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Bibliography on: Microbiome

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ESP: PubMed Auto Bibliography 30 Sep 2022 at 02:07 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: 2022-09-29

Yahfoufi N, Kadamani AK, Aly S, et al (2022)

Pubertal consumption of R. badensis subspecies acadiensis modulates LPS-induced immune responses and gut microbiome dysbiosis in a sex-specific manner.

Brain, behavior, and immunity pii:S0889-1591(22)00388-9 [Epub ahead of print].

Puberty is a critical period of development characterized by significant brain remodeling and increased vulnerability to immune challenges. Exposure to an immune challenge such as LPS during puberty can result in inflammation and gut dysbiosis which may lead to altered brain functioning and psychiatric illnesses later in life. However, treatment with probiotics during puberty has been found to mitigate LPS-induced peripheral and central inflammation, prevent LPS-induced changes to the gut microbiota and protect against enduring behavioural disorders in a sex-specific manner. Recent findings from our laboratory revealed that pubertal R. badensis subspecies acadiensis (R. badensis subsp. acadiensis) treatment prevents LPS-induced depression-like behavior and alterations in 5HT1A receptor expression in a sex-specific manner. However, the underlying mechanism remains unclear. Thus, the aim of this study was to gain mechanistic insights and to investigate the ability of R. badensis subsp. acadiensis consumption during puberty to mitigate the effects of LPS treatment on the immune system and the gut microbiome. Our results revealed that pubertal treatment with R. badensis subsp. acadiensis reduced sickness behaviors in females more than males in a time-specific manner. It also mitigated LPS-induced increases in pro-inflammatory cytokines in the blood and in TNFα mRNA expression in the prefrontal cortex and the hippocampus of female mice. There were sex-dependent differences in microbiome composition that persisted after LPS injection or R. badensis subsp. acadiensis consumption. R. badensis subsp. acadiensis had greater impact on the microbiota of male mice but female microbiota's were more responsive to LPS treatment. This suggested that female mice microbiota's may be more prone to modulation by this probiotic. These findings emphasize the sex-specific effects of probiotic use during puberty on the structure of the gut microbiome and the immune system and highlight the critical role of gut colonization with probiotics during adolescence on immunomodulation and prevention of the enduring effects of infections.

RevDate: 2022-09-29

Lupwayi NZ, Blackshaw RE, Geddes CM, et al (2022)

Multi-year and multi-site effects of recurrent glyphosate applications on the wheat rhizosphere microbiome.

Environmental research pii:S0013-9351(22)01690-5 [Epub ahead of print].

Glyphosate (N-(phosphonomethyl)glycine) is broad-spectrum herbicide that is extensively used worldwide, but its effects on the soil microbiome are inconsistent. To provide a sound scientific basis for herbicide re-review and registration decisions, we conducted a four-year (2013-2016) study in which we consecutively applied glyphosate to a wheat (Triticum aestivum L.)-field pea (Pisum sativum L.)-canola (Brassica napus L.)-wheat crop rotation at five sites in the Canadian prairies. The glyphosate rates were 0, 1, 2, 4 and 8 kg ae ha-1, applied pre-seeding and post-harvest every year. The wheat rhizosphere was sampled in the final year of the study and analysed for microbial biomass C (MBC), the composition and diversity of the microbiome, and activities of β-glucosidase, N-acetyl-β-glucosiminidase, acid phosphomonoesterase and arylsulphatase. Glyphosate did not affect MBC, the composition and diversity of prokaryotes and fungi, and the activities of three of the four enzymes measured in the wheat rhizosphere. The one effect of glyphosate was a wave-like response of N-acetyl-β-glucosaminidase activity with increasing application rates. The experimental sites had much greater effects, driven by soil pH and organic C, on the soil microbiome composition and enzyme activities than glyphosate. Soil pH was positively correlated with the relative abundance of Acidobacteriota but negatively correlated with that of Actinobacteriota and Basidiomycota. Soil organic C was positively correlated with the relative abundances of Proteobacteriota and Verrucomicrobiota, but negatively correlated with the relative abundance of Crenachaeota. The activity of acid phosphomonoesterase declined with increasing relative abundance of Acidobacteriota, but increased with that of Actinobacteriota and Basidiomycota. The activity of N-acetyl-β-glucosaminidase also increased with increasing relative abundance of Actinobacteriota but decreased with that of Mortierellomycota. β-glucosidase activity also decreased with increasing relative abundance of Mortierellomycota. The core fungal species observed in at least 90% of the samples were Humicola nigrescens, Gibberella tricincta and Giberella fujikuroi. Therefore, this multi-site study on the Canadian prairies revealed no significant effects of 4-year applications of glyphosate applied at different rates on most soil microbial properties despite differences in the properties among sites. However, it is important to keep evaluating glyphosate effects on the soil microbiome and its functioning because it is the most widely used herbicide worldwide.

RevDate: 2022-09-29

Wu KK, Zhao L, Sun ZF, et al (2022)

Synergistic effect of hydrogen and nanoscale zero-valent iron on ex-situ biogas upgrading and acetate recovery.

The Science of the total environment pii:S0048-9697(22)06199-X [Epub ahead of print].

Hydrogen (H2) assisted ex-situ biogas upgrading and liquid chemicals production can augment the fossil fuel-dominated energy market, and alleviate CO2-induced global warming. Recent investigations confirmed that nanoscale zero-valent iron (nZVI) enabled the enhancement of anaerobic digestion for biogas production. However, little is known about the effect of nZVI on the downstream ex-situ biogas upgrading. Herein, different levels (0 mg L-1, 100 mg L-1, 200 mg L-1, 500 mg L-1, 1000 mg L-1, 2000 mg L-1) of nZVI were added for H2-assisted ex-situ biogas upgrading, to study whether nZVI could impact the biomethane purity and acetate yield for the first time. Results showed that all tested nZVI levels were favorable for biogas upgrading in the presence of H2, the highest biomethane content (94.1 %, v/v), the CO2 utilization ratio (95.9 %), and acetate yield (19.4 mmol L-1) were achieved at 500 mg L-1 nZVI, respectively. Further analysis indicated that increased biogas upgrading efficiency was related to an increase in extracellular polymeric substances, which ensures the microbial activity and stability of the ex-situ biogas upgrading. Microbial community characterization showed that the Petrimonas, Romboutsia, Acidaminococcus, and Clostridium predominated the microbiome during biogas upgrading at 500 mg L-1 nZVI with H2 supply. These results suggested that nZVI and H2 contributed jointly to promoting the bioconversion of CO2 in biogas to acetate. The findings could be helpful for paving a new way for efficient simultaneous ex-situ biogas upgrading and liquid chemicals recovery.

RevDate: 2022-09-29

Yang F, Wang X, Tian X, et al (2022)

Cow manure simultaneously reshaped antibiotic and metal resistome in the earthworm gut tract by metagenomic analysis.

The Science of the total environment pii:S0048-9697(22)06109-5 [Epub ahead of print].

Earthworm conversion is an eco-friendly biological process that converts livestock waste into a benign nutrient-rich organic fertilizer. However, little is known about the impacts of earthworm-converted livestock manure on the antibiotic resistome in the earthworm gut microbiota. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift of antibiotic resistance genes (ARGs) in the earthworm gut-feeding on cow manure (CM)-by metagenomic analysis. The effects of copper (Cu) as a food addictive were also evaluated. CM substantially enriched the antibiotic resistome in the foregut and midgut, while it decreased in the hindgut. A similar trend was observed for metal resistance genes (MRGs). Notably, Cu in the CM had little effect on composition of ARGs and MRGs in earthworm gut. The earthworm gut microbiome altered by CM was responsible for the shift of ARGs and MRGs. In wormcast, Cu (100 and 300 mg/kg) significantly increased the abundance of ARGs and MRGs. Our study provides valuable insight into the response of ARGs and MRGs to CM in earthworm gut, and underscores the need for the judicious use of heavy metals as feed additives in livestock and poultry farming.

RevDate: 2022-09-29

Yang YN, Wang QC, Xu W, et al (2022)

The berberine-enriched gut commensal Blautia producta ameliorates high-fat diet (HFD)-induced hyperlipidemia and stimulates liver LDLR expression.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie, 155:113749 pii:S0753-3322(22)01138-6 [Epub ahead of print].

Berberine (BBR) is an effective cholesterol-lowering drug. Although gut microbiota has been implicated in the pharmacological activities of BBR, little evidence exists on the specific species of gut microbiota involved in its therapeutic effects, nor on linking gut bacteria to its recognized hypercholesterolemia-alleviating mechanism-upregulation of the low-density lipoprotein receptor (LDLR) in the liver. The present study was performed to identify the specific species of gut microbiota involved in the anti-hyperlipdemic effect of BBR, and interpret its mechanism through linking the gut microbiota and LDLR. The BBR-enriched gut bacterial species were identified by whole genome shotgun sequencing. Pure cultured B. producta was orally administered to C57BL/6 mice to evaluate its anti-hyperlipdemic effect. The LDLR-upregulating effect of B. producta was evaluated both in vitro and in vivo. Orally administration of BBR (200 mg/kg) decreased serum and liver lipid levels in HFD-induced hyperlipidemic mice. Microbiome analysis indicated that Blautia was closely associated with BBR's lipid-modulating activities. Further analysis revealed that BBR selectively promoted the growth of Blautia producta. Orally treatment of HFD mice with live B. producta reduced obesity and alleviated hyperlipidemia. Notably, the B. producta significantly increased LDLR expression in the liver, and its spent culture supernatant upregulated the LDLR level and promoted LDL uptake by HepG2 cells. Simultaneously, B. producta also linked butyrate-producing and bile salt hydrolase (BSH)-inhibiting effect of BBR. The gut microbiota, especially B. producta, may confers the hypercholesterolemia-alleviating effects of berberine. B. producta represents a novel probiotic that may be used for the treatment of dyslipidemia.

RevDate: 2022-09-29

Centurion VB, Campanaro S, Basile A, et al (2022)

Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics.

Microbiological research, 265:127197 pii:S0944-5013(22)00237-3 [Epub ahead of print].

Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.

RevDate: 2022-09-29

Huang JH, Wang J, Chai XQ, et al (2022)

The Intratumoral Bacterial Metataxonomic Signature of Hepatocellular Carcinoma.

Microbiology spectrum [Epub ahead of print].

Microbiota is implicated in hepatocellular carcinoma (HCC). The spectrum of intratumoral microbiota associated with HCC progression remains elusive. Fluorescence in situ hybridization revealed that microbial DNAs were distributed in the cytosol of liver hepatocytes and erythrocytes. Viable anaerobic or aerobic bacteria were recovered in HCC tissues by fresh tissue culture. We performed a comprehensive DNA sequencing of bacterial 16S rRNA genes in 156 samples from 28 normal liver, 64 peritumoral, and 64 HCC tissues, and the DNA sequencing yielded 4.2 million high-quality reads. Both alpha and beta diversity in peritumor and HCC microbiota were increased compared to normal controls. The most predominant phyla in HCC were Patescibacteria, Proteobacteria, Bacteroidota, Firmicutes, and Actinobacteriota. phyla of Proteobacteria, Firmicutes, and Actinobacteriota, and classes of Bacilli and Actinobacteria, were consistently enriched in peritumor and HCC tissues, while Gammaproteobacteria was especially abundant in HCC tissues compared to normal controls. Streptococcaceae and Lactococcus were the marker taxa of HCC cirrhosis. The Staphylococcus branch and Caulobacter branch were selectively enriched in HBV-negative HCCs. The abundance of Proteobacteria, Gammaproteobacteria, Firmicutes, Actinobacteriota, and Saccharimonadia were associated with the clinicopathological features of HCC patients. The inferred functions of different taxa were changed between the microbiota of normal liver and peritumor/HCC. Random forest machine learning achieved great discriminative performance in HCC prediction (area under the curve [AUC] = 1.00 in the training cohort, AUC = 0.950 for top five class signature, and AUC = 0.943 for the top 50 operational taxonomy units [OTUs] in the validation cohort). Our analysis highlights the complexity and diversity of the liver and HCC microbiota and established a specific intratumoral microbial signature for the potential prediction of HCC. IMPORTANCE Gut microbiome is an important regulator of hepatic inflammation, detoxification, and immunity, and contributes to the carcinogenesis of liver cancer. Intratumoral bacteria are supposed to be closer to the tumor cells, forming a microenvironment that may be relevant to the pathological process of hepatocellular carcinoma (HCC). However, the presence of viable intratumoral bacteria remains unclear. It is worth exploring whether the metataxonomic characteristics of intratumoral bacteria can be used as a potential marker for HCC prediction. Here, we present the first evidence of the existence of viable intratumoral bacteria in HCC using the tissue culture method. We revealed that microbial DNAs were distributed in the cytosol of liver hepatocytes and erythrocytes. We analyzed the diversity, structure, and abundance of normal liver and HCC microbiota. We built a machine learning model for HCC prediction using intratumoral bacterial features. We show that specific taxa represent potential targets for both therapeutic and diagnostic interventions.

RevDate: 2022-09-29

Izcue J, Palacios-García I, Rojas Traverso F, et al (2022)

Perspectives on Inequity and Health Disparities in Chile and Their Relationship to Microbial Ecology.

mSystems [Epub ahead of print].

Among countries in the Organisation for Economic Cooperation and Development (OECD), Chile stands out as having important inequalities in income distribution, dietary quality, access to urban green spaces, and health outcomes. People in lower socioeconomic groups consistently show higher rates of noncommunicable chronic diseases and are being hit the hardest by the COVID-19 pandemic. These chronic conditions are increasingly considered to be shaped, or affected by, the human gut microbiome. Moreover, inequity as an overarching concept might also be associated with microbial patterns and if so, this may represent a novel pathway through which to address health and other disparities. Focusing on the case of Chile, our goal is to contribute to a critical discussion and motivate researchers and policymakers to consider the role of the microbiome in social equity in future endeavors.

RevDate: 2022-09-29

Tang Y, Du J, Wu H, et al (2022)

Potential Therapeutic Effects of Short-chain Fatty Acids on Chronic Pain.

Current neuropharmacology pii:CN-EPUB-126564 [Epub ahead of print].

The intestinal homeostasis maintained by the gut microbiome and relevant metabolites is essential for health, and its disturbance leads to various intestinal or extraintestinal diseases. Recent studies suggest that gut microbiome-derived metabolites short-chain fatty acids (SCFAs) are involved in different neurological disorders (such as chronic pain). SCFAs are produced by bacterial fermentation of dietary fibers in the gut and contribute to multiple host processes, including gastrointestinal regulation, cardiovascular modulation, and neuroendocrine-immune homeostasis. Although SCFAs have been implicated in the modulation of chronic pain, the detailed mechanisms that underlie such roles of SCFAs remain to be further investigated. In this review, we summarize currently available research data regarding SCFAs as a potential therapeutic target for chronic pain treatment and discuss several possible mechanisms by which SCFAs modulate chronic pain.

RevDate: 2022-09-29

Xiang W, Ji B, Jiang Y, et al (2022)

Association of low-grade inflammation caused by gut microbiota disturbances with osteoarthritis: A systematic review.

Frontiers in veterinary science, 9:938629.

Background: Currently, many studies have been published on the relationship between the gut microbiome and knee osteoarthritis. However, the evidence for the association of gut microbiota with knee osteoarthritis has not been comprehensively evaluated.

Objective: This review aimed to assess existing results and provide scientific evidence for the association of low-grade inflammation caused by gut microbiota disturbances with knee osteoarthritis.

Methods: This study conducted an extensive review of the current literature using four databases, PubMed, EMBASE, Cochrane Library and Web of Science before 31 December 2021. Risk of bias was determined using ROBINS and SYRCLE, and quality of evidence was assessed using GRADE and CAMADARES criteria. Twelve articles were included.

Results: Studies have shown that a high-fat diet leads to a disturbance of the gut microbiota, mainly manifested by an increase in the abundance of Firmicutes and Proteobacteria, a decrease in Bacteroidetes, and an increase in the Firmicutes/ Bacteroidetes ratio. Exercise can reverse the pattern of gain or loss caused by high fat. These changes are associated with elevated levels of serum lipopolysaccharide (LPS) and its binding proteins, as well as various inflammatory factors, leading to osteoarthritis (OA).

Conclusion: This systematic review shows that a correlation between low-grade inflammation caused by gut microbiota disturbances and severity of knee osteoarthritis radiology and dysfunction. However, there was a very small number of studies that could be included in the review. Thus, further studies with large sample sizes are warranted to elucidate the association of low-grade inflammation caused by gut microbiota disturbances with osteoarthritis, and to explore the possible mechanisms for ameliorating osteoarthritis by modulating gut microbiota.

RevDate: 2022-09-29

Zhang K, Lin R, Chang Y, et al (2022)

16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis.

PeerJ, 10:e14043 pii:14043.

Background: The full-length 16S rRNA sequencing can better improve the taxonomic and phylogenetic resolution compared to the partial 16S rRNA gene sequencing. The 16S-FAS-NGS (16S rRNA full-length amplicon sequencing based on a next-generation sequencing platform) technology can generate high-quality, full-length 16S rRNA gene sequences using short-read sequencers, together with assembly procedures. However there is a lack of a data analysis suite that can help process and analyze the synthetic long read data.

Results: Herein, we developed software named 16S-FASAS (16S full-length amplicon sequencing data analysis software) for 16S-FAS-NGS data analysis, which provided high-fidelity species-level microbiome data. 16S-FASAS consists of data quality control, de novo assembly, annotation, and visualization modules. We verified the performance of 16S-FASAS on both mock and fecal samples. In mock communities, we proved that taxonomy assignment by MegaBLAST had fewer misclassifications and tended to find more low abundance species than the USEARCH-UNOISE3-based classifier, resulting in species-level classification of 85.71% (6/7), 85.71% (6/7), 72.72% (8/11), and 70% (7/10) of the target bacteria. When applied to fecal samples, we found that the 16S-FAS-NGS datasets generated contigs grouped into 60 and 56 species, from which 71.62% (43/60) and 76.79% (43/56) were shared with the Pacbio datasets.

Conclusions: 16S-FASAS is a valuable tool that helps researchers process and interpret the results of full-length 16S rRNA gene sequencing. Depending on the full-length amplicon sequencing technology, the 16S-FASAS pipeline enables a more accurate report on the bacterial complexity of microbiome samples. 16S-FASAS is freely available for use at

RevDate: 2022-09-29

Liu Z, Zhao J, Huo J, et al (2022)

Influence of planting yellowhorn (Xanthoceras sorbifolium Bunge) on the bacterial and fungal diversity of fly ash.

PeerJ, 10:e14015 pii:14015.

