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30 Jun 2022 at 01:47
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Bibliography on: Microbiome


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RJR: Recommended Bibliography 30 Jun 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: 2022-06-29

Deng L, Wang S, Zhang R, et al (2022)

Protective effects of (R)-enantiomers but not (S)-enantiomers of β2-adrenergic receptor agonists against acute colitis: The role of β2AR.

International immunopharmacology, 110:108997 pii:S1567-5769(22)00481-7 [Epub ahead of print].

The outcomes of ulcerative colitis (UC) treatment remain unsatisfactory. Salbutamol is a β2-adrenergic receptor (β2AR) agonist that is frequently used to treat human airway diseases, and it is a chiral drug with (RS)-isomers. However, the effects of (RS)-enantiomers of this drug on acute ulcerative colitis remain unknown. The present work determined and compared the effects of different chiral β2AR agonists in acute colitis. Acute colitis was established in mice with 3% dextran sulfate sodium and the mice were orally administered different salbutamol isomers. Body weight loss, colon length, disease activity index (DAI), and colon histopathology were assessed. Inflammatory cytokine levels were detected by ELISA. Colonic biopsies were collected from colitis patients. 16S rDNA amplicon sequencing was carried out to assess the composition and relative abundance of the gut microbiome. The expression of M1 and M2 macrophage markers in the colon were assessed by immunofluorescence staining and Western blotting. The results revealed that (R)-salbutamol prevented body weight loss and colonic shortening, decreased the DAI and histopathological scores, and reduced splenomegaly and inflammatory cytokine levels significantly better than (RS)-salbutamol and (S)-salbutamol. (R)-salbutamol downregulated levels of inflammatory protein in LPS-induced human colon tissue specimens. Furthermore, (R)-salbutamol ameliorated gut dysbiosis and macrophage polarization in mice with colitis. The β2AR antagonist ICI-118551 reversed the effect of (R)-salbutamol in ameliorating acute colitis. Taken together, (R)-salbutamol ameliorated the mice with acute colitis, which can serve as a new candidate or lead compound for UC treatment.

RevDate: 2022-06-29

Bendová B, Mikula O, Bímová BV, et al (2022)

Divergent gut microbiota in two closely related house mouse subspecies under common garden conditions.

FEMS microbiology ecology pii:6620832 [Epub ahead of print].

The gastrointestinal microbiota (GM) is considered an important component of the vertebrate holobiont. GM-host interactions influence the fitness of holobionts and are therefore an integral part of evolution. The house mouse is a prominent model for GM-host interactions, and evidence suggests a role for GM in mouse speciation. However, previous studies based on short 16S rRNA GM profiles of wild house mouse subspecies failed to detect GM divergence, which is a prerequisite for the inclusion of GM in Dobzhansky-Muller incompatibilities. Here, we used standard 16S rRNA GM profiling in two mouse subspecies, Mus musculus musculus and M. m. domesticus, including the intestinal mucosa and content of three gut sections (ileum, caecum, and colon). We reduced environmental variability by sampling GM in the offspring of wild mice bred under semi-natural conditions. Although the breeding conditions allowed a contact between the subspecies, we found a clear differentiation of GM between them, in all three gut sections. Differentiation was mainly driven by several Helicobacters and two H. ganmani variants showed a signal of co-divergence with their hosts. Helicobacters represent promising candidates for studying GM-host co-adaptations and the fitness effects of their interactions.

RevDate: 2022-06-29

van Heck JIP, Gacesa R, Stienstra R, et al (2022)

The Gut Microbiome Composition Is Altered in Long-Standing Type 1 Diabetes and Associates With Glycemic Control and Disease-Related Complications.

Diabetes care pii:147146 [Epub ahead of print].

OBJECTIVE: People with type 1 diabetes are at risk for developing micro- and macrovascular complications. Little is known about the gut microbiome in long-standing type 1 diabetes. We explored differences in the gut microbiome of participants with type 1 diabetes compared with healthy control subjects and associated the gut microbiome with diabetes-related complications.

RESEARCH DESIGN AND METHODS: Microbiome data of 238 participants with type 1 diabetes with an average disease duration of 28 ± 15 years were compared with 2,937 age-, sex-, and BMI-matched individuals. Clinical characteristics and fecal samples were collected, and metagenomic shotgun sequencing was performed. Microbial taxonomy was associated with type 1 diabetes-related characteristics and vascular complications.

RESULTS: No significant difference in the α-diversity of the gut microbiome was found between participants with type 1 diabetes and healthy control subjects. However, 43 bacterial taxa were significantly depleted in type 1 diabetes, while 37 bacterial taxa were significantly enriched. HbA1c and disease duration explained a significant part of the variation in the gut microbiome (R2 > 0.008, false discovery rate [FDR] <0.05), and HbA1c was significantly associated with the abundance of several microbial species. Additionally, both micro- and macrovascular complications explained a significant part of the variation in the gut microbiome (R2 > 0.0075, FDR < 0.05). Nephropathy was strongly associated with several microbial species. Macrovascular complications displayed similar associations with nephropathy.

CONCLUSIONS: Our data show that the gut microbiome is altered in people with (long-standing) type 1 diabetes and is associated with glycemic control and diabetes-related complications. As a result of the cross-sectional design, the causality of these relationships remains to be determined.

RevDate: 2022-06-29

Cao Y, Macori G, Naithani A, et al (2022)

A 16S rRNA Sequencing Study Describing the Environmental Microbiota of Two Powdered Infant Formula Built Facilities.

Foodborne pathogens and disease [Epub ahead of print].

Microbial safety is critically important for powdered infant formula (PIF) fed to neonates, with under-developed immune systems. The quality and safety of food products are dictated by those microorganisms found in both raw materials and the built production environment. In this study, a 2-year monitoring program of a production environment was carried out in two PIF factories located in the Republic of Ireland, and the environmental microbiome in different care areas of these sites was studied by using a 16S ribosomal RNA (rRNA)-based sequencing technique. Results highlighted a core microbiome associated with the PIF factory environment containing 24 bacterial genera representing five phyla, with Acinetobacter and Pseudomonas as the predominant genera. In different care areas of the PIF factory, as hygiene standards increased, deciphered changes in microbial community compositions became smaller over time and approached stability, and bacteria dominating the care area became less influenced by the external environment and more by human interactions and raw materials. These observations indicated that the microbial composition can be altered in response to environmental interventions. Genera Cronobacter and Salmonella were observed in trace amounts in the PIF factory environment, and bacterial genera known to be persistent in a stressed environment, such as Acinetobacter, Bacillus, Streptococcus, and Clostridium, were likely to have higher abundances in dry environment-based care areas. To our knowledge, this is the first study to characterize the PIF production environment microbiome using 16S rRNA-based sequencing. This study described the composition and changing trends of the environmental microbial communities in different care areas of the PIF manufacturing facility, and it provided valuable information to support the safer production of PIF in the future.

RevDate: 2022-06-29

Pai SR, Kurpad AV, Kuriyan R, et al (2022)

Intraindividual double burden of malnutrition: The contribution of the infant gut microbiome.

Asia Pacific journal of clinical nutrition, 31(2):157-166.

The prevalence of the double burden of malnutrition in society is well known with the coexistence of undernutrition with an increase in overweight/obesity; this has been increasing globally with nutritional imbalances and infectious diseases being the major etiological factors. However, there is also the coexistence of inappropriate adiposity or metabolic dysfunction in an individual who appears currently undernourished by anthropometric standards (stunted or underweight); this is the intraindividual double burden of malnutrition. It could also occur in temporal sequence, as anthropometric overweight in an individual who has previously endured childhood under-nutrition. IIDBM has increased the risk for diet-related non-communicable diseases over the past few decades, as it tracks into adulthood, warranting an urgent need for intervention and prevention. While gut dysbiosis has been associated with various forms of malnutrition, the early life gut microbiome composition and its related metabolites and regulatory factors, are possibly linked to the development of inflammatory and metabolic conditions in IIDBM. The possible underlying physiological mechanisms are reviewed here, working through host dietary influences, gut microbial metabolites, host inflammation and metabolic dysregulation. When validated experimentally and tested through appropriately designed randomised, controlled trials, these mechanistic insights will likely lead to development of preventive strategies.

RevDate: 2022-06-29

Kudjordjie EN, Hooshmand K, Sapkota R, et al (2022)

Fusarium oxysporum Disrupts Microbiome-Metabolome Networks in Arabidopsis thaliana Roots.

Microbiology spectrum [Epub ahead of print].

While the plant host metabolome drives distinct enrichment of detrimental and beneficial members of the microbiome, the mechanistic interomics relationships remain poorly understood. Here, we studied microbiome and metabolome profiles of two Arabidopsis thaliana accessions after Fusarium oxysporum f.sp. mathioli (FOM) inoculation, Landsberg erecta (Ler-0) being susceptible and Col-0 being resistant against FOM. By using bacterial and fungal amplicon sequencing and targeted metabolite analysis, we observed highly dynamic microbiome and metabolome profiles across FOM host progression, while being markedly different between FOM-inoculated and noninoculated Col-0 and Ler-0. Co-occurrence network analysis revealed more robust microbial networks in the resistant Col-0 compared to Ler-0 during FOM infection. Correlation analysis revealed distinct metabolite-OTU correlations in Ler-0 compared with Col-0 which could possibly be explained by missense variants of the Rfo3 and Rlp2 genes in Ler-0. Remarkably, we observed positive correlations in Ler-0 between most of the analyzed metabolites and the bacterial phyla Proteobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, and Verrucomicrobia, and negative correlations with Actinobacteria, Firmicutes, and Chloroflexi. The glucosinolates 4-methyoxyglucobrassicin, glucoerucin and indole-3 carbinol, but also phenolic compounds were strongly correlating with the relative abundances of indicator and hub OTUs and thus could be active in structuring the A. thaliana root-associated microbiome. Our results highlight interactive effects of host plant defense and root-associated microbiota on Fusarium infection and progression. Our findings provide significant insights into plant interomic dynamics during pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control. IMPORTANCE Plant health and fitness are determined by plant-microbe interactions which are guided by host-synthesized metabolites. To understand the orchestration of this interaction, we analyzed the distinct interomic dynamics in resistant and susceptible Arabidopsis ecotypes across different time points after infection with Fusarium oxysporum (FOM). Our results revealed distinct microbial profiles and network resilience during FOM infection in the resistant Col-0 compared with the susceptible Ler-0 and further pinpointed specific microbe-metabolite associations in the Arabidopsis microbiome. These findings provide significant insights into plant interomics dynamics that are likely affecting fungal pathogen invasion and could possibly facilitate future exploitation of microbiomes for plant disease control.

RevDate: 2022-06-29

Avuthu N, C Guda (2022)

Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer.

Microbiology spectrum [Epub ahead of print].

Colorectal cancer (CRC) is the second leading cause of cancer mortality worldwide. The dysbiotic gut microbiota and its metabolite secretions play a significant role in CRC development and progression. In this study, we identified microbial and metabolic biomarkers applicable to CRC using a meta-analysis of metagenomic datasets from diverse geographical regions. We used LEfSe, random forest (RF), and co-occurrence network methods to identify microbial biomarkers. Geographic dataset-specific markers were identified and evaluated using area under the ROC curve (AUC) scores and random effect size. Co-occurrence networks analysis showed a reduction in the overall microbial associations and the presence of oral pathogenic microbial clusters in CRC networks. Analysis of predicted metabolites from CRC datasets showed the enrichment of amino acids, cadaverine, and creatine in CRC, which were positively correlated with CRC-associated microbes (Peptostreptococcus stomatis, Gemella morbillorum, Bacteroides fragilis, Parvimonas spp., Fusobacterium nucleatum, Solobacterium moorei, and Clostridium symbiosum), and negatively correlated with control-associated microbes. Conversely, butyrate, nicotinamide, choline, tryptophan, and 2-hydroxybutanoic acid showed positive correlations with control-associated microbes (P < 0.05). Overall, our study identified a set of global CRC biomarkers that are reproducible across geographic regions. We also reported significant differential metabolites and microbe-metabolite interactions associated with CRC. This study provided significant insights for further investigations leading to the development of noninvasive CRC diagnostic tools and therapeutic interventions. IMPORTANCE Several studies showed associations between gut dysbiosis and CRC. Yet, the results are not conclusive due to cohort-specific associations that are influenced by genomic, dietary, and environmental stimuli and associated reproducibility issues with various analysis approaches. Emerging evidence suggests the role of microbial metabolites in modulating host inflammation and DNA damage in CRC. However, the experimental validations have been hindered by cost, resources, and cumbersome technical expertise required for metabolomic investigations. In this study, we performed a meta-analysis of CRC microbiota data from diverse geographical regions using multiple methods to achieve reproducible results. We used a computational approach to predict the metabolomic profiles using existing CRC metagenomic datasets. We identified a reliable set of CRC-specific biomarkers from this analysis, including microbial and metabolite markers. In addition, we revealed significant microbe-metabolite associations through correlation analysis and microbial gene families associated with dysregulated metabolic pathways in CRC, which are essential in understanding the vastly sporadic nature of CRC development and progression.

RevDate: 2022-06-29

Liu F, Duan M, Fu H, et al (2022)

Orthopedic Surgery Causes Gut Microbiome Dysbiosis and Intestinal Barrier Dysfunction in Prodromal Alzheimer's Disease Patients: A Prospective Observational Cohort Study.

Annals of surgery pii:00000658-990000000-00035 [Epub ahead of print].

OBJECTIVE: To investigate gut microbiota and intestinal barrier function changes after orthopedic surgery in elderly patients with either normal cognition (NC) or a prodromal Alzheimer's disease phenotype (pAD) comprising either subjective cognitive decline (SCD) or amnestic mild cognitive impairment (aMCI).

BACKGROUND: Homeostatic disturbances induced by surgical trauma and/or stress can potentially alter the gut microbiota and intestinal barrier function in elderly patients before and after orthopedic surgery.

METHODS: In this prospective cohort study, 135 patients were subject to preoperative neuropsychological assessment and then classified into: NC (n=40), SCD (n=58), or aMCI (n=37). Their gut microbiota, bacterial endotoxin (LPS), tight junction protein (TJ), and inflammatory cytokines in blood were measured prior to surgery and on postsurgical day 1, 3, and 7 (or before discharge).

RESULTS: The short-chain fatty acid (SCFA)-producing bacteria were lower whilst the Gram-negative bacteria, LPS and TJ were higher preoperatively in both the SCD and aMCI (pAD) groups compared to the NC group. After surgery, a decrease in SCFA-producing bacteria, and an increase in both Gram-negative bacteria and plasma claudin were significant in the pAD groups relative to the NC group. SCFA-producing bacteria were negatively correlated with TJ and cytokines in pAD patients on postsurgical day 7. Furthermore, surgery-induced perioperative metabolic stress and inflammatory responses were associated with gut microbiota alterations.

CONCLUSIONS: Surgery exacerbates both preexisting microbiota dysbiosis and intestinal barrier dysfunction in pAD patients, all of which may be associated with systemic inflammation and, in turn, may lead to further cognitive deterioration.

RevDate: 2022-06-29

Yang Y, C Wu (2022)

Targeting gut microbial bile salt hydrolase (BSH) by diet supplements: new insights into dietary modulation of human health.

Food & function [Epub ahead of print].

The gut microbiome is increasingly recognized as a vital organ that participates in nutrient acquisition, energy regulation and maintenance of human health. Targeted manipulation of the gut microbiota by dietary supplements has been validated as an effective approach to improve human health. Among various gut microbiome-host interactions, bile acids (BAs) are intensively metabolized by the gut microbes and control a variety of metabolic processes such as energy homeostasis, glucose and lipid metabolism by activation of farnesoid X receptor (FXR). How dietary supplements regulate FXR signaling and promote human health is thus attracting broad interest and well-reviewed. However, the exact effects of BAs on FXR activity and host metabolism are compound-specific. Different BAs are metabolized by the gut microbes into varied BA derivatives and then impose distinct modulation of FXR activity and host health. As the gateway enzymes, bile salt hydrolases (BSHs), produced by the gut microbiota, control the first step of BA transformation in the gut. Therefore, BSH is a key mediator linking the food supplements' modulation to the gut microbiota and BAs-FXR signaling. In this review, we generalized the relationship between BAs, gut microbial BSHs and FXR, and summarized the dietary regulators of BSH and FXR activities, aiming to rationalize the dietary management of human health via dietary supplement-gut microbiota-FXR signaling axis.

RevDate: 2022-06-29

Wang M, Yang F, Yan X, et al (2022)

Anti-diabetic effect of banana peel dietary fibers on type 2 diabetic mellitus mice induced by streptozotocin and high-sugar and high-fat diet.

Journal of food biochemistry [Epub ahead of print].

We used a high-fat diet (HFD) and streptozotocin (STZ) to induce type 2 diabetic mellitus (T2DM) mice and evaluated the effect of banana peel dietary fibers (BP-DFs) as potential hypoglycemic agents. After 5 weeks of intervention with banana peel dietary fibers (BP-DFs), food intake was reduced, body weight was increased, blood lipids and glucose were reduced, fasting insulin and GLP-1 levels were increased, and liver and pancreatic tissue damage was reduced. Banana peel soluble dietary fiber (BP-SDF) has the most significant effect. The results of fecal microbiota analysis showed that BP-DFs could ameliorates gut microbiome dysbiosis, and all three types of dietary fibers have obvious effects. The results of fecal short-chain fatty acids (SCFAs) showed that the content of fecal SCFAs was increased after BP-DFs dietary intervention, and BP-SDF had the most obvious effect. RT-PCR experiment results show that BP-DFs can up-regulate the mRNA expression levels of PI3K, AKT, IRS-1, and FOXO1 in the liver of diabetic mice, which indicates that BD-DFs may play a role in improving insulin resistance and insulin signal transduction via the IRS/PI3K/AKT pathway, improving insulin resistance and insulin signal transduction. Our research may be extended to BP-DFs, especially BP-SDF, as the basis for potential dietary intervention to prevent or treat type 2 diabetic mellitus. This work supports future research studies of the anti-diabetic properties of BP-SDF in humans. PRACTICAL APPLICATIONS: Diabetes can lead to a variety of complications that have a huge impact on health. Dietary fiber may help in lowering blood sugar. Our experimental results showed that banana peel dietary fibers have the effect of reducing food intake, blood sugar, improving liver and pancreas function, increasing the abundance of intestinal flora, and improving the IRS/PI3K/AKT pathway in T2DM mice. Therefore, this study could provide a theoretical basis for the development of functional foods with banana peel dietary fiber.

