developed, and its feasibility assessed.

METHODS: A non-randomised feasibility study was conducted on nine non-medicated children with ADHD, aged 8-13 years (mean 10.39 years), using a prospective one-group pre-test/post-test design. Participants were recruited from ADHD support groups in London and took part in the 6-week microbiome-targeted dietary intervention, which was specifically designed to impact the composition of gut bacteria. Children were assessed pre- and post-intervention on measures of ADHD symptomatology, cognition, sleep, gut function and stool-sample microbiome analysis. The primary aim was to assess the study completion rate, with secondary aims assessing adherence, adverse events (aiming for no severe and minimal), acceptability and suitability of outcome measures.

RESULTS: Recruitment proved to be challenging and despite targeting 230 participants directly through support groups, and many more through social media, nine families (of the planned 10) signed up for the trial. The completion rate for the study was excellent at 100%. Exploration of secondary aims revealed that (1) adherence to each aspect of the dietary protocol was very good; (2) two mild adverse events were reported; (3) parents rated the treatment as having good acceptability; (4) data collection and outcome measures were broadly feasible for use in an RCT with a few suggestions recommended; (5) descriptive data for outcome measures is presented and suggests that further exploration of gut microbiota, ADHD symptoms and sleep would be helpful in future research.

CONCLUSIONS: This study provides preliminary evidence for the feasibility of a microbiome-targeted dietary intervention in children with ADHD. Recruitment was challenging, but the diet itself was well-tolerated and adherence was very good. Families wishing to trial this diet may find it an acceptable intervention. However, recruitment, even for this small pilot study, was challenging. Because of the difficulty experienced recruiting participants, future randomised controlled trials may wish to adopt a simpler dietary approach which requires less parental time and engagement, in order to recruit the number of participants required to make meaningful statistical interpretations of efficacy.

TRIAL REGISTRATION: Identifier: NCT03737877 . Registered 13 November 2018-retrospectively registered, within 2 days of the first participant being recruited.

RevDate: 2022-05-23

Clavere-Graciette AG, McWhirt ME, Hoopes LA, et al (2022)

Microbiome differences between wild and aquarium whitespotted eagle rays (Aetobatus narinari).

Animal microbiome, 4(1):34.

BACKGROUND: Animal-associated microbiomes can be influenced by both host and environmental factors. Comparing wild animals to those in zoos or aquariums can help disentangle the effects of host versus environmental factors, while also testing whether managed conditions foster a 'natural' host microbiome. Focusing on an endangered elasmobranch species-the whitespotted eagle ray Aetobatus narinari-we compared the skin, gill, and cloaca microbiomes of wild individuals to those at Georgia Aquarium. Whitespotted eagle ray microbiomes from Georgia Aquarium were also compared to those of cownose rays (Rhinoptera bonasus) in the same exhibit, allowing us to explore the effect of host identity on the ray microbiome.

RESULTS: Long-term veterinary monitoring indicated that the rays in managed care did not have a history of disease and maintained health parameters consistent with those of wild individuals, with one exception. Aquarium whitespotted eagle rays were regularly treated to control parasite loads, but the effects on animal health were subclinical. Microbiome α- and β-diversity differed between wild versus aquarium whitespotted eagle rays at all body sites, with α-diversity significantly higher in wild individuals. β-diversity differences in wild versus aquarium whitespotted eagle rays were greater for skin and gill microbiomes compared to those of the cloaca. At each body site, we also detected microbial taxa shared between wild and aquarium eagle rays. Additionally, the cloaca, skin, and gill microbiomes of aquarium eagle rays differed from those of cownose rays in the same exhibit. Potentially pathogenic bacteria were at low abundance in all wild and aquarium rays.

CONCLUSION: For whitespotted eagle rays, managed care was associated with a microbiome differing significantly from that of wild individuals. These differences were not absolute, as the microbiome of aquarium rays shared members with that of wild counterparts and was distinct from that of a cohabitating ray species. Eagle rays under managed care appear healthy, suggesting that their microbiomes are not associated with compromised host health. However, the ray microbiome is dynamic, differing with both environmental factors and host identity. Monitoring of aquarium ray microbiomes over time may identify taxonomic patterns that co-vary with host health.

RevDate: 2022-05-23

Morowitz MJ, Katheria AC, Polin RA, et al (2022)

The NICU Antibiotics and Outcomes (NANO) trial: a randomized multicenter clinical trial assessing empiric antibiotics and clinical outcomes in newborn preterm infants.

Trials, 23(1):428.

BACKGROUND: Early-onset sepsis is an important cause of neonatal morbidity and mortality in the preterm population. Infants perceived to be at increased risk for early-onset sepsis are often treated empirically with broad-spectrum antibiotics while awaiting confirmatory blood cultures, despite an overall incidence of early-onset sepsis of 2-3% among extremely-low-birthweight (ELBW) infants. Recent observational studies associate perinatal antibiotic use with an increased incidence of necrotizing enterocolitis, late-onset sepsis, and mortality among ELBW infants. Given currently available data and variability in clinical practice, we designed a prospective multi-institutional randomized controlled trial to determine the safety of early antibiotic use in ELBW infants.

METHODS: The NICU Antibiotics and Outcomes (NANO) trial is a multicenter, double-blinded, randomized controlled trial. A sample of 802 ELBW preterm infants will undergo web-based stratified block randomization to receive empiric antibiotics (EA; ampicillin and gentamicin) or placebo during routine evaluation for early-onset sepsis. Participating sites will use preexisting institutional protocols for antibiotic dosage and duration. Infants born at participating sites with a gestational age of 29 weeks or less are eligible for enrollment. Exclusion criteria include maternal intrauterine infection, hemodynamic or respiratory instability, delivery by caesarean section for maternal indications without labor or prolonged rupture of membranes, and prior administration of antibiotics. The primary outcome is the composite incidence of necrotizing enterocolitis, late-onset sepsis, or death during participants' index hospitalization. Maternal and infant samples will be collected longitudinally and assessed for differences in microbiome composition and diversity.

DISCUSSION: The NANO trial is designed to compare the rate of adverse outcomes of EA use at birth versus placebo in ELBW preterm infants. If EA at birth worsens clinical outcomes, then the results of the trial may help providers decrease antibiotic utilization in the NICU and subsequently decrease the incidence of complications associated with early antibiotic use in ELBW infants. If we instead find that EA improve outcomes, then the trial will validate a longstanding clinical practice that has not previously been supported by high-quality data. Future studies will assess long-term clinical and microbial outcomes in infants who received empiric antibiotics following delivery.

TRIAL REGISTRATION: Trial registration data: June 25, 2019 NCT03997266 .

RevDate: 2022-05-23

Giridharan VV, Generoso JS, Lence L, et al (2022)

A crosstalk between gut and brain in sepsis-induced cognitive decline.

Journal of neuroinflammation, 19(1):114.

BACKGROUND: Sepsis is a potentially fatal disease characterized by acute organ failure that affects more than 30 million people worldwide. Inflammation is strongly associated with sepsis, and patients can experience impairments in memory, concentration, verbal fluency, and executive functioning after being discharged from the hospital. We hypothesize that sepsis disrupts the microbiota-gut-brain axis homeostasis triggering cognitive impairment. This immune activation persists during treatment, causing neurological dysfunction in sepsis survivors.

METHODS: To test our hypothesis, adult Wistar rats were subjected to cecal-ligation and perforation (CLP) or sham (non-CLP) surgeries. The animals were subjected to the [11C]PBR28 positron emission tomography (PET)/computed tomography (CT) imaging at 24 h and 10 days after CLP and non-CLP surgeries. At 24 h and 10 days after surgery, we evaluated the gut microbiome, bacterial metabolites, cytokines, microglia, and astrocyte markers. Ten days after sepsis induction, the animals were subjected to the novel object recognition (NOR) and the Morris water maze (MWM) test to assess their learning and memory.