Phytoremediation is a low-cost solution to fly ash pollution and the rhizosphere interactions between plant roots and the fly ash microbiome were important for the phytoremediation. To analyze the dynamic changes of the rhizosphere microbiome during yellowhorn cultivation in fly ash, the bacterial 16S rRNA gene V3-V4 region and the fungal ITS region of the rhizosphere microbiome were sequenced using Illumina MiSeq technology. The changes in fly ash physicochemical properties and the heavy metal content of different yellowhorn tissues were also analyzed. The results showed that both the bacterial and fungal communities were noticeably different after yellowhorn cultivation compared with the control sample. Proteobacteria and Acidobacteria levels increased (p < 0.05) and Firmicutes and Actinobacteria decreased (p < 0.05) in the bacterial community after yellowhorn cultivation. In the fungal community, Ascomycota and Mortierellomycota decreased (p < 0.05), while Chytridiomycota increased (p < 0.05). The levels of four heavy metals (Cr, Cd, Hg, Pb and As) decreased in the fly ash after yellowhorn cultivation. These metals were absorbed by the yellowhorn plants and accumulated in the fibrous root, taproot, stem and leaf tissues of these plants. Accordingly, the abundance of bacteria that could solubilize heavy metals increased (p < 0.05). In summary, the cultivation of yellowhorn affected the composition of the rhizosphere microbial communities in fly ash, which is of great significance for the biological remediation of fly ash.

RevDate: 2022-09-29

Abduweli Uyghurturk D, Lu Y, Urata J, et al (2022)

Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT).

PeerJ, 10:e14040 pii:14040.

Background: Hematopoietic cell transplantation (HCT) is a potentially curative therapy for a wide range of pediatric malignant and nonmalignant diseases. However, complications, including blood stream infection (BSI) remain a major cause of morbidity and mortality. While certain bacteria that are abundant in the oral microbiome, such as S. mitis, can cause BSI, the role of the oral microbial community in the etiology of BSI is not well understood. The finding that the use of xylitol wipes, which specifically targets the cariogenic bacteria S. mutans is associated with reduced BSI in pediatric patients, lead us to investigate dental caries as a risk factor for BSI.

Methods: A total of 41 pediatric patients admitted for allogenic or autologous HCT, age 8 months to 25 years, were enrolled. Subjects with high dental caries risk were identified as those who had dental restorations completed within 2 months of admission for transplant, or who had untreated decay. Fisher's exact test was used to determine if there was a significant association between caries risk and BSI. Dental plaque and saliva were collected on a cotton swab from a subset of four high caries risk (HCR) and four low caries risk (LCR) children following pretransplant conditioning. 16SrRNA sequencing was used to compare the microbiome of HCR and LCR subjects and to identify microbes that were significantly different between the two groups.

Results: There was a statistically significant association between caries risk and BSI (p < 0.035) (Fisher's exact test). Multivariate logistic regression analysis showed children in the high dental caries risk group were 21 times more likely to have BSI, with no significant effect of age or mucositis severity. HCR subjects showed significantly reduced microbial alpha diversity as compared to LCR subjects. LEfse metagenomic analyses, showed the oral microbiome in HCR children enriched in order Lactobacillales. This order includes Streptococcus and Lactobacillus, both which contain bacteria primarily associated with dental caries.

Discussion: These findings support the possibility that the cariogenic microbiome can enhance the risk of BSI in pediatric populations. Future metagenomic analyses to measure microbial differences at, before, and after conditioning related to caries risk, may further unravel the complex relationship between the oral microbiome, and whether it affects health outcomes such as BSI.

RevDate: 2022-09-29

Akaza N, Takasaki K, Nishiyama E, et al (2022)

The Microbiome in Comedonal Contents of Inflammatory Acne Vulgaris is Composed of an Overgrowth of Cutibacterium Spp. and Other Cutaneous Microorganisms.

Clinical, cosmetic and investigational dermatology, 15:2003-2012 pii:379609.

Background: Acne vulgaris (acne) and cutaneous resident microorganisms are considered to be closely related. However, the bacterial and fungal microbiota in the comedonal contents of inflammatory acne lesions have not yet been investigated in detail.

Purpose: To clarify the relationship between cutaneous microorganisms and acne, we examined the microbiome in the comedonal contents of inflammatory acne and on the facial skin of patients with acne using 16s rRNA and ITS gene sequencing with a next-generation sequencer (NGS).

Patients and Methods: Twenty-two untreated Japanese acne outpatients were examined. The comedonal contents of inflammatory acne lesions on the face were collected using a comedo extractor. Skin surface samples from facial skin were collected using the swab method.

Results: The results obtained revealed that the predominant bacteria in the comedonal contents of inflammatory acne were Cutibacterium spp. (more prominent in areas with large amounts of sebum), while those on the skin surface were Staphylococcus spp. Malassezia spp., particularly Malassezia restricta, were the predominant fungi in both the comedonal contents of inflammatory acne and on the skin surface. The bacterial microbiome in comedonal contents exhibited stronger metabolic activity, including the production of enzymes related to acne, than that on the skin surface.

Conclusion: These results indicate that acne is an inflammatory disease involving the overgrowth of Cutibacterium acnes and other cutaneous resident microorganisms, including Malassezia spp.

RevDate: 2022-09-29

Mousa WK (2022)

The microbiome-product colibactin hits unique cellular targets mediating host-microbe interaction.

Frontiers in pharmacology, 13:958012 pii:958012.

The human microbiota produces molecules that are evolved to interact with the diverse cellular machinery of both the host and microbes, mediating health and diseases. One of the most puzzling microbiome molecules is colibactin, a genotoxin encoded in some commensal and extraintestinal microbes and is implicated in initiating colorectal cancer. The colibactin cluster was discovered more than 15 years ago, and most of the research studies have been focused on revealing the biosynthesis and precise structure of the cryptic encoded molecule(s) and the mechanism of carcinogenesis. In 2022, the Balskus group revealed that colibactin not only hits targets in the eukaryotic cell machinery but also in the prokaryotic cell. To that end, colibactin crosslinks the DNA resulting in activation of the SOS signaling pathway, leading to prophage induction from bacterial lysogens and modulation of virulence genes in pathogenic species. These unique activities of colibactin highlight its ecological role in shaping gut microbial communities and further consequences that impact human health. This review dives in-depth into the molecular mechanisms underpinning colibactin cellular targets in eukaryotic and prokaryotic cells, aiming to understand the fine details of the role of secreted microbiome chemistry in mediating host-microbe and microbe-microbe interactions. This understanding translates into a better realization of microbiome potential and how this could be advanced to future microbiome-based therapeutics or diagnostic biomarkers.

RevDate: 2022-09-29

Li X, Sun X, Zhang A, et al (2022)

Breast microbiome associations with breast tumor characteristics and neoadjuvant chemotherapy: A case-control study.

Frontiers in oncology, 12:926920.

Background: Commensal microbiota have been proven to colonize the mammary gland, but whether their composition is altered in patients with breast cancer (BC) remains elusive. This study intends to explore the breast microbiome differences between benign and malignant diseases and to investigate the impact of neoadjuvant chemotherapy (NAC) on the breast microbiota in patients with BC.

Methods: Breast normal adipose tissues (NATs) were collected from 79 patients with BC and 15 controls between July 2019 and November 2021. The BC group consisted of 29 patients who had received NAC and 50 who were non-NAC patients. Participants diagnosed with benign breast disease were recruited as controls. 16S rRNA gene sequencing was used to analyze the bacterial diversity of NATs.

Results: The community structure of the NAT microbiome was significantly different between the BC and control groups. Proteobacteria decreased (47.40% versus 39.74%), whereas Firmicutes increased (15.71% versus 25.33%) in patients with BC when compared with that in control tissues. Nine genera were enriched in BC NATs, and four genera levels increased in the control group. The associations between differential bacterial genera and breast tumor grade were calculated by Spearman's correlation. The results showed that tumor grade was positively associated with the relative abundance of Streptococcus and negatively related to Vibrio, Pseudoalteromonas, RB41, and Photobacterium. Moreover, menopause was associated with the microbiota composition change of non-NAC BC patients and related to the significant reduction in the abundance level of Pseudoalteromonas, Veillonella, and Alcaligenes. In addition, NAC was related to the beta diversity of patients with BC and associated with the decrease of Clostridium_sensu_stricto_7 and Clostridium_sensu_stricto_2 in postmenopausal patients. Of note, Tax4Fun functional prediction analysis revealed that the metabolic state was more exuberant in the BC group with upregulating of multiple metabolism-related pathways.

Conclusion: Our results offer new insight into the relationship between NAC and breast microbiota and help to better characterize the breast microbial dysbiosis that occurs in patients with BC. Further epidemiological studies with larger sample size and well-designed animal experiments are required to elucidate the role of breast microbiota in the therapeutic outcome of BC.

RevDate: 2022-09-29

Fréville M, Estienne A, Ramé C, et al (2022)

Chronic dietary exposure to a glyphosate-based herbicide results in total or partial reversibility of plasma oxidative stress, cecal microbiota abundance and short-chain fatty acid composition in broiler hens.

Frontiers in physiology, 13:974688 pii:974688.

Glyphosate-based herbicides (GBHs) are massively used in agriculture. However, few studies have investigated the effects of glyphosate-based herbicides on avian species although they are largely exposed via their food. Here, we investigated the potential reversibility of the effects of chronic dietary exposure to glyphosate-based herbicides in broiler hens. For 42 days, we exposed 32-week-old hens to glyphosate-based herbicides via their food (47 mg/kg/day glyphosate equivalent, glyphosate-based herbicides, n = 75) corresponding to half glyphosate's no-observed-adverse-effect-level in birds. We compared their performance to that of 75 control animals (CT). Both groups (glyphosate-based herbicides and control animals) were then fed for 28 additional days without glyphosate-based herbicides exposure (Ex-glyphosate-based herbicides and Ex-control animals). Glyphosate-based herbicides temporarily increased the plasma glyphosate and AMPA (aminomethylphosphonic acid) concentrations. Glyphosate and aminomethylphosphonic acid mostly accumulated in the liver and to a lesser extent in the leg muscle and abdominal adipose tissue. Glyphosate-based herbicides also temporarily increased the gizzard weight and plasma oxidative stress monitored by TBARS (thiobarbituric acid reactive substances). Glyphosate-based herbicides temporarily decreased the cecal concentrations of propionate, isobutyrate and propionate but acetate and valerate were durably reduced. The cecal microbiome was also durably affected since glyphosate-based herbicides inhibited Barnesiella and favored Alloprevotella. Body weight, fattening, food intake and feeding behavior as well as plasma lipid and uric acid were unaffected by glyphosate-based herbicides. Taken together, our results show possible disturbances of the cecal microbiota associated with plasma oxidative stress and accumulation of glyphosate in metabolic tissues in response to dietary glyphosate-based herbicides exposure in broiler hens. Luckily, glyphosate-based herbicides at this concentration does not hamper growth and most of the effects on the phenotypes are reversible.

RevDate: 2022-09-29

Zhu H, Qiang J, Li Q, et al (2022)

Multi-kingdom microbiota and functions changes associated with culture mode in genetically improved farmed tilapia (Oreochromis niloticus).

Frontiers in physiology, 13:974398 pii:974398.

Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are intensively farmed in China, where most of the yield derives from the pond culture system (PCS). The in-pond raceway system (IPRS) is a new type of highly efficient aquaculture mode, and has been recommended as a novel system for GIFT farming. To determine the effects of these culture modes on the gut microbiome of GIFT, we conducted a 90-days experiment in IPRS and PCS units. A 16S rRNA gene profile analysis showed that the composition of gut microbiota in GIFT under IPRS and PCS conditions gradually separated as rearing progressed, with divergent responses by the midgut and hindgut bacteria. The α-diversity in hindgut decreased significantly by day 90, as compared with on day 7 (p < 0.05), with a significantly greater decrease in PCS-reared fish than in IPRS fish (p < 0.05). The α-diversity of microbiota in midgut remained stable (p > 0.05). The overall dominant gut bacteria were Bacteroidetes, Proteobacteria, and Firmicutes. Rearing mode affected the taxonomic profile of the gut bacteria; in midgut, IPRS samples had more Firmicutes and Fusobacteria compared with PCS samples, but less Proteobacteria, Verrucomicrobia, and Actinobacteria. Firmicutes was enriched in IPRS hindgut, and Fusobacteria was enriched in PCS hindgut. Using random-forest models and LEfSe, we also screened core taxa that could discriminate between the gut microbial communities under IPRS and PCS conditions. The genus Cetobacterium (of family Fusobacteriaceae) was significantly enriched in midgut in IPRS fish, and enriched in hindgut in PCS fish. The genus Clostridium sensu stricto (of family Clostridiaceae 1) was significantly enriched in both IPRS midgut and hindgut. Analysis with PICRUSt2 software revealed that the culture modes were similar in their effects on the gut microbial metabolic functions. The predicted pathways were significantly enriched in the metabolism class (level 1). Further, the relative abundance of functions related to amino acid metabolic, carbohydrate metabolic, energy metabolic, and metabolic of cofactors and vitamins were high at hierarchy level 2, as the metabolic activity of intestinal bacteria is especially active. Overall, this study enhances our understanding of the characteristics of gut microbiota in GIFT under IPRS and PCS culture modes. Moreover, our findings provide insights into the microecological balance in IPRS units, and a theoretical reference for further development of this culture system.

RevDate: 2022-09-29

Yuan M, Xu Y, Z Guo (2022)

Association of oral microbiome and pancreatic cancer: a systematic review and meta-analysis.

Therapeutic advances in gastroenterology, 15:17562848221123980 pii:10.1177_17562848221123980.

Background: Oral microbiota reported to be associated with pancreatic diseases, including pancreatic cancer. However, the association of oral microbiome and pancreatic cancer has not been reviewed systematically.

Objectives: To systematically investigate the association between the oral microbiome and pancreatic cancer risk.

Design: A systematic review and meta-analysis.

Data Sources and Methods: Systemic searches were conducted using PubMed, Medline, Cochrane Library, and Embase databases without any language restriction from conception to August 29, 2020. The studies that evaluated the association of oral microbiome and pancreatic cancer risk were included in this meta-analysis.

Results: The six included studies encompassed a total of 863 pancreatic cancer cases and 906 controls. Four studies reported the overall oral microbiome in pancreatic cancer cases. A total of 12-17 species/clusters were correlated with pancreatic cancer. Three studies reported the odds ratios (ORs) or relative abundance of several oral microbiomes pieces/clusters, and the majority were associated with pancreatic cancer.

Conclusions: Overall, this study supports the hypothesis of associations of variations of patients' oral microbiota to pancreatic cancer. Nonetheless, due to all included studies were conducted in USA or Europe, additional original studies and meta-analysis particular studies from other countries are essential for an in-depth investigation into the role of oral bacteria in pancreatic cancer.

RevDate: 2022-09-29

Sethi V, Garg M, Herve M, et al (2022)

Potential complementary and/or synergistic effects of curcumin and boswellic acids for management of osteoarthritis.

Therapeutic advances in musculoskeletal disease, 14:1759720X221124545 pii:10.1177_1759720X221124545.

For several thousand years (~4000) Boswellia serrata and Curcuma longa have been used in Aryuvedic medicine for treatment of various illnesses, including asthma, peptic ulcers, and rheumatoid arthritis, all of which are mediated through pathways associated with inflammation and pain. Although the in vivo pharmacology of both these natural ingredients is difficult to study because of poor bioavailability, in vitro data suggest that both influence gene expression mediated through nuclear factor kappa B (NF-κB). Therefore, the activity of pathways associated with inflammation (including NF-κB and lipoxygenase- and cyclooxygenase-mediated reduction in leukotrienes/prostaglandins) and those involved in matrix degradation and apoptosis are reduced, resulting in a reduction in pain. Additive activity of boswellic acids and curcumin was observed in preclinical models and synergism was suggested in clinical trials for the management of osteoarthritis (OA) pain. Overall, studies of these natural ingredients, alone or in combination, revealed that these extracts relieved pain from OA and other inflammatory conditions. This may present an opportunity to improve patient care by offering alternatives for patients and physicians, and potentially reducing nonsteroidal anti-inflammatory or other pharmacologic agent use. Additional research is needed on the effects of curcumin on the microbiome and the influence of intestinal metabolism on the activity of curcuminoids to further enhance formulations to ensure sufficient anti-inflammatory and antinociceptive activity. This narrative review includes evidence from in vitro and preclinical studies, and clinical trials that have evaluated the mechanism of action, pharmacokinetics, efficacy, and safety of curcumin and boswellic acids individually and in combination for the management of OA pain.

RevDate: 2022-09-29

Chauhan NS, Mukerji M, S Gupta (2022)

Editorial: Role of microbiome in diseases diagnostics and therapeutics.

Frontiers in cellular and infection microbiology, 12:1025837.

RevDate: 2022-09-29

Chai J, Liu X, Usdrowski H, et al (2022)

Geography, niches, and transportation influence bovine respiratory microbiome and health.

Frontiers in cellular and infection microbiology, 12:961644.

Bovine respiratory disease (BRD), one of the most common and infectious diseases in the beef industry, is associated with the respiratory microbiome and stressors of transportation. The impacts of the bovine respiratory microbiota on health and disease across different geographic locations and sampling niches are poorly understood, resulting in difficult identification of BRD causes. In this study, we explored the effects of geography and niches on the bovine respiratory microbiome and its function by re-analyzing published metagenomic datasets and estimated the main opportunistic pathogens that changed after transportation. The results showed that diversity, composition, structure, and function of the bovine nasopharyngeal microbiota were different across three worldwide geographic locations. The lung microbiota also showed distinct microbial composition and function compared with nasopharyngeal communities from different locations. Although different signature microbiota for each geographic location were identified, a module with co-occurrence of Mycoplasma species was observed in all bovine respiratory communities regardless of geography. Moreover, transportation, especially long-distance shipping, could increase the relative abundance of BRD-associated pathogens. Lung microbiota from BRD calves shaped clusters dominated with different pathogens. In summary, geography, sampling niches, and transportation are important factors impacting the bovine respiratory microbiome and disease, and clusters of lung microbiota by different bacterial species may explain BRD pathogenesis, suggesting the importance of a deeper understanding of bovine respiratory microbiota in health.

RevDate: 2022-09-28

Carda-Diéguez M, Moazzez R, A Mira (2022)

Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study.

Microbiome, 10(1):159.

BACKGROUND: Tooth decay is one of the most prevalent diseases worldwide, and efficient tooth brushing with a fluoride-containing dentifrice is considered fundamental to caries prevention. Fluoride-containing dentifrices have been extensively studied in relation to enamel resistance to demineralization. Arginine (Arg) has also been proposed as a promising prebiotic to promote pH buffering through ammonia production. Here, we present the first metagenomic (DNA sequencing of the whole microbial community) and metatranscriptomic (RNAseq of the same community) analyses of human dental plaque to evaluate the effect of brushing with fluoride (Fl) and a Fl+Arg containing dentifrices on oral microbial composition and activity. Fifty-three patients were enrolled in a longitudinal clinical intervention study with two arms, including 26 caries-active and 27 caries-free adults. After a minimum 1-week washout period, dental plaque samples were collected at this post-washout baseline, 3 months after the use of a 1450-ppm fluoride dentifrice, and after 6 months of using a 1450-ppm fluoride with 1.5% arginine dentifrice.