RevDate: 2022-06-29

Weiland SO, Detcharoen M, Schlick-Steiner BC, et al (2022)

Analyses of locomotion, wing morphology, and microbiome in Drosophila nigrosparsa after recovery from antibiotics.

MicrobiologyOpen, 11(3):e1291.

Antibiotics, such as tetracycline, have been frequently used to cure arthropods of Wolbachia endosymbionts. After the symbionts have been removed, the hosts must recover for some generations from the side effects of the antibiotics. However, most studies do not assess the direct and indirect longer-term effects of antibiotics used to remove Wolbachia, which may question the exact contribution of this endosymbiont to the effects observed. Here, we used the fly Drosophila nigrosparsa treated or not with tetracycline for three generations followed by two generations of recovery to investigate the effects of this antibiotic on the fly locomotion, wing morphology, and the gut microbiome. We found that antibiotic treatment did not affect fly locomotion two generations after being treated with the antibiotic. In addition, gut-microbiome restoration was tested as a more efficient solution to reduce the potential side effects of tetracycline on the microbiome. There was no significant difference in alpha diversity between gut restoration and other treatments, but the abundance of some bacterial taxa differed significantly between the gut-restoration treatment and the control. We conclude that in D. nigrosparsa the recovery period of two generations after being treated with the antibiotic is sufficient for locomotion, and suggest a general assessment of direct and indirect effects of antibiotics after a particular recovery time.

RevDate: 2022-06-28

Urbaniak C, Morrison MD, Thissen JB, et al (2022)

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station.

Microbiome, 10(1):100.

BACKGROUND: The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months.

METHODS: Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results.

RESULTS: Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 105 cfu/m2 CONCLUSIONS: Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity. Video Abstract.

RevDate: 2022-06-28

Chalifour BN, Elder LE, J Li (2022)

Gut microbiome of century-old snail specimens stable across time in preservation.

Microbiome, 10(1):99.

BACKGROUND: Museum biological specimens provide a unique means of gathering ecological information that spans wide temporal ranges. Museum specimens can also provide information on the microbial communities that persist within the host specimen. Together, these provide researchers valuable opportunities to study long-term trends and mechanisms of microbial community change. The effects of decades-long museum preservation on host-microbial communities have not been systematically assessed. The University of Colorado's Museum of Natural History has densely sampled Oreohelix strigosa (Rocky Mountainsnail) for the past century; many are preserved in ethanol, which provides an excellent opportunity to explore how the microbiome changes across time in preservation.

RESULTS: We used 16S rRNA (ribosomal ribonucleic acid) gene amplicon sequencing to examine Oreohelix strigosa gut microbiomes from museum specimens across a 98-year range, as well as within short-term preservation treatments collected in 2018. Treatment groups included samples extracted fresh, without preservation; samples starved prior to extraction; and samples preserved for 1 month, 6 months, and 9 months. General microbiome composition was similar across all years. Sample groups belonging to specific years, or specific short-term treatments, showed unique associations with select bacterial taxa. Collection year was not a significant predictor of microbial richness, though unpreserved short-term treatments showed significantly higher richness than preserved treatments. While the year was a significant factor in microbiome composition, it did not explain much of the variation across samples. The location was a significant driver of community composition and explained more of the variability.

CONCLUSIONS: This study is the first to examine animal host-associated microbiome change across a period of nearly one century. Generally, geographic location was a greater factor in shaping gut microbiome composition, rather than a year collected. Consistent patterns across this temporal range indicate that historic specimens can answer many ecological questions surrounding the host-associated microbiome. Video Abstract.

RevDate: 2022-06-28

Kato S, Nagasawa T, Uehara O, et al (2022)

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women.

BMC oral health, 22(1):260.

BACKGROUND: The establishment of symbiotic microbiota in pregnant women is important for both the mother and her offspring. Little is known about the salivary symbiotic bacteria in pregnancy, and analysis of composition of microbiome (ANCOM) is useful to detect small differences in the number of bacteria. The aim of this study was to investigate the differences in the salivary bacteria between healthy pregnant and non-pregnant women using ANCOM.

METHODS: Unstimulated saliva samples were collected from 35 healthy pregnant women at 35 weeks gestation and 30 healthy non-pregnant women during menstruation. All participants underwent a periodontal examination. Estradiol and progesterone levels were examined by enzyme-linked immunosorbent assay. DNA extracted from the saliva was assessed by 16S ribosomal RNA amplicon sequencing and real-time PCR.

RESULTS: Salivary estradiol and progesterone levels were significantly increased in pregnant women. The alpha and beta diversities were higher in pregnant women than in non-pregnant women. The largest effect size difference noted when the microbiota of the pregnant and non-pregnant women were analyzed was that for Bifidobacteriales. Levels of Bifidobacterium dentium, but not of Bifidobacterium adolescentis, were significantly increased in pregnant women, and the levels were significantly correlated with progesterone concentration.

CONCLUSION: The results suggest that Bifidobacterium and progesterone levels are elevated in the saliva of healthy pregnant women compared with non-pregnant women.

RevDate: 2022-06-28

Batista L, Robles V, Manichanh C, et al (2022)

Colonic bacterial diversity and dysbiosis in active microscopic colitis as compared to chronic diarrhoea and healthy controls: effect of polyethylene glycol after bowel lavage for colonoscopy.

BMC gastroenterology, 22(1):320.

BACKGROUND: Most microbiota studies in microscopic colitis patients are performed after diagnostic colonoscopy without considering the potential effect of colonic lavage. Patients may achieve clinical remission after colonoscopy and it is unknown whether lavage-induced changes play a role.

AIM: To assess the effect of polyethylene glycol (PEG) colonic lavage on clinical remission rate, microbial diversity, microbial dysbiosis index and specific microbial changes in patients with active microscopic colitis as compared to other diarrhoeal diseases and healthy controls.

METHODS: Fifty-five consecutive patients presenting chronic watery diarrhoea and 12 healthy controls were included. Faecal samples were collected three days before and 30 days after PEG in patients and controls for microbiome analysis.

RESULTS: Clinical remission was observed in 53% of microscopic colitis patients, and in 32% of non-microscopic colitis patients (p = 0.16). Considering patients with persisting diarrhoea after colonoscopy, 71% of non-microscopic colitis patients had bile acid diarrhoea. Baseline Shannon Index was lower in diarrhoea groups than in healthy controls (p = 0.0025); there were no differences between microscopic colitis, bile-acid diarrhoea and functional diarrhoea. The microbial dysbiosis index was significantly higher in microscopic colitis than in bile acid diarrhoea plus functional diarrhoea (p = 0.0095), but no bacterial species showed a significantly different relative abundance among the diarrheal groups.

CONCLUSIONS: Dysbiosis is a feature in active microscopic colitis, but loss of microbial diversity was similar in all diarrheal groups, suggesting that faecal microbial changes are not due to microscopic colitis itself but associated with stool form. A considerable number of microscopic colitis patients achieved clinical remission after colonoscopy, but we were unable to demonstrate related PEG-induced changes in faecal microbiome.

RevDate: 2022-06-28

Petrak F, Herpertz S, Hirsch J, et al (2022)

Gut microbiota differs in composition between adults with type 1 diabetes with or without depression and healthy control participants: a case-control study.

BMC microbiology, 22(1):169.

BACKGROUND: Individuals with type 1 diabetes and those with depression show differences in the composition of the gut microbiome from that of healthy people. However, these differences have not yet been studied in patients with both diseases. Therefore, we compared the gut microbiome of people with type 1 diabetes with or without depression with matched healthy controls.

METHODS: A case-control study was conducted in 20 adults with type 1 diabetes (group A), 20 adults with type 1 diabetes and depression (group B), and 20 healthy adults (group C). Gut microbiota composition was determined by sequencing of the V3-V4 region of the bacterial 16S rDNA and alpha and beta diversity was compared between the groups.

RESULTS: Groups A and B both showed higher alpha diversity than the healthy control group (P < 0.001) but alpha diversity did not differ significantly between groups A and B. Participants having type 1 diabetes with (P < 0.05) or without comorbid depression (P < 0.001) differed regarding beta diversity from healthy controls but not between each other. Group B (diabetes with depression) had significantly higher abundance of Megaspaera than groups A and C. Both diabetes groups had a higher abundance of Christensenellaceae, Succinivibrionaceae, and Rhodospirillaceae than the healthy group but similar between-group abundances.

CONCLUSIONS: While differences in alpha and beta diversity and in some bacterial taxa occurred only between participants with diabetes and healthy controls, specific characteristics regarding the abundance of Megasphaera were observed in people with diabetes and comorbid depression. In summary, the study findings indicate a possible involvement of bacterial groups in depression in people with diabetes. The results suggest replication studies in larger samples to verify these findings.

RevDate: 2022-06-28

Mars Brisbin M, Mitarai S, Saito MA, et al (2022)

Microbiomes of bloom-forming Phaeocystis algae are stable and consistently recruited, with both symbiotic and opportunistic modes.

The ISME journal [Epub ahead of print].

Phaeocystis is a cosmopolitan, bloom-forming phytoplankton genus that contributes significantly to global carbon and sulfur cycles. During blooms, Phaeocystis species produce large carbon-rich colonies, creating a unique interface for bacterial interactions. While bacteria are known to interact with phytoplankton-e.g., they promote growth by producing phytohormones and vitamins-such interactions have not been shown for Phaeocystis. Therefore, we investigated the composition and function of P. globosa microbiomes. Specifically, we tested whether microbiome compositions are consistent across individual colonies from four P. globosa strains, whether similar microbiomes are re-recruited after antibiotic treatment, and how microbiomes affect P. globosa growth under limiting conditions. Results illuminated a core colonial P. globosa microbiome-including bacteria from the orders Alteromonadales, Burkholderiales, and Rhizobiales-that was re-recruited after microbiome disruption. Consistent microbiome composition and recruitment is indicative that P. globosa microbiomes are stable-state systems undergoing deterministic community assembly and suggests there are specific, beneficial interactions between Phaeocystis and bacteria. Growth experiments with axenic and nonaxenic cultures demonstrated that microbiomes allowed continued growth when B-vitamins were withheld, but that microbiomes accelerated culture collapse when nitrogen was withheld. In sum, this study reveals symbiotic and opportunistic interactions between Phaeocystis colonies and microbiome bacteria that could influence large-scale phytoplankton bloom dynamics and biogeochemical cycles.

RevDate: 2022-06-28

Vaughan MH, Zemtsov GE, Dahl EM, et al (2022)

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture.

RevDate: 2022-06-28

Han ND, Cheng J, Delannoy-Bruno O, et al (2022)

Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans.

Cell pii:S0092-8674(22)00709-7 [Epub ahead of print].

Plant fibers in byproduct streams produced by non-harsh food processing methods represent biorepositories of diverse, naturally occurring, and physiologically active biomolecules. To demonstrate one approach for their characterization, mass spectrometry of intestinal contents from gnotobiotic mice, plus in vitro studies, revealed liberation of N-methylserotonin from orange fibers by human gut microbiota members including Bacteroides ovatus. Functional genomic analyses of B. ovatus strains grown under permissive and non-permissive N-methylserotonin "mining" conditions revealed polysaccharide utilization loci that target pectins whose expression correlate with strain-specific liberation of this compound. N-methylserotonin, orally administered to germ-free mice, reduced adiposity, altered liver glycogenesis, shortened gut transit time, and changed expression of genes that regulate circadian rhythm in the liver and colon. In human studies, dose-dependent, orange-fiber-specific fecal accumulation of N-methylserotonin positively correlated with levels of microbiome genes encoding enzymes that digest pectic glycans. Identifying this type of microbial mining activity has potential therapeutic implications.

RevDate: 2022-06-28

San León D, J Nogales (2022)

Toward merging bottom-up and top-down model-based designing of synthetic microbial communities.

Current opinion in microbiology, 69:102169 pii:S1369-5274(22)00053-4 [Epub ahead of print].

The increasing interest of microbial communities as promising biocatalyst is leading an intense effort into the development of computational frameworks assisting the analysis and rational engineering of such complex ecosystems. Here, we critically review the recent computational and model-guided advances in the system-level engineering of microbiome, including both the rational bottom-up and the evolutionary top-down approaches. Furthermore, we highlight modeling and computational methods supporting both engineering paradigms. Finally, we discuss the advantages of combining both strategies into a hybrid top-down/bottom-up (middle-out) strategy to engineer synthetic microbial communities with improved performance and scope.

RevDate: 2022-06-28

Zhu T, Jin J, Chen M, et al (2022)

The impact of infection with COVID-19 on the respiratory microbiome: A narrative review.

Virulence, 13(1):1076-1087.

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has affected millions of individuals with various implications. Consistent with the crucial role of the microbiome in determining health and disease in humans, various studies have investigated the gut and respiratory microbiome effect on the COVID-19. Microbiota dysbiosis might support the entry, replication, and establishment of SARS-CoV-2 infection by modulating various mechanisms. One of the main mechanisms that the modulation of respiratory microbiota composition during the COVID-19 infection affects the magnitude of the disease is changes in innate and acquired immune responses, including inflammatory markers and cytokines and B- and T-cells. The diversity of respiratory microbiota in COVID-19 patients is controversial; some studies reported low microbial diversity, while others found high diversity, suggesting the role of respiratory microbiota in this disease. Modulating microbiota diversity and profile by supplementations and nutrients can be applied prophylactic and therapeutic in combating COVID-19. Here, we discussed the lung microbiome dysbiosis during various lung diseases and its interaction with immune cells, focusing on COVID-19.

RevDate: 2022-06-28

Rakotonirina A, Galperine T, E Allémann (2022)

Fecal microbiota transplantation: a review on current formulations in Clostridioides difficile infection and future outlooks.

Expert opinion on biological therapy [Epub ahead of print].

INTRODUCTION: The role of the gut microbiota in health and the pathogenesis of several diseases has been highlighted in recent years. Even though the precise mechanisms involving the microbiome in these ailments are still unclear, microbiota-modulating therapies have been developed. Fecal microbiota transplantation (FMT) has shown significant results against Clostridioides difficile infection (CDI), and its potential has been investigated for other diseases. Unfortunately, the technical aspects of the treatment make it difficult to implement. Pharmaceutical technology approaches to encapsulate microorganisms could play an important role in providing this treatment and render the treatment modalities easier to handle.

AREAS COVERED: After an overview of CDI, this narrative review aims to discuss the current formulations for FMT and specifically addresses the technical aspects of the treatment. This review also distinguishes itself by focusing on the hurdles and emphasizing the possible improvements using pharmaceutical technologies.

EXPERT OPINION: FMT is an efficient treatment for recurrent CDI. However, its standardization is overlooked. The approach of industrial and hospital preparations of FMT are different, but both show promise in their respective methodologies. Novel FMT formulations could enable further research on dysbiotic diseases in the future.

RevDate: 2022-06-28

Vasishta S, Ganesh K, Umakanth S, et al (2022)

Ethnic disparities attributed to the manifestation in and response to type 2 diabetes: insights from metabolomics.

Metabolomics : Official journal of the Metabolomic Society, 18(7):45.

Type 2 diabetes (T2D) associated health disparities among different ethnicities have long been known. Ethnic variations also exist in T2D related comorbidities including insulin resistance, vascular complications and drug response. Genetic heterogeneity, dietary patterns, nutrient metabolism and gut microbiome composition attribute to ethnic disparities in both manifestation and progression of T2D. These factors differentially regulate the rate of metabolism and metabolic health. Metabolomics studies have indicated significant differences in carbohydrate, lipid and amino acid metabolism among ethnicities. Interestingly, genetic variations regulating lipid and amino acid metabolism might also contribute to inter-ethnic differences in T2D. Comprehensive and comparative metabolomics analysis between ethnicities might help to design personalized dietary regimen and newer therapeutic strategies. In the present review, we explore population based metabolomics data to identify inter-ethnic differences in metabolites and discuss how (a) genetic variations, (b) dietary patterns and (c) microbiome composition may attribute for such differences in T2D.

RevDate: 2022-06-28

Zhu H, Tian P, Qian X, et al (2022)

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders.

Food & function [Epub ahead of print].

Early life stress can considerably interfere in gut microbiome formation and nervous system development. Specific probiotic strains have been proved to exert anti-stress effects by modulating the gut-brain axis. However, little is known about whether probiotic treatment during pregnancy can protect the offspring from early life stress. In this study, Bifidobacterium breve CCFM1025, previously proven to exert microbial and neurobiological regulation effects, was given to pregnant mice. The offspring's gut and brain functions were evaluated when challenged with maternal separation. Intriguingly, treatment with probiotics during pregnancy protected the offspring from maternal separation-induced neurobiological and gastrointestinal disorders such as depression-like behaviour and delayed defecation. Quantification of CCFM1025 was performed, and perinatal transmission of CCFM1025 was further validated, which also explained the reason for increased levels of colonic 5-hydroxytryptamine and caecal short-chain fatty acids in the offspring. Our findings indicated that the effects of probiotics can be perinatally transmitted through gut microbes and that probiotic treatment during pregnancy may have great potential in managing health risks in early life.

RevDate: 2022-06-28

Roguet A, Newton RJ, Eren AM, et al (2022)

Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.

mSystems [Epub ahead of print].

Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.

RevDate: 2022-06-28

Wang XB, Azarbad H, Leclerc L, et al (2022)

A Drying-Rewetting Cycle Imposes More Important Shifts on Soil Microbial Communities than Does Reduced Precipitation.

mSystems [Epub ahead of print].