RESULTS: Compared to the control group, the 24-h and 10-day CLP groups showed increased [11C]PBR28 uptake, glial cells count, and cytokine levels in the brain. Results show that sepsis modulates the gut villus length and crypt depth, alpha and beta microbial diversities, and fecal short-chain fatty acids (SCFAs). In addition, sepsis surviving animals showed a significant cognitive decline compared with the control group.

CONCLUSIONS: Since several pharmacological studies have failed to prevent cognitive impairment in sepsis survivors, a better understanding of the function of glial cells and gut microbiota can provide new avenues for treating sepsis patients.

RevDate: 2022-05-23

Savitz J, RH Yolken (2022)

Therapeutic Implications of the Microbial Hypothesis of Mental Illness.

Current topics in behavioral neurosciences [Epub ahead of print].

There is increasingly compelling evidence that microorganisms may play an etiological role in the emergence of mental illness in a subset of the population. Historically, most work has focused on the neurotrophic herpesviruses, herpes simplex virus type 1 (HSV-1), cytomegalovirus (CMV), and Epstein-Barr virus (EBV) as well as the protozoan, Toxoplasma gondii. In this chapter, we provide an umbrella review of this literature and additionally highlight prospective studies that allow more mechanistic conclusions to be drawn. Next, we focus on clinical trials of anti-microbial medications for the treatment of psychiatric disorders. We critically evaluate six trials that tested the impact of anti-herpes medications on inflammatory outcomes in the context of a medical disorder, nine clinical trials utilizing anti-herpetic medications for the treatment of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) or schizophrenia, and four clinical trials utilizing anti-parasitic medications for the treatment of schizophrenia. We then turn our attention to evidence for a gut dysbiosis and altered microbiome in psychiatric disorders, and the potential therapeutic effects of probiotics, including an analysis of more than 10 randomized controlled trials of probiotics in the context of schizophrenia, bipolar disorder (BD), and major depressive disorder (MDD).

RevDate: 2022-05-23

Olson CA, PJ Turnbaugh (2022)

Designed secretion deters microbiome depletion.

Nature microbiology [Epub ahead of print].

RevDate: 2022-05-24

Li S, Abdulkadir N, Schattenberg F, et al (2022)

Stabilizing microbial communities by looped mass transfer.

Proceedings of the National Academy of Sciences of the United States of America, 119(17):e2117814119.

Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates μ′. Subsets of cells that did not show net growth μ′SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.

RevDate: 2022-05-23

Wei X, Yu L, Han B, et al (2022)

Spatial variations of root-associated bacterial communities of alpine plants in the Qinghai-Tibet Plateau.

The Science of the total environment pii:S0048-9697(22)03183-7 [Epub ahead of print].

Exploring the geospatial variation of root-associated microbiomes is critical for understanding plant-microbe-environment interactions and plant environmental adaptability. Root-associated bacterial communities from the three compartments [rhizosphere surrounding soil (RSS), rhizosphere soil (rhizosphere), and root endosphere (endophytic)] are influenced by multiple factors, including plant species and geographical locations. Nonetheless, these communities remain poorly understood under harsh conditions. In this study, we selected four dominant alpine plants on the Qinghai-Tibet Plateau (i.e., Elymus nutans, Festuca sinensis, Kobresia pygmaea, and Kobresia humilis) to investigate their root-associated bacterial communities across 11 geographical locations and determine the factors driving spatial variation. The results showed that the microbiota of the three compartments had significantly different community compositions, with more Pseudomonadaceae and Enterobacteriaceae present in the endosphere. Spatial variations in root endophytic microbiota were mainly governed by stochastic processes, which were different from the deterministic processes in the other two compartments. Meanwhile, the geographical location had greater effects on bacterial communities than plant species, and the spatial variation of α-diversity in the endosphere was much higher than that in the RSS and rhizosphere. We further found that the differentiation of bacterial diversity in the endosphere among sympatric plant species was enhanced by higher annual precipitation, lower soil nutrients (carbon and nitrogen), and pH. For example, the coefficient of variation of endosphere Pseudomonadaceae abundance was positively correlated with annual mean precipitation, whereas that of Enterobacteriaceae abundance was negatively correlated with soil pH. The co-occurrence network analysis identified a higher proportion of bacterial coexistence in the endosphere (70.9%) than in the RSS (49.5%) and rhizosphere soil (50.9%). Finally, we revealed the relative convergence of endophytic communities among sympatric plant species in the alpine grasslands.

RevDate: 2022-05-23

Wilson RA, JM McDowell (2022)

Recent advances in understanding of fungal and oomycete effectors.

Current opinion in plant biology, 68:102228 pii:S1369-5266(22)00057-7 [Epub ahead of print].

Fungal and oomycete pathogens secrete complex arrays of proteins and small RNAs to interface with plant-host targets and manipulate plant regulatory networks to the microbes' advantage. Research on these important virulence factors has been accelerated by improved genome sequences, refined bioinformatic prediction tools, and exploitation of efficient platforms for understanding effector gene expression and function. Recent studies have validated the expectation that oomycetes and fungi target many of the same sectors in immune signaling networks, but the specific host plant targets and modes of action are diverse. Effector research has also contributed to deeper understanding of the mechanisms of effector-triggered immunity.

RevDate: 2022-05-23

Wang K, Chen H, Fan RL, et al (2022)

Effect of carbendazim on honey bee health: Assessment of survival, pollen consumption, and gut microbiome composition.

Ecotoxicology and environmental safety, 239:113648 pii:S0147-6513(22)00488-2 [Epub ahead of print].

Gut microbiota and nutrition play major roles in honey bee health. Recent reports have shown that pesticides can disrupt the gut microbiota and cause malnutrition in honey bees. Carbendazim is the most commonly used fungicide in China, but it is not clear whether carbendazim negatively affects the gut microbes and nutrient intake levels in honey bees. To address this research gap, we assessed the effects of carbendazim on the survival, pollen consumption, and sequenced 16 S rRNA gene to determine the bacterial composition in the midgut and hindgut. Our results suggest that carbendazim exposure does not cause acute death in honey bees even at high concentrations (5000 mg/L), which are extremely unlikely to exist under field conditions. Carbendazim does not disturb the microbiome composition in the gut of young worker bees during gut microbial colonization and adult worker bees with established gut communities in the mid and hindgut. However, carbendazim exposure significantly decreases pollen consumption in honey bees. Thus, exposure of bees to carbendazim can perturb their beneficial nutrition homeostasis, potentially reducing honey bee immunity and increasing their susceptibility to infection by pathogens, which influence effectiveness as pollinators, even colony health.

RevDate: 2022-05-23

Ulrich K, Becker R, Behrendt U, et al (2022)

Physiological and genomic characterisation of Luteimonas fraxinea sp. nov., a bacterial species associated with trees tolerant to ash dieback.

Systematic and applied microbiology, 45(4):126333 pii:S0723-2020(22)00040-6 [Epub ahead of print].

A group of isolates of the genus Luteimonas was characterised, which represented a specific component of the healthy core microbiome of Fraxinus excelsior in forest districts with a high infection rate of H. fraxineus, the causal agent of ash dieback. Based on phylogenomic and phenotypic analyses, a clear differentiation from related Luteimonas species was shown. Comparisons of the overall genome relatedness indices with the closest phylogenetic neighbours resulted in values below the recommended species cut-off levels. In addition, differences in several physiological and chemotaxonomic traits allowed a clear demarcation from the type strains of closely related species. Conclusively, the strain group was considered to represent a novel species in the genus Luteimonas, for which the name Luteimonas fraxinea sp. nov. is proposed, with strain D4P002T (=DSM 113273T = LMG 32455T) as the type strain. A functional analysis of the genome revealed features particularly associated with attachment, biofilm production and motility, indicating the ability of D4P002T to effectively colonise ash leaves. In nursery trials, ash seedlings inoculated with this strain showed suppression of the pathogen over a period of three years. This effect was accompanied by a significant shift in the bacterial microbiome of the plants. Altogether, the exclusive occurrence in the microbiome of tolerant ash trees, the genetic background and the results of the inoculation experiment suggest that strain D4P002T may suppress the penetration and spreading of H. fraxineus in or on ash leaves via colonisation resistance or trigger a priming effect of plant defences against the pathogen.