RESULTS: There was a shift in both the composition and activity of the plaque microbiome after 3 months of brushing with the fluoride-containing toothpaste compared to the samples collected at the 1-week post-washout period, both for caries-active and caries-free sites. Although several caries-associated bacteria were reduced, there was also an increase in several health- and periodontitis-associated bacteria. Over 400 genes changed proportion in the metagenome, and between 180 and 300 genes changed their expression level depending on whether caries-free or caries-active sites were analyzed. The metagenome and metatranscriptome also changed after the subjects brushed with the Fl+Arg dentifrice. There was a further decrease of both caries- and periodontitis-associated organisms. In both caries-free and caries-active sites, a decrease of genes from the arginine biosynthesis pathway was also observed, in addition to an increase in the expression of genes associated with the arginine deiminase pathway, which catabolizes arginine into ammonia, thereby buffering acidic pH. Bacterial richness and diversity were not affected by either of the two treatments in the two arms of the study.

CONCLUSIONS: Our data demonstrate that long-term use of both assayed dentifrices changes the bacterial composition and functional profiles of human dental plaque towards a healthier microbial community, both in caries-free and caries-active sites. This observation was especially apparent for the Fl+Arg dentifrice. Thus, we conclude that the preventive benefits of tooth brushing go beyond the physical removal of dental plaque and that the active ingredients formulated within dentifrices have a positive effect not only on enamel chemistry but also on the metabolism of oral microbial populations. Video Abstract.

RevDate: 2022-09-28

Molina MA, Andralojc KM, Huynen MA, et al (2022)

In-depth insights into cervicovaginal microbial communities and hrHPV infections using high-resolution microbiome profiling.

NPJ biofilms and microbiomes, 8(1):75.

The cervicovaginal microbiome (CVM) correlates with women's cervical health, and variations in its composition are associated with high-risk human papillomavirus (hrHPV) infection outcomes. Cervicovaginal microbes have been grouped into five community state types (CSTs) based on microbial community composition and abundance. However, studying the impact of CSTs in health and disease is challenging because the current sequencing technologies have limited confident discrimination between closely related and yet functionally different bacterial species. Circular probe-based RNA sequencing (ciRNAseq) achieves high-resolution microbiome profiling and therefore provides in-depth and unambiguous knowledge about the composition of the CVM. Based on ciRNAseq profiling of a large cohort of cervical smears (n = 541), we here define subgroups of CSTs I, III, and IV based on intra-CST differences with respect to abundances of Lactobacillus acidophilus (CSTs I-A vs. I-B and CSTs III-A vs. III-B), Lactobacillus iners (CSTs I-A vs. I-B and CSTs III-A vs. III-B), and Megasphaera genomosp type 1 (CSTs IV-A vs. IV-B). Our results further support the existence of subgroups of CST IV-C that are dominant for non-Lactobacillus species and have intermediate microbial diversity. We also show that CST V is associated with uninfected conditions, and CST IV-A associates with hrHPV-induced cervical disease. In conclusion, we characterized new subdivisions of cervicovaginal CSTs, which may further advance our understanding of women's cervical health and hrHPV-related progression to disease.

RevDate: 2022-09-28

Lu J, Rincon N, Wood DE, et al (2022)

Metagenome analysis using the Kraken software suite.

Nature protocols [Epub ahead of print].

Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization of the microbial community. To facilitate efficient and reproducible metagenomic analysis, we introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets. Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1-2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.

RevDate: 2022-09-28

Hayes LN, An K, Carloni E, et al (2022)

Prenatal immune stress blunts microglia reactivity, impairing neurocircuitry.

Nature [Epub ahead of print].

Recent studies suggested that microglia, the primary brain immune cells, can affect circuit connectivity and neuronal function1,2. Microglia infiltrate the neuroepithelium early in embryonic development and are maintained in the brain throughout adulthood3,4. Several maternal environmental factors-such as an aberrant microbiome, immune activation and poor nutrition-can influence prenatal brain development5,6. Nevertheless, it is unknown how changes in the prenatal environment instruct the developmental trajectory of infiltrating microglia, which in turn affect brain development and function. Here we show that, after maternal immune activation (MIA) in mice, microglia from the offspring have a long-lived decrease in immune reactivity (blunting) across the developmental trajectory. The blunted immune response was accompanied by changes in chromatin accessibility and reduced transcription factor occupancy of the open chromatin. Single-cell RNA-sequencing analysis revealed that MIA does not induce a distinct subpopulation but, rather, decreases the contribution to inflammatory microglia states. Prenatal replacement of microglia from MIA offspring with physiological infiltration of naive microglia ameliorated the immune blunting and restored a decrease in presynaptic vesicle release probability onto dopamine receptor type-two medium spiny neurons, indicating that aberrantly formed microglia due to an adverse prenatal environment affect the long-term microglia reactivity and proper striatal circuit development.

RevDate: 2022-09-28

Oduaran OH, AS Bhatt (2022)

Equitable partnerships and the path to inclusive, innovative and impactful human microbiome research.

Nature reviews. Gastroenterology & hepatology [Epub ahead of print].

RevDate: 2022-09-28

Procházková N, Falony G, Dragsted LO, et al (2022)

Advancing human gut microbiota research by considering gut transit time.

Gut pii:gutjnl-2022-328166 [Epub ahead of print].

Accumulating evidence indicates that gut transit time is a key factor in shaping the gut microbiota composition and activity, which are linked to human health. Both population-wide and small-scale studies have identified transit time as a top covariate contributing to the large interindividual variation in the faecal microbiota composition. Despite this, transit time is still rarely being considered in the field of the human gut microbiome. Here, we review the latest research describing how and why whole gut and segmental transit times vary substantially between and within individuals, and how variations in gut transit time impact the gut microbiota composition, diversity and metabolism. Furthermore, we discuss the mechanisms by which the gut microbiota may causally affect gut motility. We argue that by taking into account the interindividual and intraindividual differences in gut transit time, we can advance our understanding of diet-microbiota interactions and disease-related microbiome signatures, since these may often be confounded by transient or persistent alterations in transit time. Altogether, a better understanding of the complex, bidirectional interactions between the gut microbiota and transit time is required to better understand gut microbiome variations in health and disease.

RevDate: 2022-09-28

Taylor M, Janasky L, N Vega (2022)

Convergent structure with divergent adaptations in combinatorial microbiome communities.

FEMS microbiology ecology pii:6726631 [Epub ahead of print].

Adaptation of replicate microbial communities frequently produces shared trajectories of community composition and structure. However, divergent adaptation of individual community members can occur and is associated with community-level divergence. The extent to which community-based adaptation of microbes should be convergent when community members are similar but not identical is therefore not well understood. In these experiments, adaptation of combinatorial minimal communities of bacteria with the model host Caenorhabditis elegans produces structurally similar communities over time, but with divergent adaptation of member taxa and differences in community-level resistance to invasion. These results indicate that community-based adaptation from taxonomically similar starting points can produce compositionally similar communities that differ in traits of member taxa and in ecological properties.

RevDate: 2022-09-28

Hua H, Huang C, Liu H, et al (2022)

Depression and antidepressant effects of ketamine and its metabolites: The pivotal role of gut microbiota.

Neuropharmacology pii:S0028-3908(22)00331-8 [Epub ahead of print].

The discovery of the robust antidepressant actions of ketamine is regarded as one of the greatest advancements in depression treatment in the past 60 years. Recent findings have provided strong evidence for the presence of bidirectional communication networks between the gastrointestinal tract and the brain in depression. Moreover, increasing evidence supports the antidepressant role of ketamine in regulating the gut microbiome and microbiota-derived molecules; however, the mechanisms underpinning such effects are still ambiguous. This review summarizes the current understanding of the anti-depressant mechanisms of ketamine and its metabolites regarding the bidirectional regulation by microbiota-gut-brain axis. We review the relationship between gut microbiota and the antidepressant mechanisms of ketamine, and discuss the role of stress response, brain-derived neurotrophic factor (BDNF)-mediated neurogenesis, anti-inflammatory effect and neurotransmitters.

RevDate: 2022-09-28

Hutchinson NT, Wang SS, Dokhanchi J, et al (2022)

Effects of Broad-spectrum Antibiotic Treatment or Germ-free Status on Endurance Performance and Exercise Adaptations in Mice.

Medicine and science in sports and exercise pii:00005768-990000000-00128 [Epub ahead of print].

PURPOSE: Endurance exercise alters the gut microbiome independently of diet. The extent to which gut microbes are responsible for physiologic adaptations to exercise training is unknown. The purpose of these experiments was to determine the role of gut microbes in performance and muscle adaptation to six weeks of voluntary wheel running (VWR) in mice.

METHODS: We depleted microbes with broad-spectrum antibiotic treatment (ABX) and used germ-free (GF) mice to determine effects on adaptations to VWR. Male and female C57Bl/6 mice (n = 56) were assigned to daily VWR or sedentary conditions. After the intervention, treadmill endurance and glucose tolerance were assessed, and gastrocnemius and soleus tissues were harvested and analyzed for citrate synthase (CS) enzyme activity and expression of exercise training-sensitive genes.

RESULTS: ABX treatment and GF status resulted in VWR volumes ~22% and 26% lower than controls, respectively. Analysis of variance revealed that while VWR increased treadmill endurance, ABX had no effect. GF status significantly reduced treadmill performance in trained GF mice post-training. VWR increased gastrocnemius CS enzyme activity in all groups, and ABX and GF status did not reduce the VWR effect. VWR also increased muscle expression of PGC1a, but this was not affected by ABX treatment.

CONCLUSIONS: ABX treatment and GF status reduced VWR behavior but did not affect VWR-induced adaptations in endurance capacity, CS activity, or expression of muscle metabolic genes. However, GF status reduced endurance capacity. These data indicated that reducing microbes in adulthood does not inhibit endurance-training adaptations in C57Bl/6 mice, but that GF mice possess a reduced responsiveness to endurance exercise training, perhaps due to a developmental defect associated with lack of microbes from birth.

RevDate: 2022-09-28

Shah UA, Maclachlan KH, Derkach A, et al (2022)

Sustained Minimal Residual Disease Negativity in Multiple Myeloma is Associated with Stool Butyrate and Healthier Plant-Based Diets.

Clinical cancer research : an official journal of the American Association for Cancer Research pii:709516 [Epub ahead of print].

PURPOSE: Sustained minimal residual disease (MRD) negativity is associated with long-term survival in multiple myeloma (MM). The gut microbiome is affected by diet, and in turn can modulate host immunity, for example through production of short-chain fatty acids including butyrate. We hypothesized that dietary factors affect the microbiome (abundance of butyrate-producing bacteria or stool butyrate concentration) and may be associated with MM outcomes.

EXPERIMENTAL DESIGN: We examined the relationship of dietary factors (via a food frequency questionnaire), stool metabolites (via gas chromatography-mass spectrometry), and the stool microbiome (via 16S sequencing - α-diversity and relative abundance of butyrate-producing bacteria) with sustained MRD negativity (via flow cytometry at 2 timepoints 1 year apart) in myeloma patients on lenalidomide maintenance. The Healthy Eating Index 2015 score and flavonoid nutrient values were calculated from the food frequency questionnaire. The Wilcoxon rank sum test was used to evaluate associations with two-sided p < 0.05 considered significant.

RESULTS: At 3 months, higher stool butyrate concentration (p=0.037), butyrate producers (p=0.025) and α-diversity (p=0.0035) were associated with sustained MRD-negativity. Healthier dietary proteins, (from seafood and plants), correlated with butyrate at 3 months (p=0.009) and sustained MRD-negativity (p=0.05). Consumption of dietary flavonoids, plant nutrients with antioxidant effects, correlated with stool butyrate concentration (anthocyanidins p=0.01, flavones p=0.01, and flavanols p=0.02).

CONCLUSIONS: This is the first study to demonstrate an association between a plant-based dietary pattern, stool butyrate production and sustained MRD-negativity in MM; providing rationale to evaluate a prospective dietary intervention.

RevDate: 2022-09-28

Jadhav A, Vadiveloo M, Laforge RG, et al (2022)

Dietary contributors to fermentable carbohydrate intake in healthy American college students.

Journal of American college health : J of ACH [Epub ahead of print].

OBJECTIVE: The study explored food items that contribute most toward increased fermentable carbohydrate (FC) intake and its association with diet quality in college students.

METHOD: This cross-sectional study included 571 consented college students (≥18 years) with reported energy intakes (500-3500 kcal/day for women; 800-4000 kcal/day for men). FC intake and healthy eating index-2015 (HEI-2015) scores were assessed by diet history questionnaire-II. Data were analyzed by unadjusted bivariate linear regression and Pearson correlation tests.

RESULTS: The mean intakes of total FC (β = 1.24; 95% Confidence Interval: 1.02, 1.47) significantly predicted HEI-2015 scores. Positive correlations were found between FC intake and red and orange vegetables (r = 0.62), whole fruits (r = 0.63), and dark green vegetables (r = 0.58). Conclusions: Higher FC intake was associated with higher diet quality; vegetables and fruits are primary contributors to FC content. Efforts are required to promote these food items to improve diet quality and FC intake to shape eating choices in college students.

RevDate: 2022-09-28

Kreth J, Koo H, PI Diaz (2022)

The functional oral microbiome: Biofilm environment, polymicrobial interactions, and community dynamics.

Molecular oral microbiology, 37(5):165-166.

RevDate: 2022-09-28

He Y, Y Chen (2022)

The potential mechanism of the microbiota-gut-bone axis in osteoporosis: a review.

Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA [Epub ahead of print].

Osteoporosis is the prevalent metabolic bone disease characterized by a decrease in bone quantity and/or quality and an increase in skeletal fragility, which increases susceptibility to fractures. Osteoporotic fractures severely affect the patients' quality of life and mortality. A plethora of evidences have suggested that the alterations in gut microbiome are associated with the changes in bone mass and microstructure. We summarized pre-clinical and clinical studies to elucidate the underlying mechanism of gut microbiota in osteoporosis. Probiotics, prebiotics, and traditional Chinese medicine may reverse the gut microbiota dysbiosis and consequently improve bone metabolism. However, the causality of gut microbiota on bone metabolism need to be investigated more in depth. In the present review, we focused on the potential mechanism of the microbiota-gut-bone axis and the positive therapeutic effect of probiotics, prebiotics, and traditional Chinese medicine on osteoporosis. Overall, the current scientific literatures support that the gut microbiota may be a novel therapeutic target in treatment of osteoporosis and fracture prevention.

RevDate: 2022-09-28

Simpson JB, MR Redinbo (2022)

Multi-omic analysis of host-microbial interactions central to the gut-brain axis.

Molecular omics [Epub ahead of print].

The gut microbiota impact numerous aspects of human physiology, including the central nervous system (CNS). Emerging work is now focusing on the microbial factors underlying the bi-directional communication network linking host and microbial systems within the gastrointestinal tract to the CNS, the "gut-brain axis". Neurotransmitters are key coordinators of this network, and their dysregulation has been linked to numerous neurological disease states. As the bioavailability of neurotransmitters is modified by gut microbes, it is critical to unravel the influence of the microbiota on neurotransmitters in the context of the gut-brain axis. Here we review foundational studies that defined molecular relationships between the microbiota, neurotransmitters, and the gut-brain axis. We examine links between the gut microbiome, behavior, and neurological diseases, as well as microbial influences on neurotransmitter bioavailability and physiology. Finally, we review multi-omics technologies uniquely applicable to this area, including high-throughput genetics, modern metabolomics, structure-guided metagenomics, targeted proteomics, and chemogenetics. Interdisciplinary studies will continue to drive the discovery of molecular mechanisms linking the gut microbiota to clinical manifestations of neurobiology.

RevDate: 2022-09-28

Delgadinho M, Ginete C, Santos B, et al (2022)

Microbial gut evaluation in an angolan paediatric population with sickle cell disease.

Journal of cellular and molecular medicine [Epub ahead of print].

Sickle cell disease (SCD) is one of the most common genetic conditions worldwide. It can contribute up to 90% of under-5 mortality in sub-Saharan Africa. Clinical manifestations are very heterogeneous, and the intestinal microbiome appears to be crucial in the modulation of inflammation, cell adhesion and induction of aged neutrophils, the main interveners of recurrent vaso-occlusive crisis. Enterocyte injury, increased permeability, altered microbial composition and bacterial overgrowth have all been documented as microbial and pathophysiologic changes in the gut microbiome of SCD patients in recent studies. Our aim was to sequence the bacterial 16S rRNA gene in order to characterize the gut microbiome of Angolan children with SCA and healthy siblings as a control. A total of 72 stool samples were obtained from children between 3 and 14 years old. Our data showed that the two groups exhibit some notable differences in microbiota relative abundance at different classification levels. Children with SCA have a higher number of the phylum Actinobacteria. As for the genus level, Clostridium cluster XI bacteria was more prevalent in the SCA children, whereas the siblings had a higher abundance of Blautia, Aestuariispira, Campylobacter, Helicobacter, Polaribacter and Anaerorhabdus. In this study, we have presented the first microbiota analysis in an Angolan paediatric population with SCD and provided a detailed view of the microbial differences between patients and healthy controls. There is still much to learn before fully relying on the therapeutic approaches for gut modulation, which is why more research in this field is crucial to making this a reality.

RevDate: 2022-09-28

Vargas M, Yañez F, Elias A, et al (2022)

Cervical pessary and cerclage placement for preterm birth prevention and cervicovaginal microbiome changes.

Acta obstetricia et gynecologica Scandinavica [Epub ahead of print].

INTRODUCTION: Our objective was to compare the vaginal microbiome in low-risk and high-risk pregnant women and to explore a potential association between vaginal microbiome and preterm birth.

MATERIAL AND METHODS: A pilot, consecutive, longitudinal, multicenter study was conducted in pregnant women at 18-22 weeks of gestation. Participants were assigned to one of three groups: control (normal cervix), pessary (cervical length ≤25 mm) and cerclage (cervical length ≤25 mm or history of preterm birth). Analysis and comparison of vaginal microbiota as a primary outcome was performed at inclusion and at 30 weeks of gestation, along with a follow-up of pregnancy and perinatal outcomes. We assessed the vaginal microbiome of pregnant women presenting a short cervix with that of pregnant women having a normal cervix, and compared the vaginal microbiome of women with a short cervix before and after placement of a cervical pessary or a cervical cerclage.

RESULTS: The microbiome of our control cohort was dominated by Lactobacillus crispatus and inners. Five community state types were identified and microbiome diversity did not change significantly over 10 weeks in controls. On the other hand, a short cervix was associated with a lower microbial load and higher microbial richness, and was not correlated with Lactobacillus relative abundance. After intervention, the cerclage group (n = 19) had a significant increase in microbial richness and a shift towards community state types driven by various bacterial species, including Lactobacillus mulieris, unidentified Bifidobacterium or Enterococcus. These changes were not significantly observed in the pessary (n = 26) and control (n = 35) groups. The cerclage group had more threatened preterm labor episodes and poorer outcomes than the control and pessary groups.

CONCLUSIONS: These findings indicate that a short cervix is associated with an altered vaginal microbiome community structure. The use of a cerclage for preterm birth prevention, as compared with a pessary, was associated with a microbial community harboring a relatively low abundance of Lactobacillus, with more threatened preterm labor episodes, and with poorer clinical outcomes.