Global changes will result in altered precipitation patterns, among which the increasing frequency of drought events has the highest deleterious potential for agriculture. Soil microbes have shown some promise to help crops adapt to drought events, but it is uncertain how crop-associated microorganisms will respond to altered precipitation patterns. To investigate this matter, we conducted a field experiment where we seeded two wheat cultivars (one resistant to water stress and the other sensitive) that were subjected to four precipitation exclusion (PE) regimes (0%, 25%, 50%, and 75% exclusion). These cultivars were sampled seven times (every 2 weeks, from May to August) within one growing season to investigate short-term microbiome responses to altered precipitation regimes and seasonality using 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. One of the most striking features of the data set was the dramatic shift in microbial community diversity, structure, and composition together with a doubling of the relative abundance of the archaeal ammonia oxidizer genus Nitrososphaera following an important drying-rewetting event. Comparatively small but significant effects of PE and wheat cultivar on microbial community diversity, composition, and structure were observed. Taken together, our results demonstrate an uneven response of microbial taxa to decreasing soil water content, which was dwarfed by drying-rewetting events, to which soil bacteria and archaea were more sensitive than fungi. Importantly, our study showed that an increase in drying-rewetting cycles will cause larger shifts in soil microbial communities than a decrease in total precipitation, suggesting that under climate changes, the distribution of precipitation will be more important than small variations in the total quantity of precipitation. IMPORTANCE Climate change will have a profound effect on the precipitation patterns of global terrestrial ecosystems. Seasonal and interannual uneven distributions of precipitation will lead to increasing frequencies and intensities of extreme drought and rainfall events, which will affect crop productivity and nutrient contents in various agroecosystems. However, we still lack knowledge about the responses of soil microbial communities to reduced precipitation and drying-rewetting events in agroecosystems. Our results demonstrated an uneven response of the soil microbiome and a dramatic shift in microbial community diversity and structure to a significant drying-rewetting event with a large increase in the relative abundance of archaeal ammonia oxidizers. These findings highlight the larger importance of rewetting of dry soils on microbial communities, as compared to decreased precipitation, with potential for changes in the soil nitrogen cycling.

RevDate: 2022-06-28

Liu J, Li T, Chen T, et al (2022)

Integrating Multiple Omics Identifies Phaeoacremonium rubrigenum Acting as Aquilaria sinensis Marker Fungus to Promote Agarwood Sesquiterpene Accumulation by Inducing Plant Host Phosphorylation.

Microbiology spectrum [Epub ahead of print].

The present study aimed to explore the factors that promote persistent agarwood accumulation. To this end, we first investigated the morphological changes and volatile compound distribution in five layers of "Guan Xiang" agarwood. The agarwood-normal transition layer (TL), an essential layer of persistent agarwood accumulation, showed clear metabolic differences by microscopy and GC-MS analysis. Microbiome analysis revealed that Phaeocremonium rubrigenum was the predominant biomarker fungus in the TL of "Guan Xiang" agarwood samples. Among the seven isolated fungi, P. rubrigenum exhibited a significantly heightened ability to induce the production in Aquilaria sinensis seedlings, especially for sesquiterpene. Tracing the proteome profile changes in P. rubrigenum-induced A. sinensis calli for 18 ds showed that the fungus-induced sesquiterpene biosynthesis increased mainly through the mevalonate (MVA) pathway. Specifically, the phosphorylation modification level, instead of the protein abundance of transcription factors (TFs), showed corresponding changes during sesquiterpene biosynthesis, thus indicating that induced phosphorylation is the key reason for enhanced sesquiterpene production. IMPORTANCE Agarwood is an expensive resinous portion derived from Aquilaria plants and has been widely used as medicine, incense, and perfume. The factors involved in steady agarwood accumulation remain elusive. Our current study suggests that as a TL marker fungus, P. rubrigenum could persistently promote agarwood sesquiterpene accumulation by inducing phosphorylation of the TFs-MVA network in A. sinensis. Moreover, our work provides strategies to improve agarwood industry management and sheds light on the potential molecular mechanisms of plant adaptation to native microbial conditions.

RevDate: 2022-06-28

Qin X, Zhou J, Wang Z, et al (2022)

Metagenomic analysis of the microbiome of the upper reproductive tract: combating ovarian cancer through predictive, preventive, and personalized medicine.

The EPMA journal pii:286 [Epub ahead of print].

Purpose: We investigated whether ovarian cancer could alter the genital microbiota in a specific way with clinical values. Furthermore, we proposed how such changes could be envisioned in a paradigm of predictive, preventive, and personalized medicine (PPPM).

Methods: The samples were collected using cotton swabs from the cervical, uterine cavity, fallopian tubes, and ovaries of patients subjected to the surgical procedures for the malignant/benign lesions. All samples were then analyzed by metagenomic shotgun sequencing. The distribution patterns and characteristics of the microbiota in the reproductive tract of subjects were analyzed and were interpreted in relation to the clinical outcomes of the subjects.

Results: While the ovarian cancer was able to alter the genital microbiota, the bacteria were the dominant microorganisms in all samples across all cohorts in the study (median 99%). The microbiota of the upper female reproductive tract were mainly from the cervical, identified by low bacterial biomass and high bacterial diversity. Ovarian cancer had a distinct microbiota signature. The tubal ligation affects its microbial distribution. There were no different species on the surface of platinum-sensitive ovarian tissues compared to samples from platinum-resistant patients.

Conclusion: The ovarian cancer-induced changes in microbiota magnify the potential of microbiota as a biotherapeutic modality in the treatment of ovarian cancer in this study and very likely for several malignancies and other conditions. Our findings demonstrated, for the first time, that microbiota could be dissected and applied in more specific fashion based on a predictive, preventive, and personalized medicine (PPPM) model in the treatment of ovarian cancer. Utilizing microbiota portfolio in a PPPM system in ovarian cancer would provide a unique opportunity to a clinically intelligent and novel approach in the treatment of ovarian cancer as well as several other conditions and malignancies.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13167-022-00286-1.

RevDate: 2022-06-28

Zhong L, Qin L, Ding X, et al (2022)

The regulatory effect of fermented black barley on the gut microbiota and metabolic dysbiosis in mice exposed to cigarette smoke.

Food research international (Ottawa, Ont.), 157:111465.

Smoking is a global public health event that can cause oxidative stress and gut microbiota dysbiosis and is related to the occurrence of diseases such as cancer and respiratory system disease. We previously found that fermented black barley was rich in antioxidative components such as polyphenols and flavonoids and regulated gut microbiota dysbiosis. In the present study, the protective effects of fermented black barley on cigarette smoke-induced damage, such as lung, reproduction organ injury, gut microbiota and metabolic dysbiosis, were investigated. Fermented black barley (100 μL/10 g·BW per day, containing 1 × 108 CFU/mL Lactobacillus) was administered orally to male ICR mice that were regularly exposed to cigarette smoke (one time a day, 15 cigarettes each time, 30 min/time). The intervention lasted continuously for 12 weeks. The results showed that compared to the group exposed only to cigarette smoke, fermented black barley treatment alleviated the pathological damage to lung and testis tissues and significantly increased the total sperm motility and antioxidative capacity of the lung. Fermented black barley also regulated the intestinal microbiome diversity; reduced the relative abundances of Lactobacillus, Turicibacter and Bifidobacterium; and increased the relative abundances of Oscillospira and Ruminococcus at the genus level. Furthermore, the metabolic profile was investigated via analysis of the abundances of fecal and hepatic metabolites, and it was shown that fermented black barley treatment alleviated the metabolic dysbiosis of lipids, amino acids, and the biosynthesis of steroid hormones (such as dehydroepiandrosterone sulfate, etc.) induced by cigarette smoking, which approached normal conditions. These regulatory effects may partially elucidate the beneficial role of fermented black barley in alleviating the harmful effects of cigarette smoking. In summary, supplementation with fermented cereal food may be a helpful way to ameliorate cigarette smoking-induced damage.

RevDate: 2022-06-28

Seo KH, Gyu Lee H, Young Eor J, et al (2022)

Effects of kefir lactic acid bacteria-derived postbiotic components on high fat diet-induced gut microbiota and obesity.

Food research international (Ottawa, Ont.), 157:111445.

Cellular components, surface layer protein (SLP) and exopolysaccharides (EPS) of postbiotic lactic bacteria (PLAB) can rehabilitate high-fat diet-induced dysbiosis and obese characteristic gut microbiome. However, it is not clear whether and how PLAB components affect gut microbiota and specifically adipocyte gene expression. Furthermore, SLP and EPS of PLAB in combination with polyphenolics of prebiotic wine grape seed flour (GSF) may have greater benefit on high-fat diet (HFD)-induced obesity and gut microbiota imbalance. To investigate interactions, C57BL/6 mice were fed a HFD and orally administered saline (CON), 250 mg/Kg EPS, or 120 mg/Kg SLP or saline with fed 2% GSF (GSF) or combination (42 mg/Kg EPS + 20 mg/Kg SLP + 0.5% GSF; ALL). There were significant reductions of HFD-induced body weight gain, adipose weight, serum triglyceride, and insulin resistance by the SLP and ALL diets compared to CON, with the most profound effect by ALL. ALL significantly affected the distribution of intestinal bacterial genus and species particularly those involved in production of short chain fatty acid (SCFA) and anti-obesogenic action. Microarray analysis from adipose tissue showed that ALL significantly affected expression of genes related to fatty acid biosynthesis, autophagy, inflammatory response, immune response, brown adipose tissue development and response to lipoteichoic acid and peptidoglycan (p < 0.05). Interestingly, expression of Akp13 (A-kinase anchoring protein 13) gene, which is related to body mass index and immune response, was negatively associated with the abundance of obesogenic and SCFAs producing gut bacteria. These data suggest that a combination of postbiotic kefir LAB cellular components and prebiotic GSF establishes a healthy intestinal microbiota that in part was associated with the prevention of obesity and obesity-related diseases.

RevDate: 2022-06-28

Al-Bulish MSM, Cao W, Yang R, et al (2022)

Docosahexaenoic acid-rich fish oil alleviates hepatic steatosis in association with regulation of gut microbiome in ob/ob mice.

Food research international (Ottawa, Ont.), 157:111373.

It remains to study whether docosahexaenoic acid-rich fish oil (DHA-FO) improves hepatic lipid metabolism by leptin-independent mechanisms. We used ob/ob mice as a model to investigate the effects of DHA-FO on hepatic steatosis. DHA-FO inhibited lipid droplets (LD) formation in liver of ob/ob mice. Probably because DHA-FO consumption prevented the accumulation of oleic acid, and suppressed the synthesis of triglycerides and cholesteryl esters. These beneficial effects might be concerned with the promotion of short chain fatty acids (SCFAs) production. Furthermore, DHA-FO could reverse gut bacteria dysbiosis, including increasing the abundance of SCFAs producers (e.g. Akkermansia and unclassified_Muribaculaceae), and suppressing the proliferation of conditional pathogenic bacteria, such as unclassified_Lachnospiraceae. DHA-FO also promoted colonic microbial function ("Glycerolipid metabolism") associated with lipid metabolism. As a potential ingredient for functional food, DHA-FO reduced LD accumulation, which might be associated with modulation of obesity-linked gut microbiome in ob/ob mice.

RevDate: 2022-06-28

Sun Y, Wang F, Liu Y, et al (2022)

Microbiome-metabolome responses of Fuzhuan brick tea crude polysaccharides with immune-protective benefit in cyclophosphamide-induced immunosuppressive mice.

Food research international (Ottawa, Ont.), 157:111370.

The present study investigated the immune-protective effect of polysaccharides from Fuzhuan brick tea (FBTPs) in cyclophosphamide (Cy)-induced immunosuppressive mice. The results showed that high-dose of FBTPs administration remarkably alleviated Cy-evoked immune damage through improving the body features, organ indices, immune responses and oxidative stress in the mice. Further microbiota analysis revealed that FBTPs obviously restored Cy-evoked microbial dysbiosis by increasing several beneficial bacteria Lactobacillus, Allobaculum, Unclassified_f_Lachnospiraceae and norank_f_Lachnospiraceae, while reducing Bacteroides, norank_f_Ruminococcaceae, Colidextribacter, Alloprevotella, norank_f_Desulfovibrionaceae and Helicobacter. Meanwhile, metabolomics analysis found that FBTPs significantly altered a range of microbial metabolites, including inosine, deoxyinosine, taurine, sinapic acid, maltotriose, butyric acid, lysophosphatidyl cholines (LysoPCs), lysophosphatidic acids (LysoPAs) and choline. These altered metabolites were involved in purine metabolism, ABC transporters, sulfur metabolism, neuroactive ligand-receptor interaction, biosynthesis of phenylpropanoids, carbohydrate digestion and absorption, protein digestion and absorption, choline metabolism in cancer and glycerophospholipid metabolism pathways, which were mainly related to immune responses, antioxidant capacity and energy supply of the immunosuppressive mice. Additionally, some significant correlations were observed between the specific microbiota and effective metabolites. These results provide a novel insight into the immune-protective effect of FBTPs on regulating the intestinal microbiota and metabolism, which are helpful for thoroughly understanding the nutrition of FBTPs and providing a solid basis for the deeper utilization of Fuzhuan brick tea (FBT).

RevDate: 2022-06-28

Kang J, Sun Y, Huang X, et al (2022)

Unraveling the microbial compositions, metabolic functions, and antibacterial properties of Huangshui, a byproduct of Baijiu fermentation.

Food research international (Ottawa, Ont.), 157:111320.

Huangshui (HS) is a byproduct of Chinese Baijiu production that has tremendous potential to become a high-value product in the food industry. This study comprehensively analyzed the commonalities and differences in physicochemical properties, microbial structures, metabolomes, flavor profiles, and antibacterial properties among sources of HS. The HS samples were extracted from three different pits in three different workshops within an industrial Baijiu distillery. Lactobacillus was the dominant genus of bacteria in all of them, while Kazachstania, Aspergillus, and Pichia were the dominant genera of fungi. A total of 45 volatile compounds, including ethyl hexanoate, hexanoic acid, and 1-butanol, were detected in the HS by headspace solid-phase microextraction coupled with gas chromatography mass spectrometry, suggesting HS could be used to flavor liquor. Untargeted metabolomic analysis yielded 224 nonvolatile metabolites that were common in all HS samples. These metabolites included organic acids, carbohydrates, benzenoids, nucleic acids, and fatty acids, which are mainly involved in amino acid and sugar metabolism. While the compositions of the microbiome and metabolome among HS samples were affected by workshop factors, there were essentially no differences in the bactericidal properties of the HS samples among workshops. HS exhibited potent antibacterial activities against Escherichia coli and Staphylococcus aureus, and HS was effective in inactivating mature biofilms formed on polystyrene microplates, as confirmed by scanning electron micrographs. Our results provided a theoretical basis to increase the economic value of HS for applications in the food industry.

RevDate: 2022-06-28

Wang D, Wu J, Zhu P, et al (2022)

Tryptophan-rich diet ameliorates chronic unpredictable mild stress induced depression- and anxiety-like behavior in mice: The potential involvement of gut-brain axis.

Food research international (Ottawa, Ont.), 157:111289.

Tryptophan, an essential amino acid, has been reported that it has the potential to regulate depression-like behavior. Meanwhile, Chronic stress-induced depression also has a close relationship with gut microbiota structure and composition. In the current research, we demonstrated that a tryptophan-rich diet (0.6% tryptophan w/w) significantly attenuated depression- and anxiety-like behaviors in a chronic unpredictable mild stress (CUMS)-treated mouse model. Tryptophan supplementation improved neuroinflammation, increased expression of BDNF, and improved mitochondrial energy metabolism in the brain of CUMS-treated mice. Besides, CUMS also enhanced the kynurenine pathway, but repressed the serotonin pathway and indole pathway of tryptophan metabolism, leading to a decrease in 5-HT and indole in serum, whereas tryptophan supplementation might shift the tryptophan metabolism more toward the serotonin pathway in CUMS-treated mice. The gut microbiome was restructured by increasing the relative abundance of Lachnospiracea, Clostridium, Lactobacillus, Bifidobacterium in tryptophan-treated depressive mice. Moreover, tryptophan administration inhibited stress-induced gut barrier damage and decreased inflammatory responses in the colon. Together, our study purports the gut-brain axis as a mechanism for the potential of tryptophan to improve depression and anxiety-related behavior.

RevDate: 2022-06-28

Farias da Cruz M, Baraúna Magno M, Alves Jural L, et al (2022)

Probiotics and dairy products in dentistry: A bibliometric and critical review of randomized clinical trials.

Food research international (Ottawa, Ont.), 157:111228.

The oral environment is an essential part of the human microbiome. The consumption of probiotic products may improve the oral microbiota and reduce the risk of diseases. This paper presents a bibliometric and critical review of randomized clinical trials (RCTs) that used probiotics to analyze oral parameters in humans. RCTs carried out with no age, gender, and ethnicity restrictions and published in the pre-COVID-19 period were included. Furthermore, the utilization of probiotic dairy products to improve oral health is discussed. The bibliometric review demonstrated that 'Microbiology,' 'Dental caries,' and 'Streptococcus mutants' were the most highlighted keywords. Furthermore, Sweden and India have the highest number of publications. The most prevalent outcomes were 'salivary parameters,' 'periodontal disease,' and 'dental caries.' The most used vehicles for probiotic administration were pharmaceutical formulas and dairy products. The administration of probiotic dairy products could modify the oral microbiota (reductions in S. mutans counts), influence the caries development and periodontal disease in children, adolescents, adults, and the elderly, and improve gingival health. The main probiotic dairy products investigated were milk, fermented milk, yogurt, kefir, curd, and cheese. Lacticaseibacillus paracasei SD1 was the most used probiotic culture. The studies demonstrated that the probiotic effect lasted 2-4 weeks after discontinuing consumption. However, the results depended on the subject type, study design, probiotic strain and concentration, and dairy product type. In conclusion, probiotic dairy products are promising alternatives to improve oral health.

RevDate: 2022-06-28

Yang D, Li C, Li L, et al (2022)

Novel insight into the formation mechanism of umami peptides based on microbial metabolism in Chouguiyu, a traditional Chinese fermented fish.

Food research international (Ottawa, Ont.), 157:111211.

Umami peptides formed by microbial metabolism play an important role in the umami taste of Chouguiyu. In this study, 138 umami peptides and 6 kinds of proteases in two categories from 35 microbial genera were identified from Chouguiyu during the fermentation process by peptidomics and metagenomics analysis, respectively. The interaction network maps between the umami peptides and protease-producing microbial genera in each protease classification were constructed based on Pearson's correlation coefficient after a two-way orthogonal partial least squares (O2PLS) evaluation. The proteases classified in 34 clusters of orthologous groups (COG) from Vagococcus, Peptostreptococcus, Acinetobacter, Psychrobacter, and Enterococcus played a major role in the formation of umami peptides. The core umami peptides with the highest abundance and correlation were mainly derived from troponin and myosin in mandarin fish. The lactic acid bacteria contributed most to the hydrolysis preparation of these umami peptides. This study is beneficial to screen the proteases and related microbial strains to improve the umami taste of Chouguiyu.