RevDate: 2022-05-23

Ørsted M, Yashiro E, Hoffmann AA, et al (2022)

Population bottlenecks constrain host microbiome diversity and genetic variation impeding fitness.

PLoS genetics, 18(5):e1010206 pii:PGENETICS-D-21-01334 [Epub ahead of print].

It is becoming increasingly clear that microbial symbionts influence key aspects of their host's fitness, and vice versa. This may fundamentally change our thinking about how microbes and hosts interact in influencing fitness and adaptation to changing environments. Here we explore how reductions in population size commonly experienced by threatened species influence microbiome diversity. Consequences of such reductions are normally interpreted in terms of a loss of genetic variation, increased inbreeding and associated inbreeding depression. However, fitness effects of population bottlenecks might also be mediated through microbiome diversity, such as through loss of functionally important microbes. Here we utilise 50 Drosophila melanogaster lines with different histories of population bottlenecks to explore these questions. The lines were phenotyped for egg-to-adult viability and their genomes sequenced to estimate genetic variation. The bacterial 16S rRNA gene was amplified in these lines to investigate microbial diversity. We found that 1) host population bottlenecks constrained microbiome richness and diversity, 2) core microbiomes of hosts with low genetic variation were constituted from subsets of microbiomes found in flies with higher genetic variation, 3) both microbiome diversity and host genetic variation contributed to host population fitness, 4) connectivity and robustness of bacterial networks was low in the inbred lines regardless of host genetic variation, 5) reduced microbial diversity was associated with weaker evolutionary responses of hosts in stressful environments, and 6) these effects were unrelated to Wolbachia density. These findings suggest that population bottlenecks reduce hologenomic variation (combined host and microbial genetic variation). Thus, while the current biodiversity crisis focuses on population sizes and genetic variation of eukaryotes, an additional focal point should be the microbial diversity carried by the eukaryotes, which in turn may influence host fitness and adaptability with consequences for the persistence of populations.

RevDate: 2022-05-23

Hale AR, Ruegger PM, Rolshausen P, et al (2022)

Fungi associated with the potato taste defect in coffee beans from Rwanda.

Botanical studies, 63(1):17.

BACKGROUND: Potato taste defect (PTD) of coffee is characterized by a raw potato like smell that leads to a lower quality taste in the brewed coffee, and harms the commercial value of some East African coffees. Although several causes for PTD have been proposed, none of them have been confirmed. Recently, high throughput sequencing techniques and bioinformatic analysis have shown great potential for identifying putative causal agents of plant diseases. Toward the goal of determining the cause of PTD, we examined raw coffee beans from Rwanda exhibiting varying PTD scores using an Illumina-based sequence analysis of the fungal rRNA ITS region.

RESULTS: Six fungal amplicon sequence variants (ASVs) with high relative abundances correlated with coffee taste scores. Four of these ASVs exhibited negative correlations - Aspergillus versicolor, Penicillium cinnamopurpureum, Talaromyces radicus, and Thermomyces lanuginosus - indicating that they might be causing PTD. Two of these fungi exhibited positive correlations - Kazachstania humilis and Clavispora lusitaniae - indicating that they might be inhibiting organisms that cause PTD.

CONCLUSIONS: This study addressed PTD causality from a new angle by examining fungi with high throughput sequencing. To our knowledge, this is the first study characterizing fungi associated with PTD, providing candidates for both causality and biocontrol.

RevDate: 2022-05-23

Srivastava S, Sajid M, Singh H, et al (2022)

Delineating the Bacteriome of Packaged and Loose Smokeless Tobacco Products Available in North India.

Applied microbiology and biotechnology [Epub ahead of print].

Smokeless tobacco product (STP) consumption is a significant public health threat across the globe. STPs are not only a storehouse of carcinogens and toxicants but also harbor microbes that aid in the conversion of tobacco alkaloids to carcinogenic tobacco-specific nitrosamines (TSNAs), thereby posing a further threat to the health of its consumers. The present study analyzed the bacterial diversity of popular dry and loose STPs by 16S rRNA gene sequencing. This NGS-based investigation revealed four dominant phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria and identified 549 genera, Prevotella, Bacteroides, and Lactobacillus constituting the core bacteriome of these STPs. The most significantly diverse bacteriome profile was displayed by the loose STP Mainpuri kapoori. The study further predicted the functional attributes of the prevalent genera by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) algorithm. Genes encoding for nitrate and nitrite reduction and transport enzymes, antibiotic resistance, multi-drug transporters and efflux pumps, secretion of endo- and exotoxin, and other pro-inflammatory molecules were identified. The loose STPs showed the highest level of nitrogen metabolism genes which can contribute to the synthesis of TSNAs. This study reveals the bacteriome of Indian domestic loose STPs that stagger behind in manufacturing and storage stringencies. Our results raise an alarm that the consumption of STPs harboring pathogenic genera can potentially lead to the onset of several oral and systemic diseases. Nevertheless, an in-depth correlation analysis of the microbial diversity of STPs and their elicit impact on consumer health is warranted. KEY POINTS: • Smokeless tobacco harbors bacteria that aid in synthesis of carcinogenic nitrosamines. • Most diverse bacteriome profile was displayed by loose smokeless tobacco products. • Pathogenic genera in these products can harm the oral and systemic health of users.

RevDate: 2022-05-23

Esmaeilishirazifard E, Usher L, Trim C, et al (2022)

Bacterial Adaptation to Venom in Snakes and Arachnida.

Microbiology spectrum [Epub ahead of print].

Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria. However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics. Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings. These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections.

RevDate: 2022-05-23

Cornet L, Cleenwerck I, Praet J, et al (2022)

Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity.

mSystems [Epub ahead of print].

Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee's microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.

RevDate: 2022-05-23

Nabizadeh E, Sadeghi J, Ahangarzadeh Rezaee M, et al (2022)

Interaction Between Altered Gut Microbiota and Sepsis: A Hypothesis or an Authentic Fact?.

Journal of intensive care medicine [Epub ahead of print].

Sepsis, as an important public health concern, is one of the leading causes of death in hospitals around the world, accounting for 25% of all deaths. Nowadays, several factors contribute to the development of sepsis. The role of the gut microbiota and the response state of the aberrant immune system is dominant. The effect of the human microbiome on health is undeniable, and gut microbiota is even considered a body organ. It is now clear that the alteration in the normal balance of the microbiota (dysbiosis) is associated with a change in the status of immune system responses. Owing to the strong association between the gut microbiota and its metabolites particularly short-chain fatty acids with many illnesses, the gut microbiota has a unique position in the research of microbiologists and even clinicians. This review aimed to analyze studies' results on the association between microbiota and sepsis, with a substantial understanding of their relationship. As a result, an extensive and comprehensive search was conducted on this issue in existing databases.

RevDate: 2022-05-23

Lama Tamang R, Juritsch AF, Ahmad R, et al (2022)

The diet-microbiota axis: a key regulator of intestinal permeability in human health and disease.

Tissue barriers [Epub ahead of print].

