@article {pmid34293582,
year = {2021},
author = {Zhang, Y and Choi, SH and Nogoy, KM and Liang, S},
title = {Review: The development of the gastrointestinal tract microbiota and intervention in neonatal ruminants.},
journal = {Animal : an international journal of animal bioscience},
volume = {15},
number = {8},
pages = {100316},
doi = {10.1016/j.animal.2021.100316},
pmid = {34293582},
issn = {1751-732X},
abstract = {The complex microbiome colonizing the gastrointestinal tract (GIT) of ruminants plays an important role in the development of the immune system, nutrient absorption and metabolism. Hence, understanding GIT microbiota colonization in neonatal ruminants has positive impacts on host health and productivity. Microbes rapidly colonize the GIT after birth and gradually develop into a complex microbial community, which allows the possibility of GIT microbiome manipulation to enhance newborn health and growth and perhaps induce lasting effects in adult ruminants. This paper reviews recent advances in understanding how host-microbiome interactions affect the GIT development and health of neonatal ruminants. Following initial GIT microbiome colonization, continuous exposure to host-specific microorganisms is necessary for GIT development and immune system maturation. Furthermore, the early GIT microbial community structure is significantly affected by early life events, such as maternal microbiota exposure, dietary changes, age and the addition of prebiotics, probiotics and synbiotics, supporting the idea of microbial programming in early life. However, the time window in which interventions can optimally improve production and reduce gastrointestinal disease as well as the role of key host-specific microbiota constituents and host immune regulation requires further study.},
}

@article {pmid34293459,
year = {2021},
author = {Jaye, K and Li, CG and Bhuyan, DJ},
title = {The complex interplay of gut microbiota with the five most common cancer types: From carcinogenesis to therapeutics to prognosis.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {103429},
doi = {10.1016/j.critrevonc.2021.103429},
pmid = {34293459},
issn = {1879-0461},
abstract = {The association between human gut microbiota and cancers has been an evolving field of biomedical research in recent years. The gut microbiota is composed of the microorganisms residing in the gastrointestinal system that interact with the host to regulate behaviours and biochemical processes within the gut. This symbiotic physiological interaction between the gut and the microbiota plays a significant role in the modulation of gut homeostasis, in which perturbations to the microbiota, also known as dysbiosis can lead to the onset of diseases, including cancer. In this review, we analysed the current literature to understand the role of gut microbiota in the five most prevalent cancer types, namely colon (colorectal), lung, breast, prostate, and stomach cancers. Recent studies have observed the immunomodulatory and anti-tumoural effects of gut microbiota in cancers. Furthermore, gut microbial dysbiosis can induce the release of toxic metabolites and exhibit pro-tumoural effects in the host. The gut microbiota was observed to have clinical implications in each cancer type in addition to regulating the efficacy of standard chemotherapy and natural anticancer agents. However, further research is warranted to understand the complex role of gut microbiota in the prevention, diagnosis, treatment, and prognosis of cancer.},
}

@article {pmid34293242,
year = {2021},
author = {Hwang, J and Thompson, A and Jaros, J and Blackcloud, P and Hsiao, J and Shi, VY},
title = {Updated understanding of Staphylococcus aureus in atopic dermatitis: from virulence factors to commensals and clonal complexes.},
journal = {Experimental dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/exd.14435},
pmid = {34293242},
issn = {1600-0625},
abstract = {Atopic dermatitis (AD) is a common inflammatory dermatosis that has multiple contributing factors including genetic, immunologic, and environmental. Staphylococcus aureus (SA) has long been associated with exacerbation of AD. SA produces many virulence factors that interact with the human skin and immune system. These superantigens and toxins have been shown to contribute to adhesion, inflammation, and skin barrier destruction. Recent advances in genome sequencing techniques have led to a broadened understanding of the multiple ways SA interacts with the cutaneous environment in AD hosts. For example, temporal shifts in the microbiome, specifically in clonal complexes of SA, have been identified during AD flares and remission. Herein, we review mechanisms of interaction between the cutaneous microbiome and SA and highlight known differences in SA clonal complexes that contribute to AD pathogenesis. Detailed knowledge of the genetic strains of SA and cutaneous dysbiosis is becoming increasingly relevant in paving the way for microbiome-modulating and precision therapies for AD.},
}

@article {pmid34292669,
year = {2021},
author = {Liu, H and Cai, Z and Wang, F and Hong, L and Deng, L and Zhong, J and Wang, Z and Cui, W},
title = {Colon-Targeted Adhesive Hydrogel Microsphere for Regulation of Gut Immunity and Flora.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2101619},
doi = {10.1002/advs.202101619},
pmid = {34292669},
issn = {2198-3844},
support = {2020YFA0908200//National Key Research and Development Program of China/ ; 81930051//National Natural Science Foundation of China/ ; 81970489//National Natural Science Foundation of China/ ; 2020M681319//Postdoctoral Research Foundation of China/ ; 20171906//Shanghai Municipal Education commission-Gaofeng Clinical Medicine/ ; ZH2018ZDA04//Shanghai Jiao Tong University "Medical and Research" Program/ ; },
abstract = {Intestinal immune homeostasis and microbiome structure play a critical role in the pathogenesis and progress of inflammatory bowel disease (IBD), whereas IBD treatment remains a challenge as the first-line drugs show limited therapeutic efficiency and great side effect. In this study, a colon-targeted adhesive core-shell hydrogel microsphere is designed and fabricated by the ingenious combination of advanced gas-shearing technology and ionic diffusion method, which can congregate on colon tissue regulating the gut immune-microbiota microenvironment in IBD treatment. The degradation experiment indicates the anti-acid and colon-targeted property of the alginate hydrogel shell, and the in vivo imaging shows the mucoadhesive ability of the thiolated-hyaluronic acid hydrogel core of the microsphere, which reduces the systematic exposure and prolongs the local drug dwell time. In addition, both in vitro and in vivo study demonstrate that the microsphere significantly reduces the secretion of pro-inflammatory cytokines, induces specific type 2 macrophage differentiation, and remarkably alleviates colitis in the mice model. Moreover, 16S ribosomal RNA sequencing reveals an optimized gut flora composition, probiotics including Bifidobacterium and Lactobacillus significantly augment, while the detrimental communities are inhibited, which benefits the intestinal homeostasis. This finding provides an ideal clinical candidate for IBD treatment.},
}

@article {pmid34291472,
year = {2021},
author = {Chen, S and Xiao, Y and Liu, Y and Tian, X and Wang, W and Jiang, L and Wu, W and Zhang, T and Cai, W and Wang, Y},
title = {Fish oil-based lipid emulsion alleviates parenteral nutrition-associated liver diseases and intestinal injury in piglets.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.2229},
pmid = {34291472},
issn = {1941-2444},
abstract = {BACKGROUND AND AIMS: This study aimed to investigate the impact of fish oil-based lipid emulsion (FO) on enterohepatic injuries and intestinal microbiota in piglets of total parenteral nutrition (TPN).

METHODS: Newborn piglets were divided into three groups, including enteral diet (the controls), TPN with 100% FO and TPN with MCT/LCT-based lipid emulsion (MCT/LCT) for 14 days. Serum biochemical indicators, hepatic and intestinal histology, and expression of genes associated with inflammation, oxidative stress, and lipid metabolism were measured. The bile acid profiles in serum and the taxonomic composition of the gut microbiome in different intestinal segments were analyzed.

RESULTS: Compared to MCT/LCT-piglets, FO reduced inflammation, promoted fatty acid oxidation and decreased oxidative stress in the liver. In the intestine, FO decreased intestinal inflammation and intestinal permeability, leading to reduce lipopolysaccharide entry into the blood circulation relative to MCT/LCT-piglets. TPN groups have dominant contents of Proteobacteria and Bacteroides, while the control group have Firmicutes at the phylum level. FO altered the taxonomic compositions of the gut microbiome in different segments, increased the relative abundance of Bacteroidaceae in ileum, and Rikenellaceae and Ruminococcaceae in the colon. FO treatment shifted bile acids (BAs) composition ratio in serum and had a lower ratio of secondary BAs to primary BAs.

CONCLUSION: FO alleviates PNLAD and intestinal injury by regulating the homeostasis of BAs' enterohepatic circulation and altering microbiota composition in different intestinal segments. This article is protected by copyright. All rights reserved.},
}

@article {pmid34291130,
year = {2021},
author = {Zhang, J and Xia, Y and Sun, J},
title = {Breast and gut microbiome in health and cancer.},
journal = {Genes & diseases},
volume = {8},
number = {5},
pages = {581-589},
doi = {10.1016/j.gendis.2020.08.002},
pmid = {34291130},
issn = {2352-3042},
abstract = {The microbiota plays essential roles in health and disease, in both the intestine and the extra-intestine. Dysbiosis of the gut microbiota causes dysfunction in the intestine, which leads to inflammatory, immune, and infectious diseases. Dysbiosis is also associated with diseases beyond the intestine via microbial translocation or metabolisms. The in situ breast microbiome, which may be sourced from the gut through lactation and sexual contact, could be altered and cause breast diseases. In this review, we summarize the recent progress in understanding the interactions among the gut microbiome, breast microbiome, and breast diseases. We discuss the intestinal microbiota, microbial metabolites, and roles of microbiota in immune system. We emphasize the novel roles and mechanisms of the microbiome (both in situ and gastrointestinal sourced) and bacterial products in the development and progression of breast cancer. The intestinal microbial translocation suggests that the gut microbiome is translocated to the skin and subsequently to the breast tissue. The gut bacterial translocation is also due to the increased intestinal permeability. The breast and intestinal microbiota are important factors in maintaining healthy breasts. Micronutrition queuine (Q) is derived from a de novo synthesized metabolite in bacteria. All human cells use queuine and incorporate it into the wobble anticodon position of specific transfer RNAs. We have demonstrated that Q modification regulates genes critical in tight junctions and migration in human breast cancer cells and a breast tumor model. We further discuss the challenges and future perspectives that can move the field forward for prevention, diagnosis, and treatment of breast diseases.},
}

@article {pmid34291099,
year = {2021},
author = {Ma, X and Li, G and Yang, C and He, M and Wang, C and Gu, Y and Ling, S and Cao, S and Yan, Q and Han, X and Wen, Y and Zhao, Q and Wu, R and Deng, J and Zuo, Z and Yu, S and Hu, Y and Zhong, Z and Peng, G},
title = {Skin Microbiota of the Captive Giant Panda (Ailuropoda Melanoleuca) and the Distribution of Opportunistic Skin Disease-Associated Bacteria in Different Seasons.},
journal = {Frontiers in veterinary science},
volume = {8},
number = {},
pages = {666486},
doi = {10.3389/fvets.2021.666486},
pmid = {34291099},
issn = {2297-1769},
abstract = {The giant panda is one of the rarest animals in the world. Skin diseases seriously endanger the health of giant panda and are considered the second major cause of its morbidity. Skin microbiota is a complex ecosystem, and the community structure and the pathogenic potential of bacteria on giant panda skin remain largely unclear. In order to understand the skin bacterial flora of captive giant pandas, the microbiota in giant panda skin samples collected during different seasons was profiled via 16S rRNA gene sequencing. In total, 522 genera from 53 bacterial phyla were detected, with Proteobacteria (40.5%), Actinobacteria (23.1%), Firmicutes (21.1%), Bacteroidetes (9.5%), Cyanobacteria (2.1%), and Thermi (1.2%) as the predominant phyla and Streptococcus (13.9%), Acinetobacter (9.2%), Staphylococcus (2.9%), Pseudomonas (5.9%), Dermacoccus (4.8%), Brachybacterium (2.9%), Escherichia (2.7%), Chryseobacterium (2.1%), Arthrobacter (1.6%), Kocuria (1.5%), Psychrobacter (1.2%), Deinococcus (1.1%), and Flavobacterium (1.1%) as the predominant genera. The results indicated that the diversity was lower in winter than in other seasons and higher in autumn than in other seasons, and the abundance in spring was significantly higher than that in other seasons. Several skin disease-associated bacteria were detected as opportunists in the skin microbiota of healthy giant pandas. In this study, the results indicated that the high diversity and abundance of the skin bacteria may have enhanced the occurrence of skin disease in autumn and spring and that skin disease-associated bacteria are the normal components of the skin microbiota.},
}

@article {pmid34290719,
year = {2021},
author = {Koczorski, P and Furtado, BU and Gołębiewski, M and Hulisz, P and Baum, C and Weih, M and Hrynkiewicz, K},
title = {The Effects of Host Plant Genotype and Environmental Conditions on Fungal Community Composition and Phosphorus Solubilization in Willow Short Rotation Coppice.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {647709},
doi = {10.3389/fpls.2021.647709},
pmid = {34290719},
issn = {1664-462X},
abstract = {Phosphorus (P) is an essential plant nutrient. Low availability of P in soil is mainly caused by high content of Fe2O3 in the clay fraction that binds to P making it unavailable. Beneficial microbes, such as P solubilizing microorganisms can increase the available P in soil and improve plant growth and productivity. In this study, we evaluated the effects of environmental conditions (climate, soil parameters), plant genotype, and level of plant association (rhizosphere or endophytic root organism) on the abundance and diversity of phosphorus solubilizing microorganisms in a Salix production system. We hypothesized that a lower number of endophytic fungi may possess the ability to solubilize P compared to the number of rhizosphere fungi with the same ability. We also expect that the plant genotype and the experimental site with its environmental conditions will influence fungal diversity. Two Salix genotypes grown in pure and mixed cultures were investigated for their fungal microbiome community and diversity in the rhizosphere and endosphere during two growing seasons. We found that the rhizosphere fungal community was more diverse. A general dominance of Ascomycota (Dothideomycetes) and Basidiomycota (Tremellomycetes) was observed. The classes Agaricomycetes and Pezizomycetes were more frequent in the endosphere, while Tremellomycetes and Mortierellomycetes were more abundant in the rhizosphere. Plot-specific soil properties (pH, total organic carbon, and nitrogen) significantly influenced the fungal community structure. Among the culturable fungal diversities, 10 strains of phosphate solubilizing fungi (PSFs) from roots and 12 strains from rhizosphere soil were identified using selective media supplemented with di-calcium and tri-calcium phosphates. The fungal density and the number of PSF were much higher in the rhizosphere than in the endosphere. Penicillium was the dominant genus of PSF isolated from both sites; other less frequent genera of PSFs were Alternaria, Cladosporium, and Clonostachys. Overall the main factors controlling the fungal communities (endophytic vs. rhizosphere fungi) were the soil properties and level of plant association, while no significant influence of growing season was observed. Differences between Salix genotypes were observed for culturable fungal diversity, while in metagenomic data analysis, only the class Dothideomycetes showed a significant effect from the plant genotype.},
}

@article {pmid34290690,
year = {2021},
author = {Srivastava, AK and Kashyap, PL and Santoyo, G and Newcombe, G},
title = {Editorial: Plant Microbiome: Interactions, Mechanisms of Action, and Applications.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {706049},
doi = {10.3389/fmicb.2021.706049},
pmid = {34290690},
issn = {1664-302X},
}