RevDate: 2022-06-28

Yasir M, Al-Zahrani IA, Bibi F, et al (2022)

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria.

Food research international (Ottawa, Ont.), 157:111190.

Consumption of fermented foods has grown worldwide due to the purported health benefits. It is thus critical to understand fermented foods microbiome that mainly influences the quality and safety of these foods. This study identified bacterial communities, including functional profiles of probiotics and antimicrobial resistance genes (ARGs), in pickled vegetables commonly consumed in the Middle Eastern, African, and Asian sub-continent regions. Eighteen samples from six pickled vegetables were collected from local markets in Saudi Arabia and analyzed using shotgun metagenomic sequencing. Statistical analyses revealed significant distance and separate clustering of bacterial communities among the different pickle types. Species of Levilactobacillus namurensis, Lentilactobacillus buchneri, Lentilactobacillus parafarraginis, Lactiplantibacillus pentosus, Pectobacterium carotovorum, Leuconostoc carnosum, Weissella confuse were found in a range of dominance in most of the samples. Binning revealed 33 high-quality, metagenome-assembled genomes (MAGs), including 4 MAGs representing putatively novel species of Lactobacillus, Alcanivorax, and Dichelobacter. Moreover, 285 ARGs and variants produce resistance against 20 classes of antibiotics were retrieved, mostly from Enterobacteriaceae contigs. The metagenomes harbored relatively high abundances of carbohydrate fermentation enzymes, as well as metabolic pathways for amino acid metabolism, cofactors and vitamins biosynthesis. Overall, by providing a comprehensive overview of bacterial communities and probiotic bacteria in pickled vegetables, the results suggest the need for more hygienic processing to avoid Enterobacteriaceae contamination and ARG spread.

RevDate: 2022-06-28

Garg Y, Kanwar N, Dodiya H, et al (2022)

Microbiome Medicine: Microbiota in Development and Management of Cardiovascular Diseases.

Endocrine, metabolic & immune disorders drug targets pii:EMIDDT-EPUB-124787 [Epub ahead of print].

The gut microbiome consists of the trillions of bacteria and other microbes whose metabolic activities and interactions with the immune system go beyond the gut itself. We are all aware that bacteria and other microorganisms have a significant impact on our health. Also, health of the bacteria directly reflects the health status of the body where they reside. Eventually, alterations in the microbiome at different sites of a body is associated with many different diseases such as obesity, IBD, malnutrition, CVD, etc. Microbiota directly or indirectly affects the heart with formation of plaques in the blood vessels and cell wall become prone to the lesion development. This ultimately leads to heighten the overall inflammatory status via increased bacterial translocation. Metabolites derived from the gut microbial metabolism of choline, phosphatidylcholine, and L-carnitine directly contribute to CVD pathology. These dietary nutrients have trimethylamine (TMA) moiety, which participates in the development of atherosclerotic heart disease. The objective of this review was to examine various metabolic pathways regulated by the gut microbiome that appear to alter heart function and lead to the development and progression of cardiovascular diseases, as well as how to target the gut microbiome for a healthier heart. In this review, we had also discussed about various clinical drugs having crosstalk between microbiota and heart and clinical trials for gut-heart microbiome.

RevDate: 2022-06-27

Liu Y, Yang M, Tang L, et al (2022)

TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila.

Microbiome, 10(1):98.

BACKGROUND: Well-balanced interactions between gut microbiota and the immune system are essential to prevent chronic intestinal inflammation, as observed in inflammatory bowel diseases (IBD). Toll-like receptor 4 (TLR4) functions as a sensor mediating the crosstalk between the intestinal commensal microbiome and host immunity, but the influence of TLR4 on the shaping of intestinal microbiota and immune responses during colon inflammation remains poorly characterized. We investigated whether the different susceptibilities to colitis between wild-type (WT) and TLR4-/- mice were gut microbiota-dependent and aimed to identify the potential immunity modulation mechanism.

METHODS: We performed antibiotic depletion of the microbiota, cohousing experiments, and faecal microbiota transplantation (FMT) in WT and TLR4-/- mice to assess the influence of TLR4 on intestinal microbial ecology. 16S rRNA sequencing was performed to dissect microbial discrepancies, and dysbiosis-associated immune perturbation was investigated by flow cytometry. Akkermansia muciniphila (A. muciniphila)-mediated immune modulation was confirmed through the T-cell transfer colitis model and bone marrow chimaera construction.

RESULTS: TLR4-/- mice experienced enhanced susceptibility to DSS-induced colitis. 16S rRNA sequencing showed notable discrepancy in the gut microbiota between WT and TLR4-/- mice. In particular, A. muciniphila contributed most to distinguishing the two groups. The T-cell transfer colitis model and bone marrow transplantation (BMT) consistently demonstrated that A. muciniphila ameliorated colitis by upregulating RORγt+ Treg cell-mediated immune responses. Mucosal biopsies from human manifested parallel outcomes with colon tissue from WT mice, as evidenced by the positive correlation between TLR4 expression and intestinal A. muciniphila colonization during homeostasis.

CONCLUSIONS: Our results demonstrate a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses. These findings provide a new perspective on host-commensal symbiosis, which may be beneficial for developing potential therapeutic strategies. Video abstract.

RevDate: 2022-06-27

Wynendaele E, Debunne N, Janssens Y, et al (2022)

The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the host-microbiome interaction.

BMC biology, 20(1):151.

BACKGROUND: Colorectal cancer, one of the most common malignancies worldwide, is associated with a high mortality rate, mainly caused by metastasis. Comparative metagenome-wide association analyses of healthy individuals and cancer patients suggest a role for the human intestinal microbiota in tumor progression. However, the microbial molecules involved in host-microbe communication are largely unknown, with current studies mainly focusing on short-chain fatty acids and amino acid metabolites as potential mediators. Quorum sensing peptides are not yet considered in this context since their presence in vivo and their ability to affect host cells have not been reported so far.

RESULTS: Here, we show that EntF*, a metabolite of the quorum sensing peptide EntF produced by Enterococcus faecium, is naturally present in mice bloodstream. Moreover, by using an orthotopic mouse model, we show that EntF* promotes colorectal cancer metastasis in vivo, with metastatic lesions in liver and lung tissues. In vitro tests suggest that EntF* regulates E-cadherin expression and consequently the epithelial-mesenchymal transition, via the CXCR4 receptor. In addition, alanine-scanning analysis indicates that the first, second, sixth, and tenth amino acid of EntF* are critical for epithelial-mesenchymal transition and tumor metastasis.

CONCLUSION: Our work identifies a new class of molecules, quorum sensing peptides, as potential regulators of host-microbe interactions. We prove, for the first time, the presence of a selected quorum sensing peptide metabolite in a mouse model, and we demonstrate its effects on colorectal cancer metastasis. We believe that our work represents a starting point for future investigations on the role of microbiome in colorectal cancer metastasis and for the development of novel bio-therapeutics in other disease areas.

RevDate: 2022-06-27

Sikder MM, Vestergård M, Kyndt T, et al (2022)

Genetic disruption of Arabidopsis secondary metabolite synthesis leads to microbiome-mediated modulation of nematode invasion.

The ISME journal [Epub ahead of print].

In-depth understanding of metabolite-mediated plant-nematode interactions can guide us towards novel nematode management strategies. To improve our understanding of the effects of secondary metabolites on soil nematode communities, we grew Arabidopsis thaliana genetically altered in glucosinolate, camalexin, or flavonoid synthesis pathways, and analyzed their root-associated nematode communities using metabarcoding. To test for any modulating effects of the associated microbiota on the nematode responses, we characterized the bacterial and fungal communities. Finally, as a proxy of microbiome-modulating effects on nematode invasion, we isolated the root-associated microbiomes from the mutants and tested their effect on the ability of the plant parasitic nematode Meloidogyne incognita to penetrate tomato roots. Most mutants had altered relative abundances of several nematode taxa with stronger effects on the plant parasitic Meloidogyne hapla than on other root feeding taxa. This probably reflects that M. hapla invades and remains embedded within root tissues and is thus intimately associated with the host. When transferred to tomato, microbiomes from the flavonoid over-producing pap1-D enhanced M. incognita root-invasion, whereas microbiomes from flavonoid-deficient mutants reduced invasion. This suggests microbiome-mediated effect of flavonoids on Meloidogyne infectivity plausibly mediated by the alteration of the abundances of specific microbial taxa in the transferred microbiomes, although we could not conclusively pinpoint such causative microbial taxa.

RevDate: 2022-06-27

Grego S, Welling CM, Miller GH, et al (2022)

A hands-free stool sampling system for monitoring intestinal health and disease.

Scientific reports, 12(1):10859.

Analysis of stool offers simple, non-invasive monitoring for many gastrointestinal (GI) diseases and access to the gut microbiome, however adherence to stool sampling protocols remains a major challenge because of the prevalent dislike of handling one's feces. We present a technology that enables individual stool specimen collection from toilet wastewater for fecal protein and molecular assay. Human stool specimens and a benchtop test platform integrated with a commercial toilet were used to demonstrate reliable specimen collection over a wide range of stool consistencies by solid/liquid separation followed by spray-erosion. The obtained fecal suspensions were used to perform occult blood tests for GI cancer screening and for microbiome 16S rRNA analysis. Using occult blood home test kits, we found overall 90% agreement with standard sampling, 96% sensitivity and 86% specificity. Microbiome analysis revealed no significant difference in within-sample species diversity compared to standard sampling and specimen cross-contamination was below the detection limit of the assay. Furthermore, we report on the use of an analogue turbidity sensor to assess in real time loose stools for tracking of diarrhea. Implementation of this technology in residential settings will improve the quality of GI healthcare by facilitating increased adherence to routine stool monitoring.

RevDate: 2022-06-27

McDonald AG, Mariethoz J, Davey GP, et al (2022)

In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis.

Scientific reports, 12(1):10846.

Human milk oligosaccharides (HMOs) form the third most abundant component of human milk and are known to convey several benefits to the neonate, including protection from viral and bacterial pathogens, training of the immune system, and influencing the gut microbiome. As HMO production during lactation is driven by enzymes that are common to other glycosylation processes, we adapted a model of mucin-type GalNAc-linked glycosylation enzymes to act on free lactose. We identified a subset of 11 enzyme activities that can account for 206 of 226 distinct HMOs isolated from human milk and constructed a biosynthetic reaction network that identifies 5 new core HMO structures. A comparison of monosaccharide compositions demonstrated that the model was able to discriminate between two possible groups of intermediates between major subnetworks, and to assign possible structures to several previously uncharacterised HMOs. The effect of enzyme knockouts is presented, identifying β-1,4-galactosyltransferase and β-1,3-N-acetylglucosaminyltransferase as key enzyme activities involved in the generation of the observed HMO glycosylation patterns. The model also provides a synthesis chassis for the most common HMOs found in lactating mothers.

RevDate: 2022-06-27

Attauabi M, Madsen GR, Bendtsen F, et al (2022)

Influence of Genetics, Immunity and the Microbiome on the Prognosis of Inflammatory Bowel Disease (IBD Prognosis Study): the protocol for a Copenhagen IBD Inception Cohort Study.

BMJ open, 12(6):e055779 pii:bmjopen-2021-055779.

INTRODUCTION: Inflammatory bowel diseases (IBD), encompassing Crohn's disease and ulcerative colitis, are chronic, inflammatory diseases of the gastrointestinal tract. We have initiated a Danish population-based inception cohort study aiming to investigate the underlying mechanisms for the heterogeneous course of IBD, including need for, and response to, treatment.

METHODS AND ANALYSIS: IBD Prognosis Study is a prospective, population-based inception cohort study of unselected, newly diagnosed adult, adolescent and paediatric patients with IBD within the uptake area of Hvidovre University Hospital and Herlev University Hospital, Denmark, which covers approximately 1 050 000 inhabitants (~20% of the Danish population). The diagnosis of IBD will be according to the Porto diagnostic criteria in paediatric and adolescent patients or the Copenhagen diagnostic criteria in adult patients. All patients will be followed prospectively with regular clinical examinations including ileocolonoscopies, MRI of the small intestine, validated patient-reported measures and objective examinations with intestinal ultrasound. In addition, intestinal biopsies from ileocolonoscopies, stool, rectal swabs, saliva samples, swabs of the oral cavity and blood samples will be collected systematically for the analysis of biomarkers, microbiome and genetic profiles. Environmental factors and quality of life will be assessed using questionnaires and, when available, automatic registration of purchase data. The occurrence and course of extraintestinal manifestations will be evaluated by rheumatologists, dermatologists and dentists, and assessed by MR cholangiopancreatography, MR of the spine and sacroiliac joints, ultrasonography of peripheral joints and entheses, clinical oral examination, as well as panoramic radiograph of the jaws. Fibroscans and dual-energy X-ray absorptiometry scans will be performed to monitor occurrence and course of chronic liver diseases, osteopenia and osteoporosis.

ETHICS AND DISSEMINATION: This study has been approved by Ethics Committee of the Capital Region of Denmark (approval number: H-20065831). Study results will be disseminated through publication in international scientific journals and presentation at (inter)national conferences.

RevDate: 2022-06-27

Hurych J, Vejmelka J, Hlinakova L, et al (2022)

Protocol for faecal microbiota transplantation in irritable bowel syndrome: the MISCEAT study - a randomised, double-blind cross-over study using mixed microbiota from healthy donors.

BMJ open, 12(6):e056594 pii:bmjopen-2021-056594.

INTRODUCTION: Several studies have demonstrated dysbiosis in irritable bowel syndrome (IBS). Therefore, faecal microbiota transplantation, whose effect and safety have been proven in Clostridioides difficile infections, may hold promise in other conditions, including IBS. Our study will examine the effectiveness of stool transfer with artificially increased microbial diversity in IBS treatment.

METHODS AND ANALYSIS: A three-group, double-blind,randomised, cross-over, placebo-controlled study of two pairs of gut microbiota transfer will be conducted in 99 patients with diarrhoeal or mixed type of IBS. Patients aged 18-65 will be randomised into three equally sized groups: group A will first receive two enemas of study microbiota mixture (deep-frozen stored stool microbiota mixed from eight healthy donors); after 8 weeks, they will receive two enemas with placebo (autoclaved microbiota mixture), whereas group B will first receive placebo, then microbiota mixture. Finally, group C will receive placebos only. The IBS Severity Symptom Score (IBS-SSS) questionnaires will be collected at baseline and then at weeks 3, 5, 8, 11, 13, 32. Faecal bacteriome will be profiled before and regularly after interventions using 16S rDNA next-generation sequencing. Food records, dietary questionnaires, anthropometry, bioimpedance, biochemistry and haematology workup will be obtained at study visits during the follow-up period. The primary outcome is the change in the IBS-SSS between the baseline and 4 weeks after the intervention for each patient compared with placebo. Secondary outcomes are IBS-SSS at 2 weeks after the intervention and 32 weeks compared with placebo and changes in the number of loose stools, Bristol stool scale, abdominal pain and bloating, anthropometric parameters, psychological evaluation and the gut microbiome composition.

ETHICS AND DISSEMINATION: The study was approved by the Ethics Committee of Thomayer University Hospital, Czechia (G-18-26); study results will be published in peer-reviewed journals and presented at international conferences and patient group meetings.


RevDate: 2022-06-27

Faridl M, Mellyani K, Khoirunnisa K, et al (2022)

RNA-seq analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic COVID-19 patients.

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases pii:S1201-9712(22)00368-X [Epub ahead of print].

OBJECTIVES: The characterization of asymptomatic and mildly symptomatic COVID-19 patients by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients.

METHODS: An RNA-seq analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data.

RESULTS: Both groups of patients underwent a cilia modification & mRNA splicing. Modulation in macroautophagy, epigenetics, and cell cycle processes was observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients.

CONCLUSION: A reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.

RevDate: 2022-06-27

Radka CD, Miller DJ, Frank MW, et al (2022)

Biochemical characterization of the first step in sulfonolipid biosynthesis in Alistipes finegoldii.

The Journal of biological chemistry pii:S0021-9258(22)00637-8 [Epub ahead of print].

Sulfonolipids are unusual lipids found in the outer membranes of Gram-negative bacteria in the phylum Bacteroidetes. Sulfonolipid and its deacylated derivative, capnine, are sulfur analogs of ceramide-1-phosphate and sphingosine-1-phosphate, respectively; thus, sulfonolipid biosynthesis is postulated to be similar to the sphingolipid biosynthetic pathway. Here, we identify the first enzyme in sulfonolipid synthesis in Alistipes finegoldii, an anaerobic gut commensal bacterium, as the product of the alfi_1224 gene, cysteate acyl-acyl carrier protein (ACP) transferase (SulA). We show SulA catalyzes the condensation of acyl-ACP and cysteate (3-sulfo-alanine) to form 3-ketocapnine. Acyl-CoA is a poor substrate. We show SulA has a bound pyridoxal phosphate (PLP) cofactor that undergoes a spectral redshift in the presence of cysteate, consistent with the transition of the lysine-aldimine complex to a substrate-aldimine complex. Furthermore, the SulA crystal structure shows the same prototypical fold found in bacterial serine palmitoyltransferases (Spt), enveloping the PLP cofactor bound to Lys251. We observed the SulA and Spt active sites are identical except for Lys281 in SulA, which is an alanine in Spt. Additionally, SulA(K281A) is catalytically inactive, but binds cysteate and forms the external aldimine normally, highlighting the structural role of the Lys281 side chain in walling off the active site from bulk solvent. Finally, the electropositive groove on the protein surface adjacent to the active site entrance provides a landing pad for the electronegative acyl-ACP surface. Taken together, these data identify the substrates, products, and mechanism of SulA, the PLP-dependent condensing enzyme that catalyzes the first step in sulfonolipid synthesis in a gut commensal bacterium.

RevDate: 2022-06-27

Arima K, Zhong R, Ugai T, et al (2022)

Western-style Diet, pks Island-Carrying Escherichia coli, and Colorectal Cancer: Analyses from Two Large Prospective Cohort Studies.

Gastroenterology pii:S0016-5085(22)00672-2 [Epub ahead of print].

BACKGROUND AND AIMS: Evidence supports a carcinogenic role of Escherichia coli carrying the polyketide synthase (pks) island that encodes enzymes for colibactin biosynthesis. We hypothesized that the association of western-style diet (rich in red and processed meat) with colorectal cancer incidence might be stronger for tumors containing higher amounts of pks+ E. coli.