The intestinal barrier orchestrates selective permeability to nutrients and metabolites while excluding noxious stimuli. Recent scientific advances establishing a causal role for the gut microbiota in human health outcomes have generated a resurgent interest toward intestinal permeability. Considering the well-established role of the gut barrier in protection against foreign antigens, there is mounting evidence for a causal link between gut permeability and the microbiome in regulating human health. However, an understanding of the dynamic host-microbiota interactions that govern intestinal barrier functions remains poorly defined. Furthermore, the system-level mechanisms by which microbiome-targeted therapies, such as probiotics and prebiotics, simultaneously promote intestinal barrier function and host health remain an area of active investigation. This review summarizes the recent advances in understanding the dynamics of intestinal permeability in human health and its integration with gut microbiota. We further summarize mechanisms by which probiotics/prebiotics influence the gut microbiota and intestinal barrier functions.

RevDate: 2022-05-23

Deng C, Zhang N, Liang X, et al (2022)

Bacillus aryabhattai LAD impacts rhizosphere bacterial community structure and promotes maize plant growth.

Journal of the science of food and agriculture [Epub ahead of print].

BACKGROUND: Plant growth-promoting rhizobacteria (PGPR) may significantly impact soil microbial community and the growth of plant roots and have critical roles in soil ecosystem functioning. However, the interactions between rhizobacteria and plants are extremely complicated and remain understudied.

RESULTS: In this study, a Bacillus strain was isolated from a long-term maize colonization soil and identified as Bacillus aryabhattai strain LAD. Laboratory tests showed that B. aryabhattai LAD had phosphate-solubilizing and nitrogen-fixing functions which benefit plant growth. The effects of LAD cultures on the root system development of corn seedlings and the structure of rhizosphere bacterial communities were studied. The most significant stimulations of LAD culture on plant growth were observed at a cell density of 102 CFU/mL. Treatment with LAD culture in hydroponics caused an increase of 107%, 197%, and 25% in the shoot length, total root length, and main root thickness, respectively. The LAD treatment also significantly affected the rhizosphere microbial abundance and community structure. The rhizobacterial abundance and species richness in the corn seedlings treated with LAD culture was significantly lower than that in the control group. However, the LAD-treated samples had higher relative abundances of PGPR like Bacillus and Burkholderia than the control samples suggesting that LAD treatment may facilitate the mutualistic relation between the rhizosphere microbiome and the plant.

CONCLUSION: These results collectively demonstrated that LAD is capable of shaping the rhizosphere microbial community structure and functions as plant growth-promoting agents which makes it a strong candidate for application as bio-fertilizer in agricultural system. This article is protected by copyright. All rights reserved.

RevDate: 2022-05-23

Abbott B (2022)

Unhelpful microbes inactivate diabetes drug.

Communications medicine, 2:4 pii:68.

Drugs can modify the microbiome and, reciprocally, the microbiome can impact drug efficacy. A recent study in Nature identifies a potential mechanism through which oral and gut bacteria selectively inhibit the antidiabetic drug acarbose.

RevDate: 2022-05-23

Kim D, Jeong YJ, Lee Y, et al (2022)

Correlation Between Salivary Microbiome of Parotid Glands and Clinical Features in Primary Sjögren's Syndrome and Non-Sjögren's Sicca Subjects.

Frontiers in immunology, 13:874285.

Recent studies have demonstrated that the oral microbiome in patients with Sjögren's syndrome (SS) is significantly different from that in healthy individuals. However, the potential role of the oral microbiome in SS pathogenesis has not been determined. In this study, stimulated intraductal saliva samples were collected from the parotid glands (PGs) of 23 SS and nine non-SS subjects through PG lavage and subjected to 16S ribosomal RNA amplicon sequencing. The correlation between the oral microbiome and clinical features, such as biological markers, clinical manifestations, and functional and radiological characteristics was investigated. The salivary microbial composition was examined using bioinformatic analysis to identify potential diagnostic biomarkers for SS. Oral microbial composition was significantly different between the anti-SSA-positive and SSA-negative groups. The microbial diversity in SS subjects was lower than that in non-SS sicca subjects. Furthermore, SS subjects with sialectasis exhibited decreased microbial diversity and Firmicutes abundance. The abundance of Bacteroidetes was positively correlated with the salivary flow rate. Bioinformatics analysis revealed several potential microbial biomarkers for SS at the genus level, such as decreased Lactobacillus abundance or increased Streptococcus abundance. These results suggest that microbiota composition is correlated with the clinical features of SS, especially the ductal structures and salivary flow, and that the oral microbiome is a potential diagnostic biomarker for SS.

RevDate: 2022-05-23

Gonçalves JIB, Borges TJ, APD de Souza (2022)

Microbiota and the Response to Vaccines Against Respiratory Virus.

Frontiers in immunology, 13:889945.

This mini review describes the role of gut and lung microbiota during respiratory viral infection and discusses the implication of the microbiota composition on the immune responses generated by the vaccines designed to protect against these pathogens. This is a growing field and recent evidence supports that the composition and function of the microbiota can modulate the immune response of vaccination against respiratory viruses such as influenza and SARS-CoV-2. Recent studies have highlighted that molecules derived from the microbiome can have systemic effects, acting in distant organs. These molecules are recognized by the immune cells from the host and can trigger or modulate different responses, interfering with vaccination protection. Modulating the microbiota composition has been suggested as an approach to achieving more efficient protective immune responses. Studies in humans have reported associations between a better vaccine response and specific bacterial taxa. These associations vary among different vaccine strategies and are likely to be context-dependent. The use of prebiotics and probiotics in conjunction with vaccination demonstrated that bacterial components could act as adjuvants. Future microbiota-based interventions may potentially improve and optimize the responses of respiratory virus vaccines.

RevDate: 2022-05-23

Lara F, Castro R, P Thomson (2022)

Changes in the gut microbiome and colic in horses: Are they causes or consequences?.

Open veterinary journal, 12(2):242-249.

The gut microbiome is a compound for millions of microorganisms that coexist in an organized way and contribute to the fermentation of different types of indigestible fibers by the small intestine. Some techniques, such as the massive sequencing of the 16S ribosomal RNA gene, have made it possible to obtain information about the abundance and functionality of the microorganisms that compose the equine gut microbiome and the interaction with their environment. Recent studies have identified the change in the composition of the intestinal microbiome during and after a colic episode, although is not clear if it is a cause or a consequence. The objective of this review was to elucidate whether there is a direct relationship between the changes that occur in the gut microbiome and colic in the equine. A systematized search in Embase, Web of Science, and PubMed was realized. Although there is good evidence that horses with colic have a change in their gut microbiome, it is not fully understood whether these changes are causes or effects. It is necessary to delve into this topic, considering studying larger population sizes. In addition, it would be of great value to previously know the normal intestinal microbiome of a group of healthy horses, which in the future could develop an episode of colic, to compare the before and after in the same individual.

RevDate: 2022-05-23

Aljahdali N (2022)

The contribution of gastrointestinal microbiota in the existence of type 2 diabetes in Saudi Arabia: Current information and perspectives.

Saudi journal of biological sciences, 29(6):103286.

Diabetes mellitus (DM) is a genuine international health issue, with Saudi Arabia ranking among the top nations with the largest diabetes prevalence. Following the International Diabetes Federation (IDF), 3.8 million Saudi Arabian people had diabetes in 2014. The occurrence of diabetes in Saudi Arabia is likely to elevate due to the current trend in the general rise of socio-economic status, which positively correlates with diabetes prevalence. The incidence of Type 2 diabetes (T2D) is highest within the age group ≥ 45 years, especially in Riyadh and Jeddah, the metro cities of Saudi Arabia. Previous studies have shown that the incidence of T2D is larger in urban regions (25.5%) than in rural regions (19.5%). Both Riyadh and Jeddah are urban areas with different food habits and locations in Saudi Arabia. Recent studies have indicated the correlation between altered alimentary tract microbiota with type 2 diabetes. Gut microbiota plays a critical role in degrading undigested dietary compounds and releasing a vast array of metabolites that directly and indirectly affects host health. In the current review, we shed light on the state of information on the realization of the types and functions of the alimentary tract microbiome and how it plays a causative agent in the up growth of T2D.