@article {pmid34290679,
year = {2021},
author = {He, B and Chen, X and Yang, H and Cernava, T},
title = {Microbiome Structure of the Aphid Myzus persicae (Sulzer) Is Shaped by Different Solanaceae Plant Diets.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {667257},
doi = {10.3389/fmicb.2021.667257},
pmid = {34290679},
issn = {1664-302X},
abstract = {Myzus persicae (Sulzer) is an important insect pest in agriculture that has a very broad host range. Previous research has shown that the microbiota of insects has implications for their growth, development, and environmental adaptation. So far, there is little detailed knowledge about the factors that influence and shape the microbiota of aphids. In the present study, we aimed to investigate diet-induced changes in the microbiome of M. persicae using high-throughput sequencing of bacterial 16S ribosomal RNA gene fragments in combination with molecular and microbiological experiments. The transfer of aphids to different plants from the Solanaceae family resulted in a substantial decrease in the abundance of the primary symbiont Buchnera. In parallel, a substantial increase in the abundance of Pseudomonas was observed; it accounted for up to 69.4% of the bacterial community in M. persicae guts and the attached bacteriocytes. In addition, we observed negative effects on aphid population dynamics when they were transferred to pepper plants (Capsicum annuum L.). The microbiome of this treatment group showed a significantly lower increase in the abundance of Pseudomonas when compared with the other Solanaceae plant diets, which might be related to the adaptability of the host to this diet. Molecular quantifications of bacterial genera that were substantially affected by the different diets were implemented as an additional verification of the microbiome-based observations. Complementary experiments with bacteria isolated from aphids that were fed with different plants indicated that nicotine-tolerant strains occur in Solanaceae-fed specimens, but they were not restricted to them. Overall, our mechanistic approach conducted under controlled conditions provided strong indications that the aphid microbiome shows responses to different plant diets. This knowledge could be used in the future to develop environmentally friendly methods for the control of insect pests in agriculture.},
}

@article {pmid34290588,
year = {2021},
author = {Stanton, JE and Malijauskaite, S and McGourty, K and Grabrucker, AM},
title = {The Metallome as a Link Between the "Omes" in Autism Spectrum Disorders.},
journal = {Frontiers in molecular neuroscience},
volume = {14},
number = {},
pages = {695873},
doi = {10.3389/fnmol.2021.695873},
pmid = {34290588},
issn = {1662-5099},
abstract = {Metal dyshomeostasis plays a significant role in various neurological diseases such as Alzheimer's disease, Parkinson's disease, Autism Spectrum Disorders (ASD), and many more. Like studies investigating the proteome, transcriptome, epigenome, microbiome, etc., for years, metallomics studies have focused on data from their domain, i.e., trace metal composition, only. Still, few have considered the links between other "omes," which may together result in an individual's specific pathologies. In particular, ASD have been reported to have multitudes of possible causal effects. Metallomics data focusing on metal deficiencies and dyshomeostasis can be linked to functions of metalloenzymes, metal transporters, and transcription factors, thus affecting the proteome and transcriptome. Furthermore, recent studies in ASD have emphasized the gut-brain axis, with alterations in the microbiome being linked to changes in the metabolome and inflammatory processes. However, the microbiome and other "omes" are heavily influenced by the metallome. Thus, here, we will summarize the known implications of a changed metallome for other "omes" in the body in the context of "omics" studies in ASD. We will highlight possible connections and propose a model that may explain the so far independently reported pathologies in ASD.},
}

@article {pmid34290462,
year = {2021},
author = {Qu, Q and Li, H and Bai, L and Zhang, S and Sun, J and Lv, W and Ye, C and Liu, C and Shi, D},
title = {Effects of Heat Stress on Gut Microbiome in Rats.},
journal = {Indian journal of microbiology},
volume = {61},
number = {3},
pages = {338-347},
doi = {10.1007/s12088-021-00948-0},
pmid = {34290462},
issn = {0046-8991},
abstract = {Gut microbiome, as the largest and most important micro-ecosystem, plays a critical role in health. The purpose of this study was to evaluate whether heat stress modulates the composition and diversity of the gut microbiome in rats. The heat stress model was prepared in rats with the heating temperature maintained at 35-38°C. Cecum contents were collected after heat stress for 3 h and days 1, 3 and 7. Total DNA was extracted for 16 S rRNA sequencing and analysis of intestinal microbiome composition and diversity. The study showed that the composition of the intestinal microbiome of heat stress group was changed. And the heat stress modulated key phylotypes of gut microbiota at the level of phylum and genus. In particular, the genus of Lactobacillus and Bacteroides were significantly reduced, whereas the Oscillospira and Clostridium were increased by heat stress. Meanwhile, the rats under the heat stress encountered the change in carbohydrate metabolism, amino acid metabolism, and membrane transport to defense against stress. Taken together, the composition and structure of gut microbiome were affected by heat stress and some key phylotypes were also significantly altered. We conclude that the heat stress could impact multiple biological functions, via altering the gut microbiome.},
}

@article {pmid34290346,
year = {2021},
author = {de la Cruz Peña, MJ and Gonzalez-Granado, LI and Garcia-Heredia, I and Carballa, LM and Martinez-Garcia, M},
title = {Minimal-moderate variation of human oral virome and microbiome in IgA deficiency.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14913},
pmid = {34290346},
issn = {2045-2322},
abstract = {Immunoglobulin A (IgA) is the dominant antibody found in our mucosal secretions and has long been recognized to play an important role in protecting our epithelium from pathogens. Recently, IgA has been shown to be involved in gut homeostatic regulation by 'recognizing' and shaping our commensal microbes. Paradoxically, yet selective IgA-deficiency is often described as asymptomatic and there is a paucity of studies only focused on the mice and human gut microbiome context fully ignoring other niches of our body and our commensal viruses. Here, we used as a model the human oral cavity and employed a holistic view and studied the impact of IgA deficiency and also common variable IgA and IgM immunodeficiencies (CVID), on both the human virome and microbiome. Unexpectedly, metagenomic and experimental data in human IgA deficiency and CVID indicate minimal-moderate changes in microbiome and virome composition compared to healthy control group and point out to a rather functional, resilient oral commensal viruses and microbes. However, a significant depletion (two fold) of bacterial cells (p-value < 0.01) and viruses was observed in IgA-deficiency. Our results demonstrate that, within the limits of our cohort, IgA role is not critical for maintaining a rather functional salivary microbiome and suggest that IgA is not a major influence on the composition of abundant commensal microbes.},
}

@article {pmid34290271,
year = {2021},
author = {Katani, R and Schilling, MA and Lyimo, B and Eblate, E and Martin, A and Tonui, T and Cattadori, IM and Francesconi, SC and Estes, AB and Rentsch, D and Srinivasan, S and Lyimo, S and Munuo, L and Tiambo, CK and Stomeo, F and Gwakisa, P and Mosha, F and Hudson, PJ and Buza, JJ and Kapur, V},
title = {Identification of Bacillus anthracis, Brucella spp., and Coxiella burnetii DNA signatures from bushmeat.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14876},
pmid = {34290271},
issn = {2045-2322},
support = {HDTRA1-16-1-0005//Defense Threat Reduction Agency/ ; },
abstract = {Meat from wildlife species (bushmeat) represents a major source of dietary protein in low- and middle-income countries where humans and wildlife live in close proximity. Despite the occurrence of zoonotic pathogens in wildlife, their prevalence in bushmeat remains unknown. To assess the risk of exposure to major pathogens in bushmeat, a total of 3784 samples, both fresh and processed, were collected from three major regions in Tanzania during both rainy and dry seasons, and were screened by real-time PCR for the presence of DNA signatures of Bacillus anthracis (B. anthracis), Brucella spp. (Brucella) and Coxiella burnetii (Coxiella). The analysis identified DNA signatures of B. anthracis (0.48%), Brucella (0.9%), and Coxiella (0.66%) in a total of 77 samples. Highest prevalence rates of B. anthracis, Brucella, and Coxiella were observed in wildebeest (56%), dik-dik (50%), and impala (24%), respectively. Fresh samples, those collected during the rainy season, and samples from Selous or Serengeti had a greater relative risk of being positive. Microbiome characterization identified Firmicutes and Proteobacteria as the most abundant phyla. The results highlight and define potential risks of exposure to endemic wildlife diseases from bushmeat and the need for future investigations to address the public health and emerging infectious disease risks associated with bushmeat harvesting, trade, and consumption.},
}

@article {pmid34290066,
year = {2021},
author = {Kim, S and Zhang, W and Pak, V and Aqua, JK and Hertzberg, VS and Spahr, CM and Slavich, GM and Bai, J},
title = {How stress, discrimination, acculturation and the gut microbiome affect depression, anxiety and sleep among Chinese and Korean immigrants in the USA: a cross-sectional pilot study protocol.},
journal = {BMJ open},
volume = {11},
number = {7},
pages = {e047281},
doi = {10.1136/bmjopen-2020-047281},
pmid = {34290066},
issn = {2044-6055},
abstract = {INTRODUCTION: Although a considerable proportion of Asians in the USA experience depression, anxiety and poor sleep, these health issues have been underestimated due to the model minority myth about Asians, the stigma associated with mental illness, lower rates of treatment seeking and a shortage of culturally tailored mental health services. Indeed, despite emerging evidence of links between psychosocial risk factors, the gut microbiome and depression, anxiety and sleep quality, very few studies have examined how these factors are related in Chinese and Korean immigrants in the USA. The purpose of this pilot study was to address this issue by (a) testing the usability and feasibility of the study's multilingual survey measures and biospecimen collection procedure among Chinese and Korean immigrants in the USA and (b) examining how stress, discrimination, acculturation and the gut microbiome are associated with depression, anxiety and sleep quality in this population.

METHOD AND ANALYSIS: This is a cross-sectional pilot study among first and second generations of adult Chinese and Korean immigrants in the greater Atlanta area (Georgia, USA). We collected (a) gut microbiome samples and (b) data on psychosocial risk factors, depression, anxiety and sleep disturbance using validated, online surveys in English, Chinese and Korean. We aim to recruit 60 participants (30 Chinese, 30 Korean). We will profile participants' gut microbiome using 16S rRNA V3-V4 sequencing data, which will be analysed by QIIME 2. Associations of the gut microbiome and psychosocial factors with depression, anxiety and sleep disturbance will be analysed using descriptive and inferential statistics, including linear regression.

ETHICS AND DISSEMINATION: This study has been approved by the Institutional Review Board at Emory University (IRB ID: STUDY00000935). Results will be made available to Chinese and Korean community members, the funder and other researchers and the broader scientific community.},
}

@article {pmid34289971,
year = {2021},
author = {Passarelli, MN and Mott, LA and Barry, EL and Rees, JR and Baron, JA},
title = {Oral antibiotics and risk of new colorectal adenomas during surveillance follow-up.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-21-0323},
pmid = {34289971},
issn = {1538-7755},
abstract = {BACKGROUND: Antibiotics may increase colorectal neoplasia risk by modifying the gut microbiome. It is unknown whether use is associated with the risk of new colorectal adenomas among individuals with prior adenomas.

METHODS: We performed a secondary analysis of 4 randomized clinical trials for the chemoprevention of colorectal adenomas. Participants self-reported all currently used prescription drugs shortly after an initial colorectal adenoma diagnosis and 2 or 3 times a year thereafter over 3 to 5 years of follow-up. We estimated adjusted risk ratios (RR) with 95% confidence intervals (CI) for incident adenomas analyzing the 4 trials together.

RESULTS: Cumulatively, the 4 trials enrolled 5,174 participants (3,491 men and 1,683 women), of whom 4,769 (92%) completed {greater than or equal to}1
follow-up colonoscopy. A total of 763 (15%) participants reported using oral antibiotics on {greater than or equal to}2
occasions. Overall, 39% of those using oral antibiotics at least twice developed new colorectal adenomas compared with 40% of those with no use or a single report of use (RR, 0.99; 95% CI, 0.90-1.10). No statistically significant associations were found in study-specific analyses, and results were similar for high- and low-risk adenoma findings, antibiotic class, anatomic location of adenomas, and analyses excluding those with interim colorectal exams.

CONCLUSIONS: Oral antibiotic use during colonoscopic surveillance after an initial adenoma diagnosis was not associated with risk of these polyps.

IMPACT: Any changes to the gut microbiome as a consequence of oral antibiotic use during surveillance may not affect the development of metachronous colorectal adenomas.},
}

@article {pmid34289818,
year = {2021},
author = {Heida, FH and Kooi, EMW and Wagner, J and Nguyen, TY and Hulscher, JBF and van Zoonen, AGJF and Bos, AF and Harmsen, HJM and de Goffau, MC},
title = {Weight shapes the intestinal microbiome in preterm infants: results of a prospective observational study.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {219},
pmid = {34289818},
issn = {1471-2180},
abstract = {BACKGROUND: The intestinal microbiome in preterm infants differs markedly from term infants. It is unclear whether the microbiome develops over time according to infant specific factors.

METHODS: We analysed (clinical) metadata - to identify the main factors influencing the microbiome composition development - and the first meconium and faecal samples til the 4th week via 16 S rRNA amplican sequencing.

RESULTS: We included 41 infants (gestational age 25-30 weeks; birth weight 430-990 g. Birth via Caesarean section (CS) was associated with placental insufficiency during pregnancy and lower BW. In meconium samples and in samples from weeks 2 and 3 the abundance of Escherichia and Bacteroides (maternal faecal representatives) were associated with vaginal delivery while Staphylococcus (skin microbiome representative) was associated with CS. Secondly, irrespective of the week of sampling or the mode of birth, a transition was observed as children children gradually increased in weight from a microbiome dominated by Staphylococcus (Bacilli) towards a microbiome dominated by Enterobacteriaceae (Gammaproteobacteria).

CONCLUSIONS: Our data show that the mode of delivery affects the meconium microbiome composition. They also suggest that the weight of the infant at the time of sampling is a better predictor for the stage of progression of the intestinal microbiome development/maturation than postconceptional age as it less confounded by various infant-specific factors.},
}

@article {pmid34289768,
year = {2021},
author = {Park, SH and Lee, JH and Shin, J and Kim, JS and Cha, B and Lee, S and Kwon, KS and Shin, YW and Choi, SH},
title = {Cognitive function improvement after fecal microbiota transplantation in in Alzheimer's dementia patient: a case report.},
journal = {Current medical research and opinion},
volume = {},
number = {},
pages = {1},
doi = {10.1080/03007995.2021.1957807},
pmid = {34289768},
issn = {1473-4877},
abstract = {After fecal microbiota transplantation (FMT) to treat Clostridioides difficile infection (CDI), cognitive improvement is noticeable, suggesting an essential association between the gut microbiome and neural function. Although it is known that the gut microbiome is linked with cognitive function, whether FMT may lead to cognitive improvement in patients with neurodegenerative disorders remains to be elucidated. We present the case of a 90-year-old woman with Alzheimer's dementia and severe CDI who underwent FMT. Cognitive function testing (Mini-Mental State Examination, Montreal Cognitive Assessment, and Clinical Dementia Rating assessment) was performed one month before FMT and one week and one month after FMT. We collected the patients' fecal samples before FMT and 3 weeks after FMT to compare the microbiota composition. The 16S rRNA gene amplicons were analyzed using the QIIME2 platform (version 2020.2) and Phyloseq R package. The linear discriminant analysis effect size was performed to determine the taxonomic difference between pre- and post-FMT. Functional biomarker analysis using the Kruskal-Wallis H test was performed between the pre- and post-FMT. The cognitive function tests after FMT showed an improvement compared to the tests before the procedure. FMT changed the microbiota composition in recipient feces. We found that the genera were reported to be associated with cognitive function. In addition, short-chain fatty acids was found to be significantly different between before and after FMT. This finding suggests the presence of an association between the gut microbiome and cognitive function. Further, it emphasizes the need for clinical awareness regarding the effect of FMT on the brain-gut-microbiome axis and its potential as a therapy for patients with dementia.},
}