METHODS: Western diet score was calculated using food frequency questionnaire data obtained every four years during follow-up of 134,775 participants in two U.S.-wide prospective cohort studies. Using quantitative polymerase chain reaction, we measured pks+ E. coli DNA in 1,175 tumors among 3,200 incident colorectal cancer cases that had occurred during the follow-up. We utilized the 3,200 cases and inverse probability weighting (to adjust for selection bias due to tissue availability), integrated in multivariable-adjusted duplication-method Cox proportional hazards regression analyses.

RESULTS: The association of the western diet score with colorectal cancer incidence was stronger for tumors containing higher levels of pks+ E. coli (Pheterogeneity = 0.014). Multivariable-adjusted hazard ratios (with 95% confidence interval) for the highest (vs. lowest) tertile of the western diet score were 3.45 (1.53-7.78) (Ptrend = 0.001) for pks+ E. coli-high tumors, 1.22 (0.57-2.63) for pks+ E. coli-low tumors, and 1.10 (0.85-1.42) for pks+ E. coli-negative tumors. The pks+ E. coli level was associated with lower disease stage but not with tumor location, microsatellite instability, or BRAF, KRAS, or PIK3CA mutations.

CONCLUSIONS: Western-style diet is associated with higher incidence of colorectal cancer containing abundant pks+ E. coli, supporting a potential link between diet, the intestinal microbiota, and colorectal carcinogenesis.

RevDate: 2022-06-27

Troci A, Rausch P, Waschina S, et al (2022)

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis.

Molecular nutrition & food research [Epub ahead of print].

SCOPE: The gut microbiome regulates various metabolic pathways in the host and its dysbiosis is involved in the pathogenesis of diverse diseases. Multiple factors modulate the composition of the microbiome and how it physiologically functions, but one of the major factors triggering gut microbiome establishment is diet. We aim to unravel interactions and changes between diet and gut microbiome over a period of 3 years.

METHODS AND RESULTS: We investigated the relation between 152 dietary factors, in terms of food groups and nutrients, and the microbiome of 75 individuals over a three-year time period. Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. Associations between diet and MAGs, functional KOs and metabolites were explored for each time point. We showed that there were significant changes in gut microbiome taxonomy and functional composition between two time points (Padonis < 0.05) and identified microbial taxa and KO functional units that were differentially expressed over the study period. Whereas microbial taxonomy was found to be highly individualized and unstable, overall microbial functions stayed relatively stable. Moreover, in-silico metabolic modeling of the gut microbial communities indicated that changes in dietary intake of medium-chain saturated fatty acids is accompanied by an altered utilization of amino acids by the gut microbiome.

CONCLUSION: Our study design allowed us to validate functional stability within the gut microbiome of healthy subjects over a three-year period. However, enduring changes in nutrition such as increased alcohol consumption or decreased intake of vegetables come along with enhanced microbial functions that are associated with disease etiology. This article is protected by copyright. All rights reserved.

RevDate: 2022-06-27

Campos PM, Darwish N, Shao J, et al (2022)

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota.

Poultry science, 101(8):101971 pii:S0032-5791(22)00263-2 [Epub ahead of print].

The chicken microbiota is often analyzed to address questions about the effects of diet or disease on poultry health. To analyze the microbiota, bioinformatic platforms such as QIIME 2 and mothur are used, which incorporate public taxonomic databases such as Greengenes, the ribosomal database project (RDP), and SILVA to assign taxonomies to bacterial sequences. Many chicken microbiota studies continue to incorporate the Greengenes database, which has not been updated since 2013. To determine whether a choice of database could affect results, this study compared the results of bioinformatic analyses obtained using the Greengenes, RDP, and SILVA databases on a cecal luminal microbiome dataset. The QIIME 2 platform was used to process 16S bacterial sequences and assign taxonomies with Greengenes, RDP, and SILVA. Linear discriminant analysis effect size (LEfSe) was performed, allowing for the comparison of taxonomies considered significantly differentially abundant between the three databases. Some notable differences between databases were observed in results, in particular the ability of SILVA database to classify members of the family Lachnospiraceae into separate genera, while these members remained in one group of unclassified Lachnospiraceae through Greengenes and RDP. LEfSe analyses showed that the SILVA database produced more differentially abundant genera, in large part due to the classification of these separate Lachnospiraceae genera. Additionally, the relative abundance of unclassified Lachnospiraceae in SILVA results was significantly lower than in RDP results. Our results show the choice of taxonomic database can influence the results of a microbiota study at the genus level, potentially affecting the interpretation of the results. The use of the SILVA database is recommended over Greengenes in chicken microbiota studies, as more specific classifications at the genus level may provide more accurate interpretations of changes in the microbiota.

RevDate: 2022-06-27

Mercado JV, Koyama M, K Nakasaki (2022)

Co-occurrence network analysis reveals loss of microbial interactions in anaerobic digester subjected to repeated organic load shocks.

Water research, 221:118754 pii:S0043-1354(22)00707-2 [Epub ahead of print].

Fluctuations in the anaerobic digestion (AD) organic loading rate (OLR) cause shocks to the AD microbiome, which lead to unstable methane productivity. Managing these fluctuations requires a larger digester, which is impractical for community-scale applications, limiting the potential of AD in advancing a circular economy. To allow operation of small-scale AD while managing OLR fluctuations, we need to tackle the issue through elucidation of the microbial community dynamics via 16S rRNA gene sequencing. This study elucidated the interrelation of the AD performance and the dynamics of the microbial interactions within its microbiome in response to repeated high OLR shocks at different frequencies. The OLR shocks were equivalent to 4 times the baseline OLR of 2 g VS/L/d. We found that less frequent organic load shocks result to deterioration of methane productivity. Co-occurrence network analysis shows that this coincides with the breakdown of the microbiome network structure. This suggests loss of microbial interactions necessary in maintaining stable AD. Identification of species influencing the network structure revealed that a species under the genus Anaerovorax has the greatest influence, while orders Spirochaetales and Synergistales represent the greatest number of the influential species. We inferred that the impact imposed by the OLR shocks shifted the microbiome activity towards biochemical pathways that are not contributing to methane production. Establishing a small-scale AD system that permits OLR fluctuations would require developing an AD microbiome resilient to infrequent organic loading shocks.

RevDate: 2022-06-27

Lai Y, Hayashi N, TK Lu (2022)

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology.

Current opinion in chemical biology, 70:102178 pii:S1367-5931(22)00063-1 [Epub ahead of print].

The role of the microbiome in health and disease is attracting the attention of researchers seeking to engineer microorganisms for diagnostic and therapeutic applications. Recent progress in synthetic biology may enable the dissection of host-microbiota interactions. Sophisticated genetic circuits that can sense, compute, memorize, and respond to signals have been developed for the stable commensal bacterium Bacteroides thetaiotaomicron, dominant in the human gut. In this review, we highlight recent advances in expanding the genetic toolkit for B. thetaiotaomicron and foresee several applications of this species for microbiome engineering. We provide our perspective on the challenges and future opportunities for the engineering of human gut-associated bacteria as living therapeutic agents.

RevDate: 2022-06-27

Prieto Riquelme MV, Garner E, Gupta S, et al (2022)

Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes.

Environmental science & technology [Epub ahead of print].

Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.

RevDate: 2022-06-27

Muthappa DM, Lamba S, Sivasankaran SK, et al (2022)

16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments.

Foodborne pathogens and disease [Epub ahead of print].

Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.

RevDate: 2022-06-27

Davis BT, Chen Z, Islam MBAR, et al (2022)

Fecal Microbiota Transfer Attenuates Gut Dysbiosis and Functional Deficits After Traumatic Brain Injury.

Shock (Augusta, Ga.), 57(6):251-259.

BACKGROUND: Traumatic brain injury (TBI) is an underrecognized public health threat. Survivors of TBI often suffer long-term neurocognitive deficits leading to the progressive onset of neurodegenerative disease. Recent data suggests that the gut-brain axis is complicit in this process. However, no study has specifically addressed whether fecal microbiota transfer (FMT) attenuates neurologic deficits after TBI.

HYPOTHESIS: We hypothesized that fecal microbiota transfer would attenuate neurocognitive, anatomic, and pathologic deficits after TBI.

METHODS: C57Bl/6 mice were subjected to severe TBI (n = 20) or sham-injury (n = 20) via an open-head controlled cortical impact. Post-injury, this cohort of mice underwent weekly oral gavage with a slurry of healthy mouse stool or vehicle alone beginning 1 h post-TBI followed by behavioral testing and neuropathologic analysis. 16S ribosomal RNA sequencing of fecal samples was performed to characterize gut microbial community structure pre- and post-injury. Zero maze and open field testing were used to evaluate post-traumatic anxiety, exploratory behavior, and generalized activity. 3D, contrast enhanced, magnetic resonance imaging was used to determine differences in cortical volume loss and white matter connectivity. Prior to euthanasia, brains were harvested for neuropathologic analysis.

RESULTS: Fecal microbiome analysis revealed a large variance between TBI, and sham animals treated with vehicle, while FMT treated TBI mice had restoration of gut dysbiosis back to levels of control mice. Neurocognitive testing demonstrated a rescue of normal anxiety-like and exploratory behavior in TBI mice treated with FMT. FMT treated TBI mice spent a greater percentage of time (22%, P = 0.0001) in the center regions of the Open Field as compared to vehicle treated TBI mice (13%). Vehicle-treated TBI animals also spent less time (19%) in the open areas of zero maze than FMT treated TBI mice (30%, P = 0.0001). Comparing in TBI mice treated with FMT, MRI demonstrated a marked attenuation in ventriculomegaly (P < 0.002) and a significant change in fractional anisotropy (i.e., loss of white matter connectivity) (P < 0.0001). Histologic analysis of brain sections revealed a FMT- injury dependent interaction in the microglia/macrophage-specific ionized calcium-binding protein, Iba1 (P = 0.002).

CONCLUSION: These data suggest that restoring a pre-injury gut microbial community structure may be a promising therapeutic intervention after TBI.

RevDate: 2022-06-27

Ferrini S, Grego E, Ala U, et al (2022)

Feasibility of 16S rRNA sequencing for cerebrospinal fluid microbiome analysis in cattle with neurological disorders: a pilot study.

Veterinary research communications [Epub ahead of print].

Bacterial infection of the central nervous system (CNS) in cattle requires prompt and adequate antimicrobial treatment. The current gold standard for antemortem etiological diagnosis is cerebrospinal fluid (CSF) culture, which often yields false negative results. CSF has long been considered a sterile district in healthy patients, but this notion has been recently challenged. For this pilot study, we used 16S rRNA gene sequencing to investigate the microbial composition of CSF of cattle presenting with CNS disorders and to compare it between subjects with CNS infections and with CNS disorders of other nature. The study sample was 10 animals: 4 presenting with CNS infectious-inflammatory diseases and 6 with other CNS disorders, based on definitive diagnosis. Since the initial round of a standard 16S rRNA PCR did not yield sufficient genetic material for sequencing in any of the samples, the protocol was modified to increase its sensitivity. Bacterial genetic material was identified in 6 animals and 2 groups were formed: an infectious inflammatory (n = 3) and a noninfectious inflammatory group (n = 3). The most frequently expressed bacterial families were Pseudomonadaceae (44.61%), Moraxellaceae (19.54%), Mycobacteriaceae (11.80%); the genera were Pseudomonas (45.42%), Acinetobacter (19.91%), Mycobacterium (12.01%). There were no detectable differences in the CSF microbial composition of the samples from the two groups. Sequencing of bacterial DNA present in the CSF was possible only after increasing PCR sensitivity. The results of 16S rRNA sequencing showed the presence of a microbial community in the CSF in cattle with neurological disorders. Further studies, in which CSF samples from healthy animals and samples from the environment are included as controls, are needed.

RevDate: 2022-06-27

Ghazi AR, Sucipto K, Rahnavard A, et al (2022)

High-sensitivity pattern discovery in large, paired multiomic datasets.

Bioinformatics (Oxford, England), 38(Supplement_1):i378-i385.

MOTIVATION: Modern biological screens yield enormous numbers of measurements, and identifying and interpreting statistically significant associations among features are essential. In experiments featuring multiple high-dimensional datasets collected from the same set of samples, it is useful to identify groups of associated features between the datasets in a way that provides high statistical power and false discovery rate (FDR) control.

RESULTS: Here, we present a novel hierarchical framework, HAllA (Hierarchical All-against-All association testing), for structured association discovery between paired high-dimensional datasets. HAllA efficiently integrates hierarchical hypothesis testing with FDR correction to reveal significant linear and non-linear block-wise relationships among continuous and/or categorical data. We optimized and evaluated HAllA using heterogeneous synthetic datasets of known association structure, where HAllA outperformed all-against-all and other block-testing approaches across a range of common similarity measures. We then applied HAllA to a series of real-world multiomics datasets, revealing new associations between gene expression and host immune activity, the microbiome and host transcriptome, metabolomic profiling and human health phenotypes.

An open-source implementation of HAllA is freely available at http://huttenhower.sph.harvard.edu/halla along with documentation, demo datasets and a user group.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RevDate: 2022-06-27

Torp AM, Kamguyan K, Christfort JF, et al (2022)

Local Delivery of Streptomycin in Microcontainers Facilitates Colonization of Streptomycin-Resistant Escherichia coli in the Rat Colon.

Applied and environmental microbiology [Epub ahead of print].

Oral antibiotic treatment is often applied in animal studies in order to allow establishment of an introduced antibiotic-resistant bacterium in the gut. Here, we compared the application of streptomycin dosed orally in microcontainers to dosage through drinking water. The selective effect on a resistant bacterial strain, as well as the effects on fecal, luminal, and mucosal microbiota composition, were investigated. Three groups of rats (n = 10 per group) were orally dosed with microcontainers daily for 3 days. One of these groups (STR-M) received streptomycin-loaded microcontainers designed for release in the distal ileum, while the other two groups (controls [CTR] and STR-W) received empty microcontainers. The STR-W group was additionally dosed with streptomycin through the drinking water. A streptomycin-resistant Escherichia coli strain was orally inoculated into all animals. Three days after inoculation, the resistant E. coli was found only in the cecum and colon of animals receiving streptomycin in microcontainers but in all intestinal compartments of animals receiving streptomycin in the drinking water. 16S rRNA amplicon sequencing revealed significant changes in the fecal microbiota of both groups of streptomycin-treated animals. Investigation of the inner colonic mucus layer by confocal laser scanning microscopy and laser capture microdissection revealed no significant effect of streptomycin treatment on the mucus-inhabiting microbiota or on E. coli encroachment into the inner mucus. Streptomycin-loaded microcontainers thus enhanced proliferation of an introduced streptomycin-resistant E. coli in the cecum and colon without affecting the small intestine environment. While improvements of the drug delivery system are needed to facilitate optimal local concentration and release of streptomycin, the application of microcontainers provides new prospects for antibiotic treatment. IMPORTANCE Delivery of antibiotics in microcontainer devices designed for release at specific sites of the gut represents a novel approach which might reduce the amount of antibiotic needed to obtain a local selective effect. We propose that the application of microcontainers may have the potential to open novel opportunities for antibiotic treatment of humans and animals with fewer side effects on nontarget bacterial populations. In the current study, we therefore elucidated the effects of streptomycin, delivered in microcontainers coated with pH-sensitive lids, on the selective effect on a resistant bacterium, as well as on the surrounding intestinal microbiota in rats.

RevDate: 2022-06-27

Mason CJ, Peiffer M, Chen B, et al (2022)

Opposing Growth Responses of Lepidopteran Larvae to the Establishment of Gut Microbiota.

Microbiology spectrum [Epub ahead of print].

Gut microbiota can have diverse impacts on hosts, the nature of which often depend on the circumstances. For insect gut microbes, the quality and nature of host diets can be a significant force in swinging the pendulum from inconsequential to functionally important. In our study, we addressed whether beneficial microbes in one species impart similar functions to related species under identical conditions. Using fall armyworm (Spodoptera frugiperda), beet armyworm (Spodoptera exigua), and other noctuid hosts, we implemented an axenic rearing strategy and manipulated gut bacterial populations and dietary conditions. Our results revealed that some gut Enterococcus and Enterobacter isolates can facilitate utilization of a poor diet substrate by fall armyworm, but this was not the case for other more optimized diets. While Enterococcus provided benefits to fall armyworm, it was decidedly antagonistic to beet armyworm (Spodoptera exigua) under identical conditions. Unique isolates and bacterial introductions at early growth stages were critical to how both larval hosts performed. Our results provide robust evidence of the roles in which bacteria support lepidopteran larval growth, but also indicate that the directionality of these relationships can differ among congener hosts. IMPORTANCE Insects have intimate relationships with gut microbiota, where bacteria can contribute important functions to their invertebrate hosts. Lepidopterans are important insect pests, but how they engage with their gut bacteria and how that translates to impacts on the host are lacking. Here we demonstrate the facultative nature of gut microbiota in lepidopteran larvae and the importance of diet in driving mutualistic or antagonistic relationships. Using multiple lepidopteran species, we uncover that the same bacteria that can facilitate exploitation of a challenging diet in one host severely diminishes larval performance of another larval species. Additionally, we demonstrate the beneficial functions of gut microbiota on the hosts are not limited to one lineage, but rather multiple isolates can facilitate the exploitation of a suboptimal diet. Our results illuminate the context-dependent nature of the gut microbiomes in invertebrates, and how host-specific microbial engagement can produce dramatically different interactions.

RevDate: 2022-06-27

Saito D, Lemos LN, Ferreira ATRN, et al (2022)

Draft Genome Sequences of Five Putatively Novel Saccharibacteria Species Assembled from the Human Oral Metagenome.

Microbiology resource announcements [Epub ahead of print].

We report the draft metagenome-assembled genomes (MAGs) of five putatively novel Saccharibacteria strains retrieved from the oral microbiome. MAGs were obtained from nonstimulated saliva samples from hosts with various clinical statuses and correspond to distinct species taxonomically placed within the Saccharimonadaceae family, as determined by genome-wide analysis against previously described TM7 genomes.

RevDate: 2022-06-27

Holley JC, Jackson MN, Pham AT, et al (2022)

Carpenter Bees (Xylocopa) Harbor a Distinctive Gut Microbiome Related to That of Honey Bees and Bumble Bees.

Applied and environmental microbiology [Epub ahead of print].