RevDate: 2022-05-23

Satish Kumar L, Pugalenthi LS, Ahmad M, et al (2022)

Probiotics in Irritable Bowel Syndrome: A Review of Their Therapeutic Role.

Cureus, 14(4):e24240.

Irritable bowel syndrome (IBS) is a chronic collection of symptoms and lowers the quality of life. The management of such patients has always involved mitigating the symptoms produced by this disorder. This article reviews the role of probiotics in IBS by compiling various studies to deduce the possible symptomatic relief that probiotics may provide to IBS patients. Given the encouraging part of probiotics in abundant other gastrointestinal conditions, this article focuses on understanding the specific functional effects (if any) that are brought about by adding probiotics in patients with different types of IBS such as IBS with predominant constipation, IBS with predominant diarrhea, and even the unclassified type of IBS. The purpose of analyzing the role of probiotics is to study the changes brought about by them at the level of the gut microbiota in patients suffering from IBS, as this may prove to be of prime importance in managing such conditions with time. This article has also furnished an overview of the pathogenesis, diagnostic criteria, treatment modalities, sources of probiotics, and their therapeutic significance in IBS patients.

RevDate: 2022-05-23

Vishnu RA, Alamelu S, Arun KV, et al (2022)

Comparative evaluation of subgingival microbiome in healthy periodontium and gingivitis using next-generation sequencing technology: A case-control study.

Journal of Indian Society of Periodontology, 26(3):224-229.

Background: Human dental plaque is a complex microbial community containing millions of species. Gingivitis is a dysregulated immune-inflammatory response induced by dysbiotic plaque biofilm that interrupts symbiosis. The emergence of next-generation sequencing with 16S rRNA gene has greatly contributed in understanding the complexity of microbiota. However, studies focusing on microbiome in gingivitis are limited. The whole bacterial community is important in causing periodontal disease than a small number of periodontal pathogens. In this study, we attempted to profile the subgingival microbiome from individuals with healthy gingiva and in patients with gingivitis using next-generation sequencing technology.

Materials and Methods: Subgingival plaque samples from 15 healthy periodontium (Group I) and 15 gingivitis (Group II) were collected and 16s rRNA sequencing was done in Illumina Solexa Sequencer. Data analysis using 16s metagenomics tool from BaseSpace onsite operational taxonomic units was assigned to each sequence using HOMD database. Individual variation in the microbiome of the subgingival samples between the two groups was also evaluated.

Results: The comparison of top 20 species between Group I and Group II revealed no significant species group between them. Synergistetes was absent in Group I samples but found in Group II. At the genus level, HACEK group species were found in both the groups, while Dialister and Aneroglobus were found abundantly in the Group II.

Conclusion: The presence of unique genera and species seen in Group II samples could point toward a dysbiotic shift that could be taking place in the subgingival environment leading to gingivitis.

RevDate: 2022-05-23

Li M, Xu M, Su A, et al (2022)

Combined Phenanthrene and Copper Pollution Imposed a Selective Pressure on the Rice Root-Associated Microbiome.

Frontiers in microbiology, 13:888086.

Combined organic and inorganic pollutants can greatly impact crops and microbes, but the interaction between coexisted pollutants and their effects on root-associated microbes under flooding conditions remains poorly understood. In this study, greenhouse experiments were conducted to investigate the individual and combined effects of phenanthrene (PHE) and copper (Cu) on rice uptake and root-associated microbial coping strategies. The results showed that more than 90% of phenanthrene was degraded, while the existence of Cu significantly reduced the dissipation of PHE in the rhizosphere, and the coexistence of phenanthrene and copper promoted their respective accumulation in plant roots. Copper played a dominant role in the interaction between these two chemicals. Microbes that can tolerate heavy metals and degrade PAHs, e.g., Herbaspirillum, Sphingobacteriales, and Saccharimonadales, were enriched in the contaminated soils. Additionally, microbes associated with redox processes reacted differently under polluted treatments. Fe reducers increased in Cu-treated soils, while sulfate reducers and methanogens were considerably inhibited under polluted treatments. In total, our results uncover the combined effect of heavy metals and polycyclic aromatic hydrocarbons on the assemblage of root-associated microbial communities in anaerobic environments and provide useful information for the selection of effective root-associated microbiomes to improve the resistance of common crops in contaminated sites.

RevDate: 2022-05-23

Ishaq SL, Turner SM, Tudor MS, et al (2022)

Many Questions Remain Unanswered About the Role of Microbial Transmission in Epizootic Shell Disease in American Lobsters (Homarus americanus).

Frontiers in microbiology, 13:824950.

Despite decades of research on lobster species' biology, ecology, and microbiology, there are still unresolved questions about the microbial communities which associate in or on lobsters under healthy or diseased states, microbial acquisition, as well as microbial transmission between lobsters and between lobsters and their environment. There is an untapped opportunity for metagenomics, metatranscriptomics, and metabolomics to be added to the existing wealth of knowledge to more precisely track disease transmission, etiology, and host-microbe dynamics. Moreover, we need to gain this knowledge of wild lobster microbiomes before climate change alters environmental and host-microbial communities more than it likely already has, throwing a socioeconomically critical industry into disarray. As with so many animal species, the effects of climate change often manifest as changes in movement, and in this perspective piece, we consider the movement of the American lobster (Homarus americanus), Atlantic Ocean currents, and the microorganisms associated with either.

RevDate: 2022-05-23

Mahajna A, Dinkla IJT, Euverink GJW, et al (2022)

Clean and Safe Drinking Water Systems via Metagenomics Data and Artificial Intelligence: State-of-the-Art and Future Perspective.

Frontiers in microbiology, 13:832452.

The use of next-generation sequencing technologies in drinking water distribution systems (DWDS) has shed insight into the microbial communities' composition, and interaction in the drinking water microbiome. For the past two decades, various studies have been conducted in which metagenomics data have been collected over extended periods and analyzed spatially and temporally to understand the dynamics of microbial communities in DWDS. In this literature review, we outline the findings which were reported in the literature on what kind of occupancy-abundance patterns are exhibited in the drinking water microbiome, how the drinking water microbiome dynamically evolves spatially and temporally in the distribution networks, how different microbial communities co-exist, and what kind of clusters exist in the drinking water ecosystem. While data analysis in the current literature concerns mainly with confirmatory and exploratory questions pertaining to the use of metagenomics data for the analysis of DWDS microbiome, we present also future perspectives and the potential role of artificial intelligence (AI) and mechanistic models to address the predictive and mechanistic questions. The integration of meta-omics, AI, and mechanistic models transcends metagenomics into functional metagenomics, enabling deterministic understanding and control of DWDS for clean and safe drinking water systems of the future.

RevDate: 2022-05-23

Nishimoto Y, Mizuguchi Y, Mori Y, et al (2022)

Resistant Maltodextrin Intake Reduces Virulent Metabolites in the Gut Environment: A Randomized Control Study in a Japanese Cohort.

Frontiers in microbiology, 13:644146.