@article {pmid34289613,
year = {2021},
author = {Šamanić, I and Kalinić, H and Fredotović, Ž and Dželalija, M and Bungur, AM and Maravić, A},
title = {Bacteria tolerant to colistin in coastal marine environment: Detection, microbiome diversity and antibiotic resistance genes' repertoire.},
journal = {Chemosphere},
volume = {281},
number = {},
pages = {130945},
doi = {10.1016/j.chemosphere.2021.130945},
pmid = {34289613},
issn = {1879-1298},
abstract = {The global spread of mobilized colistin resistance (mcr) genes in clinical and natural environments dangerously diminishes the effectiveness of this last-resort antibiotic, becoming an urgent health threat. We used a multidisciplinary approach to detect mcr-1 gene and colistin (CL)-resistant bacteria in seawater from two Croatian public beaches. Illumina-based sequencing of metagenomic 16S rRNA was used to assess the taxonomic, functional, and antibiotic resistance genes (ARGs) profiling of the bacterial community tolerant to CL regarding different culture-based isolation methodologies. Data revealed that the choice of methodology alters the diversity and abundance of taxa accounting for the CL-resistance phenotype. The mcr-1 gene was identified by cloning and sequencing in one sample, representing the first report of mcr-1 gene in Croatia. Culturing of CL-resistant strains revealed their resistance phenotypes and concurrent production of clinically significant β-lactamases, such as CTX-M-15, CTX-M-3 and SHV-12. We also report the first identification of blaCTX-M-15 gene in Klebsiella huaxiensis and K. michiganensis, as well as the blaTEM-1+CTX-M-3 in Serratia fonticola. ARGs profiles derived from metagenomic data and predicted by PICRUSt2, showed the highest abundance of genes encoding for multidrug efflux pumps, followed by the transporter genes accounting for the tetracycline, macrolide and phenicol resistance. Our study evidenced the multidrug resistance features of CL-tolerant bacterial communities thriving in surface beach waters. We also showed that combined application of the metagenomic approaches and culture-based techniques enabled successful detection of mcr-1 gene, which could be underreported in natural environment.},
}

@article {pmid34289377,
year = {2021},
author = {Zhang, XS and Yin, YS and Wang, J and Battaglia, T and Krautkramer, K and Li, WV and Li, J and Brown, M and Zhang, M and Badri, MH and Armstrong, AJS and Strauch, CM and Wang, Z and Nemet, I and Altomare, N and Devlin, JC and He, L and Morton, JT and Chalk, JA and Needles, K and Liao, V and Mount, J and Li, H and Ruggles, KV and Bonneau, RA and Dominguez-Bello, MG and Bäckhed, F and Hazen, SL and Blaser, MJ},
title = {Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2021.06.014},
pmid = {34289377},
issn = {1934-6069},
abstract = {Early-life antibiotic exposure perturbs the intestinal microbiota and accelerates type 1 diabetes (T1D) development in the NOD mouse model. Here, we found that maternal cecal microbiota transfer (CMT) to NOD mice after early-life antibiotic perturbation largely rescued the induced T1D enhancement. Restoration of the intestinal microbiome was significant and persistent, remediating the antibiotic-depleted diversity, relative abundance of particular taxa, and metabolic pathways. CMT also protected against perturbed metabolites and normalized innate and adaptive immune effectors. CMT restored major patterns of ileal microRNA and histone regulation of gene expression. Further experiments suggest a gut-microbiota-regulated T1D protection mechanism centered on Reg3γ, in an innate intestinal immune network involving CD44, TLR2, and Reg3γ. This regulation affects downstream immunological tone, which may lead to protection against tissue-specific T1D injury.},
}

@article {pmid34288947,
year = {2021},
author = {Tyagi, K and Tyagi, I and Kumar, V},
title = {Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0251790},
doi = {10.1371/journal.pone.0251790},
pmid = {34288947},
issn = {1932-6203},
abstract = {Spiders being one of the most diverse group in phylum arthropod are of great importance due to their role as predators, silk producer, and in medicinal applications. Spiders in prey-predator relationships play a crucial role in balancing the food-chain of any ecosystem; therefore it is essential to characterize the gut microbiota of spiders collected from natural environments. In the present work, the largest effort so far has been made to characterize the gut microbiota of 35 spider species belonging to four different families using 16S amplicon targeting sequencing. Further, we compared the gut microbiota composition including endosymbiont abundance in spider species collected from different geographical locations. The results obtained revealed the presence of genera like Acinetobacter (15%), V7clade (9%), Wolbachia (8%), Pseudomonas (5%), Bacillus (6%). Although comparative analysis revealed that the gut bacterial composition in all the spider families has a similar pattern, in terms of community richness and evenness. The bacterial diversity in the spider family, Lycosidae are more diverse than in Salticidae, Tetragnathidae and Araneidae. Furthermore, it was observed that the abundance of endosymbiont genera, i.e. Wolbachia and Rickettsia, leads to shift in the abundance of other bacterial taxa and may cause sexual alterations in spider species. Moreover, predicted functional analysis based on PICRUSt2 reveals that gut microbiota of spider species were involved in functions like metabolism of carbohydrates, cofactors and vitamins, amino acids; biosynthesis of organic compounds, fatty acids, lipids etc. Based on the results obtained, it can be said that different locations do not correlate with community composition of gut microbiota in spider species collected from natural environments.},
}

@article {pmid34288545,
year = {2021},
author = {Wang, C and Li, Q and Tang, C and Zhao, X and He, Q and Tang, X and Ren, J},
title = {Characterization of the blood and neutrophil-specific microbiomes and exploration of potential bacterial biomarkers for sepsis in surgical patients.},
journal = {Immunity, inflammation and disease},
volume = {},
number = {},
pages = {},
doi = {10.1002/iid3.483},
pmid = {34288545},
issn = {2050-4527},
support = {2020Z188//Jiangsu Postdoctoral Research Foundation/ ; 81772052//National Natural Science Foundation of China/ ; },
abstract = {INTRODUCTION: Recent studies have demonstrated the presence of a circulating microbiome in the blood of healthy subjects and chronic inflammatory patients. However, our knowledge regarding the blood microbiome and its potential roles in surgical patients remains very limited. The objective of this study was to determine the blood microbial landscape in surgical patients and to explore its potential associations with postoperative sepsis.

MATERIALS AND METHODS: 2825 patients who underwent surgical treatments were screened for enrollment and 204 cases were recruited in this study. The patients were sub-grouped into noninfected, infected, sepsis, and septic shock according to postoperative clinical manifestations. A total of 222 blood samples were obtained for neutrophil isolation, DNA extraction and high-throughput sequencing, quantitative proteomics analysis, and flow cytometric analyses.

RESULTS: Blood and neutrophils in surgical patients and healthy controls contained highly diverse microbiomes, mainly comprising Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. The majority (80.7%-91.5%) of the microbiomes were composed of gut-associated bacteria. The microbiomes in septic patients were significantly distinct from those of healthy controls, and marked differences in microbiome composition were observed between sepsis and septic shock groups. Several specific bacterial genera, including Flavobacterium, Agrococcus, Polynucleobacter, and Acidovorax, could distinguish patients with septic shock from those with sepsis, with higher area under curve values. Moreover, Agrococcus, Polynucleobacter, and Acidovorax were positively associated with the sequential (sepsis-related) organ failure assessment scores and/or acute physiology and chronic health examination scores in septic shock patients. The proteins involved in bactericidal activities of neutrophils were downregulated in septic patients.

CONCLUSIONS: We present evidence identifying significant changes of blood and neutrophil-specific microbiomes across various stages of sepsis, which might be associated with the progression of sepsis after surgical treatments. Several certain bacterial genera in blood microbiome could have potential as microbial markers for early detection of sepsis.},
}

@article {pmid34288433,
year = {2021},
author = {Liu, TY and Ye, N and Wang, X and Das, D and Tan, Y and You, X and Long, M and Hu, T and Dai, L and Zhang, J and Chen, MX},
title = {Drought stress and plant ecotype drive microbiome recruitment in switchgrass.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.13154},
pmid = {34288433},
issn = {1744-7909},
abstract = {The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass that can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S rRNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought-stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome. This article is protected by copyright. All rights reserved.},
}

@article {pmid34287929,
year = {2021},
author = {Wagner, MR},
title = {Prioritizing host phenotype to understand microbiome heritability in plants.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.17622},
pmid = {34287929},
issn = {1469-8137},
abstract = {Breeders and evolutionary geneticists have grappled with the complexity of the "genotype-to-phenotype map" for decades. Now, recent studies highlight the relevance of this concept for understanding heritability of plant microbiomes. Because host phenotype is a more proximate cause of microbiome variation than host genotype, microbiome heritability varies across plant anatomy and development. Fine-scale variation of plant traits within organs suggests that the well-established concept of "microbiome compartment" should be refined. Additionally, recent work shows that the balance of deterministic processes (including host genetic effects) vs. stochastic processes also varies over time and space. Together, these findings suggest that re-centering plant phenotype-both as a predictor and a readout of microbiome function-will accelerate new insights into microbiome heritability.},
}

@article {pmid34287641,
year = {2021},
author = {Chen, Z and Luo, J and Li, J and Kim, G and Chen, ES and Xiao, S and Snapper, SB and Bao, B and An, D and Blumberg, RS and Lin, CH and Wang, S and Zhong, J and Liu, K and Li, Q and Wu, C and Kuchroo, VK},
title = {Foxo1 controls gut homeostasis and commensalism by regulating mucus secretion.},
journal = {The Journal of experimental medicine},
volume = {218},
number = {9},
pages = {},
doi = {10.1084/jem.20210324},
pmid = {34287641},
issn = {1540-9538},
support = {479689//Crohn's and Colitis Foundation/ ; 1-16-INI-16//American Diabetes Association/ ; P30-EY026877/EY/NEI NIH HHS/United States ; //Research to Prevent Blindness/ ; TA 3059-A-2//National Multiple Sclerosis Society/ ; R01 AI139536/NH/NIH HHS/United States ; },
abstract = {Mucus produced by goblet cells in the gastrointestinal tract forms a biological barrier that protects the intestine from invasion by commensals and pathogens. However, the host-derived regulatory network that controls mucus secretion and thereby changes gut microbiota has not been well studied. Here, we identify that Forkhead box protein O1 (Foxo1) regulates mucus secretion by goblet cells and determines intestinal homeostasis. Loss of Foxo1 in intestinal epithelial cells (IECs) results in defects in goblet cell autophagy and mucus secretion, leading to an impaired gut microenvironment and dysbiosis. Subsequently, due to changes in microbiota and disruption in microbiome metabolites of short-chain fatty acids, Foxo1 deficiency results in altered organization of tight junction proteins and enhanced susceptibility to intestinal inflammation. Our study demonstrates that Foxo1 is crucial for IECs to establish commensalism and maintain intestinal barrier integrity by regulating goblet cell function.},
}

@article {pmid34287544,
year = {2021},
author = {Coelho, GDP and Ayres, LFA and Barreto, DS and Henriques, BD and Prado, MRMC and Passos, CMD},
title = {Acquisition of microbiota according to the type of birth: an integrative review.},
journal = {Revista latino-americana de enfermagem},
volume = {29},
number = {},
pages = {e3446},
doi = {10.1590/1518.8345.4466.3446},
pmid = {34287544},
issn = {1518-8345},
abstract = {OBJECTIVE: to analyze scientific evidence regarding the relationship between the type of birth and the microbiota acquired by newborns.

METHOD: this integrative review addresses the role of the type of delivery on newborns' microbial colonization. A search was conducted in the Medical Literature Analysis and Retrieval System Online/PubMed and Virtual Health Library databases using the descriptors provided by Medical Subject Headings (MeSH) and Health Science Descriptors (DeCS).

RESULTS: infants born vaginally presented a greater concentration of Bacteroides, Bifidobacteria, and Lactobacillus in the first days of life and more significant microbial variability in the following weeks. The microbiome of infants born via C-section is similar to the maternal skin and the hospital setting and less diverse, mainly composed of Staphylococcus, Streptococcus, and Clostridium.

CONCLUSION: the maternal vaginal microbiota provides newborns with a greater variety of colonizing microorganisms responsible for boosting and preparing the immune system. Vaginal birth is the ideal birth route, and C-sections should only be performed when there are medical indications.},
}

@article {pmid34287371,
year = {2021},
author = {Sasaki, Y and Honyashiki, M and Kinoshita, T and Matsui, A and Nakashoji, A and Inagawa, T and Ikezawa, S and Yoshimura, N and Yamamura, R and Amano, M and Tomo, Y and Tachimori, H and Matsuoka, YJ and Okubo, R},
title = {Perilla Oil and Bifidobacterium for Alleviating Fear of Cancer Recurrence in Breast Cancer Survivors: Study Protocol for a Three-Arm Phase II Randomized Controlled Study (POB Study).},
journal = {Methods and protocols},
volume = {4},
number = {3},
pages = {},
doi = {10.3390/mps4030046},
pmid = {34287371},
issn = {2409-9279},
support = {19K20171//the Japan Society for the Promotion of Science/ ; 2019 Ota Oil Promotion Award//the Japan Society for Lipid Nutrition/ ; },
abstract = {The fear of cancer recurrence (FCR) is the most common and most severe unmet need among cancer survivors. Safe treatments for the FCR that are easily disseminated are greatly needed. Our primary aim is a preliminary evaluation of the efficacy and effect size of perilla oil, which is rich in omega-3 fatty acids, and Bifidobacterium, a probiotic, on FCR in breast cancer survivors after the completion of chemotherapy. This study has been planned as an exploratory clinical study (phase II) and will be conducted as a three-arm, 12-week parallel group, masked-rater randomized controlled trial. Fifteen participants will be randomized with 1:1:1 allocation to receive Bifidobacterium plus perilla oil, Bifidobacterium alone, or no intervention (control). Interventions will end within 12 weeks after the random allocation of each participant. The participants will be outpatients with invasive breast cancer aged 20 years or older whose chemotherapy was completed at least 6 months before registration; hormone therapy may be ongoing. The primary outcome will be severity of FCR at 12 weeks assessed by masked raters using the 4-item Concerns about Recurrence Scale concerning overall fear of recurrence. The study protocol for the current study is registered in the Japan Registry of Clinical Trials (jRCTs031200029).},
}

@article {pmid34287254,
year = {2021},
author = {Agrawal, R and Ajami, NJ and Malhotra, S and Chen, L and White, DL and Sharafkhaneh, A and Hoffman, KL and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L},
title = {Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Pilot Study.},
journal = {Clocks & sleep},
volume = {3},
number = {3},
pages = {387-397},
doi = {10.3390/clockssleep3030025},
pmid = {34287254},
issn = {2624-5175},
support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 0000//Gillson Longenbaugh Foundation/ ; 0000//Golfers Against Cancer Organization/ ; CIN13-413//the Houston Veterans Affairs Health Services Research Center of Innovations/ ; R01CA172880/CA/NCI NIH HHS/United States ; CX001430.//U.S. Department of Veterans Affairs/ ; },
abstract = {We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6-8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.},
}