Eusocial corbiculate bees, including bumble bees and honey bees, maintain a socially transmitted core gut microbiome that contributes to digestion and pathogen defense. In contrast, solitary bees, which have fewer opportunities for direct interhost transmission, typically have less consistent microbiomes dominated by bacteria associated with pollen and food reserves. Carpenter bees (genus Xylocopa) are long-lived bees that are not eusocial but that often live in shared nesting sites. We characterized gut microbiomes for Xylocopa micans, X. mexicanorum, X. tabaniformis parkinsoniae, and X. virginica and for five solitary bee species from other genera (Andrena, Habropoda, Megachile, and Svastra), sampled in the same localities in central Texas. Unexpectedly, all four Xylocopa species had microbiomes dominated by bacterial lineages previously known only from social bees or other insect groups. Microbiomes were similar across three Xylocopa species and included lineages in the families Bifidobacteriaceae, Orbaceae, Lactobacillaceae, Pseudomonadaceae, and Enterobacteriaceae. In contrast, X. virginica had a distinct microbiome dominated by the genus Bombilactobacillus, a group abundant in guts of eusocial bees. Phylogenetic analyses support a past transfer of bacterial lineages into Xylocopa from bumble bees or honey bees. Gut microbiome compositions of Xylocopa species were distinct from those of other co-occurring solitary bees that had variable gut microbiomes dominated by bacteria from environmental sources. IMPORTANCE Gut microbiomes from social bees, such as honey bees and bumble bees, are conserved and consist of host-restricted bacteria that are transmitted among sterile female workers within a colony and that are important to the health of these key insect pollinators. In contrast, solitary bee species typically have more erratic, environmentally acquired microbiomes. Carpenter bees (genus Xylocopa) can be solitary as they lack a worker caste, and each female can excavate nests and raise offspring alone, although females are often social share nests at least in some species. This study showed that the gut microbiomes of four Xylocopa species have distinctive and consistent compositions and are dominated by bacterial lineages previously known from honey bees and bumble bees. Thus, eusociality is not required for bees to maintain a specialized, host-restricted gut microbiome. These findings suggest that gut bacteria are transmitted at shared nesting sites and that they play a role in host ecology.

RevDate: 2022-06-27

Sang J, Zhuang D, Zhang T, et al (2022)

Convergent and Divergent Age Patterning of Gut Microbiota Diversity in Humans and Nonhuman Primates.

mSystems [Epub ahead of print].

The gut microbiome has significant effects on healthy aging and aging-related diseases, whether in humans or nonhuman primates. However, little is known about the divergence and convergence of gut microbial diversity between humans and nonhuman primates during aging, which limits their applicability for studying the gut microbiome's role in human health and aging. Here, we performed 16S rRNA gene sequencing analysis for captive rhesus macaques (Macaca mulatta) and compared this data set with other freely available gut microbial data sets containing four human populations (Chinese, Japanese, Italian, and British) and two nonhuman primates (wild lemurs [Lemur catta] and wild chimpanzees [Pan troglodytes]). Based on the consistent V4 region of the 16S rRNA gene, beta diversity analysis suggested significantly separated gut microbial communities associated with host backgrounds of seven host groups, but within each group, significant gut microbial divergences were observed, and indicator bacterial genera were identified as associated with aging. We further discovered six common anti-inflammatory gut bacteria (Prevotellamassilia, Prevotella, Gemmiger, Coprococcus, Faecalibacterium, and Roseburia) that had butyrate-producing potentials suggested by pangenomic analysis and that showed similar dynamic changes in at least two selected host groups during aging, independent of distinct host backgrounds. Finally, we found striking age-related changes in 66 plasma metabolites in macaques. Two highly changed metabolites, hydroxyproline and leucine, enriched in adult macaques were significantly and positively correlated with Prevotella and Prevotellamassilia. Furthermore, genus-level pangenome analysis suggested that those six common indicator bacteria can synthesize leucine and arginine as hydroxyproline and proline precursors in both humans and macaques. IMPORTANCE This study provides the first comprehensive investigation of age patterning of gut microbiota of four human populations and three nonhuman primates and found that Prevotellamassilia, Prevotella, Gemmiger, Coprococcus, Faecalibacterium, and Roseburia may be common antiaging microbial markers in both humans and nonhuman primates due to their potential metabolic capabilities for host health benefits. Our results also provide key support for using macaques as animal models in studies of the gut microbiome's role during human aging.

RevDate: 2022-06-27

Zhou X, Liu Y, Xiong X, et al (2022)

Intestinal accumulation of microbiota-produced succinate caused by loss of microRNAs leads to diarrhea in weanling piglets.

Gut microbes, 14(1):2091369.

Diarrheal disease is a common health problem with complex causality. Although diarrhea is accompanied by disturbances in microbial diversity, how gut microbes are involved in the occurrence of diarrhea remains largely unknown. Here, using a pig model of post-weaning stress-induced diarrhea, we aim to elucidate and enrich the mechanistic basis of diarrhea. We found significant alterations in fecal microbiome, their metabolites, and microRNAs levels in piglets with diarrhea. Specifically, loss of ssc-miRNA-425-5p and ssc-miRNA-423-3p, which inhibit the gene expression of fumarate reductase (frd) in Prevotella genus, caused succinate accumulation in piglets, which resulted in diarrhea. Single-cell RNA sequencing indicated impaired epithelial function and increased immune response in the colon of piglet with diarrhea. Notably, the accumulated succinate increased colonic fluid secretion by regulating transepithelial Cl-secretion in the epithelial cells. Meanwhile, succinate promoted colonic inflammatory responses by activating MyD88-dependent TLR4 signaling in the macrophages. Overall, our findings expand the mechanistic basis of diarrhea and suggest that colonic accumulation of microbiota-produced succinate caused by loss of miRNAs leads to diarrhea in weanling piglets.

RevDate: 2022-06-27

Kim R, Wang Y, Sims CE, et al (2022)

A Platform for Co-Culture of Primary Human Colonic Epithelium With Anaerobic Probiotic Bacteria.

Frontiers in bioengineering and biotechnology, 10:890396 pii:890396.

An in vitro platform was designed and optimized for the co-culture of probiotic anaerobic bacteria with a primary human colonic epithelium having a goal of assessing the anti-inflammatory impact of the probiotic bacteria. The device maintained a luminal O2 concentration at <1% while also supporting an oxygenated basal compartment at 10% for at least 72 h. Measurement of the transepithelial resistance of a confluent colonic epithelium showed high monolayer integrity while fluorescence assays demonstrated that the monolayer was comprised primarily of goblet cells and colonocytes, the two major differentiated cell subtypes of the colonic epithelium. High monolayer barrier function and viability were maintained during co-culture of the epithelium with the probiotic obligate anaerobe Anaerobutyricum hallii (A. hallii). Importantly the device supported a static co-culture of microbes and colonic epithelium mimicking the largely static or low flow conditions within the colonic lumen. A model inflamed colonic epithelium was generated by the addition of tumor necrosis factor-α (TNF-α) and lipopolysaccharide (LPS) to the basal and luminal epithelium sides, respectively. Co-culture of A. hallii with the LPS/TNF-α treated intestine diminished IL-8 secretion by ≥40% which could be mimicked by co-culture with the A. hallii metabolite butyrate. In contrast, co-culture of the inflamed epithelium with two strains of lactic acid-producing bacteria, Lactobacillus rhamnosus GG (LGG) and Bifidobacterium adolescentis (B. adolescentis), did not diminish epithelial IL-8 secretion. Co-culture with colonic epithelial cells from different donors demonstrated a consistent anti-inflammatory effect by A. hallii, but distinct responses to co-culture with LGG and B. adolescentis. The demonstrated system offers a simple and easily adopted platform for examining the physiologic impact of alterations in the intestinal epithelium that occur in the presence of probiotic bacteria and their metabolites.

RevDate: 2022-06-27

Chang HW, Yan D, Singh R, et al (2022)

Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations.

JID innovations : skin science from molecules to population health, 2(3):100115 pii:S2667-0267(22)00023-6.

Psoriasis is a chronic, inflammatory skin disease that affects 2‒3% of the global population. Besides skin manifestations, patients with psoriasis have increased susceptibility to a number of comorbidities, including psoriatic arthritis, cardiovascular disease, and inflammatory bowel disease. To understand the systemic component of psoriasis pathogenesis, we performed a pilot study to examine the fecal metagenome, host colonic transcriptome, and host peripheral blood immune profiles of patients with psoriasis and healthy controls. Our study showed increased functional diversity in the gut microbiome of patients with psoriasis. In addition, we identified microbial species that preferentially associate with patients with psoriasis and which have been previously found to associate with other autoimmune diseases. Intriguingly, our data revealed three psoriasis subgroups that have distinct microbial and host features. Integrating these features revealed host‒microbe associations that are specific to psoriasis or particular psoriasis subgroups. Our findings provide insight into the factors that may affect the development of comorbidities in patients with psoriasis and may hold diagnostic potential for early identification of patients with psoriasis at risk for these comorbidities.

RevDate: 2022-06-27

Zhang Z, Yu Y, Zhu G, et al (2022)

The Emerging Role of Plant-Derived Exosomes-Like Nanoparticles in Immune Regulation and Periodontitis Treatment.

Frontiers in immunology, 13:896745.

Periodontitis is an infectious oral disease, which leads to the destruction of periodontal tissues and tooth loss. Although the treatment of periodontitis has improved recently, the effective treatment of periodontitis and the periodontitis-affected periodontal tissues is still a challenge. Therefore, it is urgent to explore new therapeutic strategies for periodontitis. Natural products show anti-microbial, anti-inflammatory, anti-oxidant and bone protective effects to periodontitis and most of these natural products are safe and cost-effective. Among these, the plant-derived exosome-like nanoparticles (PELNs), a type of natural nanocarriers repleted with lipids, proteins, RNAs, and other active molecules, show the ability to enter mammalian cells and regulate cellular activities. Reports from the literature indicate the great potential of PELNs in the regulation of immune functions, inflammation, microbiome, and tissue regeneration. Moreover, PELNs can also be used as drug carriers to enhance drug stability and cellular uptake in vivo. Since regulation of immune function, inflammation, microbiome, and tissue regeneration are the key phenomena usually targeted during periodontitis treatment, the PELNs hold the promising potential for periodontitis treatment. This review summarizes the recent advances in PELNs-related research that are related to the treatment of periodontitis and regeneration of periodontitis-destructed tissues and the underlying mechanisms. We also discuss the existing challenges and prospects of the application of PELNs-based therapeutic approaches for periodontitis treatment.

RevDate: 2022-06-27

Soto Chervin C, TF Gajewski (2020)

Microbiome-based interventions: therapeutic strategies in cancer immunotherapy.

Immuno-oncology technology, 8:12-20 pii:S2590-0188(20)30036-8.

The composition of the commensal microbiota has recently emerged as a key element influencing the efficacy of cancer treatments. It has become apparent that the interplay between the microbiome and immune system within the host influences the response to immunotherapy, particularly immune checkpoint inhibitor therapy. Identifying the key components of the gut microbiota that influence this response is paramount for designing therapeutic interventions to enhance the response to cancer therapy. This review will discuss strategies being considered to modulate the gut microbiota, including fecal microbiota transplantation, administration of defined bacterial isolates as well as bacterial consortia, supplementation with probiotics, and lifestyle modifications such as dietary changes. Understanding the influence of the complex variables of the human microbiota on the effectiveness of cancer therapy will help drive the clinical design of microbial-based interventions in the field of oncology.

RevDate: 2022-06-27

Sharma NK, Wu SB, Morgan NK, et al (2022)

Artificial gut and the applications in poultry: A review.

Animal nutrition (Zhongguo xu mu shou yi xue hui), 10:156-166 pii:S2405-6545(22)00036-1.

Artificial gut models including both the gastric and intestinal phases have been used in poultry research for decades to predict the digestibility of nutrients, the efficacy of feed enzymes and additives, and caecal fermentation. However, the models used in the past are static and cannot be used to predict interactions between the feed, gut environment and microbiome. It is imperative that a standard artificial gut model for poultry is established, to enable these interactions to be examined without continual reliance on animals. To ensure the validity of an artificial model, it should be validated with in vivo studies. This review describes current practices in the use of artificial guts in research, their importance in poultry nutrition studies and highlights an opportunity to develop a dynamic gut model for poultry to reduce the number of in vivo experiments.

RevDate: 2022-06-27

Tran DM (2022)

Taxonomic and functional profiles of Coffea canephora endophytic microbiome in the Central Highlands region, Vietnam, revealed by analysis of 16S rRNA metagenomics sequence data.

Data in brief, 43:108372 pii:S2352-3409(22)00569-8.

Vietnam is the largest producer of Robusta coffee (Coffea canephora L.) [1]. Among regions in Vietnam, the Central Highlands is the capital of the coffee plantation and production [2]. Previous works have established a dataset of rhizospheric microbial diversity and its functionality to develop sustainable Robusta coffee production techniques in this region [3], [4], [5], [6]; however, a dataset of the endophytic microbiome of this plant species has been found is still unknown. The work presented here is the first report on the microbial and functional diversity of the endophytic microbiome of Coffea canephora L. grown in the region. A representative root sample was obtained by mixing five different root samples collected from a 6-year-old Robusta coffee field in Dak Lak Province, the Central Highlands, on 30 October 2021. After that, 16S rRNA metagenomic next-generation sequencing was conducted on the sample using the Illumina MiSeq platform. The raw sequence of endophytic microbiome data in this work was uploaded in Fastq format on NCBI with Bioproject PRJNA821717 and can be accessed at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA821717. The dataset can be useful for understanding basic information about the prokaryotic ecology of this important plant in the Central Highlands, Vietnam. The data can also be valuable for developing cultivation techniques for sustainable Coffea canephora L. production by applying indigenous microbial resources.

RevDate: 2022-06-27

Li L, Chen L, Yang Y, et al (2022)

Characteristics of Gut Microbiome and Its Metabolites, Short-Chain Fatty Acids, in Children With Idiopathic Short Stature.

Frontiers in endocrinology, 13:890200.

Background: The gut microbiome is important for host nutrition and metabolism. Whether the gut microbiome under normal diet regulate human height remains to be addressed. Our study explored the possible relationship between gut microbiota, its metabolic products and the pathogenesis of idiopathic short stature disease (ISS) by comparing the gut microbiota between children with ISS and of normal height, and also the short-chain fatty acids (SCFAs) produced by the gut microbiota.

Methods: The subjects of this study were 32 prepubescent children aged 4-8 years. The fecal microbial structure of the subjects was analyzed by 16S rRNA high-throughput sequencing technology. The concentrations of SCFAs in feces were determined by gas chromatography-mass spectrometry.

Results: The richness of gut microbiota in ISS group was decreased, and the composition of gut microbiota was significantly different between ISS group and control group. The relative abundance of nine species including family Ruminococcaceae and genera Faecalibacterium and Eubacterium, in ISS group was significantly lower than that in control group (P<0.05). The relative abundance of 10 species, such as those belonging to genus Parabacteroides and genus Clostridium, in ISS group was significantly higher than that in control group (P<0.05). The concentration of total SCFAs and butyrate in ISS group was significantly lower than that in control group. The correlation analysis among different species, clinical indicators, and SCFAs showed that the relative abundance of family Ruminococcaceae and genera Faecalibacterium and Eubacterium was positively correlated with the standard deviation score of height. Furthermore, the concentrations of total SCFAs and butyrate were positively correlated with serum insulin-like growth factor 1 (IGF-1)-SDS. Disease prediction model constructed based on the bacteria who abundance differed between healthy children and ISS children exhibited high diagnostic value (AUC: 0.88).

Conclusions: The composition of gut microbiota and the change in its metabolite levels may be related to ISS pathogenesis. Strains with increased or decreased specificity could be used as biomarkers to diagnose ISS.

RevDate: 2022-06-27

Lin X, Wang Y, Liu Z, et al (2022)

Intestinal strictures in Crohn's disease: a 2021 update.

Therapeutic advances in gastroenterology, 15:17562848221104951 pii:10.1177_17562848221104951.

Intestinal strictures remain one of the most intractable and common complications of Crohn's disease (CD). Approximately 70% of CD patients will develop fibrotic strictures after 10 years of CD diagnosis. Since specific antifibrotic therapies are unavailable, endoscopic balloon dilation and surgery remain the mainstay treatments despite a high recurrence rate. Besides, there are no reliable methods for accurately evaluating intestinal fibrosis. This is largely due to the fact that the mechanisms of initiation and propagation of intestinal fibrosis are poorly understood. There is growing evidence implying that the pathogenesis of stricturing CD involves the intricate interplay of factors including aberrant immune and nonimmune responses, host-microbiome dysbiosis, and genetic susceptibility. Currently, the progress on intestinal strictures has been fueled by the advent of novel techniques, such as single-cell sequencing, multi-omics, and artificial intelligence. Here, we perform a timely and comprehensive review of the substantial advances in intestinal strictures in 2021, aiming to provide prompt information regarding fibrosis and set the stage for the improvement of diagnosis, treatment, and prognosis of intestinal strictures.

RevDate: 2022-06-27

German JB, Lebrilla C, DA Mills (2022)

Milk: A Scientific Model for Diet and Health Research in the 21st Century.

Frontiers in nutrition, 9:922907.

The origin of lactation and the composition, structures and functions of milk's biopolymers highlight the Darwinian pressure on lactation as a complete, nourishing and protective diet. Lactation, under the driving pressure to be a sustainable bioreactor, was under selection pressure of its biopolymers with diverse functions acting from the mammary gland through the digestive system of the infant. For example, milk is extensively glycosylated and the glycan structures and their functions are now emerging. Milk contains free oligosaccharides; complex polymers of sugars whose stereospecific linkages are not matched by glycosidic enzymes within the mammalian infant gut. These glycan polymers reach the lower intestine undigested. In this microbe-rich environment, bacteria compete to release and ferment the sugars via different hydrolytic strategies. One specific type of bacteria, Bifidobacterium longum subsp. infantis, (B. infantis) is uniquely equipped with a repertoire of genes encoding enzymes capable of taking up, hydrolyzing and metabolizing the complex glycans of human milk. This combination of a distinct food supply and unique genetic capability shapes the composition and metabolic products of the entire microbial community within the lower intestine of breast fed infants. The intestinal microbiome dominated by B. infantis, shields the infant from the growth of gram negative enteropathogens and their endotoxins as a clear health benefit. The world is facing unprecedented challenges to produce a food supply that is both nourishing, safe and sustainable. Scientists need to guide the future of agriculture and food in response to these 21st century challenges. Lactation provides an inspiring model of what that future research strategy could be.