In recent years, there have been many reports on the effects of prebiotics on intestinal health. In particular, the consumption of resistant maltodextrin (RMD) has been reported to be beneficial. However, there has been no comprehensive quantification of the effect of RMD on the intestinal environment. Therefore, this study aimed to quantify the effects of RMD on the intestine, especially the intestinal microbiome and metabolome profiles. A randomized, double-blind, and controlled trial was conducted in 29 Japanese subjects, whose hemoglobin A1c (HbA1c) levels are larger than 6% (Clinical trial no. UMIN000023970, The subjects consumed RMD or placebo twice per day for 24 weeks. Blood and fecal samples were collected before and after the intake. The intestinal environment was assessed by a metabologenomics approach, involving 16S rRNA gene-based microbiome analysis and mass spectrometry-based metabolome analysis. The intake of RMD increased the levels of Bifidobacterium and Fusicatenibacter and decreased deoxycholate levels. Additionally, intake of RMD lowered the levels of some opportunistic virulent metabolites, such as imidazole propionate and trimethylamine, in subjects with an initially high amount of those metabolites. RMD may have beneficial effects on the gut environment, such as commensal microbiota modulation and reduction of virulence metabolites, which is known as a causative factor in metabolic disorders. However, the effects of RMD partially depend on the gut environmental baseline.

RevDate: 2022-05-23

Cabugao KGM, Gushgari-Doyle S, Chacon SS, et al (2022)

Characterizing Natural Organic Matter Transformations by Microbial Communities in Terrestrial Subsurface Ecosystems: A Critical Review of Analytical Techniques and Challenges.

Frontiers in microbiology, 13:864895.

Determining the mechanisms, traits, and pathways that regulate microbial transformation of natural organic matter (NOM) is critical to informing our understanding of the microbial impacts on the global carbon cycle. The capillary fringe of subsurface soils is a highly dynamic environment that remains poorly understood. Characterization of organo-mineral chemistry combined with a nuanced understanding of microbial community composition and function is necessary to understand microbial impacts on NOM speciation in the capillary fringe. We present a critical review of the popular analytical and omics techniques used for characterizing complex carbon transformation by microbial communities and focus on how complementary information obtained from the different techniques enable us to connect chemical signatures with microbial genes and pathways. This holistic approach offers a way forward for the comprehensive characterization of the formation, transformation, and mineralization of terrestrial NOM as influenced by microbial communities.

RevDate: 2022-05-23

Liu P, Hu S, He Z, et al (2022)

Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome.

Frontiers in microbiology, 13:828254.

Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have been proposed to decipher strains in metagenomes. However, strain-level complexity is far from being well characterized up to date. As the indicator of strain-level complexity, metagenomic single-nucleotide polymorphisms (SNPs) have been utilized to disentangle conspecific strains. Lots of SNP-based tools have been developed to identify strains in metagenomes. However, the sufficient sequencing depth for SNP and strain-level analysis remains unclear. We conducted ultra-deep sequencing of the human gut microbiome and constructed an unbiased framework to perform reliable SNP analysis. SNP profiles of the human gut metagenome by ultra-deep sequencing were obtained. SNPs identified from conventional and ultra-deep sequencing data were thoroughly compared and the relationship between SNP identification and sequencing depth were investigated. The results show that the commonly used shallow-depth sequencing is incapable to support a systematic metagenomic SNP discovery. In contrast, ultra-deep sequencing could detect more functionally important SNPs, which leads to reliable downstream analyses and novel discoveries. We also constructed a machine learning model to provide guidance for researchers to determine the optimal sequencing depth for their projects (SNPsnp, To conclude, the SNP profiles based on ultra-deep sequencing data extend current knowledge on metagenomics and highlights the importance of evaluating sequencing depth before starting SNP analysis. This study provides new ideas and references for future strain-level investigations.

RevDate: 2022-05-23

Bueno MR, Ishikawa KH, Almeida-Santos G, et al (2022)

Lactobacilli Attenuate the Effect of Aggregatibacter actinomycetemcomitans Infection in Gingival Epithelial Cells.

Frontiers in microbiology, 13:846192.

Probiotics may be considered as an additional strategy to achieve a balanced microbiome in periodontitis. However, the mechanisms underlying the use of probiotics in the prevention or control of periodontitis are still not fully elucidated. This in vitro study aimed to evaluate the effect of two commercially available strains of lactobacilli on gingival epithelial cells (GECs) challenged by Aggregatibacter actinomycetemcomitans. OBA-9 GECs were infected with A. actinomycetemcomitans strain JP2 at an MOI of 1:100 and/or co-infected with Lactobacillus acidophilus La5 (La5) or Lacticaseibacillus rhamnosus Lr32 (Lr32) at an MOI of 1:10 for 2 and 24 h. The number of adherent/internalized bacteria to GECs was determined by qPCR. Production of inflammatory mediators (CXCL-8, IL-1β, GM-CSF, and IL-10) by GECs was determined by ELISA, and the expression of genes encoding cell receptors and involved in apoptosis was determined by RT-qPCR. Apoptosis was also analyzed by Annexin V staining. There was a slight loss in OBA-9 cell viability after infection with A. actinomycetemcomitans or the tested probiotics after 2 h, which was magnified after 24-h co-infection. Adherence of A. actinomycetemcomitans to GECs was 1.8 × 107 (± 1.2 × 106) cells/well in the mono-infection but reduced to 1.2 × 107 (± 1.5 × 106) in the co-infection with Lr32 and to 6 × 106 (± 1 × 106) in the co-infection with La5 (p < 0.05). GECs mono-infected with A. actinomycetemcomitans produced CXCL-8, GM-CSF, and IL-1β, and the co-infection with both probiotic strains altered this profile. While the co-infection of A. actinomycetemcomitans with La5 resulted in reduced levels of all mediators, the co-infection with Lr32 promoted reduced levels of CXCL-8 and GM-CSF but increased the production of IL-1β. The probiotics upregulated the expression of TLR2 and downregulated TLR4 in cells co-infected with A. actinomycetemcomitans. A. actinomycetemcomitans-induced the upregulation of NRLP3 was attenuated by La5 but increased by Lr32. Furthermore, the transcription of the anti-apoptotic gene BCL-2 was upregulated, whereas the pro-apoptotic BAX was downregulated in cells co-infected with A. actinomycetemcomitans and the probiotics. Infection with A. actinomycetemcomitans induced apoptosis in GECs, whereas the co-infection with lactobacilli attenuated the apoptotic phenotype. Both tested lactobacilli may interfere in A. actinomycetemcomitans colonization of the oral cavity by reducing its ability to interact with gingival epithelial cells and modulating cells response. However, L. acidophilus La5 properties suggest that this strain has a higher potential to control A. actinomycetemcomitans-associated periodontitis than L. rhamnosus Lr32.

RevDate: 2022-05-23

Ampatzoglou A, Gruszecka-Kosowska A, Torres-Sánchez A, et al (2022)

Incorporating the Gut Microbiome in the Risk Assessment of Xenobiotics and Identifying Beneficial Components for One Health.

Frontiers in microbiology, 13:872583.

Three areas of relevance to the gut microbiome in the context of One Health were explored; the incorporation of the microbiome in food safety risk assessment of xenobiotics; the identification and application of beneficial microbial components to various areas under One Health, and; specifically, in the context of antimicrobial resistance. Although challenging, focusing on the microbiota resilience, function and active components is critical for advancing the incorporation of microbiome data in the risk assessment of xenobiotics. Moreover, the human microbiota may be a promising source of beneficial components, with the potential to metabolize xenobiotics. These may have possible applications in several areas, e.g., in animals or plants for detoxification or in the environment for biodegradation. This approach would be of particular interest for antimicrobials, with the potential to ameliorate antimicrobial resistance development. Finally, the concept of resistance to xenobiotics in the context of the gut microbiome may deserve further investigation.

RevDate: 2022-05-23

Monger XC, Saucier L, Gilbert AA, et al (2022)

Stabilization of swine faecal samples influences taxonomic and functional results in microbiome analyses.

MethodsX, 9:101716 pii:S2215-0161(22)00097-8.