RevDate: 2022-09-28

Mørup N, Main AM, Jørgensen N, et al (2022)

The seminal plasma microbiome of men with testicular germ cell tumours described by small RNA sequencing.

Andrology [Epub ahead of print].

BACKGROUND: It has been estimated that microorganisms are involved in the pathogenesis of approximately 20% of all cancers. Testicular germ cell tumours (TGCTs) are the most common type of malignancy in young men and arise from the precursor cell, Germ Cell Neoplasia in Situ (GCNIS). The microbiome of seminal plasma and testicular tissue has not been thoroughly investigated in regard to TGCTs.

OBJECTIVES: To investigate the differences in the seminal plasma microbiome between men with TGCT or GCNIS-only compared with controls.

MATERIALS AND METHODS: The study population consisted of patients with GCNIS-only (n = 5), TGCT (n = 18), and controls (n = 25) with different levels of sperm counts in the ejaculate. RNA was isolated from the seminal plasma and sequenced. Reads not mapping to the human genome were aligned against a set of 2784 bacterial/archaeal and 4336 viral genomes using the Kraken pipeline.

RESULTS: We identified reads from 2172 species and most counts were from Alteromonas mediterranea, Falconid herpesvirus 1, and Stigmatella aurantiaca. Six species (Acaryochloris marina, Halovirus HGTV-1, Thermaerobacter marianensis, Thioalkalivibrio sp. K90mix, Burkholderia sp. YI23, and Desulfurivibrio alkaliphilus) were found in significantly (q-value <0.05) higher levels in the seminal plasma of TGCT and GCNIS-only patients compared with controls. In contrast, Streptomyces phage VWB, was found at significantly higher levels among controls compared with TGCT and GCNIS-only patients combined.

DISCUSSION: Often the microbiome is analysed by shotgun or 16S ribosomal sequencing whereas our present data builds on small RNA sequencing. This allowed us to identify more viruses and phages compared to previous studies, but also makes the results difficult to directly compare.

CONCLUSION: Our study is the first to report identification of the microbiome species in seminal plasma of men with TGCT and GCNIS-only, which potentially could be involved in the pathogenesis of TGCTs. Further studies are, however, needed to confirm our findings. This article is protected by copyright. All rights reserved.

RevDate: 2022-09-28

Chen S, Li T, Yang L, et al (2022)

Artificial intelligence-driven prediction of multiple drug interactions.

Briefings in bioinformatics pii:6720429 [Epub ahead of print].

When a drug is administered to exert its efficacy, it will encounter multiple barriers and go through multiple interactions. Predicting the drug-related multiple interactions is critical for drug development and safety monitoring because it provides foundations for practical, safe compatibility and rational use of multiple drugs. With the progress of artificial intelligence (AI) technology, a variety of novel prediction methods for single interaction have emerged and shown great advantages compared to the traditional, expensive and time-consuming laboratory research. To promote the comprehensive and simultaneous predictions of multiple interactions, we systematically reviewed the application of AI in drug-drug, drug-food (excipients) and drug-microbiome interactions. We began by outlining the model methods, evaluation indicators, algorithms and databases commonly used to build models for three types of drug interactions. The models based on the metabolic enzyme P450, drug similarity and drug targets have empathized among the machine learning models of drug-drug interactions. In particular, we discussed the limitations of current approaches and identified potential areas for future research. It is anticipated the in-depth review will be helpful for the development of the next-generation of systematic prediction models for simultaneous multiple interactions.

RevDate: 2022-09-28

Bidell MR, Hobbs ALV, TP Lodise (2022)

Gut Microbiome Health and Dysbiosis: A Clinical Primer.

Pharmacotherapy [Epub ahead of print].

The gut microbiome has been referred to as the "forgotten organ." Although much about the gut microbiome remains incompletely understood, data on its clinical importance is emerging at rapid speed. Many practicing clinicians may be unaware of the essential role that the microbiome plays in both health and disease. This review aims to improve clinical understanding of the gut microbiome by discussing key terminology and foundational concepts. The role of a healthy microbiome in normal host function is described, as well as the consequences of a disrupted microbiome (i.e., dysbiosis). Management strategies to restore the gut microbiome from a disrupted to a healthy state are also briefly discussed. Lastly, we review emerging areas for therapeutic potential and opportunity to bring determinants of microbiome health from the bench to bedside.

RevDate: 2022-09-28

Shi J, Gao G, Yu Z, et al (2022)

The Relevance of Host Gut Microbiome Signature Alterations on de novo Fatty Acids Synthesis in Patients with Multi-Drug Resistant Tuberculosis.

Infection and drug resistance, 15:5589-5600 pii:372122.

Background: Tuberculosis (TB) is still the single pathogen infectious disease with the largest number of deaths worldwide. The relationship that intestinal microbiota disorder and de novo fatty acid synthesis metabolism have with disease progression in multi-drug resistant TB (MDR-TB) has not yet been fully studied.

Objective: To investigate the effects of long periods of MDR-TB, pre-extensively drug-resistant TB (pre-XDR-TB), or rifampicin-resistant TB (RR-TB) on gut microbiome dysbiosis and advanced disease.

Methods: The sample was chosen between March 2019 and September 2019 in Wenzhou Central Hospital and comprised 11 patients with pre-XDR-TB, 23 patients with RR-TB, and 28 patients with MDR-TB. Healthy individuals were chosen as the control group (CK group). An overnight fast blood sample was drawn via venipuncture into tubes without anticoagulant. For analysis, 300 mg of faeces from patients from the same group was mixed and analysed using DNA extraction, NGS sequencing, and bioinformatics. A QIAamp Fecal DNA Mini Kit was used to isolate the DNA. The extracted DNA was stored at -20°C.

Results: Advanced TB was concurrent with an elevated level of the proportions of acetyl-CoA carboxylase (ACC1) to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and fatty acid synthase (FASN) to GAPDH in de novo fatty acids synthesis, and Eubacterium, Faecalibacterium, Roseburia, and Ruminococcus were increased significantly in RR-TB patients compared to healthy individuals, whereas their abundance in the pre-XDR-TB and MDR-TB groups showed little change in comparison with the control group. Proteobacteria levels were greatly increased in the RR-TB and MDR-TB patient groups but not in the patients with pre-XDR-TB or the healthy subjects. The pre-XDR-TB group exhibited alterations of the intestinal microbiome: coliform flora showed the highest abundance of Verrucomicrobiales, Enterobacteriales, Bifidobacteriales and Lactobacillales. De novo fatty acids synthesis was enhanced in patients and was associated with the gut microbiome dysbiosis induced by the antimicrobials, with Bacteroidetes, Bacteroidales, and Bacteroidaceae displaying the most important correlations on a phylum, order, and family level, respectively.

Conclusion: The progression to advanced TB was observed to be a result of the interaction between multiple interrelated pathways, with gut-lung crosstalk potentially playing a role in patients with drug-resistant TB.

RevDate: 2022-09-28

Inam Z, Felton E, Burrell A, et al (2022)

Impact of Antibiotics on the Lung Microbiome and Lung Function in Children With Cystic Fibrosis 1 Year After Hospitalization for an Initial Pulmonary Exacerbation.

Open forum infectious diseases, 9(9):ofac466 pii:ofac466.

Background: Cystic fibrosis (CF) is characterized by recurrent pulmonary exacerbations (PEx) and lung function decline. PEx are frequently treated with antibiotics. However, little is known about the effects of antibiotics on the airway microbiome of persons with CF over time. The purpose of this study was to evaluate changes in the microbiome and lung function in persons with CF over 1 year following an initial study pulmonary exacerbation (iPEx).

Methods: Twenty children aged ≤18 years with CF were enrolled in the study, which occurred prior to the routine administration of highly effective modulator therapy. Respiratory samples and spirometry were obtained at a minimum of quarterly visits and up to 1 year after an iPEx. Metagenomic sequencing was performed, and bacterial taxa were assigned using MetaPhlAn 2.0. Paired t test, analysis of variance, and generalized least squares regression were used to compare outcome variables.

Results: The mean age of study participants at the time of the iPEx was 10.6 years. There were 3 ± 1.6 PEx treated with antibiotics per person during the study period. Bacterial richness was similar at 1 year compared to iPEx (40.3 vs 39.3, P = .852), whereas the mean Shannon diversity index was significantly higher at 1 year (2.84 vs 1.62, P < .001). The number of PEx treated with antibiotics was not associated with changes in microbial diversity but was associated with changes in lung function.

Conclusions: In our 1-year prospective study, we found that microbial diversity increased despite decreases in lung function associated with repeated PEx events requiring antibiotic therapy.

RevDate: 2022-09-28

Remy R, Kemnitz N, Trefz P, et al (2022)

Profiling of exhaled volatile organics in the screening scenario of a COVID-19 test center.

iScience pii:S2589-0042(22)01467-5 [Epub ahead of print].

Breath volatile organics (VOCs) may provide immediate information on infection mechanisms and host response. We conducted real-time mass-spectrometry based breath profiling in 708 non-preselected consecutive subjects in the screening scenario of a COVID-19 test center. Recruited subjects were grouped based on PCR confirmed infection status and presence or absence of flu like symptoms. Exhaled VOC profiles of SARS-CoV-2 positive cases (n=36) differed from healthy (n=256) and those with other respiratory infections (n=416). Concentrations of most VOCs were supressed in COVID-19. VOC concentrations also differed between symptomatic and asymptomatic cases. Breath markers mirror effects of infections onto host's cellular metabolism and microbiome. Down-regulation of specific VOCs were attributed to suppressive effects of SARS-CoV-2 onto gut or pulmonary microbial metabolism. Breath analysis holds potential for monitoring SARS-CoV-2 infections rather than for primary diagnosis. Breath profiling offers unconventional insight into host-virus cross-talk and infection microbiology and enables non-invasive assessment of disease manifestation.

RevDate: 2022-09-28

Qasim H, Nasr M, Mohammad A, et al (2022)

Dysbiosis and Migraine Headaches in Adults With Celiac Disease.

Cureus, 14(8):e28346.

One of the most significant illnesses associated with gluten is celiac disease, which encompasses many conditions. It is generally recognized that neurological manifestations can occur either at the time of the disease onset or as the illness continues to develop. One of the main clinical presentations of celiac disease is headache, either in the form of migraine or in an unspecific form. Migraine pathophysiology is intricate and still poorly understood. Several mechanisms involving the gut-brain axis have been proposed to explain this association. These include the interaction of chronic inflammation with inflammatory and vasoactive mediators, the modulation of the intestinal immune environment of the microbiota, and the dysfunction of the autonomic nervous system. However, further research is required to fully comprehend the fundamental mechanisms and pathways at play. This review aims to give a narrative summary of the literature on celiac disease's neurological symptoms, particularly migraines, and to assess any potential associations to dysbiosis, an imbalance in the microbiome.

RevDate: 2022-09-28

Sheldon JM, N Alonso (2022)

The Therapeutic Benefits of Single and Multi-Strain Probiotics on Mean Daily Crying Time and Key Inflammatory Markers in Infantile Colic.

Cureus, 14(8):e28363.

Infantile colic is a functional gastrointestinal disorder in which a healthy infant displays paroxysms of intense crying or fussiness. Although this condition is self-limited, it causes significant distress for parents and may be linked to long-term health concerns for children. The microbiome of infants with colic has been correlated with increased dysbiosis or imbalance of commensal bacteria. This dysbiosis may ultimately lead to changes in infants' immunological profiles, favoring markers linked to inflammation, including specific cytokines, calprotectin, and genetic markers. Therapeutic regimens such as probiotics may be helpful in modifying the gut microbial composition, thereby influencing the presence of inflammatory markers and potentially reducing colic symptoms in infants. This review provides a summary of the findings from 10 randomized, placebo-controlled, double-blinded studies conducted in the past five years with the aim of examining the potential therapeutic benefits of probiotics in infantile colic. The articles were selected through PubMed and Google Scholar using the keywords infantile colic, microbiome, probiotics, cytokines, dysbiosis, inflammatory markers, and lactobacilli. We summarize the results of these studies to explore the potential anti-inflammatory therapeutic benefits of single and multi-strain probiotic formulations on daily crying time and key inflammatory markers in infants with colic. The research largely shows the beneficial role of probiotics, largely of the lactobacillus genus, in the reduction of colic symptoms and the reduction of key inflammatory markers. However, some studies demonstrated an insignificant effect of certain probiotic strains in symptom management. Further research is necessary to better understand the anti-inflammatory properties of probiotics and determine the role this could have on the manifestation of colic in infants.

RevDate: 2022-09-28

Du C, Li B, Yu W, et al (2022)

Characteristics of annual mold variations and association with childhood allergic symptoms/diseases via combining surveys and home visit measurements.

Indoor air, 32(9):e13113.

The presence of dampness and visible molds leads to concerns of poor indoor air quality which has been consistently linked with increased exacerbation and development of allergy and respiratory diseases. Due to the limitations of epidemiological surveys, the actual fungal exposure characteristics in residences has not been sufficiently understood. This study aimed to characterize household fungal diversity and its annual temporal and spatial variations. We developed combined cross-sectional survey, repeated air sampling around a year, and DNA sequencing methods. The questionnaire survey was conducted in 2019, and 4943 valid cases were received from parents; a follow-up case-control study (11 cases and 12 controls) was designed, and onsite measurements of indoor environments were repeated in typical summer, transient season, and winter; dust from floor and beddings in children's room were collected and ITS based DNA sequencing of totally 68 samples was conducted. Results from 3361 children without changes to their residences since birth verified the significant associations of indoor dampness/mold indicators and prevalence of children-reported diseases, with increased adjusted odd ratios (aORs) >1 for studied asthma, wheeze, allergic rhinitis, and eczema. The airborne fungal concentrations from air sampling were higher than 1000 CFU/m3 in summer, regardless of indoors and outdoors, indicating an intermediate pollution level. The DNA sequencing for dust showed the Aspergillus was the predominant at genus level and the Aspergillus_penicillioides was the most common at species level; while the fungal community and composition varied significantly in different homes and seasons, according to α and β diversity analyses. The comprehensive research methods contribute to a holistic understanding of indoor fungal exposure, including the concentrations, seasonal variations, community, and diversity, and verifies the relations with children's adverse health outcomes. The study further elucidates the role of microbiome in human health, which helps setting health-protective thresholds and managing mold treatments in buildings, to promote indoor air quality and human well-beings.

RevDate: 2022-09-28

Yang JIL, Lee BG, Park JH, et al (2022)

Airborne fungal and bacterial microbiome in classrooms of elementary schools during the COVID-19 pandemic period: Effects of school disinfection and other environmental factors.

Indoor air, 32(9):e13107.

The aim of the study was to examine the effects of environmental factors including disinfection on airborne microbiome during the coronavirus disease 2019 pandemic, we evaluated indoor and outdoor air collected from 19 classrooms regularly disinfected. Extracted bacterial and fungal DNA samples were sequenced using the Illumina MiSeq™ platform. Using bacterial DNA copy number concentrations from qPCR analysis, multiple linear regressions including environmental factors as predictors were performed. Microbial diversity and community composition were evaluated. Classrooms disinfected with spray ≤1 week before sampling had lower bacterial DNA concentration (3116 DNA copies/m3) than those >1 week (5003 copies/m3) (p-values = 0.06). The bacterial DNA copy number concentration increased with temperature and was higher in classrooms in coastal than inland cities (p-values <0.01). Bacterial diversity in outdoor air was higher in coastal than inland cities while outdoor fungal diversity was higher in inland than coastal cities. These outdoor microbiomes affected classroom microbial diversity but bacterial community composition at the genus level in occupied classrooms were similar between coastal and inland cities. Our findings emphasize that environmental conditions including disinfection, climate, and school location are important factors in shaping classroom microbiota. Yet, further research is needed to understand the effects of modified microbiome by disinfection on occupants' health.

RevDate: 2022-09-28

Niraula S, Rose M, WS Chang (2022)

Microbial co-occurrence network in the rhizosphere microbiome: its association with physicochemical properties and soybean yield at a regional scale.

Journal of microbiology (Seoul, Korea), 60(10):986-997.

Microbial communities in the rhizosphere play a crucial role in determining plant growth and crop yield. A few studies have been performed to evaluate the diversity and co-occurrence patterns of rhizosphere microbiomes in soybean (Glycine max) at a regional scale. Here, we used a culture-independent method to compare the bacterial communities of the soybean rhizosphere between Nebraska (NE), a high-yield state, and Oklahoma (OK), a low-yield state. It is well known that the rhizosphere microbiome is a subset of microbes that ultimately get colonized by microbial communities from the surrounding bulk soil. Therefore, we hypothesized that differences in the soybean yield are attributed to the variations in the rhizosphere microbes at taxonomic, functional, and community levels. In addition, soil physicochemical properties were also evaluated from each sampling site for comparative study. Our result showed that distinct clusters were formed between NE and OK in terms of their soil physicochemical property. Among 3 primary nutrients (i.e., nitrogen, phosphorus, and potassium), potassium is more positively correlated with the high-yield state NE samples. We also attempted to identify keystone communities that significantly affected the soybean yield using co-occurrence network patterns. Network analysis revealed that communities formed distinct clusters in which members of modules having significantly positive correlations with the soybean yield were more abundant in NE than OK. In addition, we identified the most influential bacteria for the soybean yield in the identified modules. For instance, included are class Anaerolineae, family Micromonosporaceae, genus Plantomyces, and genus Nitrospira in the most complex module (ME9) and genus Rhizobium in ME23. This research would help to further identify a way to increase soybean yield in low-yield states in the U.S. as well as worldwide by reconstructing the microbial communities in the rhizosphere.

RevDate: 2022-09-28

Kim DW, Ahn JH, CJ Cha (2022)

Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches.

Journal of microbiology (Seoul, Korea), 60(10):969-976.

Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.

RevDate: 2022-09-27

Xiao R, Luo G, Liao W, et al (2022)

Association of human gut microbiota composition and metabolic functions with Ficus hirta Vahl dietary supplementation.

NPJ science of food, 6(1):45.

Ficus hirta Vahl (FHV), a traditional herbal ingredient of the tonic diet, receives increasing popularity in southern China. However, it is largely unknown that how a FHV diet (FHVD) affects the human gut microbiome. In this exploratory study, a total of 43 healthy individuals were randomized into the FHVD (n = 25) and Control (n = 18) groups to receive diet intervention for 8 weeks. 16S rRNA gene sequencing, metagenomic sequencing and metabolic profile of participants were measured to assess the association between FHV diet and gut microbiome. A preservation effect of Faecalibacterium and enrichment of Dialister, Veillonella, Clostridium, and Lachnospiraceae were found during the FHVD. Accordingly, the pathway of amino acid synthesis, citrate cycle, coenzyme synthesis, and partial B vitamin synthesis were found to be more abundant in the FHVD. In addition, serine, glutamine, gamma-aminobutyric acid, tryptamine, and short-chain fatty acids (SCFAs) were higher after the FHVD. The conjoint analysis of FHV components and in-vitro fermentation confirmed that the improved SCFAs concentration was collectively contributed by the increasing abundance of key enzyme genes and available substrates. In conclusion, the muti-omics analysis showed that the FHVD optimized the structure of the gut microbial community and its metabolic profile, leading to a healthy tendency, with a small cluster of bacteria driving the variation rather than a single taxon.