@article {pmid34287059,
year = {2021},
author = {Lukowski, JK and Bhattacharjee, A and Yannarell, SM and Schwarz, K and Shor, LM and Shank, EA and Anderton, CR},
title = {Expanding Molecular Coverage in Mass Spectrometry Imaging of Microbial Systems Using Metal-Assisted Laser Desorption/Ionization.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0052021},
doi = {10.1128/Spectrum.00520-21},
pmid = {34287059},
issn = {2165-0497},
abstract = {Mass spectrometry imaging (MSI) is becoming an increasingly popular analytical technique to investigate microbial systems. However, differences in the ionization efficiencies of distinct MSI methods lead to biases in terms of what types and classes of molecules can be detected. Here, we sought to increase the molecular coverage of microbial colonies by employing metal-assisted laser desorption/ionization (MetA-LDI) MSI, and we compared our results to more commonly utilized matrix-assisted laser desorption/ionization MALDI MSI. We found substantial (∼67%) overlap in the molecules detected in our analysis of Bacillus subtilis colony biofilms using both methods, but each ionization technique did lead to the identification of a unique subset of molecular species. MetA-LDI MSI tended to identify more small molecules and neutral lipids, whereas MALDI MSI more readily detected other lipids and surfactin species. Putative annotations were made using METASPACE, Metlin, and the BsubCyc database. These annotations were then confirmed from analyses of replicate bacterial colonies using liquid extraction surface analysis tandem mass spectrometry. Additionally, we analyzed B. subtilis biofilms in a polymer-based emulated soil micromodel using MetA-LDI MSI to better understand bacterial processes and metabolism in a native, soil-like environment. We were able to detect different molecular signatures within the micropore regions of the micromodel. We also show that MetA-LDI MSI can be used to analyze microbial biofilms from electrically insulating material. Overall, this study expands the molecular universe of microbial metabolism that can be visualized by MSI. IMPORTANCE Matrix-assisted laser desorption/ionization mass spectrometry imaging is becoming an important technique to investigate molecular processes within microbial colonies and microbiomes under different environmental conditions. However, this method is limited in terms of the types and classes of molecules that can be detected. In this study, we utilized metal-assisted laser desorption/ionization mass spectrometry imaging, which expanded the range of molecules that could be imaged from microbial samples. One advantage of this technique is that the addition of a metal helps facilitate ionization from electrically nonconductive substrates, which allows for the investigation of biofilms grown in polymer-based devices, like soil-emulating micromodels.},
}

@article {pmid34287035,
year = {2021},
author = {Vanderwolf, KJ and Campbell, LJ and Taylor, DR and Goldberg, TL and Blehert, DS and Lorch, JM},
title = {Mycobiome Traits Associated with Disease Tolerance Predict Many Western North American Bat Species Will Be Susceptible to White-Nose Syndrome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0025421},
doi = {10.1128/Spectrum.00254-21},
pmid = {34287035},
issn = {2165-0497},
abstract = {White-nose syndrome (WNS), a fungal disease that has caused catastrophic population declines of bats in eastern North America, is rapidly spreading across the continent and now threatens previously unexposed bat species in western North America. The causal agent of WNS, the fungus Pseudogymnoascus destructans, can infect many species of hibernating bats, but susceptibility to WNS varies by host species. We previously reported that certain traits of the skin microbiome, particularly yeast diversity and abundance, of bat species in eastern North America are strongly associated with resistance to WNS. Using these traits, we developed models to predict WNS susceptibility of 13 species of western North American bats. Based on models derived from yeast species diversity, only one bat species, Myotis velifer, was predicted to be WNS resistant (i.e., may develop the disease, but with low mortality rates). We also screened yeasts found on western bats for P. destructans-antagonistic properties by spore germination and growth inhibition/competition assays and found the ability of yeasts to inhibit P. destructans in vitro to be strain specific. Similar to results of inhibition assays performed with yeasts isolated from bats in eastern North America, few yeasts isolated from bats in western North America inhibited P. destructans in vitro. Continued monitoring of western bat populations will serve to validate the accuracy of the mycobiome analysis in predicting WNS susceptibility, document population and susceptibility trends, and identify additional predictors to assess the vulnerability of naive bat populations to WNS. IMPORTANCE White-nose syndrome is one of the most devastating wildlife diseases ever documented. Some bat species are resistant to or tolerant of the disease, and we previously reported that certain traits of the skin mycobiome of bat species in eastern North America are strongly associated with resistance to WNS. Predicting which western bat species will be most susceptible to WNS would be of great value for establishing conservation priorities. Based on models derived from yeast species diversity, only one bat species was predicted to be WNS resistant. High susceptibility to WNS would pose a significant conservation threat to bats in western North America.},
}

@article {pmid34287009,
year = {2021},
author = {Aljabr, W and Alruwaili, M and Penrice-Randal, R and Alrezaihi, A and Harrison, AJ and Ryan, Y and Bentley, E and Jones, B and Alhatlani, BY and AlShahrani, D and Mahmood, Z and Rickett, NY and Alosaimi, B and Naeem, A and Alamri, S and Alsran, H and Hamed, ME and Dong, X and Assiri, AM and Alrasheed, AR and Hamza, M and Carroll, MW and Gemmell, M and Darby, A and Donovan-Banfield, I and Stewart, JP and Matthews, DA and Davidson, AD and Hiscox, JA},
title = {Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0021921},
doi = {10.1128/mSphere.00219-21},
pmid = {34287009},
issn = {2379-5042},
abstract = {Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.},
}

@article {pmid34287005,
year = {2021},
author = {Kang, Y and Sun, B and Chen, Y and Lou, Y and Zheng, M and Li, Z},
title = {Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0016221},
doi = {10.1128/mSphere.00162-21},
pmid = {34287005},
issn = {2379-5042},
abstract = {The human oral microbial community has been considered a reservoir of antibiotic resistance. Currently, the effects of periodontitis and the scaling and root planing (SRP) treatment on the performance of antibiotic-resistant genes (ARGs) and metal-resistant genes (MRGs) in the dental plaque microbiota are not well characterized. To explore this issue, we selected 48 healthy-state (HS), 40 periodontitis-state (PS; before treatment), and 24 resolved-state (RS; after SRP treatment) metagenomic data of dental plaque samples from the Sequence Read Archive (SRA) database. NetShift analysis identified Fretibacterium fastidiosum, Tannerella forsythia, and Campylobacter rectus as key drivers during dental plaque microbiota alteration in the progression of periodontitis. Periodontitis and SRP treatment resulted in an increase in the number of ARGs and MRGs in dental plaque and significantly altered the composition of ARG and MRG profiles. Bacitracin, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and multidrug resistance genes were the main classes of ARGs with high relative abundance, whereas multimetal, iron, chromium, and copper resistance genes were the primary types of MRGs in dental plaque microbiota. The cooccurrence of ARGs, MRGs, and mobile genetic elements (MGEs) indicated that a coselection phenomenon exists in the resistomes of dental plaque microbiota. Overall, our data provide new insights into the standing of the distribution of ARGs and MRGs in oral microbiota of periodontitis patients, and it was possible to contribute to the understanding of the complicated correlations among microorganisms, resistomes, and MGEs. IMPORTANCE The emergence and development of resistance to antibiotics in periodontal pathogens have affected the success rate of treatment for periodontitis. The development of new antibacterial strategies is urgently needed to help control and treat periodontal disease, and dental plaque microbiome studies offer a promising new angle of attack. In this study, we investigated the dental plaque microbiota and resistomes in periodontal health and disease states and their changes after SRP therapy. This is the first analysis of the profile of the microbial community and antibiotic and metal resistance genes in dental plaque by the metagenomic approach, to the best of our knowledge. Monitoring the profile of these resistomes has huge potential to provide reference levels for proper antibiotics use and the development of new antimicrobial strategies in periodontitis therapy and thereby improve actual efficacy of the treatment regimens.},
}

@article {pmid34287003,
year = {2021},
author = {Schloss, PD},
title = {Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0019121},
doi = {10.1128/mSphere.00191-21},
pmid = {34287003},
issn = {2379-5042},
abstract = {Amplicon sequencing variants (ASVs) have been proposed as an alternative to operational taxonomic units (OTUs) for analyzing microbial communities. ASVs have grown in popularity, in part because of a desire to reflect a more refined level of taxonomy since they do not cluster sequences based on a distance-based threshold. However, ASVs and the use of overly narrow thresholds to identify OTUs increase the risk of splitting a single genome into separate clusters. To assess this risk, I analyzed the intragenomic variation of 16S rRNA genes from the bacterial genomes represented in an rrn copy number database, which contained 20,427 genomes from 5,972 species. As the number of copies of the 16S rRNA gene increased in a genome, the number of ASVs also increased. There was an average of 0.58 ASVs per copy of the 16S rRNA gene for full-length 16S rRNA genes. It was necessary to use a distance threshold of 5.25% to cluster full-length ASVs from the same genome into a single OTU with 95% confidence for genomes with 7 copies of the 16S rRNA, such as Escherichia coli. This research highlights the risk of splitting a single bacterial genome into separate clusters when ASVs are used to analyze 16S rRNA gene sequence data. Although there is also a risk of clustering ASVs from different species into the same OTU when using broad distance thresholds, these risks are of less concern than artificially splitting a genome into separate ASVs and OTUs. IMPORTANCE 16S rRNA gene sequencing has engendered significant interest in studying microbial communities. There has been tension between trying to classify 16S rRNA gene sequences to increasingly lower taxonomic levels and the reality that those levels were defined using more sequence and physiological information than is available from a fragment of the 16S rRNA gene. Furthermore, the naming of bacterial taxa reflects the biases of those who name them. One motivation for the recent push to adopt ASVs in place of OTUs in microbial community analyses is to allow researchers to perform their analyses at the finest possible level that reflects species-level taxonomy. The current research is significant because it quantifies the risk of artificially splitting bacterial genomes into separate clusters. Far from providing a better representation of bacterial taxonomy and biology, the ASV approach can lead to conflicting inferences about the ecology of different ASVs from the same genome.},
}

@article {pmid34286500,
year = {2021},
author = {Dessì, A and Bosco, A and Pintus, R and Orrù, G and Fanos, V},
title = {Fusobacterium nucleatum and alteration of the oral microbiome: from pregnancy to SARS-COV-2 infection.},
journal = {European review for medical and pharmacological sciences},
volume = {25},
number = {13},
pages = {4579-4596},
doi = {10.26355/eurrev_202107_26251},
pmid = {34286500},
issn = {2284-0729},
abstract = {OBJECTIVE: The human being has evolved in close symbiosis with its own ecological community of commensal, symbiotic and pathogenic bacteria. After the intestinal microbiome, that of the oral cavity is the largest and most diversified. Its importance is reflected not only in local and systemic diseases, but also in pregnancy since it would seem to influence the placental microbiome.

MATERIALS AND METHODS: This is a literature review of articles published in PubMed about Fusobacterium Nucleatum and both its implications with systemic and oral health, adverse pregnancy outcomes, flavors perception and its interference in the oral-nasal mucosal immunity.

RESULTS: It is in maintaining the microbiome's homeostasis that the Fusobacterium nucleatum, an opportunistic periodontal pathogen of the oral cavity, plays a crucial role both as a bridge microorganism of the tongue biofilm, and in maintaining the balance between the different species in the oral-nasal mucosal immunity also by taste receptors interaction. It is also involved in the flavor perception and its detection in the oral microbiome of children from the first days of life suggests a possible physiological role. However, the dysbiosis can determine its pathogenicity with local and systemic consequences, including the pathogenesis of respiratory infections.

CONCLUSIONS: It is interesting to evaluate its possible correlation with Sars-CoV-2 and the consequences on the microflora of the oral cavity, both to promote a possible broad-spectrum preventive action, in favor of all subjects for whom, by promoting the eubiosis of the oral microbiome, a defensive action could be envisaged by the commensals themselves but, above all, for patients with specific comorbidities and therefore already prone to oral dysbiosis.},
}

@article {pmid34286025,
year = {2018},
author = {Alves, ES and Ferreira, RBR and Antunes, LCM},
title = {Extraction of Small Molecules from Fecal Samples and Testingof Their Activity on Microbial Physiology.},
journal = {Bio-protocol},
volume = {8},
number = {8},
pages = {e2808},
doi = {10.21769/BioProtoc.2808},
pmid = {34286025},
issn = {2331-8325},
abstract = {The human body is colonized by vast communities of microbes, collectively known as microbiota, or microbiome. Although microbes colonize every surface of our bodies that is exposed to the external environment, the biggest collection of microbes colonizing humans and other mammals can be found in the gastrointestinal tract. Given the fact that the human gut is colonized by several hundred microbial species, our group hypothesized that the chemical diversity of this environment should be significant, and that many of the molecules present in that environment would have important signaling roles. Therefore, we devised a protocol to extract these molecules from human feces and test their signaling properties. Potentially bioactive extracts can be tested through addition to culture medium and analyses of bacterial growth and gene expression, among other properties. The protocol described herein provides an easy and rapid method for the extraction and testing of metabolites from fecal samples using Salmonella enterica as a model organism. This protocol can also be adapted to the extraction of small molecules from other matrices, such as cultured mammalian cells, tissues, body fluids, and axenic microbial cultures, and the resulting extracts can be tested against various microbial species.},
}

@article {pmid34285994,
year = {2018},
author = {Edwards, J and Santos-Medellín, C and Sundaresan, V},
title = {Extraction and 16S rRNA Sequence Analysis of Microbiomes Associated with Rice Roots.},
journal = {Bio-protocol},
volume = {8},
number = {12},
pages = {e2884},
doi = {10.21769/BioProtoc.2884},
pmid = {34285994},
issn = {2331-8325},
abstract = {Plant roots associate with a wide diversity of bacteria and archaea across the root-soil spectrum. The rhizosphere microbiota, the communities of microbes in the soil adjacent to the root, can contain up to 10 billion bacterial cells per gram of soil (Raynaud and Nunan, 2014) and can play important roles for the fitness of the host plant. Subsets of the rhizospheric microbiota can colonize the root surface (rhizoplane) and the root interior (endosphere), forming an intimate relationship with the host plant. Compositional analysis of these communities is important to develop tools in order to manipulate root-associated microbiota for increased crop productivity. Due to the reduced cost and increasing throughput of next-generation sequencing, major advances in deciphering these communities have recently been achieved, mainly through the use of amplicon sequencing of the 16S rRNA gene. Here we first present a protocol for dissecting the microbiota from various root compartments, developed using rice as a model. We next present a method for amplifying fragments of the 16S rRNA gene using a dual index approach. Finally, we present a simple workflow for analyzing the resulting sequencing data to make ecological inferences.},
}

@article {pmid34285793,
year = {2021},
author = {Gilbert, KJ and Renner, T},
title = {Acid or base? How do plants regulate the ecology of their phylloplane?.},
journal = {AoB PLANTS},
volume = {13},
number = {4},
pages = {plab032},
doi = {10.1093/aobpla/plab032},
pmid = {34285793},
issn = {2041-2851},
abstract = {Plants interface with and modify the external environment across their surfaces, and in so doing, can control or mitigate the impacts of abiotic stresses and also mediate their interactions with other organisms. Botanically, it is known that plant roots have a multi-faceted ability to modify rhizosphere conditions like pH, a factor with a large effect on a plant's biotic interactions with microbes. But plants can also modify pH levels on the surfaces of their leaves. Plants can neutralize acid rain inputs in a period of hours, and either acidify or alkalinize the pH of neutral water droplets in minutes. The pH of the phylloplane-that is, the outermost surface of the leaf-varies across species, from incredibly acidic (carnivorous plants: as low as pH 1) to exceptionally alkaline (species in the plant family, Malvaceae, up to pH 11). However, most species mildly acidify droplets on the phylloplane by 1.5 orders of magnitude in pH. Just as rhizosphere pH helps shape the plant microbiome and is known to influence belowground interactions, so too can phylloplane pH influence aboveground interactions in plant canopies. In this review, we discuss phylloplane pH regulation from the physiological, molecular, evolutionary, and ecological perspectives and address knowledge gaps and identify future research directions.},
}

@article {pmid34285069,
year = {2021},
author = {Wagner, MR and Tang, C and Salvato, F and Clouse, KM and Bartlett, A and Vintila, S and Phillips, L and Sermons, S and Hoffmann, M and Balint-Kurti, PJ and Kleiner, M},
title = {Microbe-dependent heterosis in maize.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {30},
pages = {},
doi = {10.1073/pnas.2021965118},
pmid = {34285069},
issn = {1091-6490},
abstract = {Hybrids account for nearly all commercially planted varieties of maize and many other crop plants because crosses between inbred lines of these species produce first-generation [F1] offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research. The leading hypotheses-which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)-have been able to explain some but not all of the observed patterns of heterosis. Abiotic stressors are known to impact the expression of heterosis; however, the potential role of microbes in heterosis has largely been ignored. Here, we show that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved versus live soil slurries in a growth chamber and for plants grown in steamed or fumigated versus untreated soil in the field. In a different field site, however, soil steaming increased rather than decreased heterosis, indicating that the direction of the effect depends on community composition, environment, or both. Together, our results demonstrate an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize.},
}