Studies on the microbiome of different species are on the rise, due to a growing interest in animal health and the safety of food products of animal origin. A challenge with studying animals' microbiomes is to find methods that obtain a good representation of the microbial community of interest. Good unbiased sampling protocols are the basis for a solid experimental design, but may need to be done in environments where sample preservation could be difficult. In this study, we evaluate by shotgun sequencing the impact of stabilizing swine faeces samples using a commercial stabilizer (PERFORMAbiome • GUT | PB-200, DNA Genotek). Using stabilizer makes it possible to obtain DNA that is significantly less degraded than when the samples are not stabilized. Also, the results on the taxonomy and on the bacterial functions encoded in the microbiome are impacted by whether or not the samples are stabilized. Finally, the stabilization of samples that had already been frozen and stored at -80°C led to extraction and DNA quality results similar to those obtained from samples that were stabilized before freezing.

RevDate: 2022-05-23

Gallo M, Vento JM, Joncour P, et al (2022)

Beneficial commensal bacteria promote Drosophila growth by downregulating the expression of peptidoglycan recognition proteins.

iScience, 25(6):104357 pii:S2589-0042(22)00628-9.

Commensal bacteria are known to promote host growth. Such effect partly relies on the capacity of microbes to regulate the host's transcriptional response. However, these evidences mainly come from comparing the transcriptional response caused by commensal bacteria with that of axenic animals, making it difficult to identify the animal genes that are specifically regulated by beneficial microbes. Here, we employ Drosophila melanogaster associated with Lactiplantibacillus plantarum to understand the host genetic pathways regulated by beneficial bacteria and leading to improved host growth. We show that microbial benefit to the host relies on the downregulation of peptidoglycan-recognition proteins. Specifically, we report that bacterial proliferation triggers the lower expression of PGRP-SC1 in larval midgut, which ultimately leads to improved host growth and development. Our study helps elucidate the mechanisms underlying the beneficial effect exerted by commensal bacteria, defining the role of immune effectors in the relationship between Drosophila and its gut microbes.

RevDate: 2022-05-23

Sharpton SR, Podlaha O, Chuang JC, et al (2022)

Changes in the gut microbiome associated with liver stiffness improvement in nonalcoholic steatohepatitis.

Therapeutic advances in gastroenterology, 15:17562848221098243 pii:10.1177_17562848221098243.

Background: Longitudinal studies are needed to decipher mechanistic links between the gut microbiome and nonalcoholic steatohepatitis (NASH). We examined shifts in the gut microbiome in persons with NASH with improvement in liver stiffness measurement (LSM) by magnetic resonance (MR) elastography.

Methods: Gut microbial profiling was performed at baseline and study completion (24 weeks) using 16 S rRNA gene sequencing in 69 adults with biopsy-confirmed NASH and significant fibrosis (stages 2-3) enrolled in a multi-center randomized controlled trial evaluating selonsertib alone or in combination with simtuzumab. Differential abundance of bacterial taxa at baseline and end of study were examined in participants with and without longitudinal improvement in LSM. Gut microbial shifts that correlated with secondary outcomes, including reduction in MR imaging-derived proton density fat faction (MRI-PDFF) and histologic fibrosis regression were evaluated. Fecal samples from 32 healthy adults were profiled and genus-level multidimensional scaling was used to determine if microbial shifts in persons with NASH improvement represented a shift toward a healthy gut microbiome.

Results: Shifts in abundance of 36 bacterial taxa including Lactobacillus (log2FC = -4.51, FDR < 0.001), Enterococcus (log2FC = -6.72, FDR < 0.001), and Megasphaera (log2FC = 7.74, FDR < 0.001) were associated with improvement in LSM. Improvement in LSM was associated with microbial shifts toward healthy reference (p = 0.05). Significant shifts in 10 and 12 bacterial taxa were associated with improvement in LSM in addition to MRI-PDFF and fibrosis regression, respectively, indicating consistent taxonomic changes across multiple clinical endpoints.

Conclusion: Longitudinal changes in the gut microbiota are observed in adults with NASH and clinical improvement and represent a shift toward a healthy microbiome.

RevDate: 2022-05-23

Pan AY, Weinstock GM, JL Maron (2022)

Editorial: Pediatric Microbiome in Health and Disease: Recent Advances.

Frontiers in pediatrics, 10:908741.

RevDate: 2022-05-23

Wang Y, Xu H, Jing M, et al (2022)

Gut Microbiome Composition Abnormalities Determined Using High-Throughput Sequencing in Children With Tic Disorder.

Frontiers in pediatrics, 10:831944.

Object: To investigate the distribution characteristics of gut microbiota in children with tic disorder (TD) and the possible role of these characteristics in the pathogenesis of TD.

Methods: The medical records of 28 children with TD treated at Wuxi Children's Hospital from January 1 to October 31, 2020, and 21 age-matched healthy children (controls) were included. The relative quantification of bacterial taxa was performed using 16S ribosomal RNA gene amplicon sequencing.

Results: There was no significant difference in the alpha diversity of gut microbiota between the TD and control groups. Analyses of beta diversity were able to differentiate the TD patients from the healthy controls based on their gut microbiota. At the phylum level, the two groups were mainly composed of four phyla, Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria. There were significant differences in Firmicutes and Actinobacteria between the two groups (P <0.05). At the level of genera, the abundance of Bifidobacterium and Collinsella reduced while that of Ruminococcaceae unclassified, Prevotella, Faecalibacterium, Coprobacillus, and Odoribacter increased in the TD group compared to that in the control group. The intergroup differences were significant (P < 0.05).

Conclusion: The abnormal composition of gut microbiota in children with TD suggests that the change in gut microbiota may play an important role in TD development.

RevDate: 2022-05-23

Wu P, Zhu T, Tan Z, et al (2022)

Role of Gut Microbiota in Pulmonary Arterial Hypertension.

Frontiers in cellular and infection microbiology, 12:812303.

Gut microbiota and its metabolites play an important role in maintaining host homeostasis. Pulmonary arterial hypertension (PAH) is a malignant clinical syndrome with a frightening mortality. Pulmonary vascular remodeling is an important feature of PAH, and its pathogenesis is not well established. With the progress of studies on intestinal microbes in different disease, cumulative evidence indicates that gut microbiota plays a major role in PAH pathophysiology. In this review, we will systematically summarize translational and preclinical data on the correlation between gut dysbiosis and PAH and investigate the role of gut dysbiosis in the causation of PAH. Then, we point out the potential significance of gut dysbiosis in the diagnosis and treatment of PAH as well as several problems that remain to be resolved in the field of gut dysbiosis and PAH. All of this knowledge of gut microbiome might pave the way for the extension of novel pathophysiological mechanisms, diagnosis, and targeted therapies for PAH.

RevDate: 2022-05-23

Que T, Pang X, Huang H, et al (2022)

Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing.

Frontiers in cellular and infection microbiology, 12:872841.

The Trachypithecus leucocephalus (white-headed langur) is a highly endangered, karst-endemic primate species, inhabiting the karst limestone forest in Guangxi, Southwest China. How white-headed langurs adapted to karst limestone and special dietary remains unclear. It is the first time to study the correlation between the gut microbiome of primates and special dietary, and environment in Guangxi. In the study, 150 fecal samples are collected from nine primates in Guangxi, China. Metagenomic sequencing is used to analyze and compare the gut microbiome composition and diversity between white-headed langurs and other primates. Our results indicate that white-headed langurs has a higher diversity of microbiome than other primates, and the key microbiome are phylum Firmicutes, class Clostridia, family Lachnospiraceae, and genera Clostridiates and Ruminococcus, which are related to the digestion and degradation of cellulose. Ten genera are significantly more abundant in white-headed langurs and François' langur than in other primates, most of which are high-temperature microbiome. Functional analysis reveals that energy synthesis-related pathways and sugar metabolism-related pathways are less abundant in white-headed langurs and François' langur than in other primates. This phenomenon could be an adaptation mechanism of leaf-eating primates to low-energy diet. The gut microbiome of white-headed langurs is related to diet and karst limestone environment. This study could serve as a reference to design conservation breeding, manage conservation units, and determine conservation priorities.