RevDate: 2022-09-27

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

Multi-omic factors associated with future wheezing in infants.

Pediatric research [Epub ahead of print].

BACKGROUND: The pathophysiology of wheezing is multifactorial, impacted by medical, demographic, environmental, and immunologic factors. We hypothesized that multi-omic analyses of host and microbial factors in saliva would enhance the ability to identify infants at risk for wheezing.

METHODS: This longitudinal cohort study included 161 term infants. Infants who developed wheezing (n = 27) within 24 months of delivery were identified using the International Study of Asthma and Allergies in Childhood Written Questionnaire and review of the medical record. Standardized surveys were used to assess infant traits and environmental exposures. Saliva was collected for multi-omic assessment of cytokines, microRNAs, mRNAs, and microbiome/virome RNAs.

RESULTS: Two infant factors (daycare attendance, family history of asthma) and three salivary "omic" features (miR-26a-5p, Elusimicrobia, Streptococcus phage phiARI0131-1) differed between the two groups (adjusted p < 0.05). miR-26a-5p levels were correlated with Elusimicrobia (R = -0.87, p = 3.7 × 10-31). A model employing the three omic features plus daycare attendance and family asthma history yielded the highest predictive accuracy for future wheezing episodes (AUC = 0.74, 95% CI: 0.703-0.772, 77% sensitivity, 62% specificity).

CONCLUSIONS: Host-microbiome interactions in saliva may yield pathophysiologic clues about the origins of wheezing and aid identification of infants at risk of future wheezing episodes.

IMPACT: Wheezing is multi-factorial, but the relative contributions of infant traits, environment, and underlying biology are poorly understood. This multi-omic study identifies three molecular factors, including salivary microRNAs, microbes, and viral phages associated with increased risk of infant wheezing. Measurement of these molecular factors enhanced predictive accuracy for future wheezing when combined with family asthma history and daycare attendance. Validation of this approach could be used to identify infants at risk for wheezing and guide personalized medical management.

RevDate: 2022-09-27

Seong HJ, Roux S, Hwang CY, et al (2022)

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.

Microbiome, 10(1):157.

BACKGROUND: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.

RESULTS: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.

CONCLUSIONS: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.

RevDate: 2022-09-27

Preethy S, Ikewaki N, Levy GA, et al (2022)

Two unique biological response-modifier glucans beneficially regulating gut microbiota and faecal metabolome in a non-alcoholic steatohepatitis animal model, with potential applications in human health and disease.

BMJ open gastroenterology, 9(1):.

OBJECTIVE: The gut microbiome and its metabolites are influenced by age and stress and reflect the metabolism and health of the immune system. We assessed the gut microbiota and faecal metabolome in a static animal model of non-alcoholic steatohepatitis (NASH).

DESIGN: This model was subjected to the following treatments: reverse osmosis water, AFO-202, N-163, AFO-202+N-163 and telmisartan treatment. Faecal samples were collected at 6 and 9 weeks of age. The gut microbiome was analysed using 16S ribosomal RNA sequences acquired by next-generation sequencing, and the faecal metabolome was analysed using gas chromatography-mass spectrometry.

RESULTS: Gut microbial diversity increased greatly in the AFO-202+N-163 group. Postintervention, the abundance of Firmicutes decreased, whereas that of Bacteroides increased and was the highest in the AFO-202+N-163 group. The decrease in the abundance of Enterobacteriaceae and other Firmicutes and the abundance of Turicibacter and Bilophila were the highest in the AFO-202 and N-163 groups, respectively. Lactobacillus abundance was highest in the AFO-202+N-163 group. The faecal metabolite spermidine, which is beneficial against inflammation and NASH, was significantly decreased (p=0.012) in the N-163 group. Succinic acid, which is beneficial in neurodevelopmental and neurodegenerative diseases, was increased in the AFO-202 group (p=0.06). The decrease in fructose was the highest in the N-163 group (p=0.0007). Isoleucine and Leucine decreased with statistical significance (p=0.004 and 0.012, respectively), and tryptophan also decreased (p=0.99), whereas ornithine, which is beneficial against chronic immune-metabolic-inflammatory pathologies, increased in the AFO-202+N-163 group.

CONCLUSION: AFO-202 treatment in mice is beneficial against neurodevelopmental and neurodegenerative diseases, and has prophylactic potential against metabolic conditions. N-163 treatment exerts anti-inflammatory effects against organ fibrosis and neuroinflammation. In combination, these compounds exhibit anticancer activity.

RevDate: 2022-09-27

Deng Y, Yang S, Zhao H, et al (2022)

Antibiotics-induced changes in intestinal bacteria result in the sensitivity of honey bee to virus.

Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(22)01492-0 [Epub ahead of print].

Antibiotics are omnipresent in the environment due to their widespread use, and they have wide-ranging negative impacts on organisms. Virus resistance differs substantially between domesticated Apis mellifera and wild Apis cerana, although both are commonly raised in China. Here, we investigated whether antibiotics can increase the sensitivity of honey bees to viral infection using the Israeli acute paralysis virus (IAPV) and tetracycline as representative virus and antibiotic. Although IAPV multiplied to lower levels in A. cerana than A. mellifera, resulting in decreased mortality (P < 0.01), there was no significant difference in immune responses to viral infection between the two species. Adult worker bees (A. cerana and A. mellifera) were treated with or without tetracycline to demonstrate the prominent role of gut microbiota against viral infection, and found Lactobacillus played a vital antiviral role in A. cerana. In A. cerana but not A. mellifera, tetracycline treatment reduced clearly bee survival and increased susceptibility to IAPV infection (P < 0.01). Our findings revealed that long-term antibiotic treatment in A. mellifera had altered the native gut microbiome and promoted the sensitivity to viral infection. We highlight the effects of antibiotics exposure on resistance to microbial and viral infection.

RevDate: 2022-09-27

Yang C, Qiu M, Zhang Z, et al (2022)

Galacto-oligosaccharides and xylo-oligosaccharides affect meat flavor by altering the cecal microbiome, metabolome, and transcriptome of chickens.

Poultry science, 101(11):102122 pii:S0032-5791(22)00411-4 [Epub ahead of print].

Studies have shown that prebiotics can affect meat quality; however, the underlying mechanisms remain poorly understood. This study aimed to investigate whether prebiotics affect the flavor of chicken meat via the gut microbiome and metabolome. The gut content was collected from chickens fed with or without prebiotics (galacto-oligosaccharides or xylo-oligosaccharides) and subjected to microbiome and metabolome analyses, whereas transcriptome sequencing was performed using chicken breast. Prebiotic supplementation yielded a slight improvement that was not statistically significant in the growth and production performance of chickens. Moreover, treatment with prebiotics promoted fat synthesis and starch hydrolysis, thus increasing meat flavor by enhancing lipase and α-amylase activity in the blood of broiler chickens. The prebiotics altered the proportions of microbiota in the gut at different levels, especially microbiota in the phyla Bacteroidetes and Firmicutes, such as members of the Alistipes, Bacteroides, and Faecalibacterium genera. Furthermore, the prebiotics altered the content of cecal metabolites related to flavor substances, including 8 types of lysophosphatidylcholine (lysoPC) and 4 types of amino acid. Differentially expressed genes (DEGs) induced by prebiotics were significantly involved in fatty acid accumulation processes, such as lipolysis in adipocytes and the adipocytokine signaling pathway. Changes in gut microbiota were correlated with metabolites, for example, Bacteroidetes and Firmicutes were positively and negatively correlated with lysoPC, respectively. Finally, DEGs interacted with cecal metabolites, especially meat-flavor-related amino acids and their derivatives. The findings of this study integrated and incorporated associations among the gut microbiota, metabolites, and transcriptome, which suggests that prebiotics affect the flavor of chicken meat.

RevDate: 2022-09-27

Chen SL, Lundy DJ, Ruan SC, et al (2022)

The gut microbiota regulates acute foreign body reaction and tissue repair after biomaterial implantation.

Biomaterials, 289:121807 pii:S0142-9612(22)00447-1 [Epub ahead of print].

We hypothesized that the host microbiome may influence foreign body responses following biomaterial implantation. To test this, we implanted a variety of clinically relevant biomaterials into germ-free or antibiotic-treated mice. Surprisingly, these mice displayed less fibrous tissue deposition, reduced host cell recruitment to the implant site, and differential expression of angiogenic and inflammatory markers. These observations were reversed upon fecal microbiome reconstitution, confirming a causal role of the host microbiome. In a clinically relevant disease model, microbiome-depleted mice cleared hyaluronic acid and bone marrow mononuclear cells from ischemic hind limb tissues more slowly, resulting in an improved therapeutic response. Findings were confirmed in pigs which showed reduced fibrotic responses to a variety of implanted materials. Lastly, we profiled changes in the host microbiome following material implantation, implicating several key bacteria phyla.

RevDate: 2022-09-27

Lucchinetti E, Lou PH, Holtzhauer G, et al (2022)

Novel lipid emulsion for total parenteral nutrition based on 18-carbon n-3 fatty acids elicits a superior immunometabolic phenotype in the murine model compared to standard lipid emulsions.

The American journal of clinical nutrition pii:6724385 [Epub ahead of print].

BACKGROUND: While lipid emulsions in modern formulations for total parenteral nutrition (TPN) provide essential fatty acids and dense calories, they also promote inflammation and immunometabolic disruptions.

OBJECTIVE: We aimed to develop a novel lipid emulsion for TPN use with superior immunometabolic actions compared with available standard lipid emulsions.

METHODS: A novel lipid emulsion (Vegaven, VV) containing 30% of 18-carbon n-3 fatty acids (α-linolenic acid and stearidonic acid) was developed for TPN (VV-TPN) and compared with TPN containing soybean oil-based lipid emulsion (IL-TPN) and fish oil-based lipid emulsion (OV-TPN). In vivo studies were performed in instrumented male C57BL/6 mice subjected to seven-day TPN prior to analysis of cytokines, indices of whole body and hepatic glucose metabolism, immune cells, lipid mediators and mucosal bowel microbiome.

RESULTS: Interleukin-6 to interleukin-10 (IL10) ratios were significantly lower in liver and skeletal muscle of VV-TPN mice when compared with IL-TPN or OV-TPN. VV-TPN and OV-TPN each increased hepatic insulin receptor abundance and resulted in similar HOMA-IR (Homeostatic Model Assessment for Insulin Resistance) values, whereas only VV-TPN increased hepatic insulin receptor substrate 2 and maintained normal hepatic glycogen content, effects that were IL10-dependent and mediated by glucokinase activation. The percentages of interferon-γ- and interleukin-17-expressing CD4+ T-cells were increased in livers of VV-TPN mice, and liver macrophages exhibited primed phenotypes when compared with IL-TPN. This immunomodulation was associated with successful elimination of the microinvasive bacterium Akkermansia muciniphila from the bowel mucosa by VV-TPN as opposed to standard lipid emulsions. Assay of hepatic lipid mediators revealed a distinct profile with VV-TPN including increases in 9(S)-hydroxy-octadecatrienoic acid. When co-administered with IL-TPN, hydroxy-octadecatrienoic acids mimicked the VV-TPN immunometabolic phenotype.

CONCLUSIONS: We here report the unique anti-inflammatory, insulin-sensitizing and immunity-enhancing properties of a newly developed lipid emulsion designed for TPN use based on 18-carbon n-3 fatty acids.

RevDate: 2022-09-27

Bhanja A, Sutar PP, M Mishra (2022)

Inulin-A polysaccharide: Review on its functional and prebiotic efficacy.

Journal of food biochemistry [Epub ahead of print].

The intake of dietary fibers in the regular diet results in boosting the gut microbiome and health of the host in several ways. The misapprehension about such dietary fibers of being only an indigestible product has changed into indispensable ingredient that has to be included in every healthy diet. Inulin is considered to be an important naturally occurring fructan classified under such dietary fibers. The present review intends to provide a thorough knowledge on inulin in maintaining the gut microbiome of the human, supported by several studies conducted on the Drosophila melanogaster, mice, rat models as well as effect on human being. The extraction process of inulin has also been described in this review that would provide a brief knowledge about its stability and the conditions that have been optimized by the researchers in order to obtain a stable product. PRACTICAL APPLICATIONS: In order to meet the consumers demand, the food industries are trying to come up with new products that could eventually replace or lower the utilization of medically avail drugs and satisfy consumers by providing them with health benefits. The availability of functional food is the new trend that can improve health of the consumers with minimal use of the drugs. Therefore, inulin as a prebiotic can be utilized to produce several functional food products that could promote health benefits to the consumers. Apart from this, the review also justifies the efficacy of inulin as a fat replacer, stabilizer, and humectant in cosmetic industries. Research also suggests that inulin has also been used as nanoparticles in pharmaceutical industries. The overall review also depicts the different extraction process of inulin from different sources.

RevDate: 2022-09-27

Liu H, Wu W, Y Luo (2022)

Oral and intravenous iron treatment alter the gut microbiome differentially in dialysis patients.

International urology and nephrology [Epub ahead of print].

OBJECTIVE: Chronic kidney disease (CKD) is often complicated by anemia, which seriously affects the quality-of-life and prognosis of patients. These patients usually need iron replacement therapy. Oral iron affects the composition and abundance of intestinal flora by increasing intestinal iron concentration.

METHODS: We undertook an interventional study to investigate the effects of oral versus intravenous iron therapy on the gut microbiota. Oral ferrous succinate tablets (n = 14) or intravenous iron sucrose (n = 14) was administered to anemic maintenance hemodialysis (MHD) patients for 2 months.

RESULTS: Oral and intravenous iron treatments had different effects on gut microbial composition and diversity. After oral iron treatment, the α-diversity was decreased, while at the phylum level, the abundance of Firmicutes was reduced and the abundance of Bacteroides was increased. At the genus level, the abundance of Blautia and Coprococcus was decreased, and the abundance of Bacteroidetes was increased. Oral iron therapy was associated with a higher abundance of Lactobacillus compared with that measured in intravenous iron-treated patients. According to metagenome function prediction analysis, oral iron increased the metabolic processes of phenylalanine, valine, leucine, and isoleucine. These changes may increase uremic toxin levels, thereby increasing the progression of renal disease.

CONCLUSION: Iron therapy affects the diversity and composition of gut flora in MHD patients. Oral iron affects the number of bacteria and increases amino acid metabolism compared with intravenous iron. These results indicate that intravenous iron may be more appropriate for MHD patients.

RevDate: 2022-09-27

Hahn AW, Menk AV, Rivadeneira DB, et al (2022)

Obesity is associated with altered tumor metabolism in metastatic melanoma.

Clinical cancer research : an official journal of the American Association for Cancer Research pii:709490 [Epub ahead of print].

PURPOSE: Overweight/obese (OW/OB) patients with metastatic melanoma unexpectedly have improved outcomes with immune checkpoint inhibitors (ICIs) and BRAF-targeted therapies. The mechanism(s) underlying this association remain unclear, thus we assessed the integrated molecular, metabolic, and immune profile of tumors, as well as gut microbiome features, for associations with patient BMI.

EXPERIMENTAL DESIGN: Associations between BMI [normal (NL < 25) or OW/OB (BMI ≥ 25] and tumor or microbiome characteristics were examined in specimens from 782 metastatic melanoma patients across 7 cohorts. DNA associations were evaluated in the TCGA cohort. RNASeq from 4 cohorts (n=357) was batch corrected and gene set enrichment analysis (GSEA) by BMI category was performed. Metabolic profiling was conducted in a subset of patients (x=36) by LC/MS, and in flow-sorted melanoma tumor cells (x=37) and patient-derived melanoma cell lines (x=17) using the Seahorse XF assay. Gut microbiome features were examined in an independent cohort (n=371).

RESULTS: DNA mutations and copy number variations were not associated with BMI. GSEA demonstrated that tumors from OW/OB patients were metabolically quiescent, with downregulation of oxidative phosphorylation and multiple other metabolic pathways. Direct metabolite analysis and functional metabolic profiling confirmed decreased central carbon metabolism in OW/OB metastatic melanoma tumors and patient-derived cell lines. The overall structure, diversity, and taxonomy of the fecal microbiome did not differ by BMI.

CONCLUSIONS: These findings suggest that the host metabolic phenotype influences melanoma metabolism and provide insight into the improved outcomes observed in OW/OB patients with metastatic melanoma treated with ICIs and targeted therapies.

RevDate: 2022-09-28

Afzal S, NK Singh (2022)

Effect of zinc and iron oxide nanoparticles on plant physiology, seed quality and microbial community structure in a rice-soil-microbial ecosystem.

Environmental pollution (Barking, Essex : 1987), 314:120224 pii:S0269-7491(22)01438-5 [Epub ahead of print].

In this study, we assessed the impact of zinc oxide (ZnO) and iron oxide (FeO) (<36 nm) nanoparticles (NPs) as well as their sulphate salt (bulk) counterpart (0, 25, 100 mg/kg) on rice growth and seed quality as well as the microbial community in the rhizosphere environment of rice. During the rice growing season 2021-22, all experiments were conducted in a greenhouse (temperature: day 30 °C; night 20 °C; relative humidity: 70%; light period: 16 h/8 h, day/night) in rice field soil. Results showed that low concentrations of FeO and ZnO NPs (25 mg/kg) promoted rice growth (height (29%, 16%), pigment content (2%, 3%)) and grain quality parameters such as grains per spike (8%, 9%), dry weight of grains (12%, 14%) respectively. As compared to the control group, the Zn (2%) and Fe (5%) accumulations at their respective low concentrations of NP treatments showed stimulation. Interestingly, our results showed that at low concentration of both the NPs the soil microbes had more diversity and richness than those in the bulk treated and control soil group. Although a number of phyla were affected by the presence of NPs, the strongest effects were observed for change in the abundance of the three phyla for Proteobacteria, Actinobacteria, and Planctomycetes. The rhizosphere environment was notably enriched with potential streptomycin producers, carbon and nitrogen fixers, and lignin degraders with regard to functional groups of microorganisms. However, microbial communities mainly responsible for chitin degradation, ammonia oxidation, and nitrite reduction were found to be decreased. The results from this study highlight significant changes in several plant-based endpoints, as well as the rhizosphere soil microorganisms. It further adds information to our understanding of the nanoscale-specific impacts of important micronutrient oxides on both rice and its associated soil microbiome.

RevDate: 2022-09-28

Bertucci A, Hoede C, Dassié E, et al (2022)

Impact of environmental micropollutants and diet composition on the gut microbiota of wild european eels (Anguilla anguilla).

Environmental pollution (Barking, Essex : 1987), 314:120207 pii:S0269-7491(22)01421-X [Epub ahead of print].