RevDate: 2022-06-27

Nurcahyanti ADR, Cokro F, Wulanjati MP, et al (2022)

Curcuminoids for Metabolic Syndrome: Meta-Analysis Evidences Toward Personalized Prevention and Treatment Management.

Frontiers in nutrition, 9:891339.

The metabolic syndrome (MS) is a multifactorial syndrome associated with a significant economic burden and healthcare costs. MS management often requires multiple treatments (polydrug) to ameliorate conditions such as diabetes mellitus, insulin resistance, obesity, cardiovascular diseases, hypertension, and non-alcoholic fatty liver disease (NAFLD). However, various therapeutics and possible drug-drug interactions may also increase the risk of MS by altering lipid and glucose metabolism and promoting weight gain. In addition, the medications cause side effects such as nausea, flatulence, bloating, insomnia, restlessness, asthenia, palpitations, cardiac arrhythmias, dizziness, and blurred vision. Therefore, is important to identify and develop new safe and effective agents based on a multi-target approach to treat and manage MS. Natural products, such as curcumin, have multi-modalities to simultaneously target several factors involved in the development of MS. This review discusses the recent preclinical and clinical findings, and up-to-date meta-analysis from Randomized Controlled Trials regarding the effects of curcumin on MS, as well as the metabonomics and a pharma-metabolomics outlook considering curcumin metabolites, the gut microbiome, and environment for a complementary personalized prevention and treatment for MS management.

RevDate: 2022-06-27

Betrapally N (2022)

Editorial: The Role of Nutrition in the Management of Liver and Associated Diseases.

Frontiers in nutrition, 9:919057.

RevDate: 2022-06-27

Spacova I, Ahannach S, Breynaert A, et al (2022)

Spontaneous Riboflavin-Overproducing Limosilactobacillus reuteri for Biofortification of Fermented Foods.

Frontiers in nutrition, 9:916607.

Riboflavin-producing lactic acid bacteria represent a promising and cost-effective strategy for food biofortification, but production levels are typically insufficient to support daily human requirements. In this study, we describe the novel human isolate Limosilactobacillus reuteri AMBV339 as a strong food biofortification candidate. This strain shows a high natural riboflavin (vitamin B2) overproduction of 18.36 μg/ml, biomass production up to 6 × 1010 colony-forming units/ml (in the typical range of model lactobacilli), and pH-lowering capacities to a pH as low as 4.03 in common plant-based (coconut, soy, and oat) and cow milk beverages when cultured up to 72 h at 37°C. These properties were especially pronounced in coconut beverage and butter milk fermentations, and were sustained in co-culture with the model starter Streptococcus thermophilus. Furthermore, L. reuteri AMBV339 grown in laboratory media or in a coconut beverage survived in gastric juice and in a simulated gastrointestinal dialysis model with colon phase (GIDM-colon system) inoculated with fecal material from a healthy volunteer. Passive transport of L. reuteri AMBV339-produced riboflavin occurred in the small intestinal and colon stage of the GIDM system, and active transport via intestinal epithelial Caco-2 monolayers was also demonstrated. L. reuteri AMBV339 did not cause fecal microbiome perturbations in the GIDM-colon system and inhibited enteric bacterial pathogens in vitro. Taken together, our data suggests that L. reuteri AMBV339 represents a promising candidate to provide riboflavin fortification of plant-based and dairy foods, and has a high application potential in the human gastrointestinal tract.

RevDate: 2022-06-27

Gopalakrishnan V, Weiner B, Ford CB, et al (2020)

Intervention strategies for microbial therapeutics in cancer immunotherapy.

Immuno-oncology technology, 6:9-17 pii:S2590-0188(20)30013-7.

Immunotherapies have drastically improved clinical outcomes in a wide range of malignancies. Nevertheless, patient responses remain highly variable, and reliable biomarkers that predict responses accurately are not yet fully understood. Compelling evidence from preclinical studies and observational data from clinical cohorts have shown that commensal microorganisms that reside in the human gastrointestinal tract, collectively termed the 'microbiome', can actively modify responses to chemotherapeutic agents and immunotherapies by influencing host immunosurveillance. Notably, microbial correlates are largely context specific, and response signatures may vary by patient population, geographic location and type of anticancer treatment. Therefore, the incongruence of beneficial microbiome signatures across studies, along with an emerging understanding of the mechanisms underlying the interactions between the microbiome, metabolome and host immune system, highlight a critical need for additional comprehensive and standardized multi-omics studies. Future research should consider key host factors, such as diet and use of medication, in both preclinical animal models and large-scale, multicenter clinical trials. In addition, there is a strong rationale to evaluate the microbiome as a tumor-extrinsic biomarker of clinical outcomes and to test the therapeutic potential of derived microbial products (e.g. defined microbial consortia), with the eventual goal of improving the efficacy of existing anticancer treatments. This review discusses the importance of the microbiome from the perspective of cancer immunotherapies, and outlines future steps that may contribute to wide-ranging clinical and translational benefits that may improve the health and quality of life of patients with cancer.

RevDate: 2022-06-27

Michel-Mata S, Wang XW, Liu YY, et al (2022)

Predicting microbiome compositions from species assemblages through deep learning.

iMeta, 1(1):.

Microbes can form complex communities that perform critical functions in maintaining the integrity of their environment or their hosts' well-being. Rationally managing these microbial communities requires improving our ability to predict how different species assemblages affect the final species composition of the community. However, making such a prediction remains challenging because of our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. To overcome this challenge, we present a deep learning framework that automatically learns the map between species assemblages and community compositions from training data only, without knowing any of the above processes. First, we systematically validate our framework using synthetic data generated by classical population dynamics models. Then, we apply our framework to data from in vitro and in vivo microbial communities, including ocean and soil microbiota, Drosophila melanogaster gut microbiota, and human gut and oral microbiota. We find that our framework learns to perform accurate out-of-sample predictions of complex community compositions from a small number of training samples. Our results demonstrate how deep learning can enable us to understand better and potentially manage complex microbial communities.

RevDate: 2022-06-27

Yahfoufi N, Ah-Yen EG, Chandrasegaram R, et al (2021)

Adolescent use of potential novel probiotic Rouxiella badensis subsp. acadiensis (Canan SV-53) mitigates pubertal LPS-Induced behavioral changes in adulthood in a sex-specific manner by modulating 5HT1A receptors expression in specific brain areas.

Comprehensive psychoneuroendocrinology, 7:100063 pii:S2666-4976(21)00037-0.

Adolescence is a critical period of development during which the brain undergoes significant remodeling that impacts behavior later in life. Exposure to stress, and especially immune challenge, during this period triggers changes in brain function resulting in the development of mental disorders in adulthood, such as depression and anxiety. Previous studies from our laboratory have shown that a single exposure to LPS (lipopolysaccharide) during puberty causes enduring depression-like behaviour in females and anxiety-like behaviours in males. However, administration of probiotics during puberty blocked the enduring effects of LPS on depression-like and anxiety-like behaviors in female and male mice, respectively. These results suggest that the gut microbiome is a mediator of the effects of stress on mental health. The objective of the current study is to examine the effectiveness of a novel probiotic Rouxiella badensis subsp. acadiensis (Canan SV-53) in blocking LPS-induced anxiety-like and depression-like behaviors in adult male and female mice. Our results showed that Rouxiella badensis subsp. acadiensis (Canan SV-53) blocked LPS-induced depression-like behavior in female mice. We also found that pubertal treatment with Rouxiella badensis subsp. acadiensis (Canan SV-53) mitigated the LPS-induced decrease in 5HT1A expression in CA1 as well as the LPS-induced increase in 5HT1A expression in the raphe-nuclei in female mice. Contrary to our predictions, pubertal LPS treatment at 6 weeks of age did not induce enduring anxiety-like behavior in males. There was also no difference in anxiety-like behavior between the LPS-sucrose and LPS-probiotic male groups. However, pubertal LPS treatment increased the expression of 5HT1A receptors in the DRN in males, while probiotic exposure mitigated this increase. Our study highlights the consequences of stress exposure (immune challenge) on mental health in adulthood taking into consideration 5HT1A receptors expression at different regions of the brain. It also emphasizes on the importance of considering adolescence as window of opportunities during which probiotic use can alleviate the long-term neural and behavioral alterations induced by stress.

RevDate: 2022-06-27

Parodi G, Leite G, Pimentel ML, et al (2022)

The Response of the Rodent Gut Microbiome to Broad-Spectrum Antibiotics Is Different in Males and Females.

Frontiers in microbiology, 13:897283.

Gut microbiome composition is different in males and females, but sex is rarely considered when prescribing antibiotics, and sex-based differences in gut microbiome recovery following antibiotic treatment are poorly understood. Here, we compared the effects of broad-spectrum antibiotics on both the stool and small bowel microbiomes in male and female rats. Adult male and female Sprague Dawley rats were exposed to a multi-drug antibiotic cocktail for 8 days, or remained unexposed as controls. Following cessation of antibiotics, rats were monitored for an additional 13-day recovery period prior to euthanasia. Baseline stool microbiome composition was similar in males and females. By antibiotic exposure day 8 (AbxD8), exposed male rats exhibited greater loss of stool microbial diversity compared to exposed females, and the relative abundance (RA) of numerous taxa were significantly different in exposed males vs. exposed females. Specifically, RA of phylum Proteobacteria and genera Lactobacillus, Sutterella, Akkermansia, and Serratia were higher in exposed males vs. exposed females, whereas RA of phyla Firmicutes and Actinobacteria and genera Turicibacter and Enterococcus were lower. By 13 days post antibiotics cessation (PAbxD13), the stool RA of these and other taxa remained significantly different from baseline, and also remained significantly different between exposed males and exposed females. RA of phyla Firmicutes and Actinobacteria and genus Enterococcus remained lower in exposed males vs. exposed females, and genus Sutterella remained higher. However, RA of phylum Proteobacteria and genus Akkermansia were now also lower in exposed males vs. females, whereas RA of phylum Bacteroidetes and genus Turicibacter were now higher in exposed males. Further, the small bowel microbiome of exposed rats on PAbxD13 was also significantly different from unexposed controls, with higher RA of Firmicutes, Turicibacter and Parabacteroides in exposed males vs. females, and lower RA of Bacteroidetes, Proteobacteria, Actinobacteria, Oscillospira, Sutterella, and Akkermansia in exposed males vs. females. These findings indicate that broad-spectrum antibiotics have significant and sex-specific effects on gut microbial populations in both stool and the small bowel, and that the recovery of gut microbial populations following exposure to broad-spectrum antibiotics also differs between sexes. These findings may have clinical implications for the way antibiotics are prescribed.

RevDate: 2022-06-27

Nalla K, Manda NK, Dhillon HS, et al (2022)

Impact of Probiotics on Dairy Production Efficiency.

Frontiers in microbiology, 13:805963.

There has been growing interest on probiotics to enhance weight gain and disease resistance in young calves and to improve the milk yield in lactating animals by reducing the negative energy balance during the peak lactation period. While it has been well established that probiotics modulate the microbial community composition in the gastrointestinal tract, and a probiotic-mediated homeostasis in the rumen could improve feed conversation competence, volatile fatty acid production and nitrogen flow that enhances the milk composition as well as milk production, detailed changes on the molecular and metabolic level prompted by probiotic feed additives are still not understood. Moreover, as living biotherapeutic agents, probiotics have the potential to directly change the gene expression profile of animals by activating the signalling cascade in the host cells. Various direct and indirect components of probiotic approaches to improve the productivity of dairy animals are discussed in this review.

RevDate: 2022-06-27

Haryono MAS, Law YY, Arumugam K, et al (2022)

Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling.

Frontiers in microbiology, 13:869135.

The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.

RevDate: 2022-06-27

Zhang J, Gao H, Jiang F, et al (2022)

Comparative Analysis of Gut Microbial Composition and Functions in Przewalski's Gazelle (Procapra przewalskii) From Various Habitats.

Frontiers in microbiology, 13:913358.

Gut microbiota of mammals participates in host nutrient metabolism and plays an important role in host adaptation to the environment. Herein, to understand the relationship between environment differences and the composition and abundance of the gut microbiota of Przewalski's gazelle (Procapra przewalskii) in almost all its habitats, high throughput sequencing of the 16S rRNA gene was used to compared the characteristics of the gut microbiota based on total 120 fecal samples. The results showed that Przewalski's gazelle exhibited different characteristics of microbiota diversity in different habitats. The Jiangxigou Rescue Station (JX), Nongchang (NC), and Ganzihe and Haergai townships (GH) groups had a relatively high microbiota diversity, while the Niaodao scenic area (ND) group had the lowest diversity. This finding seemed to follow a similar pattern of change in the population of Przewalski's gazelle. Bacteroidetes and Actinobacteria were the phyla with significant differences, especially between the Wayu township (WY) and the other groups. The difference in the microbiota mainly included the Ruminococcaceae UCG-005, Christensenellaceae R-7 group, and Bacteroidaceae and was enriched in the ND, WY, and other regions. We speculated that the difference in the gut microbiota was due to a difference in environmental characteristics, particularly the food resources that the host can obtain. We speculated that a similar microbiome has important functions for species survival and represents the evolutionary commonality of Przewalski's gazelle, while a different microbiome plays an important role in the adaptation of Przewalski's gazelle to a different environment. The results of this study illustrate how the same species adapts to different environments from the perspective of gut microbiota plasticity and therefore are of great significance for the protection and restoration of the population of this species.

RevDate: 2022-06-27

Joyce C, Halverson T, Gonzalez C, et al (2022)

The Urobiomes of Adult Women With Various Lower Urinary Tract Symptoms Status Differ: A Re-Analysis.

Frontiers in cellular and infection microbiology, 12:860408.

The discovery of the urinary microbiome (urobiome) has created opportunities for urinary health researchers who study a wide variety of human health conditions. This manuscript describes an analysis of catheterized urine samples obtained from 1,004 urobiome study participants with the goal of identifying the most abundant and/or prevalent (common) taxa in five clinically relevant cohorts: unaffected adult women (n=346, 34.6%), urgency urinary incontinence (UUI) (n=255, 25.5%), stress urinary incontinence (SUI) (n=50, 5.0%), urinary tract infection (UTI) (n=304, 30.4%), and interstitial cystitis/painful bladder syndrome (IC/PBS) (n=49, 4.9%). Urine was collected via transurethral catheter and assessed for microbes with the Expanded Quantitative Urine Culture (EQUC) technique. For this combined analytic cohort, the mean age was 59 ± 16; most were Caucasian (n=704, 70.2%), Black (n=137, 13.7%), or Hispanic (n=130, 13.0%), and the mean BMI was 30.4 ± 7.7. Whereas many control or IC/PBS cohort members were EQUC-negative (42.4% and 39.8%, respectively), members of the other 3 cohorts were extremely likely to have detectable microbes. The detected urobiomes of the controls and IC/PBS did not differ by alpha diversity or genus level composition and differed by only a few species. The other 3 cohorts differed significantly from the controls. As expected, Escherichia was both prevalent and highly abundant in the UTI cohort, but other taxa also were prevalent at more moderate abundances, including members of the genera Lactobacillus, Streptococcus, Staphylococcus, Corynebacterium, Actinomyces, and Aerococcus. Members of these genera were also prevalent and highly abundant in members of the UUI cohort, especially Streptococcus anginosus. Intriguingly, these taxa were also detected in controls but at vastly lower levels of both prevalence and abundance, suggesting the possibility that UUI-associated symptoms could be the result of an overabundance of typical urobiome constituents. Finally, prevalence and abundance of microbes in the SUI cohort were intermediate to those of the UUI and control cohorts. These observations can inform the next decade of urobiome research, with the goal of clarifying the mechanisms of urobiome community composition and function. There is tremendous potential to improve diagnosis, evaluation and treatment for individuals affected with a wide variety of urinary tract disorders.

RevDate: 2022-06-27

Kumar M, Saadaoui M, S Al Khodor (2022)

Infections and Pregnancy: Effects on Maternal and Child Health.

Frontiers in cellular and infection microbiology, 12:873253.

Pregnancy causes physiological and immunological adaptations that allow the mother and fetus to communicate with precision in order to promote a healthy pregnancy. At the same time, these adaptations may make pregnant women more susceptible to infections, resulting in a variety of pregnancy complications; those pathogens may also be vertically transmitted to the fetus, resulting in adverse pregnancy outcomes. Even though the placenta has developed a robust microbial defense to restrict vertical microbial transmission, certain microbial pathogens have evolved mechanisms to avoid the placental barrier and cause congenital diseases. Recent mechanistic studies have begun to uncover the striking role of the maternal microbiota in pregnancy outcomes. In this review, we discuss how microbial pathogens overcome the placental barrier to cause congenital diseases. A better understanding of the placental control of fetal infection should provide new insights into future translational research.

RevDate: 2022-06-27

Campillo-Gimenez L, Yang Y, De Los Reyes-Gavilan CG, et al (2022)

Editorial: "The Host-Microbiome Interplay in Colorectal Cancer".

Frontiers in cellular and infection microbiology, 12:906719.

RevDate: 2022-06-27

Proffitt C, Bidkhori G, Lee S, et al (2022)

Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders.

iScience, 25(7):104513 pii:S2589-0042(22)00784-2.

The human gut microbiome has been associated with metabolic disorders including obesity, type 2 diabetes, and atherosclerosis. Understanding the contribution of microbiome metabolic changes is important for elucidating the role of gut bacteria in regulating metabolism. We used available metagenomics data from these metabolic disorders, together with genome-scale metabolic modeling of key bacteria in the individual and community-level to investigate the mechanistic role of the gut microbiome in metabolic diseases. Modeling predicted increased levels of glutamate consumption along with the production of ammonia, arginine, and proline in gut bacteria common across the disorders. Abundance profiles and network-dependent analysis identified the enrichment of tartrate dehydrogenase in the disorders. Moreover, independent plasma metabolite levels showed associations between metabolites including proline and tyrosine and an increased tartrate metabolism in healthy obese individuals. We, therefore, propose that an increased tartrate metabolism could be a significant mediator of the microbiome metabolic changes in metabolic disorders.