@article {pmid34284901,
year = {2021},
author = {Donker, AE and van der Staaij, H and Swinkels, DW},
title = {The critical roles of iron during the journey from fetus to adolescent: Developmental aspects of iron homeostasis.},
journal = {Blood reviews},
volume = {},
number = {},
pages = {100866},
doi = {10.1016/j.blre.2021.100866},
pmid = {34284901},
issn = {1532-1681},
abstract = {Iron is indispensable for human life. However, it is also potentially toxic, since it catalyzes the formation of harmful oxidative radicals in unbound form and may facilitate pathogen growth. Therefore, iron homeostasis needs to be tightly regulated. Rapid growth and development require large amounts of iron, while (especially young) children are vulnerable to infections with iron-dependent pathogens due to an immature immune system. Moreover, unbalanced iron status early in life may have effects on the nervous system, immune system and gut microbiota that persist into adulthood. In this narrative review, we assess the critical roles of iron for growth and development and elaborate how the body adapts to physiologically high iron demands during the journey from fetus to adolescent. As a first step towards the development of clinical guidelines for the management of iron disorders in children, we summarize the unmet needs regarding the developmental aspects of iron homeostasis.},
}

@article {pmid34284550,
year = {2021},
author = {Bohatyrewicz, R and Sołek-Pastuszka, J and Walas, W and Sznajder, K and Falba, A and Chamier-Ciemińska, K and Poncyljusz, W and Dąbrowski, W and Rybojad, B and Woźniak, M and Wojczal, J and Luchowski, P and Zielińska, M and Guziński, M and Sierakowska, K and Kołakowska, T and Serafin, Z and Bartkowska-Śniatkowska, A and Jończyk-Potoczna, K and Kobylarz, K and Byrska-Maciejasz, E and Wyrobek, Ł and Piotrowski, A and Jurkiewicz, E and Kościesza, A and Migdał, M and Tałałaj, M and Jakubów, P and Robert Janica, J and Pągowska-Klimek, I and Brzewski, M and Jurszewicz, P and Dziejowska, M and Milewicz-Podgórska, E and Bekiesinska-Figatowska, M and Szurowska, E and Owczuk, R and Kusza, K and Sawicki, M},
title = {Invitation to participate in a multi-center study for validation of cerebral computed tomography angiography and computed tomography perfusion in the determination of cerebral circulatory arrest during brain death/death by neurological criteria diagnosis procedure in paediatric population below 12 years of age.},
journal = {Anaesthesiology intensive therapy},
volume = {53},
number = {2},
pages = {97-102},
doi = {10.5114/ait.2021.107189},
pmid = {34284550},
issn = {1731-2531},
abstract = {In recent years commensal microorganisms are not just "passive occupants", but important element of homeostasis. There are numerous reports documenting the composition and role of the gut, skin or vagina microbiome but the role of commensal organisms living in the lungs is relatively unknown. Pulmonary microbiome impact on the immune response of the host organism and may indicate new therapeutic directions. Lung microbiome, by modulating the expression of innate immunity genes, causes an increase in the concentration of IL-5, IL-10, IFNγ and CCL11, affects the TLR4 dependent response of pulmonary macrophages and modulate the production of antibacterial peptides contained in the mucus. It is documented that disorders of the lung microbiome contribute to asthma or chronic obstructive pulmonary disease. However it is known that pulmonary dysbiosis also occurs in critically ill patients. It is possible, therefore, that microbiota-targeted therapy may constitute the future therapeutic direction in ICU.},
}

@article {pmid34282723,
year = {2021},
author = {Diebold, PJ and New, FN and Hovan, M and Satlin, MJ and Brito, IL},
title = {Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
doi = {10.7554/eLife.66834},
pmid = {34282723},
issn = {2050-084X},
support = {OADS BAA 2016-N-17812/CC/CDC HHS/United States ; 1661338//National Science Foundation/ ; 1650122//National Science Foundation/ ; K23 AI114994/NH/NIH HHS/United States ; 1DP2HL141007-01/NH/NIH HHS/United States ; OADS BAA 2016-N-17812/CC/CDC HHS/United States ; K23 AI114994/NH/NIH HHS/United States ; 1DP2HL141007-01/NH/NIH HHS/United States ; },
abstract = {The horizonal transfer of plasmid-encoded genes allows bacteria to adapt to constantly shifting environmental pressures, bestowing functional advantages to their bacterial hosts such as antibiotic resistance, metal resistance, virulence factors, and polysaccharide utilization. However, common molecular methods such as short- and long-read sequencing of microbiomes cannot associate extrachromosomal plasmids with the genome of the host bacterium. Alternative methods to link plasmids to host bacteria are either laborious, expensive, or prone to contamination. Here we present the One-step Isolation and Lysis PCR (OIL-PCR) method, which molecularly links plasmid-encoded genes with the bacterial 16S rRNA gene via fusion PCR performed within an emulsion. After validating this method, we apply it to identify the bacterial hosts of three clinically relevant beta-lactamases within the gut microbiomes of neutropenic patients, as they are particularly vulnerable multidrug-resistant infections. We successfully detect the known association of a multi-drug resistant plasmid with Klebsiella pneumoniae, as well as the novel associations of two low-abundance genera, Romboutsia and Agathobacter. Further investigation with OIL-PCR confirmed that our detection of Romboutsia is due to its physical association with Klebsiella as opposed to directly harboring the beta-lactamase genes. Here we put forth a robust, accessible, and high-throughput platform for sensitively surveying the bacterial hosts of mobile genes, as well as detecting physical bacterial associations such as those occurring within biofilms and complex microbial communities.},
}

@article {pmid34284412,
year = {2021},
author = {Pasiakos, SM and Karl, JP and Margolis, LM},
title = {Challenging traditional carbohydrate intake recommendations for optimizing performance at high altitude.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000000782},
pmid = {34284412},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: To highlight emerging evidence challenging traditional recommendations to increase carbohydrate intake to optimize performance at high altitude.

RECENT FINDINGS: Several studies have now clearly demonstrated that, compared with sea level, exogenous carbohydrate oxidation during aerobic exercise is blunted in lowlanders during initial exposure to high altitude. There is also no apparent ergogenic effect of ingesting carbohydrate during aerobic exercise on subsequent performance at high altitude, either initially after arriving or even after up to 22 days of acclimatization. The inability to oxidize and functionally benefit from exogenous carbohydrate intake during exercise after arriving at high altitude coincides with hyperinsulinemia, accelerated glycogenolysis, and reduced peripheral glucose uptake. Collectively, these responses are consistent with a hypoxia-mediated metabolic dysregulation reflective of insulin resistance. Parallel lines of evidence have also recently demonstrated roles for the gut microbiome in host metabolism, bioenergetics, and physiologic responses to high altitude, implicating the gut microbiome as one potential mediator of hypoxia-mediated metabolic dysregulation.

SUMMARY: Identification of novel and well tolerated nutrition and/or pharmacological approaches for alleviating hypoxia-mediated metabolic dysregulation and enhancing exogenous carbohydrate oxidation may be more effective for optimizing performance of lowlanders newly arrived at high altitude than traditional carbohydrate recommendations.},
}

@article {pmid34284178,
year = {2021},
author = {Morris, MT and Hauton, C and Baylay, AJ and Peruzza, L and Targett, TE and Ciotti, BJ},
title = {Spatial variation in the gastrointestinal microbiome, diet, and nutritional condition of a juvenile flatfish among coastal habitats.},
journal = {Marine environmental research},
volume = {170},
number = {},
pages = {105413},
doi = {10.1016/j.marenvres.2021.105413},
pmid = {34284178},
issn = {1879-0291},
abstract = {Gut microbiota are important for the health, fitness and development of animal hosts, but little is known about these assemblages in wild populations of fish. Such knowledge is particularly important for juvenile life stages where nutritional intake critically determines early development, growth, and ultimately recruitment. We characterise the microbiome inhabiting the gut of young-of-the-year European plaice ('YOY plaice') on sandy beaches, their key juvenile habitat, and examine how these microbial communities vary spatially in relation to diet and nutritional condition of their plaice hosts. Body size, diet (stomach fullness and eukaryotic 18S ribosomal sequencing), nutritional condition (RNA:DNA) and gut microbiota (16S prokaryotic ribosomal sequencing) were compared in fish at two spatial scales: between beaches separated by 10s of kilometres and between sites at different depths on the same beach, separated by 10s of metres. The main microbial phyla in YOY plaice guts were Proteobacteria, Spirochaetes, Tenericutes and Verrucomicrobiae. Within the Proteobacteria there was an unusual dominance of Alphaproteobacteria. Differences in body size, diet and nutritional condition of YOY plaice between beaches were accompanied by differences in gut microbial assemblage structure. Notably, substantially reduced nutritional condition and size at one of the beaches was associated with lower stomach fullness, reduced consumption of annelids and differences in the abundance and presence of specific microbial taxa. Differences were also detected in microbial assemblages, body size, and diet between depths within the same nursery beach, although stomach fullness and nutritional condition did not vary significantly. The functional links between the environment, gut microbiota, and their hosts are potentially important mediators of the development of young fish through critical life stages. Our study indicates that these links need to be addressed at 10 km and even 10 m scales to capture the variability observed in wild populations of juvenile fish.},
}

@article {pmid34283920,
year = {2021},
author = {Zembroski, AS and Xiao, C and Buhman, KK},
title = {The Roles of Cytoplasmic Lipid Droplets in Modulating Intestinal Uptake of Dietary Fat.},
journal = {Annual review of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-nutr-110320-013657},
pmid = {34283920},
issn = {1545-4312},
abstract = {Dietary fat absorption is required for health but also contributes to hyperlipidemia and metabolic disease when dysregulated. One step in the process of dietary fat absorption is the formation of cytoplasmic lipid droplets (CLDs) in small intestinal enterocytes; these CLDs serve as dynamic triacylglycerol storage organelles that influence the rate at which dietary fat is absorbed. Recent studies have uncovered novel factors regulating enterocyte CLD metabolism that in turn influence the absorption of dietary fat. These include peroxisome proliferator-activated receptor α activation, compartmentalization of different lipid pools, the gut microbiome, liver X receptor and farnesoid X receptor activation, obesity, and physiological factors stimulating CLD mobilization. Understanding how enterocyte CLD metabolism is regulated is key in modulating the absorption of dietary fat in the prevention of hyperlipidemia and its associated metabolic disorders. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid34283919,
year = {2021},
author = {Mehta, S and Huey, SL and McDonald, D and Knight, R and Finkelstein, JL},
title = {Nutritional Interventions and the Gut Microbiome in Children.},
journal = {Annual review of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-nutr-021020-025755},
pmid = {34283919},
issn = {1545-4312},
abstract = {The gut microbiome plays an integral role in health and disease, and diet is a major driver of its composition, diversity, and functional capacity. Given the dynamic development of the gut microbiome in infants and children, it is critical to address two major questions: (a) Can diet modify the composition, diversity, or function of the gut microbiome, and (b) will such modification affect functional/clinical outcomes including immune function, cognitive development, and overall health? We synthesize the evidence on the effect of nutritional interventions on the gut microbiome in infants and children across 26 studies. Findings indicate the need to study older children, assess the whole intestinal tract, and harmonize methods and interpretation of findings, which are critical for informing meaningful clinical and public health practice. These findings are relevant for precision health, may help identify windows of opportunity for intervention, and may inform the design and delivery of such interventions. Expected final online publication date for the Annual Review of Nutrition, Volume 41 is September 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.},
}

@article {pmid34283837,
year = {2021},
author = {Velasco, C and Dunn, C and Sturdy, C and Izda, V and Martin, J and Rivas, A and McNaughton, J and Jeffries, MA},
title = {Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation.},
journal = {PloS one},
volume = {16},
number = {7},
pages = {e0248322},
doi = {10.1371/journal.pone.0248322},
pmid = {34283837},
issn = {1932-6203},
abstract = {OBJECTIVE: Adult elastic cartilage has limited repair capacity. MRL/MpJ (MRL) mice, by contrast, are capable of spontaneously healing ear punctures. This study was undertaken to characterize microbiome differences between healer and non-healer mice and to evaluate whether this healing phenotype can be transferred via gut microbiome transplantation.

METHODS: We orally transplanted C57BL/6J (B6) mice with MRL/MpJ cecal contents at weaning and as adults (n = 57) and measured ear hole closure 4 weeks after a 2.0mm punch and compared to vehicle-transplanted MRL and B6 (n = 25) and B6-transplanted MRL (n = 20) mice. Sex effects, timing of transplant relative to earpunch, and transgenerational heritability were evaluated. In a subset (n = 58), cecal microbiomes were profiled by 16S sequencing and compared to ear hole closure. Microbial metagenomes were imputed using PICRUSt.

RESULTS: Transplantation of B6 mice with MRL microbiota, either in weanlings or adults, improved ear hole closure. B6-vehicle mice healed ear hole punches poorly (0.25±0.03mm, mm ear hole healing 4 weeks after a 2mm ear hole punch [2.0mm-final ear hole size], mean±SEM), whereas MRL-vehicle mice healed well (1.4±0.1mm). MRL-transplanted B6 mice healed roughly three times as well as B6-vehicle mice, and half as well as MRL-vehicle mice (0.74±0.05mm, P = 6.9E-10 vs. B6-vehicle, P = 5.2E-12 vs. MRL-vehicle). Transplantation of MRL mice with B6 cecal material did not reduce MRL healing (B6-transplanted MRL 1.3±0.1 vs. MRL-vehicle 1.4±0.1, p = 0.36). Transplantation prior to ear punch was associated with the greatest ear hole closure. Offspring of transplanted mice healed significantly better than non-transplanted control mice (offspring:0.63±0.03mm, mean±SEM vs. B6-vehicle control:0.25±0.03mm, n = 39 offspring, P = 4.6E-11). Several microbiome clades were correlated with healing, including Firmicutes (R = 0.84, P = 8.0E-7), Lactobacillales (R = 0.65, P = 1.1E-3), and Verrucomicrobia (R = -0.80, P = 9.2E-6). Females of all groups tended to heal better than males (B6-vehicle P = 0.059, MRL-transplanted B6 P = 0.096, offspring of MRL-transplanted B6 P = 0.0038, B6-transplanted MRL P = 1.6E-6, MRL-vehicle P = 0.0031). Many clades characteristic of female mouse cecal microbiota vs. males were the same as clades characteristic of MRL and MRL-transplanted B6 mice vs. B6 controls, including including increases in Clostridia and reductions in Verrucomicrobia in female mice.