In fish, the gut microbiome plays a crucial role in homeostasis and health and is affected by several organic and inorganic environmental contaminants. Amphidromous fish are sentinel species, particularly exposed to these stressors. We used whole metagenome sequencing to characterize the gut microbiome of wild European eels (Anguilla anguilla) at a juvenile stage captured from three sites with contrasted pollution levels in term of heavy metals and persistent organic pollutants. The objectives were to identify what parameters could alter the gut microbiome of this catadromous fish and to explore the potential use of microbiota as bioindicators of environment quality. We identified a total of 1079 microbial genera. Overall, gut microbiome was dominated by Proteobacteria, Firmicutes and Actinobacteria. Alpha and beta diversity were different amongst sites and could be explained by a reduced number of environmental and biological factors, specifically the relative abundance of fish preys in eels' diet, PCB101, γHCH (lindane), transnonachlor and arsenic. Furthermore, we identified a series of indicator taxa with differential abundance between the three sites. Changes in the microbial communities in the gut caused by environmental pollutants were previously undocumented in European eels. Our results indicate that microbiota might represent another route by which pollutants affect the health of these aquatic sentinel organisms.

RevDate: 2022-09-27

Gadsby NJ, DM Musher (2022)

The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures.

Clinical microbiology reviews [Epub ahead of print].

All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Enterobacteriaceae, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying Legionella and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.

RevDate: 2022-09-27

Lerch F, Vötterl JC, Schwartz-Zimmermann HE, et al (2022)

Exposure to plant-oriented microbiome altered jejunal and colonic innate immune response and barrier function more strongly in suckling than in weaned piglets.

Journal of animal science pii:6722649 [Epub ahead of print].

Weaning often leaves the piglet vulnerable to gut dysfunction. Little is known about the acute response of a gut mucosa primed by a milk-oriented microbiome before weaning to a plant-oriented microbiome (POM) after weaning. We evaluated the epithelial structure, secretory response and permeability in the small and large intestines of piglets receiving a milk-based (i.e. preweaning) or plant-based diet (i.e. postweaning) to POM inocula using intestinal loop perfusion assays (ILPA). The POM were prepared from jejunal and colonic digesta of four 7 week-old weaned (day 28 of life) piglets, having gut-site specific microbial and metabolite composition. Two consecutive ILPA were performed in 16 piglets pre- (day 24-27) and 16 piglets postweaning (day 38-41) in two replicate batches. Two jejunal and colonic loops per piglet were perfused with Krebs-Henseleit buffer (control) or the respective POM. The outflow fluid was analyzed for antimicrobial secretions. Jejunal and colonic loop tissue was collected after each ILPA for histomorphology and electrophysiology using Ussing chambers. ANOVA was performed using the MIXED procedure in SAS. The POM stimulated the secretory response by increasing mucin in the jejunal and colonic outflow by 99.7 and 54.1%, respectively, and jejunal IgA by 19.2%, whereas colonic lysozyme decreased 25.6% compared to the control (P < 0.05). Fittingly, the POM raised the number of goblet cells by 96.7% in jejunal and 56.9% in colonic loops compared to control loops (P < 0.05). The POM further flattened jejunal villi by 18.3% and reduced crypt depth in jejunal and colonic loops by 53.8 and 9.0% compared to the control (P < 0.05); observations typically made postweaning and indicative for mucosal recognition of 'foreign' compounds. The POM altered the jejunal and colonic net ion flux as indicated by 22.7 and 59.2% greater short-circuit current compared to control loops, respectively; the effect being stronger postweaning (P < 0.05). Colonic barrier function improved with age (P < 0.05), whereas POM perfusion compromised the mucosal barrier as suggested by 17.7 and 54.1% greater GT and mucosal-to-serosal flux of fluorescein-isothiocyanate dextran, respectively, compared to the control (P < 0.05). In conclusion, results demonstrated that the preweaning gut epithelium acutely responds to novel compounds in postweaning digesta by upregulating the first line of defense (i.e. mucin and lysozyme secretion) and impairment of the structural integrity.

RevDate: 2022-09-27

Mo XB, Sun YH, Wu LF, et al (2022)

A novel long noncoding RNA, lnc-RNU12, influences the T-cell cycle via c-JUN and CCNL2 in rheumatoid arthritis.

Rheumatology (Oxford, England) pii:6722613 [Epub ahead of print].

OBJECTIVES: Long noncoding RNAs (lncRNAs) play important roles in rheumatoid arthritis (RA) pathogenesis. However, specific lncRNAs that regulate gene expression in RA pathogenesis are poorly known. This study was undertaken to characterize a novel lncRNA (lnc-RNU12) that has a lower-than-normal expression level in RA patients.

METHODS: We performed initial genome-wide lncRNA microarray screening in peripheral blood mononuclear cells (PBMCs) of 28 RA cases and 18 controls. Multiple methods were used to validate the detected associations between lncRNAs and RA. Furthermore, we identified the source and characteristics of the highlighted lncRNAs, detected the target genes, and determined the functional effect on immune cells through lncRNA knockdown in Jurkat T cell lines.

RESULTS: lnc-RNU12 was downregulated in PBMCs and T cell subtypes of RA patients and genetically associated with RA risk. lnc-RNU12 mediates the effect of microbiome alterations on RA risk. Activation of T cells caused low expression of lnc-RNU12. Knockdown of lnc-RNU12 in Jurkat T cells caused cell cycle S-phase arrest and altered the expression of protein-coding genes related to the cell cycle and apoptosis (e.g. c-JUN, CCNL2, CDK6, MYC, RNF40, PKM, VPS35, DNAJB6 and FLCN). Finally, c-JUN and CCNL2 were identified as target genes of lnc-RNU12 at the mRNA and protein expression levels. RNA-binding protein immunoprecipitation assays verified the interaction between lnc-RNU12 and the two proteins (c-Jun and cyclin L2) in Jurkat cells.

CONCLUSION: Our study suggested that lnc-RNU12 was involved in the pathogenesis of RA by influencing the T cell cycle by targeting c-JUN and CCNL2.

RevDate: 2022-09-27

Rubin IMC, Mollerup S, Broholm C, et al (2022)

Synbiotic Intervention with Lactobacilli, Bifidobacteria, and Inulin in Healthy Volunteers Increases the Abundance of Bifidobacteria but Does Not Alter Microbial Diversity.

Applied and environmental microbiology [Epub ahead of print].

Synbiotics combine probiotics and prebiotics and are being investigated for potential health benefits. In this single-group-design trial, we analyzed changes in the gut microbiome, stool quality, and gastrointestinal well-being in 15 healthy volunteers after a synbiotic intervention comprising Lacticaseibacillus rhamnosus (LGG), Lactobacillus acidophilus (LA-5), Lacticaseibacillus paracasei subsp. paracasei (L. CASEI 431), and Bifidobacterium animalis subsp. lactis BB-12 and 20 g of chicory-derived inulin powder consumed daily for 4 weeks. Fecal samples were collected at baseline and at completion of the intervention, and all participants completed a fecal diary based on the Bristol Stool Scale and recorded their gastrointestinal well-being. No adverse effects were observed after consumption of the synbiotic product, and stool consistency and frequency remained almost unchanged during the trial. Microbiome analysis of the fecal samples was achieved using shotgun sequencing followed by taxonomic profiling. No changes in alpha and beta diversity were seen after the intervention. Greater relative abundances of Bifidobacteriaceae were observed in 12 subjects, with indigenous bifidobacteria species constituting the main increase. All four probiotic organisms increased in abundance, and L. rhamnosus, B. animalis, and L. acidophilus were differentially abundant, compared to baseline. Comparison of the fecal strains to the B. animalis subsp. lactis BB-12 reference genome and the sequenced symbiotic product revealed only a few single-nucleotide polymorphisms differentiating the probiotic B. animalis subsp. lactis BB-12 from the fecal strains identified, indicating that this probiotic strain was detectable after the intervention. IMPORTANCE The effects of probiotics/synbiotics are seldom investigated in healthy volunteers; therefore, this study is important, especially considering the safety aspects of multiple probiotics together with prebiotic fiber in consumption by humans. The study explores at the potential of a synbiotic intervention with lactobacilli, bifidobacteria, and inulin in healthy volunteers and tracks the ingested probiotic strain B. animalis subsp. lactis.

RevDate: 2022-09-27

Williams CE, Kueneman JG, Nicholson DJ, et al (2022)

Sustained Drought, but Not Short-Term Warming, Alters the Gut Microbiomes of Wild Anolis Lizards.

Applied and environmental microbiology [Epub ahead of print].

As rising temperatures threaten biodiversity across the globe, tropical ectotherms are thought to be particularly vulnerable due to their narrow thermal tolerance ranges. Nevertheless, physiology-based models highlighting the vulnerability of tropical organisms rarely consider the contributions of their gut microbiota, even though microbiomes influence numerous host traits, including thermal tolerance. We combined field and lab experiments to understand the response of the slender anole lizard (Anolis apletophallus) gut microbiome to climatic shifts of various magnitude and duration. First, to examine the effects of long-term climate warming in the wild, we transplanted lizards from the mainland Panama to a series of warmer islands in the Panama Canal and compared their gut microbiome compositions after three generations of divergence. Next, we mimicked the effects of a short-term "heat-wave" by using a greenhouse experiment and explored the link between gut microbiome composition and lizard thermal physiology. Finally, we examined variation in gut microbiomes in our mainland population in the years both before and after a naturally occurring drought. Our results suggest that slender anole microbiomes are surprisingly resilient to short-term warming. However, both the taxonomic and predicted functional compositions of the gut microbiome varied by sampling year across all sites, suggesting that the drought may have had a regional effect. We provide evidence that short-term heat waves may not substantially affect the gut microbiota, while more sustained climate anomalies may have effects at broad geographic scales. IMPORTANCE As climate change progresses, it is crucial to understand how animals will respond to shifts in their local environments. One component of this response involves changes in the microbial communities living in and on host organisms. These "microbiomes" can affect many processes that contribute to host health and survival, yet few studies have measured changes in the microbiomes of wild organisms experiencing novel climatic conditions. We examined the effects of shifting climates on the gut microbiome of the slender anole lizard (Anolis apletophallus) by using a combination of field and laboratory studies, including transplants to warm islands in the Panama Canal. We found that slender anole microbiomes remain stable in response to short-term warming but may be sensitive to sustained climate anomalies, such as droughts. We discuss the significance of these findings for a species that is considered highly vulnerable to climate change.

RevDate: 2022-09-27

Schneider AM, Nolan ZT, Banerjee K, et al (2022)

Evolution of the facial skin microbiome during puberty in normal and acne skin.

Journal of the European Academy of Dermatology and Venereology : JEADV [Epub ahead of print].

BACKGROUND: The composition of the skin microbiome varies from infancy to adulthood and becomes most stable in adulthood. Adult acne patients harbor an "acne microbiome" dominated by specific strains of C. acnes. However, the precise timing of skin microbiome evolution, the development of the acne microbiome, and the shift to virulent C. acnes strain composition during puberty is unknown.

OBJECTIVES: We performed a cross-sectional pilot study in a pediatric population to understand how and when the skin microbiome composition transitions during puberty and whether a distinct "acne microbiome" emerges in pediatric subjects.

METHODS: Forty-eight volunteers including males and females, ages 7-17 yrs., with and without acne were enrolled and evaluated for pubertal development using the Tanner staging criteria. Sebum levels were measured and skin microbiota were collected by sterile swab on the subject's forehead. DNA was sequenced by whole genome shotgun sequencing.

RESULTS: A significant shift in microbial diversity emerged between early (T1-T2) and late (T3-T5) stages of puberty, coinciding with increased sebum production on the face. The overall relative abundance of C. acnes in both normal and acne skin increased during puberty and individual C. acnes strains were uniquely affected by pubertal stage and the presence of acne. Further, an acne microbiome signature associated with unique C. acnes strain composition and metabolic activity emerges in late puberty in those with acne. This unique C. acnes strain composition is predicted to have increased porphyrin production, which may contribute to skin inflammation.

CONCLUSIONS: Our data suggest that the stage of pubertal development influences skin microbiome composition. As children mature, a distinct acne microbiome composition emerges in those with acne. Understanding how both puberty and acne influence the microbiome may support novel therapeutic strategies to combat acne in the pediatric population.

RevDate: 2022-09-28

Oliveira IMF, Ng DYK, van Baarlen P, et al (2022)

Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches.

Microbial genomics, 8(9):.

Rothia species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity, including the palatine tonsils, is colonized by a complex microbial community, which compete for resources, actively suppress competitors and influence host physiology. We analysed genomic data from 43 new porcine Rothia isolates, together with 112 publicly available draft genome sequences of Rothia isolates from humans, animals and the environment. In all Rothia genomes, we identified biosynthetic gene clusters predicted to produce antibiotic non-ribosomal peptides, iron scavenging siderophores and other secondary metabolites that modulate microbe-microbe and potentially microbe-host interactions. In vitro overlay inhibition assays corroborated the hypothesis that specific strains produce natural antibiotics. Rothia genomes encode a large number of carbohydrate-active enzymes (CAZy), with varying CAZy activities among the species found in different hosts, host niches and environments. These findings reveal competition mechanisms and metabolic specializations linked to ecological adaptation of Rothia species in different hosts.

RevDate: 2022-09-27

Hanitsch LG (2022)

Bronchiectasis and obstructive lung diseases in primary antibody deficiencies and beyond: update on management and pathomechanisms.

Current opinion in allergy and clinical immunology pii:00130832-990000000-00015 [Epub ahead of print].

PURPOSE OF REVIEW: Pulmonary complications are among the most frequent manifestations in patients with primary antibody deficiency (PAD), contributing significantly to morbidity and mortality. Here, we focus on recent findings in obstructive pulmonary disease and bronchiectasis in PAD. Since specific data on patients with PAD is limited and management mostly follows general recommendations, this review also aims to summarize data from the immunocompetent population.

RECENT FINDINGS: Potential risk factors for the development and progression of bronchiectasis include reduced immunoglobulins and lower CD4 cells. In addition, Pseudomonas aeruginosa and an altered microbiome might contribute to local inflammation and disease progression. Findings on the contribution of neutrophils and eosinophils in the affected immunocompetent population require confirmation in PAD. Despite its high global burden, there is an extreme paucity of data on chronic obstructive pulmonary disease in PAD. Lower IgA and IgM are associated with asthma in PAD, but the heterogeneity of prevalence among PAD groups is poorly understood. Recent observations of non-IgE-mediated pathomechanisms in asthma may be of particular interest in PAD patients.

SUMMARY: Management of PAD patients with chronic lung disease requires a multidisciplinary team approach including immunology, pulmonology, infectious disease and physiotherapy. Diagnostic processes should be harmonized to ensure a more precise perspective on prevalence and disease courses.

RevDate: 2022-09-27

Shareefdeen H, C Hill (2022)

The gut virome in health and disease: new insights and associations.

Current opinion in gastroenterology [Epub ahead of print].

PURPOSE OF REVIEW: Recent years have seen great strides made in the field of viral metagenomics. Many studies have reported alterations in the virome in different disease states. The vast majority of the human intestinal virome consists of bacteriophages, viruses that infect bacteria. The dynamic relationship between gut bacterial populations and bacteriophages is influenced by environmental factors that also impact host health and disease. In this review, we focus on studies highlighting the dynamics of the gut virome and fluctuations associated with disease states.

RECENT FINDINGS: Novel correlations have been identified between the human gut virome and diseases such as obesity, necrotizing enterocolitis and severe acute respiratory syndrome coronavirus 2 infection. Further associations between the virome and cognition, diet and geography highlight the complexity of factors that can influence the dynamic relationship between gut bacteria, bacteriophages and health.

SUMMARY: Here, we highlight some novel associations between the virome and health that will be the foundation for future studies in this field. The future development of microbiome-based interventions, identification of biomarkers, and novel therapeutics will require a thorough understanding of the gut virome and its dynamics.

RevDate: 2022-09-27

Freedberg DE, L Chang (2022)

Gastrointestinal symptoms in COVID-19: the long and the short of it.

Current opinion in gastroenterology pii:00001574-990000000-00023 [Epub ahead of print].

PURPOSE OF REVIEW: A large and growing number of patients have persistent gastrointestinal symptoms that they attribute to COVID-19. SARS-CoV-2, the virus that causes COVID-19, replicates within the gut and acute COVID-19 is associated with alteration of the gut microbiome. This article reviews recent observational data related to gastrointestinal symptoms in 'long COVID' and discusses pathophysiologic mechanisms that might explain persistent post-COVID gastrointestinal symptoms.

RECENT FINDINGS: Gastrointestinal symptoms are present in half of the patients with acute COVID-19, persist 6 months after COVID-19 in 10-25% of patients, and are rated as the most bothersome symptom in 11% of all patients. These symptoms include heartburn, constipation, diarrhoea and abdominal pain and decline in prevalence with the passage of time. Long COVID gastrointestinal symptoms are associated with mental health symptoms (anxiety and depression) that predate COVID-19 and also with mental health symptoms that are concurrent, after recovery from COVID-19. The cause of long COVID gastrointestinal symptoms is unknown and hypotheses include the SARS-CoV-2 virus itself, which infects the gastrointestinal tract; COVID-19, which can be accompanied by gut microbiome changes, a profound systemic inflammatory response and critical illness; and/or effects of pandemic stress on gastrointestinal function and symptom perception, which may be unrelated to either SARS-CoV-2 or to COVID-19.

SUMMARY: New, persistent gastrointestinal symptoms are commonly reported after recovery from COVID-19. The pathophysiology of these symptoms is unknown but likely to be multifactorial.

RevDate: 2022-09-27

Vitetta L (2022)

The vermiform cecal appendix, expendable or essential? A narrative review.

Current opinion in gastroenterology [Epub ahead of print].

PURPOSE OF REVIEW: The vermiform cecal appendix is a small thin pouch-like tube of intestinal tissue situated in the lower right abdomen. It is attached at the junction of the large intestine between the ascending colon and small intestine. Historically, the appendix has been labeled redundant with no significant function, a remnant of evolution. This idea was thought to represent a function that may have been critical for survival that became nonsignificant over time. Evolutionary biologists deemed it to be a vestigial organ that early in human evolution was a dedicated organ that was useful and exploited by herbivorous ancestors.

RECENT FINDINGS: Currently, the vermiform cecal appendix has generated significant renewed research interest. As such it has been reported to present a site with a high concentration of lymphoid tissue and a biofilm microbiome that approximately mirrors that which is found in the large bowel.

SUMMARY: Research suggests that the vermiform cecal appendix may be the site of a safe-house biofilm that could re-inoculate the large bowel. Given that the appendix has no known role in digestion, the network of lymphoid tissue and microbiome could constitute an initial site of bacterial translocations that can influence early life ontology and immunological tolerance. A dysbiotic microbiome in the appendix is posited to trigger inflammatory sequelae.

RevDate: 2022-09-27

Murphy KM, Watkins MM, Finger JW, et al (2022)

Xenobiotic estradiol-17ß alters gut microbiota of hatchling American Alligators (Alligator mississippiensis).

Environmental microbiology [Epub ahead of print].