RevDate: 2022-05-23

Singh R, Stogios N, Smith E, et al (2022)

Gut microbiome in schizophrenia and antipsychotic-induced metabolic alterations: a scoping review.

Therapeutic advances in psychopharmacology, 12:20451253221096525 pii:10.1177_20451253221096525.

Schizophrenia (SCZ) is a severe mental disorder with high morbidity and lifetime disability rates. Patients with SCZ have a higher risk of developing metabolic comorbidities such as obesity and diabetes mellitus, leading to increased mortality. Antipsychotics (APs), which are the mainstay in the treatment of SCZ, increase the risk of these metabolic perturbations. Despite extensive research, the mechanism underlying SCZ pathophysiology and associated metabolic comorbidities remains unclear. In recent years, gut microbiota (GMB) has been regarded as a 'chamber of secrets', particularly in the context of severe mental illnesses such as SCZ, depression, and bipolar disorder. In this scoping review, we aimed to investigate the underlying role of GMB in the pathophysiology of SCZ and metabolic alterations associated with APs. Furthermore, we also explored the therapeutic benefits of prebiotic and probiotic formulations in managing SCZ and AP-induced metabolic alterations. A systematic literature search yielded 46 studies from both preclinical and clinical settings that met inclusion criteria for qualitative synthesis. Preliminary evidence from preclinical and clinical studies indicates that GMB composition changes are associated with SCZ pathogenesis and AP-induced metabolic perturbations. Fecal microbiota transplantation from SCZ patients to mice has been shown to induce SCZ-like behavioral phenotypes, further supporting the plausible role of GMB in SCZ pathogenesis. This scoping review recapitulates the preclinical and clinical evidence suggesting the role of GMB in SCZ symptomatology and metabolic adverse effects associated with APs. Moreover, this scoping review also discusses the therapeutic potentials of prebiotic/probiotic formulations in improving SCZ symptoms and attenuating metabolic alterations related to APs.

RevDate: 2022-05-23

Song Z, Sun Y, Liu P, et al (2022)

Invasion of Spartina alterniflora on Zostera japonica enhances the abundances of bacteria by absolute quantification sequencing analysis.

Ecology and evolution, 12(5):e8939 pii:ECE38939.

Plant invasion can alter soil organic matter composition and indirectly impact estuary ecology; therefore, it is paramount to understand how plant invasion influences the bacterial community. Here, we present an absolute quantification 16S rRNA gene sequencing to investigate the bacterial communities that were collected from Zostera japonica and Spartina alterniflora covered areas and Z. japonica degradation areas in the Yellow River Estuary. Our data revealed that the absolute quantity of bacteria in the surface layer was significantly (p < .05) higher than that in the bottom and degradation areas. Following the invasion of S. alterniflora, the abundances of Bacteroidia, Acidimicrobiaceae, and Dehalococcoidaceaewere enriched in the S. alterniflora sediment. In addition, variations in the composition of sediment bacterial communities at the phylum level were the most intimately related to total organic carbon (TOC), and the content of heavy metals could reduce the abundance of bacteria. This study provided some information to understand the effects of S. alterniflora invasion on Z. japonica from the perspective of microbiome level.

RevDate: 2022-05-23

Fusco F, Perottoni S, Giordano C, et al (2022)

The microbiota-gut-brain axis and epilepsy from a multidisciplinary perspective: Clinical evidence and technological solutions for improvement of in vitro preclinical models.

Bioengineering & translational medicine, 7(2):e10296 pii:BTM210296.

Epilepsy is a common neurological disease characterized by the enduring predisposition of the brain to generate seizures. Among the recognized causes, a role played by the gut microbiota in epilepsy has been hypothesized and supported by new investigative approaches. To dissect the microbiota-gut-brain (MGB) axis involvement in epilepsy, in vitro modeling approaches arouse interest among researchers in the field. This review summarizes, first of all, the evidence of a role of the MGB axis in epilepsy by providing an overview of the recent clinical and preclinical studies and showing how dietary modification, microbiome supplementations, and hence, microbiota alterations may have an impact on seizures. Subsequently, the currently available strategies to study epilepsy on animal and in vitro models are described, focusing attention on these latter and the technological challenges for integration with already existing MGB axis models. Finally, the implementation of existing epilepsy in vitro systems is discussed, offering a complete overview of the available technological tools which may improve reliability and clinical translation of the results towards the development of innovative therapeutic approaches, taking advantage of complementary technologies.

RevDate: 2022-05-23

Shah A, Talley NJ, G Holtmann (2022)

Current and Future Approaches for Diagnosing Small Intestinal Dysbiosis in Patients With Symptoms of Functional Dyspepsia.

Frontiers in neuroscience, 16:830356.

The development and application of next generation sequencing technologies for clinical gastroenterology research has provided evidence that microbial dysbiosis is of relevance for the pathogenesis of gastrointestinal and extra-intestinal diseases. Microbial dysbiosis is characterized as alterations of diversity, function, and density of the intestinal microbes. Emerging evidence suggests that alterations of the gastrointestinal microbiome are important for the pathophysiology of a variety of functional gastrointestinal conditions, e.g., irritable bowel syndrome (IBS) and functional dyspepsia (FD), also known as disorders of brain-gut axis interaction. Clinicians have for many years recognized that small intestinal bacterial overgrowth (SIBO) is typified by a microbial dysbiosis that is underpinned by abnormal bacterial loads in these sites. SIBO presents with symptoms which overlap with symptoms of FD and IBS, point toward the possibility that SIBO is either the cause or the consequence of functional gastrointestinal disorders (FGIDs). More recently, new terms including "intestinal methanogen overgrowth" and "small intestinal fungal overgrowth" have been introduced to emphasize the contribution of methane production by archea and fungi in small intestinal dysbiosis. There is emerging data that targeted antimicrobial treatment of SIBO in patients with FD who simultaneously may or may not have IBS, results in symptom improvement and normalization of positive breath tests. However, the association between SIBO and FGIDs remains controversial, since widely accepted diagnostic tests for SIBO are lacking. Culture of jejunal fluid aspirate has been proposed as the "traditional gold standard" for establishing the diagnosis of SIBO. Utilizing jejunal fluid culture, the results can potentially be affected by cross contamination from oropharyngeal and luminal microbes, and there is controversy regarding the best cut off values for SIBO diagnosis. Thus, it is rarely used in routine clinical settings. These limitations have led to the development of breath tests, which when compared with the "traditional gold standard," have sub-optimal sensitivity and specificity for SIBO diagnosis. With newer diagnostic approaches-based upon applications of the molecular techniques there is an opportunity to characterize the duodenal and colonic mucosa associated microbiome and associated gut microbiota dysbiosis in patients with various gastrointestinal and extraintestinal diseases. Furthermore, the role of confounders like psychological co-morbidities, medications, dietary practices, and environmental factors on the gastrointestinal microbiome in health and disease also needs to be explored.


ESP Quick Facts

ESP Origins

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

ESP Support

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

ESP Rationale

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

ESP Goal

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

ESP Usage

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

ESP Content

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

ESP Help

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

ESP Plans

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

Electronic Scholarly Publishing
961 Red Tail Lane
Bellingham, WA 98226

E-mail: RJR8222 @

Papers in Classical Genetics

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

Digital Books

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


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


Biographical information about many key scientists.

Selected Bibliographies

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

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