CONCLUSION: In this study, we found an association between the microbiome and tissue regeneration in MRL mice and demonstrate that this trait can be transferred to non-healer mice via microbiome transplantation. We identified several microbiome clades associated with healing.},
}

@article {pmid34282942,
year = {2021},
author = {Umbach, AK and Stegelmeier, AA and Neufeld, JD},
title = {Archaea Are Rare and Uncommon Members of the Mammalian Skin Microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0064221},
doi = {10.1128/mSystems.00642-21},
pmid = {34282942},
issn = {2379-5077},
abstract = {Although previous research demonstrates that skin-associated archaea are rarely detected within human skin microbiome data, exist at relatively low abundance, and are primarily affiliated with the Methanobacteriota and Halobacteriota phyla, other studies suggest that archaea are consistently detected and relatively abundant on human skin, with skin "archaeomes" dominated by putative ammonia oxidizers of the Nitrososphaeria class (Thermoproteota phylum, formerly Thaumarchaeota). Here, we evaluated new and existing 16S rRNA gene sequence data sourced from mammalian skin and skin-associated surfaces and generated with two commonly used universal prokaryotic primer sets to assess archaeal prevalence, relative abundance, and taxonomic distribution. Archaeal 16S rRNA gene sequences were detected in only 17.5% of 1,688 samples by high-throughput sequence data, with most of the archaeon-positive samples associated with nonhuman mammalian skin. Only 5.9% of human-associated skin sample data sets contained sequences affiliated with archaeal 16S rRNA genes. When detected, the relative abundance of sequences affiliated with archaeal amplicon sequence variants (ASVs) was less than 1% for most mammalian skin samples and did not exceed 2% for any samples. Although several computer keyboard microbial profiles were dominated by Nitrososphaeria sequences, all other skin microbiome data sets tested were primarily composed of sequences affiliated with Methanobacteriota and Halobacteriota phyla. Our findings revise downward recent estimates of human skin archaeal distributions and relative abundances, especially those affiliated with the Nitrososphaeria, reflecting a limited and infrequent archaeal presence within the mammalian skin microbiome. IMPORTANCE The current state of research on mammalian skin-associated archaea is limited, with the few papers focusing on potential skin archaeal communities often in disagreement with each other. As such, there is no consensus on the prevalence or taxonomic composition of archaea on mammalian skin. Mammalian skin health is in part influenced by its complex microbiota and consortium of bacteria and potential archaea. Without a clear foundational analysis and characterization of the mammalian skin archaeome, it will be difficult for future research to explore the potential impact of skin-associated archaea on skin health and function. The current work provides a much-needed analysis of the mammalian skin archaeome and contributes to building a foundation from which further discussion and exploration of the skin archaeome might continue.},
}

@article {pmid34282937,
year = {2021},
author = {Patel, S and Vlasblom, AA and Verstappen, KM and Zomer, AL and Fluit, AC and Rogers, MRC and Wagenaar, JA and Claesson, MJ and Duim, B},
title = {Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0015221},
doi = {10.1128/mSystems.00152-21},
pmid = {34282937},
issn = {2379-5077},
abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) is an important human pathogen and often colonizes pigs. To lower the risk of MRSA transmission to humans, a reduction of MRSA prevalence and/or load in pig farms is needed. The nasal microbiome contains commensal species that may protect against MRSA colonization and may be used to develop competitive exclusion strategies. To obtain a comprehensive understanding of the species that compete with MRSA in the developing porcine nasal microbiome, and the moment of MRSA colonization, we analyzed nasal swabs from piglets in two litters. The swabs were taken longitudinally, starting directly after birth until 6 weeks. Both 16S rRNA and tuf gene sequencing data with different phylogenetic resolutions and complementary culture-based and quantitative real-time PCR (qPCR)-based MRSA quantification data were collected. We employed a compositionally aware bioinformatics approach (CoDaSeq + rmcorr) for analysis of longitudinal measurements of the nasal microbiota. The richness and diversity in the developing nasal microbiota increased over time, albeit with a reduction of Firmicutes and Actinobacteria, and an increase of Proteobacteria. Coabundant groups (CAGs) of species showing strong positive and negative correlation with colonization of MRSA and S. aureus were identified. Combining 16S rRNA and tuf gene sequencing provided greater Staphylococcus species resolution, which is necessary to inform strategies with potential protective effects against MRSA colonization in pigs. IMPORTANCE The large reservoir of methicillin-resistant Staphylococcus aureus (MRSA) in pig farms imposes a significant zoonotic risk. An effective strategy to reduce MRSA colonization in pig farms is competitive exclusion whereby MRSA colonization can be reduced by the action of competing bacterial species. We complemented 16S rRNA gene sequencing with Staphylococcus-specific tuf gene sequencing to identify species anticorrelating with MRSA colonization. This approach allowed us to elucidate microbiome dynamics and identify species that are negatively and positively associated with MRSA, potentially suggesting a route for its competitive exclusion.},
}

@article {pmid34282936,
year = {2021},
author = {Madill, MBW and Luo, Y and Sampara, P and Ziels, RM},
title = {Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0071221},
doi = {10.1128/mSystems.00712-21},
pmid = {34282936},
issn = {2379-5077},
abstract = {Managing and engineering activated sludge wastewater treatment microbiomes for low-energy nitrogen removal requires process control strategies to stop the oxidation of ammonium at nitrite. Our ability to out-select nitrite-oxidizing bacteria (NOB) from activated sludge is challenged by their metabolic and physiological diversity, warranting measurements of their in situ physiology and activity under selective growth pressures. Here, we examined the stability of nitrite oxidation in activated sludge during a press disturbance induced by treating a portion of return activated sludge with a sidestream flow containing free ammonia (FA) at 200 mg NH3-N/liter. The nitrite accumulation ratio peaked at 42% by day 40 in the experimental bioreactor with the press disturbance, while it did not increase in the control bioreactor. A subsequent decrease in nitrite accumulation within the experimental bioreactor coincided with shifts in dominant Nitrospira 16S rRNA amplicon sequence variants (ASVs). We applied bioorthogonal noncanonical amino acid tagging (BONCAT) coupled with fluorescence-activated cell sorting (FACS) to investigate changes in the translational activity of NOB populations throughout batch exposure to FA. BONCAT-FACS confirmed that the single Nitrospira ASV washed out of the experimental bioreactor had reduced translational activity following exposure to FA, whereas the two Nitrospira ASVs that emerged after process acclimation were not impacted by FA. Thus, the coexistence of functionally degenerate and physiologically resistant Nitrospira populations provided resilience to the nitrite-oxidizing function during the press disturbance. These results highlight how BONCAT-FACS can resolve ecological niche differentiation within activated sludge and inform strategies to engineer and control microbiome function. IMPORTANCE Nitrogen removal from activated sludge wastewater treatment systems is an energy-intensive process due to the large aeration requirement for nitrification. This energy footprint could be minimized with engineering control strategies that wash out nitrite-oxidizing bacteria (NOB) to limit oxygen demands. However, NOB populations can have a high degree of physiological diversity, and it is currently difficult to decipher the behavior of individual taxa during applied selective pressures. Here, we utilized a new substrate analog probing approach to measure the activity of NOB at the cellular translational level in the face of a press disturbance applied to the activated sludge process. Substrate analog probing corroborated the time series reactor sampling, showing that coexisting and functionally degenerate Nitrospira populations provided resilience to the nitrite oxidation process. Taken together, these results highlight how substrate analog approaches can illuminate in situ ecophysiologies within shared niches, and can inform strategies to improve microbiome engineering and management.},
}

@article {pmid34282935,
year = {2021},
author = {Wang, X and Howe, S and Wei, X and Deng, F and Tsai, T and Chai, J and Xiao, Y and Yang, H and Maxwell, CV and Li, Y and Zhao, J},
title = {Comprehensive Cultivation of the Swine Gut Microbiome Reveals High Bacterial Diversity and Guides Bacterial Isolation in Pigs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0047721},
doi = {10.1128/mSystems.00477-21},
pmid = {34282935},
issn = {2379-5077},
abstract = {Despite the substantial progress made in human gut culturomics, little is known about the culturability of the swine gut microbiota. In this study, we cultured swine gut microbiota using 53 bacterial cultivation methods with different medium and gas combinations from three pigs at four different growth stages. Both culture-dependent (CD; colony mixtures from each method) and culture-independent (CI; original fecal suspensions) samples were subjected to 16S rRNA gene amplicon sequencing. Increasing microbial diversities were observed in both CI and CD samples from successive growth stages. While a total of 378, 482, 565, and 555 bacterial amplicon sequence variants (ASVs) were observed in the CI samples, higher microbial diversities (415, 675, 808, and 823 observed ASVs) were detected using the CD methods at the lactation, nursery, growing, and finishing stages, respectively. We constructed reference culture maps showing the preferred cultivation conditions for specific bacterial taxa and examined the effects of culturing factors such as oxygen, medium, donor pig age, antibiotics, and blood culture preincubation on swine gut microbiota cultivation. We focused on a wide range of beneficial bacteria, chose 1,299 colonies based on the reference map, and Sanger sequenced their 16S rRNA genes. These isolates clustered into 148 different bacterial taxa covering 28 genera. We observed 11, 19, 33, and 25 pairs of cooccurring ASVs in both CD and CI samples at four successive growth stages. This study provides guidance in culturing the swine gut microbiota of interest, which is critical when characterizing their functions in this important animal species. IMPORTANCE The swine gut microbiome has been the focus of many investigations due to the fact that pigs serve as both an excellent biomedical model for human diseases and an important protein source. Substantial progress has been made in swine gut microbiome studies using next-generation sequencing-based culture-independent approaches, but little is known about the culturability of the swine gut microbiota. To understand their roles in swine production, it is critical to culture bacterial strains of interest. In this study, we cultured the gut microbiota from pigs at different growth stages using 53 bacterial cultivation methods with different medium and gas combinations. This study provides evidence that the swine gut microbiota is much more diverse based on a culture-dependent approach than previously known. It provides preliminary guidance for isolating certain bacteria of interest from pigs, which is critical in establishing causal relationships between the gut microbiota and the health status of pigs.},
}

@article {pmid34282934,
year = {2021},
author = {Fan, W and Kan, H and Liu, HY and Wang, TL and He, YN and Zhang, M and Li, YX and Li, YJ and Meng, W and Li, Q and Hu, AQ and Zheng, YJ},
title = {Association between Human Genetic Variants and the Vaginal Bacteriome of Pregnant Women.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0015821},
doi = {10.1128/mSystems.00158-21},
pmid = {34282934},
issn = {2379-5077},
abstract = {The influence of human genetic variants on the vaginal bacterial traits (VBTs) of pregnant women is still unknown. Using a genome-wide association approach based on the 16S rRNA bacteriome analysis, a total of 72 host genetic variant (single nucleotide polymorphisms [SNPs], indels, or copy number variations [CNVs])-VBT associations were found that reached the genome-wide significance level (P < 5 × 10-8) with an acceptable genomic inflation factor λ of <1.1. The majority of these SNPs that reached the genome-wide significance level had a relatively low minor allele frequency (MAF), and only seven of them had MAFs greater than 0.05. rs303212, located at the IFIT1 gene on chromosome 10, was the most eye-catching variant, which had a genome-wide association with the relative abundance (RAB) of Actinobacteria and Bifidobacteriaceae and also had a suggestive association with the RAB of a few common vaginal bacteria including Actinobacteriota, Firmicutes, Lactobacillus, and Gardnerella vaginalis and the beta diversity weighted UniFrac (P < 1 × 10-5). The findings of the study suggest that the vaginal bacteriome may be influenced by a number of genetic variants across the human genome and that interferon signaling may have an important influence on vaginal bacterial communities during pregnancy. IMPORTANCE Knowledge about the influence of host genetics on the vaginal bacteriome in pregnancy is still limited. Although a number of environmental and behavioral factors may exert influences on the structure of vaginal bacterial communities, the vaginal bacteriome often undergoes a relatively fixed transition to a more stable and less diverse state as the menstrual cycle stops, which raises questions on the effects of human genetics. We utilized a genome-wide approach to identify the associations between genetic variants and multiple VBTs and performed enrichment analyses. The human genetics during pregnancy may be involved in multiple pathways. The results may disclose innate functional factors involved in shaping the vaginal bacteriome during pregnancy and provide insight into the establishment of specific strategies for prevention and clinical treatment of pregnancy complications.},
}

@article {pmid34282932,
year = {2021},
author = {Brubaker, L and Gourdine, JF and Siddiqui, NY and Holland, A and Halverson, T and Limeria, R and Pride, D and Ackerman, L and Forster, CS and Jacobs, KM and Thomas-White, KJ and Putonti, C and Dong, Q and Weinstein, M and Lukacz, ES and Karstens, L and Wolfe, AJ},
title = {Forming Consensus To Advance Urobiome Research.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0137120},
doi = {10.1128/mSystems.01371-20},
pmid = {34282932},
issn = {2379-5077},
abstract = {Urobiome research has the potential to advance the understanding of a wide range of diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early research method consensus to facilitate the greater, common good. This consensus document, developed by a group of expert investigators currently engaged in urobiome research (UROBIOME 2020 conference participants), aims to promote standardization and advances in this field by the adoption of common core research practices. We propose a standardized nomenclature as well as considerations for specimen collection, preservation, storage, and processing. Best practices for urobiome study design include our proposal for standard metadata elements as part of core metadata collection. Although it is impractical to follow fixed analytical procedures when analyzing urobiome data, we propose guidelines to document and report data originating from urobiome studies. We offer this first consensus document with every expectation of subsequent revision as our field progresses.},
}

@article {pmid34282804,
year = {2021},
author = {Alberti, G and Mazzola, M and Gagliardo, C and Pitruzzella, A and Fucarini, A and Giammanco, M and Tomasello, G and Carini, F},
title = {Extracellular vesicles derived from gut microbiota in inflammatory bowel disease and colorectal cancer: new players?.},
journal = {Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia},
volume = {},
number = {},
pages = {},
doi = {10.5507/bp.2021.042},
pmid = {34282804},
issn = {1213-8118},
abstract = {The human gut microbiome encompasses inter alia, the myriad bacterial species that create the optimal host-microorganism balance essential for normal metabolic and immune function. Various lines of evidence suggest that dysregulation of the microbiota-host interaction is linked to pathologies such as inflammatory bowel disease (IBD) and colorectal cancer (CRC). Extracellular vesicles (EVs), found in virtually all body fluids and produced by both eukaryotic cells and bacteria are involved in cell-cell communication and crosstalk mechanisms, such as the immune response, barrier function and intestinal flora. This review highlights advancements in knowledge of the functional role that EVs may have in IBD and CRC, and discusses the possible use of EVs derived from intestinal microbiota in therapeutic strategies for treating these conditions.},
}

@article {pmid34282636,
year = {2021},
author = {Peng, K and Chen, K and Teply, BA and Yee, GC and Farazi, PA and Lyden, ER},
title = {Impact of Proton Pump Inhibitor Use on the Effectiveness of Immune Checkpoint Inhibitors in Advanced Cancer Patients.},
journal = {The Annals of pharmacotherapy},
volume = {},
number = {},
pages = {10600280211033938},
doi = {10.1177/10600280211033938},
pmid = {34282636},
issn = {1542-6270},
abstract = {BACKGROUND: The gut microbiome plays a critical role in modulating the therapeutic effect of immune checkpoint inhibitors (ICIs). Proton pump inhibitors (PPIs) are commonly used in cancer patients and may affect the gut microbiome by altering gut pH.

OBJECTIVE: To evaluate if concurrent use of PPI is associated with overall survival (OS) and progression-free survival (PFS) in patients with stage IV non-small-cell lung cancer (NSCLC), melanoma, renal cell carcinoma, transitional cell carcinoma, or head and neck squamous cell carcinoma.

METHODS: This was a single-center retrospective cohort study of advanced cancer adult patients who received nivolumab or pembrolizumab between September 1, 2014, and August 31, 2019. Concomitant PPI exposure was defined as PPI use 0 to 30 days before or after initiation of ICIs. Treatment outcome was OS and PFS.

RESULTS: A total of 233 patients were included in our study. Concomitant PPI use was not significantly associated with OS (hazard ratio [HR] = 1.22; 95% CI = 0.80-1.86) or PFS (HR = 1.05; 95% CI = 0.76-1.45) in patients with ICI use. The effect estimates were robust after adjusting for covariates in multivariate analysis and in patients with NSCLC.