Environmental estrogens pose serious concerns for ecosystems through their effects on organismal survival and physiology. The gut microbiome is highly vulnerable to environmental influence, yet the effects of estrogens on gut homeostasis are unknown because they are poorly studied in wildlife populations. To determine the influence of environmental estrogens (i.e., xenoestrogens) on the diversity and abundance of gut microbiota, we randomly assigned 23 hatchling American alligators (Alligator mississippiensis) to three ecologically relevant treatments (control, low, and high estrogen concentrations) for ten weeks. We predicted that xenoestrogen exposure would decrease microbial diversity and abundance within the digestive tract and that this effect would be dose-dependent. Microbial samples were collected following diet treatments and microbial diversity was determined using 16S rRNA gene-sequencing. Individuals in estrogen-treatment groups had decreased microbial diversity, but a greater relative abundance of operational taxonomic units than those in the control group. Additionally, this effect was dose-dependent; as individuals were exposed to more estrogen, their microbiota became less diverse, less rich, and less even. Findings from this study suggest that estrogen contamination can influence wildlife populations at the internal microbial-level, which may lead to future deleterious health effects.

RevDate: 2022-09-27

Li Z, Wang K, Ding Y, et al (2022)

Dapagliflozin modulates the fecal microbiota after myocardial infarction in non-diabetic mice.

Clinical and experimental pharmacology & physiology [Epub ahead of print].

The gut microbiota is seemed to be a major modulator of cardiovascular diseases, such as myocardial infarction. Dapagliflozin, sodium-glucose cotransporter 2 inhibitors (SGLT2i), is an antidiabetic agent that was recently utilized in patients with cardiovascular diseases. This study aims to investigate the effects of dapagliflozin on the fecal microbiota of postinfarction non-diabetic mice. A total of 19 male mice were randomly divided into three groups, where two groups were performed with myocardial infarction (MI) by left anterior descending ligation. One day after the surgery, each group was administered normal saline (15ml/kg/day, 0.9%) or dapagliflozin (1.5mg/kg/day) for 4 weeks. Echocardiography was obtained on day 28 post MI. Masson's trichrome staining was used to determine the degree of fibrosis. Fecal samples were collected to assess the microbiome by 16S ribosomal RNA gene sequencing. We found that dapagliflozin significantly improved cardiac function in the non-diabetic myocardial infarction mice model after the 28-day treatment, especially in ejection fraction and fractional shortening (p<0.01). Enterotypes were composed of Muribaculaceae and Lactobacillaceae after dapagliflozin treatment, while Muribaculaceae and Erysipelotrichaceae were the main enterotypes post-MI. Dapagliflozin increased the abundance of beneficial bacteria like Lactobacillaceae, while decreasing the abundance of beneficial bacteria like Bifidobacteriaceae. It was interesting to discover that Proteobacteria (especially Desulfovibrionaceae) were enriched after the dapagliflozin treatment for myocardial infarction. Dapagliflozin increased the abundance of main beneficial bacteria. In post-myocardial infarction treatments, using dapagliflozin could positively contribute to the improvement of cardiac function and alter the structure of fecal microbiota.

RevDate: 2022-09-27

Hooi SL, Dwiyanto J, Rasiti H, et al (2022)

A case report of improvement on ADHD symptoms after fecal microbiota transplantation with gut microbiome profiling pre- and post-procedure.

Current medical research and opinion [Epub ahead of print].

BACKGROUND: Recent studies demonstrate the association of the gut microbiome in regulating interactions between the central nervous system and intestinal function. Individuals with ADHD have been shown to have unique gut microbial signature, with depletion of beneficial commensal microbes. Fecal microbiota transplant (FMT) restores the imbalanced gut microbiome and may replete missing microbes to increase production of hormones and neurotransmitters regulating human behavior and cognition.

RESEARCH DESIGN & METHODS: Here, we present an interesting case of a 22-year-old woman treated with FMT primarily to treat recurrent Clostridioides difficile infection, which coincidentally alleviated her ADHD symptoms. We also present the pre- and post-FMT gut microbiota profiles conducted using shotgun metagenomic sequencing on the patient's fecal samples to thereby highlight potential microbial-associated mechanisms associated with the relief of ADHD symptoms.

RESULTS & CONCLUSIONS: Our case report provides preliminary evidence regarding the use of FMT in a patient with Clostridioides difficile and ADHD. We speculate that gut microbiome modulation, in particular the gain or loss of specific microbial species and pathways involving the metabolism of SCFAs, tryptophan and GABA, may merit further exploration as a potential therapeutic strategy for ADHD.

RevDate: 2022-09-27

Dear K, Gan D, Stavrakoglou A, et al (2022)

Hyperkeratotic flexural erythema (more commonly known as granular parakeratosis) with use of laundry sanitizers containing benzalkonium chloride.

Clinical and experimental dermatology [Epub ahead of print].

BACKGROUND: Hyperkeratotic flexural erythema (HKFE), also known as granular parakeratosis, is a scaly, erythematous or brown eruption, which usually occurs in the intertriginous and flexural areas. It has been linked to the use of benzalkonium chloride (BAK).

AIM: To review the clinical presentation of patients diagnosed with HKFE who had been exposed to laundry sanitizer containing BAK, and the therapies trialled to treat these patients.

METHODS: This was a retrospective cases series of 45 patients seen by dermatologists in Victoria, Australia. Information was collected on clinical presentation, investigation and management.

RESULTS: The patients varied in age from 18 months to 89 years. The rash typically presented as a symmetrical erythema with characteristic multilayered brownish epidermal scaling. The most common location of the rash was the inguinal/anogenital area (32 of 45 patients; 71.1%) and there was a female predominance. Regarding treatment, topical corticosteroids were frequently prescribed and antibiotics were trialled in 11 patients; however, the condition resolved spontaneously over time in all patients with use of emollients, along with cleaning of the washing machine by running an empty wash, and repeated washing or sometimes disposal of BAK-contaminated clothing.

CONCLUSION: This large case series highlighted the characteristic clinical presentation of HKFE in the setting of BAK used in laundry sanitizer, demonstrating a potential causal link. Further studies are required to evaluate the role of the skin microbiome.

RevDate: 2022-09-28

Yunes RA, Poluektova EU, Belkina TV, et al (2022)

Lactobacilli: Legal Regulation and Prospects for New Generation Drugs.

Applied biochemistry and microbiology, 58(5):652-664.

The global probiotics industry has been undergoing major changes in recent years. Approaches to finding and creating new probiotics, as well as a paradigm of their use in food, medicine, and pharmacology are changing. The catalyst proved to be the increasing popularity and availability of omics technologies, in particular, metagenomic studies of human and animal microbiomes. However, the efficiency and safety of drugs based on probiotic strains, as well as their marketing rates, largely depend on the levels of legal and technical regulation in the field. The present review discusses the aspects of legal regulation in Russia, the European Union and the United States, along with the advantages and disadvantages of probiotics and postbiotics. A consensus is emerging that postbiotics have a number of advantages over classical live probiotic cultures. The review also focuses on the lactobacilli family, which includes the largest number of probiotic strains studied so far and still holds a leading position among probiotics. On the legislative front, Russia is often ahead of its time with adopting such laws as the Federal Law No. 492-FZ on biosecurity, which defined the concept of human and animal microbiota and set forth legislative guidelines for its preservation. The new field of research referred to as microbiome nutrigenomics aims to achieve this goal.

RevDate: 2022-09-28
CmpDate: 2022-09-28

Shahi SK, Ghimire S, Lehman P, et al (2022)

Obesity induced gut dysbiosis contributes to disease severity in an animal model of multiple sclerosis.

Frontiers in immunology, 13:966417.

Background: Multiple sclerosis (MS) is an inflammatory and demyelinating disease of the CNS. The etiology of MS is complex, and results from the interaction of multiple environmental and genetic factors. Although human leukocyte antigen-HLA alleles such as HLA-DR2 and -DR3 are considered the strongest genetic factors, the environmental factors responsible for disease predisposition are not well understood. Recently, diet and gut microbiota have emerged as an important environmental factors linked to the increased incidence of MS. Especially, western diets rich in protein and fat have been linked to the increased incidence of obesity. Numerous clinical data indicate a role of obesity and gut microbiota in MS; however, the mechanistic link between gut microbiota and obesity in the pathobiology of MS remains unclear. The present study determines the mechanisms driving MS severity in the context of obesity utilizing a high-fat diet (HFD) induced obese HLA-DR3 class-II transgenic mouse model of MS.

Methods: HLA-DR3 transgenic mice were kept on a standard HFD diet or Normal Chow (NC) for eight weeks. Gut microbiota composition and functional analysis were performed from the fecal DNA of mice. Experimental autoimmune encephalomyelitis-EAE (an animal model of MS) was induced by immunization with the proteolipid protein-PLP91-110 peptide in complete Freud's Adjuvant (CFA) and pertussis toxin.

Results: We observed that HFD-induced obesity caused gut dysbiosis and severe disease compared to mice on NC. Amelioration of disease severity in mice depleted of gut microbiota suggested an important role of gut bacteria in severe EAE in obese mice. Fecal microbiota analysis in HFD mice shows gut microbiota alterations with an increase in the abundance of Proteobacteria and Desulfovibrionaceae bacteria and modulation of various bacterial metabolic pathways including bacterial hydrogen sulfide biosynthetic pathways. Finally, mice on HFD showed increased gut permeability and systemic inflammation suggesting a role gut barrier modulation in obesity induced disease severity.

Conclusions: This study provides evidence for the involvement of the gut microbiome and associated metabolic pathways plus gut permeability in obesity-induced modulation of EAE disease severity. A better understanding of the same will be helpful to identify novel therapeutic targets to reduce disease severity in obese MS patients.

RevDate: 2022-09-28

Dearing MD, Kaltenpoth M, J Gershenzon (2022)

Demonstrating the role of symbionts in mediating detoxification in herbivores.

Symbiosis (Philadelphia, Pa.), 87(1):59-66.

Plant toxins constitute an effective defense against herbivorous animals. However, many herbivores have evolved adaptations to cope with dietary toxins through detoxification, excretion, sequestration, target site insensitivity and/or via behavioral avoidance. While these adaptations are often directly encoded in herbivore genomes, evidence is accumulating that microbial symbionts can reduce the dose of plant toxins by metabolizing or sequestering them prior to absorption by the herbivore. Here, we describe a few well-studied examples to assess such symbiont-mediated detoxification and showcase different approaches that have been used for their analyses. These include: (i) a host phenotypic route in which the symbiotic association is manipulated to reveal host fitness costs upon toxin exposure in the presence/absence of detoxifying symbionts, including function restoration after symbiont re-infection, (ii) a molecular microbiological approach that focuses on the identification and characterization of microbial genes involved in plant toxin metabolism, and (iii) an analytical chemical route that aims to characterize the conversion of the toxin to less harmful metabolites in vivo and link conversion to the activities of a detoxifying symbiont. The advantages and challenges of each approach are discussed, and it is argued that a multi-pronged strategy combining phenotypic, molecular, and chemical evidence is needed to unambiguously demonstrate microbial contributions to plant toxin reduction and the importance of these processes for host fitness. Given the interdisciplinary nature of the topic, we aim to provide a guideline to researchers interested in symbiont-mediated detoxification and hope to encourage future studies that contribute to a more comprehensive and mechanistic understanding of detoxification in herbivores and their symbionts.

RevDate: 2022-09-27

Miller RD, Iinishi A, Modaresi SM, et al (2022)

Computational identification of a systemic antibiotic for gram-negative bacteria.

Nature microbiology [Epub ahead of print].

Discovery of antibiotics acting against Gram-negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which inserts proteins into the outer membrane, is an attractive target due to its surface location. Darobactins produced by Photorhabdus, a nematode gut microbiome symbiont, target BamA. We reasoned that a computational search for genes only distantly related to the darobactin operon may lead to novel compounds. Following this clue, we identified dynobactin A, a novel peptide antibiotic from Photorhabdus australis containing two unlinked rings. Dynobactin is structurally unrelated to darobactins, but also targets BamA. Based on a BamA-dynobactin co-crystal structure and a BAM-complex-dynobactin cryo-EM structure, we show that dynobactin binds to the BamA lateral gate, uniquely protruding into its β-barrel lumen. Dynobactin showed efficacy in a mouse systemic Escherichia coli infection. This study demonstrates the utility of computational approaches to antibiotic discovery and suggests that dynobactin is a promising lead for drug development.

RevDate: 2022-09-27

Beck LC, Masi AC, Young GR, et al (2022)

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants.

Nature microbiology [Epub ahead of print].

The development of the gut microbiome from birth plays important roles in short- and long-term health, but factors influencing preterm gut microbiome development are poorly understood. In the present study, we use metagenomic sequencing to analyse 1,431 longitudinal stool samples from 123 very preterm infants (<32 weeks' gestation) who did not develop intestinal disease or sepsis over a study period of 10 years. During the study period, one cohort had no probiotic exposure whereas two cohorts were given different probiotic products: Infloran (Bifidobacterium bifidum and Lactobacillus acidophilus) or Labinic (B. bifidum, B. longum subsp. infantis and L. acidophilus). Mothers' own milk, breast milk fortifier, antibiotics and probiotics were significantly associated with the gut microbiome, with probiotics being the most significant factor. Probiotics drove microbiome transition into different preterm gut community types (PGCTs), each enriched in a different Bifidobacterium sp. and significantly associated with increased postnatal age. Functional analyses identified stool metabolites associated with PGCTs and, in preterm-derived organoids, sterile faecal supernatants impacted intestinal, organoid monolayer, gene expression in a PGCT-specific manner. The present study identifies specific influencers of gut microbiome development in very preterm infants, some of which overlap with those impacting term infants. The results highlight the importance of strain-specific differences in probiotic products and their impact on host interactions in the preterm gut.

RevDate: 2022-09-28
CmpDate: 2022-09-28

Yang Q, Van Haute M, Korth N, et al (2022)

Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome.

Nature communications, 13(1):5641.

Prebiotic fibers, polyphenols and other molecular components of food crops significantly affect the composition and function of the human gut microbiome and human health. The abundance of these, frequently uncharacterized, microbiome-active components vary within individual crop species. Here, we employ high throughput in vitro fermentations of pre-digested grain using a human microbiome to identify segregating genetic loci in a food crop, sorghum, that alter the composition and function of human gut microbes. Evaluating grain produced by 294 sorghum recombinant inbreds identifies 10 loci in the sorghum genome associated with variation in the abundance of microbial taxa and/or microbial metabolites. Two loci co-localize with sorghum genes regulating the biosynthesis of condensed tannins. We validate that condensed tannins stimulate the growth of microbes associated with these two loci. Our work illustrates the potential for genetic analysis to systematically discover and characterize molecular components of food crops that influence the human gut microbiome.

RevDate: 2022-09-28

De Vrieze J (2020)

The next frontier of the anaerobic digestion microbiome: From ecology to process control.

Environmental science and ecotechnology, 3:100032.

The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.

RevDate: 2022-09-28

Wang M, T Cernava (2020)

Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity.

Environmental science and ecotechnology, 4:100061.

Recent studies have shown that various agrochemicals can substantially affect microbial communities; especially those that are associated with cultivated plants. Under certain circumstances, up to 50% of the naturally occurring microorganisms can be negatively affected by common agricultural practices such as seed coating with fungicide-based matrices. Nevertheless, the off-target effects of commonly applied agrochemicals are still understudied in terms of their interferences with microbial communities. At the same time, agrochemical inputs are steadily increasing due to the intensification of agriculture and the increasing pathogen pressure that is currently observed worldwide. In this article, we briefly reflect on the current knowledge related to pesticide interference with microbial communities and discuss negative implications for the plant holobiont as well as such that are spanning beyond local system borders. Cumulative effects of pesticide inputs that cause alterations in microbial functioning likely have unforeseen implications on geochemical cycles that should be addressed with a high priority in ongoing research. A holistic assessment of such implications will allow us to objectively select the most suitable means for food production under the scenario of a growing global population and aggravating climatic conditions. We present three hypothetical solutions that might facilitate a more sustainable and less damaging application of pesticides in the future.

RevDate: 2022-09-28
CmpDate: 2022-09-28

Hong SY, Yang YY, Xu JZ, et al (2022)

The renal pelvis urobiome in the unilateral kidney stone patients revealed by 2bRAD-M.

Journal of translational medicine, 20(1):431.

BACKGROUND: The pathogenesis of kidney stone disease (KSD) is not fully understood, and potential contributing factors remain to be explored. Several studies have revealed that the urinary microbiome (urobiome) of stone formers was distinct from that of healthy individuals using 16S rRNA gene sequencing, most of which only provided microbial identification at the genus level. 2bRAD sequencing for Microbiome (2bRAD-M) is a novel sequencing technique that enables accurate characterization of the low-biomass microbiome at the species resolution. We aimed to apply 2bRAD-M to profile the renal pelvis urobiome of unilateral kidney stone patients and compared the urobiome with and without stone(s).

METHOD: A total of 30 patients with unilateral stones were recruited, and their renal pelvis urine from both sides was collected. A ureteroscope was inserted into the renal pelvis with stone(s) and a ureteral catheter was placed into the ureteroscope to collect renal pelvis urine. This procedure was repeated again with new devices to collect the urine of the other side. 2bRAD-M was performed to characterize the renal pelvis urobiome of unilateral stone formers to explore whether microbial differences existed between the stone side and the non-stone side.

RESULTS: The microbial community composition of the stone side was similar to that of the non-stone side. Paired comparison showed that Corynebacterium was increased and Prevotella and Lactobacillus were decreased in the stone side. Four species (Prevotella bivia, Lactobacillus iners, Corynebacterium aurimucosum, and Pseudomonas sp_286) were overrepresented in the non-stone side. 24 differential taxa were also identified between two groups by linear discriminant analysis effect size (LEfSe). Extensive and close connections among genera and species were observed in the correlation analysis. Moreover, a random forest classifier was constructed using specific enriched species, which can distinguish the stone side from the non-stone side with an accuracy of 71.2%.

CONCLUSION: This first 2bRAD-M microbiome survey gave an important hint towards the potential role of urinary dysbiosis in KSD and provided a better understanding of mechanism of stone formation.

RevDate: 2022-09-28
CmpDate: 2022-09-28

Lakshmanan AP, Murugesan S, Al Khodor S, et al (2022)

The potential impact of a probiotic: Akkermansia muciniphila in the regulation of blood pressure-the current facts and evidence.

Journal of translational medicine, 20(1):430.

Akkermansia muciniphila (A. muciniphila) is present in the human gut microbiota from infancy and gradually increases in adulthood. The potential impact of the abundance of A. muciniphila has been studied in major cardiovascular diseases including elevated blood pressure or hypertension (HTN). HTN is a major factor in premature death worldwide, and approximately 1.28 billion adults aged 30-79 years have hypertension. A. muciniphila is being considered a next-generation probiotic and though numerous studies had highlighted the positive role of A. muciniphila in lowering/controlling the HTN, however, few studies had highlighted the negative impact of increased abundance of A. muciniphila in the management of HTN. Thus, in the review, we aimed to discuss the current facts, evidence, and controversy about the role of A. muciniphila in the pathophysiology of HTN and its potential effect on HTN management/regulation, which could be beneficial in identifying the drug target for the management of HTN.

RevDate: 2022-09-27

Montenegro Junior RM, Ponte CMM, Castelo MHCG, et al (2022)

Reduced gut microbiota diversity in patients with congenital generalized lipodystrophy.