RevDate: 2022-06-27

Gupta A, Sinha DK, S Nair (2022)

Shifts in Pseudomonas species diversity influence adaptation of brown planthopper to changing climates and geographical locations.

iScience, 25(7):104550 pii:S2589-0042(22)00822-7.

The brown planthopper (BPH) is a monophagous sap-sucking pest of rice that causes immense yield loss. The rapid build-up of pesticide resistance combined with the ability of BPH populations to quickly overcome host plant resistance has rendered conventional control strategies ineffective. One of the likely ways in which BPH adapts to novel environments is by undergoing rapid shifts in its microbiome composition. To elucidate the rapid adaptation to novel environments and the contributions of Pseudomonas toward insect survival, we performed Pseudomonas-specific 16S rRNA gut-microbiome profiling of BPH populations. Results revealed the differential occurrence of Pseudomonas species in BPH populations with changing climates and geographical locations. Further, the observed variation in Pseudomonas species composition and abundance correlated with BPH survivability. Collectively, this study, while adding to our current understanding of symbiont-mediated insect adaptation, also demonstrated a complex interplay between insect physiology and microbiome dynamics, which likely confers BPH its rapid adaptive capacity.

RevDate: 2022-06-27

Brewster WR, Burkett WC, Ko EM, et al (2022)

An evaluation of the microbiota of the upper reproductive tract of women with and without epithelial ovarian cancer.

Gynecologic oncology reports, 42:101017 pii:S2352-5789(22)00097-2.

Objective: The microbiome of the female upper reproductive tract (URT) has not been characterized. We hypothesize that distinct bacterial species may be identified in different areas of the URT in women with or without ovarian cancers.

Methods: Postmenopausal women scheduled for salpingooophorectomy were prospectively identified. We excluded those who used antibiotics within three months of surgery or had a diagnosed gynecologic cancer. Bacteria were extracted from tissue samples of the proximal fallopian tube, fimbriae and ovaries of 10 women. Using molecular-phylogenetic methods based on the highly conserved 16S bacteria rRNA gene, we assessed the complexity of URT microbiota in tissue samples by high throughput sequencing of the V1-V3 region of the 16S gene. Sequences were processed through QIIME and an average of 69,625 reads per sample was obtained after quality filtering. Multivariate analyses were conducted using PRIMER VI software.

Results: The initial analysis of samples suggests that bacteria exist in the URT. Analysis of similarity matrix (ANOSIM) suggests that the microbiome differs in the areas examined (ANOSIM R = 0.26, p = 0.015). The microbiome differs significantly between the fallopian tube and ovary (ANOSIM R = 0.23, p = 0.02). The proximal fallopian tube microbiome also differs from the fimbriae (ANOSIM R = 0.66, p = 0.025). There were borderline differences in the microbial profiles of the specimens with and without epithelial ovarian cancer (p = 0.06).

Conclusions: We identified distinct microbiota of the ovaries and fallopian tubes with a profile unique to women with epithelial ovarian cancer. Further investigation is necessary to determine whether the microbiome is related to ovarian carcinogenesis.

RevDate: 2022-06-27

Frei R, Heye K, C Roduit (2022)

Environmental influences on childhood allergies and asthma - The Farm effect.

Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology, 33(6):e13807.

Asthma and allergies are major health problems and exert an enormous socioeconomic burden. Besides genetic predisposition, environmental factors play a crucial role in the development of these diseases in childhood. Multiple worldwide epidemiological studies have shown that children growing up on farms are immune to allergic diseases and asthma. Farm-related exposures shape children's immune homeostasis, via mediators such as N-glycolylneuraminic acid or arabinogalactan, or by diverse environmental microbes. Moreover, nutritional factors, such as breastfeeding or farm milk and food diversity, inducing short-chain fatty acids-producing bacteria in the intestine, contribute to farm-related effects. All farm-related exposures induce an anti-inflammatory response of the innate immunity and increase the differentiation of regulatory T cells and T helper cell type 1. A better understanding of the components of the farm environment, that are protective to the development of allergy and asthma, and their underlying mechanisms, will help to develop new strategies for the prevention of allergy and asthma.

RevDate: 2022-06-27

Beheshti R, Halstead S, McKeone D, et al (2022)

Understanding immunological origins of atopic dermatitis through multi-omic analysis.

Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology, 33(6):e13817.

BACKGROUND: The pathophysiology of atopic dermatitis (AD) is multifactorial, impacted by individual medical, demographic, environmental, and immunologic factors. This study used multi-omic analyses to assess how host and microbial factors could contribute to infant AD development.

METHODS: This longitudinal cohort study included 129 term infants, identified as AD (n = 37) or non-AD (n = 92) using the Infant Feeding Practices-II survey and review of medical records. Standardized surveys were used to assess medical and demographic traits (gestational age, sex, race, maternal AD, and atopy family history), and environmental exposures (delivery method, maternal tobacco use, pets, breastfeeding duration, and timing of solid food introduction). Saliva was collected at 6 months for multi-omic assessment of cytokines, microRNAs, mRNAs, and the microbiome. The contribution of each factor to AD status was assessed with logistic regression.

RESULTS: Medical, demographic, and environmental factors did not differ between AD and non-AD infants. Five "omic" factors (IL-8/IL-6, miR-375-3p, miR-21-5p, bacterial diversity, and Proteobacteria) differed between groups (p < .05). The severity of AD was positively associated with levels of miR-375-3p (R = .17, p = .049) and Proteobacteria (R = .22, p = .011), and negatively associated with levels of miR-21-5p (R = .20, p = .022). Multi-omic features accounted for 17% of variance between groups, significantly improving an AD risk model employing medical, demographic, and environmental factors (X2 = 32.47, p = .006).

CONCLUSION: Interactions between the microbiome and host signaling may predispose certain infants to AD by promoting a pro-inflammatory environment.

RevDate: 2022-06-26

Nagao KC (2022)

Dissecting the Roles of Innate Cells in the Skin and Intractable Skin Diseases.

The Keio journal of medicine, 71(2):53.

The skin is not merely a physical barrier but also an active immunological interface, exposed to various external stimuli including microbes. Over the recent years, our laboratory has defined hair follicles as control towers that regulates immune cells residing in the skin. Hair follicles produce chemokines and cytokines that are crucial for the localization and tissue-residency of immune cells including the Langerhans cells, resident memory T cells, and innate lymphoid cells. We also discovered that disruption of the ADAM17-EGF receptor axis and ADAM10-Notch signaling axis leads to dysbiosis on the skin surface and in the hair follicles, respectively. The former leads to microbiome predominance of Staphylococcus aureus and results in atopic skin inflammation, whereas the latter leads to Corynebacterium species predominance that trigger irreversible hair follicle destruction. These findings highlight the distinct mechanisms that regulate the microbiome in different compartments of the skin. In this talk, I will focus on the deeper layers of the skin-the hypodermis (a.k.a subcutaneous tissue), a common site for cellulitis, which we found to be enriched with macrophages. We enabled layer-specific depletion of macrophages, which had prominent effects on the organization of the extracellular matrix, counterintuitively rendering mice highly protected against S. aureus-mediated cellulitis. I will also introduce our ongoing efforts to understand the histology and pathophysiology of Degos disease, an extremely rare and highly fatal disease of unknown etiology.

RevDate: 2022-06-26

Chen Y, X Lai (2022)

Modeling the effect of gut microbiome on therapeutic efficacy of immune checkpoint inhibitors against cancer.

Mathematical biosciences pii:S0025-5564(22)00068-2 [Epub ahead of print].

Immune checkpoint inhibitors have been shown to be highly successful against some solid metastatic malignancies, but only for a subset of patients who show durable clinical responses. The overall patient response rate is limited due to the interpatient heterogeneity. Preclinical and clinical studies have recently shown that the therapeutic responses can be improved through the modulation of gut microbiome. However, the underlying mechanisms are not fully understood. In this paper, we explored the effect of favorable and unfavorable gut bacteria on the therapeutic efficacy of anti-PD-1 against cancer by modeling the tumor-immune-gut microbiome interactions, and further examined the predictive markers of responders and non-responders to anti-PD-1. The dynamics of the gut bacteria was fitted to the clinical data of melanoma patients, and virtual patients data were generated based on the clinical patient survival data. Our simulation results show that low initial growth rate and low level of favorable bacteria at the initiation of anti-PD-1 therapy are predictive of non-responders, while high level of favorable bacteria at the initiation of anti-PD-1 therapy is predictive of responders. Simulation results also confirmed that it is possible to promote patients' response rate to anti-PD-1 by manipulating the gut bacteria composition of non-responders, whereby achieving long-term progression-free survival.

RevDate: 2022-06-26

Claudia S, Marta C, Đorde T, et al (2022)

Impact of organic soil amendments in antibiotic levels, antibiotic resistance gene loads, and microbiome composition in corn fields and crops.

Environmental research pii:S0013-9351(22)01087-8 [Epub ahead of print].

The potential spreading of antibiotic resistance genes (ARG) into agricultural fields and crops represent a fundamental limitation on the use of organic fertilization in food production systems. We present here a study of the effect of spreading four types of organic soil amendments (raw pig slurry, liquid and solid fractions, and a digested derivative) on demonstrative plots in two consecutive productive cycles of corn harvest (Zea mays), using a mineral fertilizer as a control, following the application of organic amendments at 32-62 T per ha (150 kg total N/ha) and allowing 5-8 months between fertilization and harvest. A combination of qPCR and high-throughput 16S rDNA sequencing methods showed a small, but significant impact of the fertilizers in both ARG loads and microbiomes in soil samples, particularly after the second harvesting cycle. The slurry solid fraction showed the largest impact on both ARG loads and microbiome variation, whereas its digestion derivatives showed a much smaller impact. Soil samples with the highest ARG loads also presented increased levels of tetracyclines, indicating a potential dual hazard by ARG and antibiotic residues linked to some organic amendments. Unlike soils, no accumulation of ARG or antibiotics was observed in corn leaves (used as fodder) or grains, and no grain sample reached detection limits for neither parameter. These results support the use of organic soil amendments in corn crops, while proposing the reduction of the loads of ARGs and antibiotics from the fertilizers to greatly reduce their potential risk.

RevDate: 2022-06-26

Liu H, Zha S, Yang Z, et al (2022)

Acute sulfide exposure induces hemocyte toxicity and microbiota dysbiosis in blood clam Tegillarca granosa.

Aquatic toxicology (Amsterdam, Netherlands), 249:106224 pii:S0166-445X(22)00150-3 [Epub ahead of print].

Sulfide are widely accumulated in aquatic environments under anaerobic conditions, which cause health problems of aquatic animals, yet their toxic effects to benthic bivalves are not well understood. We investigated the effects of sulfide on innate immunity of the blood clam Tegillarca granosa. Immunity-related indicators and hemolymph microbiota were investigated in the clams exposed to sulfide (via 10, 100 and 1000 μmol/L of Na2S) over a 7-day period. The results showed that cellular immune responses in T. granosa were affected by exposure to high sulfide concentration (1000 μmol/L Na2S), as indicated by total counts of hemocytes (THC), cell viability, ROS levels and phagocytic activities, suggesting that sulfide stress induces T. granosa more vulnerable to pathogen challenges. In addition, the Na2S-induced stress also reshaped the hemolymph microbial community structure of T. granosa that some original genera decreased, such as Lactobacillus, Desulfovibrio and Akkermansia; some genera increased, such as Vibrio and Pseudoalteromonas in sulfide stress group. Sulfide exposure promoted the proliferation of opportunistic pathogen and reduced the diversity of microbial community in the hemolymph of T. granosa. In summary, sulfide stress had marked hemocytotoxicity, reduced immune-cell activity and increased bacterial infections in the blood clam.

RevDate: 2022-06-26

Cao Z, Sugimura N, Burgermeister E, et al (2022)

The gut virome: A new microbiome component in health and disease.

EBioMedicine, 81:104113 pii:S2352-3964(22)00294-8 [Epub ahead of print].

The human gastrointestinal tract harbours an abundance of viruses, collectively known as the gut virome. The gut virome is highly heterogeneous across populations and is linked to geography, ethnicity, diet, lifestyle, and urbanisation. The currently known function of the gut virome varies greatly across human populations, and much remains unknown. We review current literature on the human gut virome, and the intricate trans-kingdom interplay among gut viruses, bacteria, and the mammalian host underlying health and diseases. We summarise evidence on the use of the gut virome as diagnostic markers and a therapeutic target. We shed light on novel avenues of microbiome-inspired diagnosis and therapies. We also review pre-clinical and clinical studies on gut virome-rectification-based therapies, including faecal microbiota transplantation, faecal virome transplantation, and refined phage therapy. Our review suggests that future research effort should focus on unravelling the mechanisms exerted by gut viruses/phages in human pathophysiology, and on developing phage-prompted precision therapies.

RevDate: 2022-06-25

Zhang S, Li Z, Shu J, et al (2022)

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense.

Microbiome, 10(1):97.

BACKGROUND: Herbivorous insects acquire their gut microbiota from diverse sources, and these microorganisms play significant roles in insect hosts' tolerance to plant secondary defensive compounds. Camellia weevil (Curculio chinensis) (CW) is an obligate seed parasite of Camellia oleifera plants. Our previous study linked the CW's gut microbiome to the tolerance of the tea saponin (TS) in C. oleifera seeds. However, the source of these gut microbiomes, the key bacteria involved in TS tolerance, and the degradation functions of these bacteria remain unresolved.

RESULTS: Our study indicated that CW gut microbiome was more affected by the microbiome from soil than that from fruits. The soil-derived Acinetobacter served as the core bacterial genus, and Acinetobacter sp. was putatively regarded responsible for the saponin-degradation in CW guts. Subsequent experiments using fluorescently labeled cultures verified that the isolate Acinetobacter sp. AS23 can migrate into CW larval guts, and ultimately endow its host with the ability to degrade saponin, thereby allowing CW to subsist as a pest within plant fruits resisting to higher concentration of defensive chemical.

CONCLUSIONS: The systematic studies of the sources of gut microorganisms, the screening of taxa involved in plant secondary metabolite degradation, and the investigation of bacteria responsible for CW toxicity mitigation provide clarified evidence that the intestinal microorganisms can mediate the tolerance of herbivorous insects against plant toxins. Video Abstract.

RevDate: 2022-06-25

Darcy JL, Amend AS, Swift SOI, et al (2022)

specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.

Environmental microbiome, 17(1):34.

BACKGROUND: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.

RESULTS: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.

CONCLUSIONS: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.

RevDate: 2022-06-25

Lephart ED, F Naftolin (2022)

Estrogen Action and Gut Microbiome Metabolism in Dermal Health.

Dermatology and therapy [Epub ahead of print].

Emerging scientific advances in microbial research linking estrogens and the gut-skin microbiome in reference to dermal health are featured in this narrative review of journal reports and reviews from January 2018 through February 2022. Background information on advances in microbial research along with defining the microbiota and microbiome is presented in brief. The development of and factors that influence the gut microbiome in health and disease as well as the intrinsic and extrinsic factors influencing the skin microbiome and skin aging are summarized. New information on the development and changes of organ microbiomes have exposed similarities between skin and gut structure/function, microbial components/diversity/taxonomy and how they impact the immune response for combating disease and enhancing wellness. Estrogens promote health and support homeostasis in general and directly impact dermal health. Moreover, the gut, based upon the level of the microbial enzyme β-glucuronidase, which regulates estrogen's enterohepatic recirculation, constitutes a gut-skin microbial axis. This axis revolves around the systemically available estrogen to support immune function, counteract inflammation and oxidative stress, and decrease the risk of hormone-dependent skin cancers. These data support the direct effect of estrogens on skin health and the interaction of diet on dermal health via effects on the gut microflora. Finally, the potential for bioactive botanicals containing phytoestrogens or selective estrogen receptor modulators (SERMs) to evade the effects of gut β-glucuronidase expressing flora is proposed that may have a positive impact on skin.

RevDate: 2022-06-25

Lemos LN, de Carvalho FM, Santos FF, et al (2022)

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans.

Scientific data, 9(1):366.

The One Health concept is a global strategy to study the relationship between human and animal health and the transfer of pathogenic and non-pathogenic species between these systems. However, to the best of our knowledge, no data based on One Health genome-centric metagenomics are available in public repositories. Here, we present a dataset based on a pilot-study of 2,915 metagenome-assembled genomes (MAGs) of 107 samples from the human (N = 34), cattle (N = 28), swine (N = 15) and poultry (N = 30) gut microbiomes. Samples were collected from the five Brazilian geographical regions. Of the draft genomes, 1,273 were high-quality drafts (≥90% of completeness and ≤5% of contamination), and 1,642 were medium-quality drafts (≥50% of completeness and ≤10% of contamination). Taxonomic predictions were based on the alignment and concatenation of single-marker genes, and the most representative phyla were Bacteroidota, Firmicutes, and Proteobacteria. Many of these species represent potential pathogens that have already been described or potential new families, genera, and species with potential biotechnological applications. Analyses of this dataset will highlight discoveries about the ecology and functional role of pathogens and uncultivated Archaea and Bacteria from food-producing animals and humans. Furthermore, it also represents an opportunity to describe new species from underrepresented taxonomic groups.

RevDate: 2022-06-25

Dumitriu A (2022)

Hypersymbiotics™: An artistic reflection on the ethical and environmental implications of microbiome research and new technologies.

Endeavour pii:S0160-9327(22)00020-5 [Epub ahead of print].

This essay describes my ongoing series "Hypersymbiotics™," which began in 2012 and explores the potential ways in which our microbiome, genetics, epigenetics and even our environment could potentially be enhanced to turn us into human 'super-organisms.' The series includes performances and installations involving BioArt, as well as photographic documentation of ephemeral artworks and takes the form of a vehicle for public discussion about new healthcare technologies. The essay discusses artworks made using synthetic biology techniques including CRISPR genetic modification in bacteria and yeasts, and gene editing in plants, as well as using artificial intelligence and stem cell research. It critiques the role of the media and advertising in the promotion of complex new biomedical technologies. The "Hypersymbiotics™" series is deeply concerned with promoting public understanding of the ethical implications of new scientific developments and enabling reflection and debate. At its core the artwork is about knowledge, power, and control and where that resides.


RJR Experience and Expertise


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


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


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


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


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


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


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


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

963 Red Tail Lane
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E-mail: RJR8222@gmail.com

Collection of publications by R J Robbins

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

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

short personal version

Curriculum Vitae for R J Robbins

long standard version

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