CONCLUSION AND RELEVANCE: Concomitant PPI use was not associated with the effectiveness of nivolumab or pembrolizumab. Certain predictors of survival outcomes related to PPI use in patients receiving immunotherapy, such as the time window and indication of PPI exposure and autoimmune disorders, should be explored in the future to better carve out the impact of PPI on the effectiveness of ICI use.},
}

@article {pmid34282606,
year = {2021},
author = {Choi, SJ and Kim, Y and Jeon, J and Gwak, HJ and Kim, M and Kang, K and Kim, Y and Jeong, J and Jung, YK and Lee, KG and Choi, HS and Jung, DH and Lee, SG and Lee, Y and Shin, SJ and Jang, K and Rho, M and Choi, D},
title = {Association of Microbial Dysbiosis with Gallbladder Diseases Identified by Bile Microbiome Profiling.},
journal = {Journal of Korean medical science},
volume = {36},
number = {28},
pages = {e189},
doi = {10.3346/jkms.2021.36.e189},
pmid = {34282606},
issn = {1598-6357},
support = {NRF-2014R1A1A1005144/NRF/National Research Foundation of Korea/Korea ; NRF-2021M3E5D1A01015177/NRF/National Research Foundation of Korea/Korea ; },
abstract = {BACKGROUND: Cholecystitis is an important risk factor for gallbladder cancer, but the bile microbiome and its association with gallbladder disease has not been investigated fully. We aimed to analyze the bile microbiome in normal conditions, chronic cholecystitis, and gallbladder cancer, and to identify candidate bacteria that play an important role in gallbladder carcinogenesis.

METHODS: We performed metagenome sequencing on bile samples of 10 healthy individuals, 10 patients with chronic cholecystitis, and 5 patients with gallbladder cancer, and compared the clinical, radiological, and pathological characteristics of the participants.

RESULTS: No significant bacterial signal was identified in the normal bile. The predominant dysbiotic bacteria in both chronic cholecystitis and gallbladder cancer were those belonging to the Enterobacteriaceae family. Klebsiella increased significantly in the order of normal, chronic cholecystitis, and gallbladder cancer. Patients with chronic cholecystitis and dysbiotic microbiome patterns had larger gallstones and showed marked epithelial atypia, which are considered as precancerous conditions.

CONCLUSION: We investigated the bile microbiome in normal, chronic cholecystitis, and gallbladder cancer. We suggest possible roles of Enterobacteriaceae, including Klebsiella, in gallbladder carcinogenesis. Our findings reveal a possible link between a dysbiotic bile microbiome and the development of chronic calculous cholecystitis and gallbladder cancer.},
}

@article {pmid34282477,
year = {2021},
author = {Martins, J and Veríssimo, P and Canhoto, J},
title = {Isolation and identification of Arbutus unedo L. fungi endophytes and biological control of Phytophthora cinnamomi in vitro.},
journal = {Protoplasma},
volume = {},
number = {},
pages = {},
pmid = {34282477},
issn = {1615-6102},
support = {SFRH/BD/122478/2016 PhD Scholarship//Fundação para a Ciência e a Tecnologia/ ; CENTRO-01-0145-FEDER-000007//Projecto ReNATURE/ ; CENTRO-08-5864-FSE-000031//F4F Forest for Future/ ; CENTRO-01-0145-FEDER-000020//Projecto Cultivar/ ; UIDB/04539/2020//Center for Neuroscience and Cell Biology (CNC)/ ; UIDB/04004/2020//Centre for Functional Ecology/ ; },
abstract = {Strawberry tree (Arbutus unedo, Ericaceae) is an evergreen tree with a circum-Mediterranean distribution. It has a great ecological and economic importance as a source of bioactive compounds with industrial applications and for fruit production. This study aims to characterize the fungi microbiome of this forestry species in order to develop biological control strategies in the increasing orchard production area. For this purpose, fungi endophytes were isolated from wild strawberry tree plants, and a molecular identification was carried out. In vitro assays were carried out to evaluate and characterize the antagonism of some endophytes. Among the several fungi endophytes isolated from strawberry tree (a total of 53 from 20 genera), a Trichoderma atroviride strain proved to have antagonism effect against several phytopathogens, including Alternaria alternata, Botrytis cinerea, Glomerella cingulata, and Mycosphaerella aurantia. This antagonism was particularly effective against Phytophthora cinnamomi, causing a reduction in growth of about 80% on this invasive oomycete. An enzymatic assay revealed the production of several enzymes by T. atroviride, such as cellulases, chitinases, glucosidases, alkaline phosphatases, and proteases, which is one of the several mechanisms known to be involved on Trichoderma biological control ability. The enzymatic activity, in particular that of cell wall-degrading enzymes, was accentuated when in a dual culture with P. cinnamomi. The production of serine proteases, aspartyl proteases, metalloproteases, and cysteine proteases was also detected in an experiment carried out in liquid medium, suggesting the involvement of these proteases on Trichoderma mycoparasitism mechanisms. Finally, in a three-way interaction with in vitro strawberry tree plants, the T. atroviride strain identified on this study (Au50) was able to protect the plants against P. cinnamomi, thus proving its potential as a biological control agent.},
}

@article {pmid34282338,
year = {2021},
author = {Vogl, T and Klompus, S and Leviatan, S and Kalka, IN and Weinberger, A and Wijmenga, C and Fu, J and Zhernakova, A and Weersma, RK and Segal, E},
title = {Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {34282338},
issn = {1546-170X},
support = {J 4256//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; CVON grant 2018-27//Royal Netherlands Academy of Arts and Sciences | ICIN Netherlands Heart Institute (Interuniversity Cardiology Institute Netherlands-Netherlands Heart Institute)/ ; },
abstract = {Serum antibodies can recognize both pathogens and commensal gut microbiota. However, our current understanding of antibody repertoires is largely based on DNA sequencing of the corresponding B-cell receptor genes, and actual bacterial antigen targets remain incompletely characterized. Here we have profiled the serum antibody responses of 997 healthy individuals against 244,000 rationally selected peptide antigens derived from gut microbiota and pathogenic and probiotic bacteria. Leveraging phage immunoprecipitation sequencing (PhIP-Seq) based on phage-displayed synthetic oligo libraries, we detect a wide breadth of individual-specific as well as shared antibody responses against microbiota that associate with age and gender. We also demonstrate that these antibody epitope repertoires are more longitudinally stable than gut microbiome species abundances. Serum samples of more than 200 individuals collected five years apart could be accurately matched and could serve as an immunologic fingerprint. Overall, our results suggest that systemic antibody responses provide a non-redundant layer of information about microbiota beyond gut microbial species composition.},
}

@article {pmid34282239,
year = {2021},
author = {Al Bataineh, MT and Dash, NR and Bel Lassen, P and Banimfreg, BH and Nada, AM and Belda, E and Clément, K},
title = {Author Correction: Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15102},
doi = {10.1038/s41598-021-94439-3},
pmid = {34282239},
issn = {2045-2322},
}

@article {pmid34281627,
year = {2021},
author = {Hui, Y and Tamez-Hidalgo, P and Cieplak, T and Satessa, GD and Kot, W and Kjærulff, S and Nielsen, MO and Nielsen, DS and Krych, L},
title = {Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets.},
journal = {Journal of animal science and biotechnology},
volume = {12},
number = {1},
pages = {85},
pmid = {34281627},
issn = {1674-9782},
support = {No 720755 (Macro Cascade project)//Bio-Based Industries Joint Undertaking under the European Union Horizon 2020 research and innovation program/ ; No 720755 (Macro Cascade project)//Bio-Based Industries Joint Undertaking under the European Union Horizon 2020 research and innovation program/ ; No 720755 (Macro Cascade project)//Bio-Based Industries Joint Undertaking under the European Union Horizon 2020 research and innovation program/ ; No. 5157-00003B (PhD grant)//The Innovation Fund Denmark/ ; No. 201706350028//Chinese Government Scholarship/ ; },
abstract = {BACKGROUND: The direct use of medical zinc oxide in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders.

RESULTS: This study investigated the effect of using rapeseed-seaweed blend (rapeseed meal added two brown macroalgae species Ascophylum nodosum and Saccharina latissima) fermented by lactobacilli (FRS) as feed ingredients in piglet weaning. From d 28 of life to d 85, the piglets were fed one of three different feeding regimens (n = 230 each) with inclusion of 0%, 2.5% and 5% FRS. In this period, no significant difference of piglet performance was found among the three groups. From a subset of piglets (n = 10 from each treatment), blood samples for hematology, biochemistry and immunoglobulin analysis, colon digesta for microbiome analysis, and jejunum and colon tissues for histopathological analyses were collected. The piglets fed with 2.5% FRS manifested alleviated intraepithelial and stromal lymphocytes infiltration in the gut, enhanced colon mucosa barrier relative to the 0% FRS group. The colon microbiota composition was determined using V3 and V1-V8 region 16S rRNA gene amplicon sequencing by Illumina NextSeq and Oxford Nanopore MinION, respectively. The two amplicon sequencing strategies showed high consistency between the detected bacteria. Both sequencing strategies indicated that inclusion of FRS reshaped the colon microbiome of weaned piglets with increased Shannon diversity. Prevotella stercorea was verified by both methods to be more abundant in the piglets supplied with FRS feed, and its abundance was positively correlated with colonic mucosa thickness but negatively correlated with blood concentrations of leucocytes and IgG.

CONCLUSIONS: FRS supplementation relieved the gut lymphocyte infiltration of the weaned piglets, improved the colon mucosa barrier with altered microbiota composition. Increasing the dietary inclusion of FRS from 2.5% to 5% did not lead to further improvements.},
}

@article {pmid34281401,
year = {2021},
author = {Chu, ND and Crothers, JW and Nguyen, LTT and Kearney, SM and Smith, MB and Kassam, Z and Collins, C and Xavier, R and Moses, PL and Alm, EJ},
title = {Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease.},
journal = {mBio},
volume = {},
number = {},
pages = {e0097521},
doi = {10.1128/mBio.00975-21},
pmid = {34281401},
issn = {2150-7511},
abstract = {For fecal microbiota transplantation (FMT) to be successful in immune diseases like inflammatory bowel disease, it is assumed that therapeutic microbes and their beneficial functions and immune interactions must colonize a recipient patient and persist in sufficient quantity and for a sufficient period of time to produce a clinical benefit. Few studies, however, have comprehensively profiled the colonization and persistence of transferred microbes along with the transfer of their microbial functions and interactions with the host immune system. Using 16S, metagenomic, and immunoglobulin A (IgA) sequencing, we analyzed hundreds of longitudinal microbiome samples from a randomized controlled trial of 12 patients with ulcerative colitis who received fecal transplant or placebo for 12 weeks. We uncovered diverse competitive dynamics among donor and patient strains, showing that persistence of transferred microbes is far from static. Indeed, one patient experienced a dramatic loss of donor bacteria 10 weeks into the trial, coinciding with a bloom of pathogenic bacteria and worsening symptoms. We evaluated the transfer of microbial functions, including desired ones, such as butyrate production, and unintended ones, such as antibiotic resistance. By profiling bacteria coated with IgA, we identified bacteria associated with inflammation and found that microbial interactions with the host immune system can be transferred across people, which could play a role in gut microbiome therapeutics for immune-related diseases. Our findings shed light on the colonization dynamics of gut microbes and their functions in the context of FMT to treat a complex disease-information that may provide a foundation for developing more-targeted therapeutics. IMPORTANCE Fecal microbiota transplantation (FMT)-transferring fecal microbes from a healthy donor to a sick patient-has shown promise for gut diseases such as inflammatory bowel disease. Unlike pharmaceuticals, however, fecal transplants are complex mixtures of living organisms, which must then interact with the microbes and immune system of the recipient. We sought to understand these interactions by tracking the microbes of 12 inflammatory bowel disease patients who received fecal transplants for 12 weeks. We uncovered a range of dynamics. For example, one patient experienced successful transfer of donor bacteria, only to lose them after 10 weeks. We similarly evaluated transfer of microbial functions, including how they interacted with the recipient's immune system. Our findings shed light on the colonization dynamics of gut microbes, as well as their functions in the context of FMT-information that may provide a critical foundation for the development of more-targeted therapeutics.},
}

@article {pmid34281388,
year = {2021},
author = {Hersch, SJ and Lam, L and Dong, TG},
title = {Engineered Type Six Secretion Systems Deliver Active Exogenous Effectors and Cre Recombinase.},
journal = {mBio},
volume = {},
number = {},
pages = {e0111521},
doi = {10.1128/mBio.01115-21},
pmid = {34281388},
issn = {2150-7511},
abstract = {Genetic editing has revolutionized biotechnology, but delivery of endonuclease genes as DNA can lead to aberrant integration or overexpression, leading to off-target effects. Here, we develop a mechanism to deliver Cre recombinase as a protein by engineering the bacterial type six secretion system (T6SS). Using multiple T6SS fusion proteins, Aeromonas dhakensis or attenuated Vibrio cholerae donor strains, and a gain-of-function cassette for detecting Cre recombination, we demonstrate successful delivery of active Cre directly into recipient cells. The most efficient transfer was achieved using a truncated version of PAAR2 from V. cholerae, resulting in a relatively small (118-amino-acid) delivery tag. We further demonstrate the versatility of this system by delivering an exogenous effector, TseC, enabling V. cholerae to kill Pseudomonas aeruginosa. This implies that P. aeruginosa is naturally resistant to all native effectors of V. cholerae and that the TseC chaperone protein is not required for its activity. Moreover, it demonstrates that the engineered system can improve T6SS efficacy against specific pathogens, proposing future application in microbiome manipulation or as a next-generation antimicrobial. Inexpensive and easy to produce, this protein delivery system has many potential applications, ranging from studying T6SS effectors to genetic editing. IMPORTANCE Delivery of protein-based drugs, antigens, and gene-editing agents has broad applications. The type VI protein secretion system (T6SS) can target both bacteria and eukaryotic cells and deliver proteins of diverse size and function. Here, we harness the T6SS to successfully deliver Cre recombinase to genetically edit bacteria without requiring the introduction of exogenous DNA into the recipient cells. This demonstrates a promising advantage over current genetic editing tools that require transformation or conjugation of DNA. The engineered secretion tag can also deliver a heterologous antimicrobial toxin that kills an otherwise unsusceptible pathogen, Pseudomonas aeruginosa. These results demonstrate the potential of T6SS-mediated delivery in areas including genome editing, killing drug-resistant pathogens, and studying toxin functions.},
}

@article {pmid34281323,
year = {2021},
author = {Gargiulo Isacco, C and Inchingolo, AD and Nguyen Cao, KD and Malcangi, G and Paduanelli, G and Pham Hung, V and Tran Cong, T and Bordea, IR and Scarano, A and Laforgia, A and Marinelli, G and Limongelli, L and Inchingolo, F and Lorusso, F and Inchingolo, AM and Dipalma, G},
title = {The bad relationship, osteo-decay and diabetes type 2 searching for a link: a literature review.},
journal = {Journal of biological regulators and homeostatic agents},
volume = {35},
number = {2 Suppl. 1},
pages = {253-269},
doi = {10.23812/21-2supp1-26},
pmid = {34281323},
issn = {0393-974X},
abstract = {The diabetes and osteoporotic metabolic diseases are characterized by a wide prevalence of the population worldwide and correlated to alteration of the bone tissues. Several cofactors could influence the clinical course and the biochemistry of the pathologies such as human microbiome, nutrition characteristics, gut microbiota activity and interactions with vitamin K and D across IGF/GH and TP53 signaling pathways and the glucose/energy as mechanism for bone tissue health. Moreover, also the calories and sugar consumption seem to be correlated to an increased inflammatory state with several consequences for hematopoiesis and host tissues response. The aim of the present literature review was to highlight the role of osteoporotic diseases and diabetes type 2 link for the bone metabolism. The literature cases showed that a correlation between bone-gut-kidney-heart-CNS-Immunity crosstalk seems to be linked with bone metabolism and health regulation. Moreover, also the aging process could represent a valuable co-factor for the sustaining of the metabolic disorders upon a multi-systemic level.},
}