Diabetology & metabolic syndrome, 14(1):136.

BACKGROUND: Previous studies suggest intestinal dysbiosis is associated with metabolic diseases. However, the causal relationship between them is not fully elucidated. Gut microbiota evaluation of patients with congenital generalized lipodystrophy (CGL), a disease characterized by the absence of subcutaneous adipose tissue, insulin resistance, and diabetes since the first years of life, could provide insights into these relationships.

METHODS: A cross-sectional study was conducted with patients with CGL (n = 17) and healthy individuals (n = 17). The gut microbiome study was performed by sequencing the 16S rRNA gene through High-Throughput Sequencing (BiomeHub Biotechnologies, Brazil).

RESULTS: The median age was 20.0 years old, and 64.7% were female. There was no difference between groups in pubertal stage, BMI, ethnicity, origin (rural or urban), delivery, breastfeeding, caloric intake, macronutrient, or fiber consumption. Lipodystrophic patients presented a lower alpha diversity (Richness index: 54.0 versus 67.5; p = 0.008). No differences were observed in the diversity parameters when analyzing the presence of diabetes, its complications, or the CGL subtype.

CONCLUSION: In this study, we demonstrate for the first time a reduced gut microbiota diversity in individuals with CGL. Dysbiosis was present despite dietary treatment and was also observed in young patients. Our findings allow us to speculate that the loss of intestinal microbiota diversity may be due to metabolic abnormalities present since the first years of life in CGL. Longitudinal studies are needed to confirm these findings, clarifying the possible causal link between dysbiosis and insulin resistance in humans.

RevDate: 2022-09-28
CmpDate: 2022-09-28

Djukovic A, Garzón MJ, Canlet C, et al (2022)

Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae.

Nature communications, 13(1):5617.

Infections by multidrug-resistant Enterobacteriaceae (MRE) are life-threatening to patients. The intestinal microbiome protects against MRE colonization, but antibiotics cause collateral damage to commensals and open the way to colonization and subsequent infection. Despite the significance of this problem, the specific commensals and mechanisms that restrict MRE colonization remain largely unknown. Here, by performing a multi-omic prospective study of hospitalized patients combined with mice experiments, we find that Lactobacillus is key, though not sufficient, to restrict MRE gut colonization. Lactobacillus rhamnosus and murinus increase the levels of Clostridiales bacteria, which induces a hostile environment for MRE growth through increased butyrate levels and reduced nutrient sources. This mechanism of colonization resistance, an interaction between Lactobacillus spp. and Clostridiales involving cooperation between microbiota members, is conserved in mice and patients. These results stress the importance of exploiting microbiome interactions for developing effective probiotics that prevent infections in hospitalized patients.

RevDate: 2022-09-26

Sawada A, Hayakawa T, Kurihara Y, et al (2022)

Seasonal responses and host uniqueness of gut microbiome of Japanese macaques in lowland Yakushima.

Animal microbiome, 4(1):54.

BACKGROUND: Changes in the gut microbial composition is an important response to cope with the seasonal fluctuations in the environment such as food availability. We examined the bacterial gut microbiome of the wild nonhuman primate, Japanese macaque (Macaca fuscata) in Yakushima over 13 months by noninvasive continuous sampling from three identified adult females.

RESULTS: Dietary composition varied considerably over the study period and displayed marked shifts with the seasons. Feeding of leaves, fruits, and invertebrates were their main foods for at least one month. Diet had a significant influence on the gut microbiome. We also confirmed significant effect of host uniqueness in the gut microbiome among the three macaques. Leaf-dominated diet shaped unique gut microbiome structures where the macaques had the highest alpha diversity and their gut microbiome was enriched with Spirochaetes and Tenericutes. Diet-related differences in the putative function were detected, such as a differentially abundant urea cycle during the leaf-feeding season.

CONCLUSION: Both diet and host individuality exerted similar amounts of effect on gut microbe community composition. Major bacterial taxa showed a similar response to monthly fluctuations of fruit and invertebrate feeding, which was largely opposite to that of leaf feeding. The main constituents of fruits and invertebrates are both digestible with the enzyme of the host animals, but that of leaves is not available as an energy source without the aid of the fermentation of the gut microbiome.

RevDate: 2022-09-26

Lavinder TR, Fachko DN, Stanton J, et al (2022)

Effects of Early Antiretroviral Therapy on the Composition and Diversity of the Fecal Microbiome of SIV-infected Rhesus Macaques (Macaca mulatta).

Comparative medicine [Epub ahead of print].

HIV-infected people develop reproducible disruptions in their gastrointestinal microbiota. Despite the suppression ofHIV viremia via long-term antiretroviral therapy (ART), alterations still occur in gut microbial diversity and the commensal microbiota. Mounting evidence suggests these microbial changes lead to the development of gut dysbiosis-persistent inflammation that damages the gut mucosa-and correlate with various immune defects. In this study, we examined how earlyART intervention influences microbial diversity in SIV-infected rhesus macaques. Using 16S rRNA sequencing, we defined the fecal microbiome in macaques given daily ART beginning on either 3 or 7 d after SIV infection (dpi) and characterized changes in composition, α diversity, and β diversity from before infection through 112 dpi. The dominant phyla in the fecal samples before infection were Bacteroidetes, Firmicutes, Spirochaetes, and Proteobacteria. After SIV infection and ART, the relative abundance of Firmicutes and Bacteroidetes did not change significantly. Significant reductions in α diversity occurred across time when ART was initiated at 3 dpi but not at 7 dpi. Principal coordinate analysis of samples revealed adivergence in β diversity in both treatment groups after SIV infection, with significant differences depending on the timingof ART administration. These results indicate that although administration of ART at 3 or 7 dpi did not substantially alterfecal microbial composition, the timing of early ART measurably altered phylogenetic diversity.

RevDate: 2022-09-28
CmpDate: 2022-09-28

Wu L, Gao Y, Su Y, et al (2022)

Probiotics with anti-type 2 diabetes mellitus properties: targets of polysaccharides from traditional Chinese medicine.

Chinese journal of natural medicines, 20(9):641-655.

Traditional Chinese medicine polysaccharides is a biologically active ingredient that is not easy to be digested. It is fermented by intestinal microflora to promote qualitative and selective changes in the composition of the intestinal microbiome, which often result in beneficial effects on the health of the host. People call it "prebiotics". In this review, we systematically summarized the anti-diabetic effect of traditional Chinese medicine polysaccharides. These polysaccharides regulate the metabolism of sugar and lipids by inter-influence with the intestinal microflora, and maintain human health, while improving type 2 diabetes-like symptoms such as high blood glucose, and abnormal glucose and lipid metabolism.

RevDate: 2022-09-26

Arkwright PD, JJ Koplin (2022)

Impact of a decade of research into atopic dermatitis.

The journal of allergy and clinical immunology. In practice pii:S2213-2198(22)00957-6 [Epub ahead of print].

The last decade has seen an unprecedented pace of change, particularly of clinical research in atopic dermatitis (AD). This review summarizes some key discoveries. Over the last 10 years, nearly half of all studies investigated the efficacy and safety of novel therapeutic agents, particularly biologics and small molecules. Clear demonstration of benefit in clinical trials with no significant safety concerns provided strong evidence leading to subsequent Food and Drug Administration (FDA) approval and routine use of the anti-IL-4Rα antagonist dupilumab in patients 6 months and older; the selective JAK1 inhibitors upadacitinib for patients 12 years and older; abrocitinib, the IL-13 antagonist tralokinumab, and the JAK1/2 inhibitor baricitinib for adults 18 years and older. Several other drugs are in the pipeline. Other areas under the spotlight have been trials of skin moisturizers and probiotics in prevention of AD, investigating the role of filaggrin and skin barrier function, and the role of skin and gut microbiome, with Staphylococcus aureus Sbi having been found to uniquely trigger allergic skin responses in AD. Skin microbiome, epidermal metabolites/structural components, and local inflammatory biomarkers are now commonly assessed using genomic and proteomic analysis of tape strips rather than more invasive biopsy to identify factors such as CCL17 which correlate with disease severity and response to therapy. Overall, the last decade has ushered in a new and exciting era in our understanding, diagnosis and treatment of this common allergic skin disease.

RevDate: 2022-09-26

Nejati S, Wang J, Sedaghat S, et al (2022)

Smart Capsule for Targeted Proximal Colon Microbiome Sampling.

Acta biomaterialia pii:S1742-7061(22)00619-5 [Epub ahead of print].

The gastrointestinal (GI) tract, particularly the colon region, holds a highly diverse microbial community that plays an important role in the metabolism, physiology, nutrition, and immune function of the host body. Accumulating evidence has revealed that alteration in these microbial communities is the pivotal step in developing various metabolic diseases, including obesity, inflammatory bowel disease (IBD), and colorectal cancer. However, there is still a lack of clear understanding of the interrelationship between microbiota and diet as well as the effectiveness of chemoprevention strategies, including pre and probiotic agents in modifying the colonic microbiota and preventing digestive diseases. Existing methods for assessing these microbiota-diet interactions are often based on samples collected from the feces or endoscopy techniques which are incapable of providing information on spatial variations of the gut microbiota or are considered invasive procedures. To address this need, here we have developed an electronic-free smart capsule that enables site-specific sampling of the gut microbiome within the proximal colon region of the GI tract. The 3D printed device houses a superabsorbent hydrogel bonded onto a flexible polydimethylsiloxane (PDMS) disk that serves as a milieu to collect the fluid in the gut lumen and its microbiome by rapid swelling and providing the necessary mechanical actuation to close the capsule after the sampling is completed. The targeted colonic sampling is achieved by coating the sampling aperture on the capsule with a double-layer pH-sensitive enteric coating, which delays fluid in the lumen from entering the capsule until it reaches the proximal colon of the GI tract. To identify the appropriate pH-responsive double-layer coating and processing condition, a series of systematic dissolution characterizations in different pH conditions that mimicked the GI tract was conducted. The effective targeted microbial sampling performance and preservation of the smart capsule with the optimized design were validated using both realistic in vitro GI tract models with mixed bacteria cultures and in vivo with pigs as an animal model. The results from 16sRNA and WideSeq analysis in both in vitro and in vivo studies showed that the bacterial population sampled within the retrieved capsule closely matched the bacterial population within the targeted sampling region (proximal colon). Herein, it is envisioned that such smart sampling capsule technology will provide new avenues for gastroenterological research and clinical applications, including diet-host-microbiome relationships, focused on human GI function and health. STATEMENT OF SIGNIFICANCE: The colonic microbiota plays a major role in the etiology of numerous diseases. Extensive efforts have been conducted to monitor the gut microbiome using sequencing technologies based on samples collected from feces or mucosal biopsies that are typically obtained by colonoscopy. Despite the simplicity of fecal sampling procedures, they are incapable of preserving spatial and temporal information about the bacteria through the gastrointestinal (GI) tract. In contrast, colonoscopy is an invasive and impractical approach to frequently assess the effect of dietary and therapeutic intake on the microbiome and their impact on the health of the patient. Here, we developed a non-invasive capsule that enables targeted sampling from the ascending colon, thereby providing crucial information for disease prediction and monitoring.

RevDate: 2022-09-26

Nelson R (2022)

Changes in infant microbiome linked to prenatal opioids.

The Lancet. Microbe pii:S2666-5247(22)00284-1 [Epub ahead of print].

RevDate: 2022-09-28

Pasokh A, Farzipour M, Mahmoudi J, et al (2022)

The effect of fecal microbiota transplantation on stroke outcomes: A systematic review.

Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association, 31(11):106727 pii:S1052-3057(22)00421-9 [Epub ahead of print].

BACKGROUND AND PURPOSE: Fecal microbiota transplantation (FMT) is a novel microbiota-based therapeutic method that transfers stool from donor into a recipient and its application is under investigating for neurological disorders such as stroke. In this systematic review, we assessed the effect of FMT in progression and treatment of stroke and recovery of post-stroke complications.

METHODS: Preliminary studies were searched in MEDLINE via PubMed, Scopus, COCHRANE library and Google Scholar, databases up to February 2022. The search strategy was restricted to articles about FMT in stroke. The initial search yielded 4570 articles, of which 19 publications were included in our systematic review.

RESULTS: Based on outcomes transferring microbiome from healthy or ischemic donor to other ischemic recipient can affect brain infarct volume and survival rate, neurological and behavioral outcomes, and inflammatory pathways.

CONCLUSIONS: Our systematic review on preclinical studies showed that manipulating gut microbiota via FMT can be a possible therapeutic approach for treatment of stroke and recovery of post-stroke complications.

RevDate: 2022-09-28

Huang S, Zhang C, Xie X, et al (2022)

GRID2 aberration leads to disturbance in neuroactive ligand-receptor interactions via changes to the species richness and composition of gut microbes.

Biochemical and biophysical research communications, 631:9-17 pii:S0006-291X(22)01248-7 [Epub ahead of print].

OBJECTIVE: To explore the association between phenotype and the gut microbiome following damage to the GRID2 gene.

METHODS: Ten wild-type (WT) mice and 11 GRID2 knockout heterozygous mice (GRID2(±)) of a similar age and weight were randomly selected. Fresh feces were collected from both groups of mice under specified pathogen-free (SPF) conditions. The bacterial genomes were extracted from the feces, the 16S rRNA genes were sequenced, and the data were analyzed to determine clustering, diversity, abundance, LEfSe, and functional differences. Differential expression and enrichment analyses of the RNA-seq and protein levels of the GRID2 gene were also performed using data in the GENE database and the new version of the Human Protein Atlas portal (

RESULTS: The diversity analysis showed differences in species composition between the two groups at different levels. At phylum level, compared with the WT group, the distribution was more bacteriophages but showed a lower content of Tenericutes in the GRID2(±) group. At the order level, compared with the WT group, a higher content of Actinomycetales and Bacteriophages were found in the GRID2(±) group. The species difference analysis showed that 17 species, including E. faecalis and Paracoccus spp., showed differences in content between the two groups. LEfSe analysis showed that the abundance of Clostridiaceae, Allobaculum, and other groups decreased in the GRID2(±) group compared with the WT group, while Mycoplasma, Sphingomonas, and Alphaproteobacteria increased in abundance. Functional analysis revealed eight differential functions between the WT and GRID2(±) group (P < 0.05). The most significantly disrupted were neuroactive ligand-receptor interactions (P < 9.99e-4). In addition, the differential expression and enrichment analyses performed at RNA-seq and protein levels revealed that the GRID2 gene showed organ-specific expression and was mainly enriched in the brain tissue.

CONCLUSIONS: Compared with the WT group, the defective GRID2 gene affected the species richness and composition of gut microbes in the GRID2(±) mice, which in turn affected the function of gut microbes, leading to the disruption of neuroactive ligand-receptor interactions. Our findings indicate that the host gene, GRID2, can influence the abundance of a subset of gut microbes but the exact mechanisms still need further investigation.

RevDate: 2022-09-28

Heinzer K, Lang S, Farowski F, et al (2022)

Dietary omega-6/omega-3 ratio is not associated with gut microbiota composition and disease severity in patients with nonalcoholic fatty liver disease.

Nutrition research (New York, N.Y.), 107:12-25 pii:S0271-5317(22)00071-9 [Epub ahead of print].

In this cross-sectional study, we hypothesized that a high dietary ratio of omega-6 (n-6) to omega-3 (n-3) fatty acids could be associated with an altered gut bacterial composition and with the disease severity in patients with nonalcoholic fatty liver disease (NAFLD). A total of 101 NAFLD patients were included in the study, of which 63 underwent a liver biopsy. All 101 patients completed a 14-day food and activity record. Ebispro 2016 professional software was used to calculate individual macronutrients and micronutrients consumed. Patients were grouped into 3 quantiles (Q) according to a low (Q1: <6.1, n = 34), moderate (Q2: 6.1-7.8, n = 33), or high (Q3: >7.8, n = 34) dietary n-6/n-3 ratio. Stool samples were analyzed using 16S rRNA gene sequencing. Spearman correlation coefficients and principal coordinate analysis were used to detect differences in the bacterial composition of the gut microbiota. The median dietary n-6/n-3 ratio of all patients was 6.7 (range, 3.1-14.9). No significant associations between the dietary n-6/n-3 ratio and the gut microbiota composition or disease severity were observed. However, the abundance of specific bacteria such as Catenibacterium or Lactobacillus ruminis were found to be positively correlated and the abundance of Clostridium were negatively correlated with dietary n-6 fatty acid intake. The results indicate that a high dietary n-6/n-3 ratio is probably not a highly relevant factor in the pathogenesis of human NAFLD. Further studies are needed to clarify the importance of interactions between gut bacterial taxa and n-6 fatty acids in the pathophysiology of NAFLD.

RevDate: 2022-09-28
CmpDate: 2022-09-28

Boger-May A, Reed T, LaTorre D, et al (2022)

Altered microbial biogeography in an innate model of colitis.

Gut microbes, 14(1):2123677.

Changes in the spatial organization, or biogeography, of colonic microbes have been observed in human inflammatory bowel disease (IBD) and mouse models of IBD. We have developed a mouse model of IBD that occurs spontaneously and consistently in the absence of adaptive immunity. Mice expressing tumor necrosis factor-induced protein 3 (TNFAIP3) in intestinal epithelial cells (villin-TNFAIP3) develop colitis when interbred with Recombination Activating 1-deficient mice (RAG1-/-). The colitis in villin-TNFAIP3 × RAG1-/- (TRAG) mice is prevented by antibiotics, indicating a role for microbes in this innate colitis. We therefore explored the biogeography of microbes and responses to antibiotics in TRAG colitis. Laser capture microdissection and 16S rRNA sequencing revealed altered microbial populations across the transverse axis of the colon as the inner mucus layer of TRAG, but not RAG1-/-, mice was infiltrated by microbes, which included increased abundance of the classes Gammaproteobacteria and Actinobacteria. Along the longitudinal axis differences in the efficacy of antibiotics to prevent colitis were evident. Neomycin was most effective for prevention of inflammation in the cecum, while ampicillin was most effective in the proximal and distal colon. RAG1-/-, but not TRAG, mice exhibited a structured pattern of bacterial abundance with decreased Firmicutes and Proteobacteria but increased Bacteroidetes along the proximal to distal axis of the gut. TRAG mice exhibited increased relative abundance of potential pathobionts including Bifidobacterium animalis along the longitudinal axis of the gut whereas others, like Helicobacter hepaticus were increased only in the cecum. Potential beneficial organisms including Roseburia were decreased in the proximal regions of the TRAG colon, while Bifidobacterium pseudolongulum was decreased in the TRAG distal colon. Thus, the innate immune system maintains a structured, spatially organized, gut microbiome along the transverse and longitudinal axis of the gut, and disruption of this biogeography is a feature of innate immune colitis.


ESP Quick Facts

ESP Origins

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

ESP Support

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

ESP Rationale

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

ESP Goal

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

ESP Usage

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

ESP Content

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

ESP Help

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

ESP Plans

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

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Papers in Classical Genetics

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

Digital Books

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


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


Biographical information about many key scientists.

Selected Bibliographies

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

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