@article {pmid34280840,
year = {2021},
author = {Gao, H and Wan, X and Xiao, B and Yang, K and Wang, Y and Zhang, C and Li, P and Liu, L and Xia, T and Wang, A and Zhang, S},
title = {Impacts of PBDE-47 exposure before, during and after pregnancy on the maternal gut microbiome and its association with host metabolism.},
journal = {Ecotoxicology and environmental safety},
volume = {222},
number = {},
pages = {112530},
doi = {10.1016/j.ecoenv.2021.112530},
pmid = {34280840},
issn = {1090-2414},
abstract = {Maternal gut microbiota play an important role in the modulation of offspring disease susceptibility and gut microbiota dysbiosis has been proposed as a mechanism through which toxic environmental chemicals exert their adverse impacts on health. The brominated flame retardants polybrominated diphenyl ethers (PBDEs) are developmental toxicants and induce dysbiotic gut microbiota in offspring. Yet, whether and how PBDEs impact the maternal gut microbiota remain unclear. Here, we sought to investigate the effect of 2,2',4,4'-tetrabromodiphenyl ether (PBDE-47) exposure from preconception through lactation cessation on maternal gut microbiota and its link to host serum metabolic consequences. Female Sprague-Dawley rats were daily exposed to 10 mg/kg PBDE-47 via oral gavage from ten days before conception until offspring were weaned on postnatal day 21, then maternal fecal and blood samples were collected for microbiome and metabolome analyses by using 16S ribosomal RNA gene sequencing and gas chromatography-mass spectrometry, respectively. Maternal exposure to PBDE-47 showed a distinct profile in gut microbiota compared to control dams, as evidenced by increased Actinobacteria phylum and genera Blautia, Gemella and Phascolarctobacterium, and decreased genera AF12 and Oscillospira. Additionally, global metabolomics analysis identified 26 differential serum metabolites to distinguish PBDE-47 from controls, which were mainly involved in amino acid, lipid, carbohydrate and energy metabolism, further confirmed by pathway analysis. Importantly, the differential serum metabolites are closely correlated with the disturbed gut microbiota in response to PBDE-47. Collectively, our results suggest that maternal gut microbial dysbiosis may serve as a potential mechanism underlying PBDE-47-elicited health hazards to mothers or even offspring.},
}

@article {pmid34280807,
year = {2021},
author = {De Vrieze, J and Heyer, R and Props, R and Van Meulebroek, L and Gille, K and Vanhaecke, L and Benndorf, D and Boon, N},
title = {Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles.},
journal = {Water research},
volume = {202},
number = {},
pages = {117422},
doi = {10.1016/j.watres.2021.117422},
pmid = {34280807},
issn = {1879-2448},
abstract = {The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.},
}

@article {pmid34280721,
year = {2021},
author = {Fan, H and Wu, S and Dong, W and Li, X and Dong, Y and Wang, S and Zhu, YG and Zhuang, X},
title = {Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H218O-based DNA-Stable isotope probing and metagenomics.},
journal = {Journal of hazardous materials},
volume = {420},
number = {},
pages = {126440},
doi = {10.1016/j.jhazmat.2021.126440},
pmid = {34280721},
issn = {1873-3336},
abstract = {The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H218O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.},
}

@article {pmid34280650,
year = {2021},
author = {Wu, Y and Zhang, H and Zhang, R and Cao, G and Li, Q and Zhang, B and Wang, Y and Yang, C},
title = {Serum metabolome and gut microbiome alterations in broiler chickens supplemented with lauric acid.},
journal = {Poultry science},
volume = {100},
number = {9},
pages = {101315},
doi = {10.1016/j.psj.2021.101315},
pmid = {34280650},
issn = {1525-3171},
abstract = {Antibiotic overuse in poultry husbandry poses a potential threat to meat safety and human health. Lauric acid (LA) is a primary medium-chain fatty acid (MCFA) with a strong antibacterial capacity. The goal of this study was to evaluate the beneficial effects of LA on the growth performance, immune responses, serum metabolism, and cecal microbiota of broiler chickens. One-day-old male Ross 308 broilers were randomly divided into 4 groups: CON, fed a basal diet; ANT, a basal diet supplemented with 75 mg/kg antibiotic; LA500, a basal diet supplemented with 500 mg/kg LA; LA1000, a basal diet supplemented with 1000 mg/kg LA. The feeding period was 42 d. The results showed that LA significantly improved broiler growth and immune functions, as evidenced by increased body weight (BW) and average daily gain (ADG), enhanced intestinal mucosal barrier, upregulated immunoglobulins (IgA, IgM, and IgY), and downregulated inflammatory cytokines (IL-1β, IL-6, TNF-α, IL-4, and IL-10) (P < 0.05). HPLC/MS-based metabolome analysis revealed that the serum metabolites in the LA group differed from those of CON and ANT groups. LA markedly decreased the abundance of phosphatidylcholines (PCs), increased lysophosphatidylcholines (LysoPCs), and inhibited the sphingolipid metabolism pathway, indicating its capacity to modulate lipid metabolism. 16S rRNA sequencing indicated that LA significantly altered cecal microbiota composition by reducing Phascolarctobacterium, Christensenellaceae_R-7_group, and Bacteroides, and increasing Faecalibacterium and Ruminococcaceae_UCG-014 (P < 0.05). Furthermore, Spearman correlation analysis revealed that changes in metabolism and microbiota were highly correlated with the growth and immune indices; strong links were also found between lipid metabolism and microbial composition. Taken together, LA promotes broiler growth and immune functions by regulating lipid metabolism and gut microbiota. The above findings highlight the substantial potential of LA as a supplement in poultry diets and provide a new strategy to reduce antibiotic usage and improve food safety.},
}

@article {pmid34280643,
year = {2021},
author = {Emami, NK and Dalloul, RA},
title = {Centennial Review: Recent developments in host-pathogen interactions during necrotic enteritis in poultry.},
journal = {Poultry science},
volume = {100},
number = {9},
pages = {101330},
doi = {10.1016/j.psj.2021.101330},
pmid = {34280643},
issn = {1525-3171},
abstract = {Necrotic enteritis (NE) is a significant enteric disease in commercial poultry with considerable economic effect on profitability manifested by an estimated $6 billion in annual losses to the global industry. NE presents a unique challenge, being a complex enteric disease that often leads to either clinical (acute) or subclinical (chronic) form. The latter typically results in poor performance (reduced feed intake, weight gain and eventually higher feed conversion ratio [FCR]) with low mortality rates, and represents the greatest economic impact on poultry production. The use of antibiotic growth promoters (AGPs) has been an effective tool in protecting birds from enteric diseases by maintaining enteric health and modifying gut microbiota, thus improving broilers' production efficiency and overall health. The removal of AGPs presented the poultry industry with several challenges, including reduced bird health and immunity as well as questioning the safety of poultry products. Consequently, research on antibiotic alternatives that can support gut health was intensified. Probiotics, prebiotics, essential oils, and organic acids were among various additives that have been tested for their efficacy against NE with some being effective but not to the level of AGPs. The focus of this review is on the relationship between NE pathogenesis, microbiome, and host immune responses, along with references to recent reviews addressing production aspects of NE. With a comprehensive understanding of these dynamic changes, new and programmed strategies could be developed to make use of the current products more effectively or build a stepping stone toward the development of a new generation of supplements.},
}

@article {pmid34280500,
year = {2021},
author = {Zhu, S and Li, X and Song, L and Huang, Y and Xiao, Y and Chu, Q and Kang, Y and Duan, S and Wu, D and Ren, Z},
title = {Stachyose inhibits vancomycin-resistant Enterococcus colonization and affects gut microbiota in mice.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {105094},
doi = {10.1016/j.micpath.2021.105094},
pmid = {34280500},
issn = {1096-1208},
abstract = {Vancomycin-resistant Enterococcus (VRE) caused nosocomial infections are rising globally. Multiple measures have been investigated to address this issue, altering gut microbiota through dietary intervention represents one of such effort. Stachyose can promote probiotic growth, which makes it a good candidate for potentially inhibiting VRE infection. This study aimed to determine whether stachyose inhibits VRE colonization and investigated the involvement of gut microbiota this effect of stachyose. In VRE-infection experiment, 6-week old female C57/6 J mice pre-treated with vancomycin were infected with 2 × 108 CFU VRE via gavage. These mice then received oral administration of stachyose or PBS as control for 7days. Two groups of uninfected mice were also received daily gavage of stachyose or PBS for 7 days to observe the impact of stachyose treatment on normal mice. Fresh fecal and colon samples were collected, then VRE colonization, gut microbiota and gene expression were respectively assessed using cultivation, 16s rRNA sequencing and RNA-sequencing in two parallel experiment, respectively. In VRE-infected mice, stachyose treatment significantly reduced VRE colonization on days 9 and 10 post-infection. Stachyose treatment increased the relative abundance of Porphyromonadaceae, Parabacteroides, and Parabacteroides distasonis compared to the PBS-treated infection mice (P < 0.01). Uninfected mice treated with stachyose showed a significant increase in Lactobacillaceae and Lactobacillus compared to the PBS-treated uninfected mice(P < 0.05). RNA-sequencing results showed that stachyose treatment in VRE-infected mice increased expression of genes involved in TNF and IL-17 signaling pathways. Stachyose treatment also up-regulated Hsd17b14, Cyp3a44, Arg1, and down-regulated Pnliprp2, Ces1c, Pla2g4c genes involving in metabolic pathway in uninfected mice. In conclusion, stachyose supplementation can effectively inhibit VRE colonization and probably altering composition of the microbiome, which can in turn result in changes in expression of genes. Stachyose may also benefit health by increasing the abundance of Lactobacillus and expression of genes involving in metabolic pathway in normal mice.},
}

@article {pmid34280457,
year = {2021},
author = {Hantsoo, L and Zemel, BS},
title = {Stress Gets into the Belly: Early Life Stress and the Gut Microbiome.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {113474},
doi = {10.1016/j.bbr.2021.113474},
pmid = {34280457},
issn = {1872-7549},
abstract = {Research has established that stress "gets under the skin," impacting neuroendocrine and neuroimmune pathways to influence risk for physical and mental health outcomes. These effects can be particularly significant for early life stress (ELS), or adverse childhood experiences (ACEs). In this review, we explore whether stress gets "into the belly," that is, whether psychosocial stress affects the gut microbiome. We review animal and human research utilizing a variety of stress paradigms (acute laboratory stressors, chronic stress, stressful life events, perceived stress, ELS, in utero stress) and their impacts on the gut microbiota, with a particular focus on ELS. We also review data on dietary interventions to moderate impact of stress on the gut microbiome. Our review suggests strong evidence that acute laboratory stress, chronic stress, and ELS affect the gut microbiota in rodents, and growing evidence that perceived stress and ELS may impact the gut microbiota in humans. Emerging data also suggests, particularly in rodents, that dietary interventions such as omega-3 fatty acids and pre- and pro-biotics may buffer against the effects of stress on the gut microbiome, but more research is needed. In sum, growing evidence suggests that stress impacts not only the neuroendocrine and neuroimmune axes, but also the microbiota-gut-brain-axis, providing a pathway by which stress may get "into the belly" to influence health risk.},
}

@article {pmid34280073,
year = {2021},
author = {Fernandez-Cantos, MV and Garcia-Morena, D and Iannone, V and El-Nezami, H and Kolehmainen, M and Kuipers, OP},
title = {Role of microbiota and related metabolites in gastrointestinal tract barrier function in NAFLD.},
journal = {Tissue barriers},
volume = {},
number = {},
pages = {1879719},
doi = {10.1080/21688370.2021.1879719},
pmid = {34280073},
issn = {2168-8370},
abstract = {The Gastrointestinal (GI) tract is composed of four main barriers: microbiological, chemical, physical and immunological. These barriers play important roles in maintaining GI tract homeostasis. In the crosstalk between these barriers, microbiota and related metabolites have been shown to influence GI tract barrier integrity, and alterations of the gut microbiome might lead to an increase in intestinal permeability. As a consequence, translocation of bacteria and their products into the circulatory system increases, reaching proximal and distal tissues, such as the liver. One of the most prevalent chronic liver diseases, Nonalcoholic Fatty Liver Disease (NAFLD), has been associated with an altered gut microbiota and barrier integrity. However, the causal link between them has not been fully elucidated yet. In this review, we aim to highlight relevant bacterial taxa and their related metabolites affecting the GI tract barriers in the context of NAFLD, discussing their implications in gut homeostasis and in disease.},
}

@article {pmid34280051,
year = {2021},
author = {Lau, TC and Fiebig-Comyn, AA and Shaler, CR and McPhee, JB and Coombes, BK and Schertzer, JD},
title = {Low dietary fiber promotes enteric expansion of a Crohn's disease-associated pathobiont independent of obesity.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00134.2021},
pmid = {34280051},
issn = {1522-1555},
support = {FDN-154295//Gouvernement du Canada | Canadian Institutes of Health Research (CIHR)/ ; MOP-136968//Gouvernement du Canada | Canadian Institutes of Health Research (CIHR)/ ; PJ4-175368//Crohn's and Colitis Canada (Crohn et Colite Canada)/ ; },
abstract = {Obesity is associated with metabolic, immunological, and infectious disease comorbidities, including an increased risk of enteric infection and inflammatory bowel disease such as Crohn's disease (CD). Expansion of intestinal pathobionts such as adherent-invasive Escherichia coli (AIEC) is a common dysbiotic feature of CD, which is amplified by prior use of oral antibiotics. Although high-fat, high-sugar diets are associated with dysbiotic expansion of E. coli, it is unknown if the content of fat or another dietary component in obesogenic diets is sufficient to promote AIEC expansion. Here, we found that administration of an antibiotic combined with feeding mice an obesogenic low fiber, high sucrose, high fat diet (HFD) that is typically used in rodent obesity studies promoted AIEC intestinal expansion. Even a short-term (i.e., 1-day) pulse of HFD feeding before infection was sufficient to promote AIEC expansion, indicating that the magnitude of obesity was not the main driver of AIEC expansion. Controlled diet experiments demonstrated that neither dietary fat nor sugar were the key determinants of AIEC colonization, but that lowering dietary fiber from approximately 13% to 5-6% was sufficient to promote intestinal expansion of AIEC when combined with antibiotics in mice. When combined with antibiotics, lowering fiber promoted AIEC intestinal expansion to a similar extent as widely used HFDs in mice. However, lowering dietary fiber was sufficient to promote AIEC intestinal expansion without affecting body mass. Our results show that low dietary fiber combined with oral antibiotics are environmental factors that promote expansion of Crohn's disease-associated pathobionts in the gut.},
}

@article {pmid34280036,
year = {2021},
author = {Raffatellu, M and Bäumler, AJ},
title = {Special Collection on the Microbiome and Infection.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {IAI0035621},
doi = {10.1128/IAI.00356-21},
pmid = {34280036},
issn = {1098-5522},
abstract = {Few recent developments in the biological sciences have been as profound or impactful as the budding field of microbiome research.….},
}

@article {pmid34280003,
year = {2021},
author = {Abdul-Rahim, O and Wu, Q and Price, TK and Pistone, G and Diebel, K and Bugni, TS and Wolfe, AJ},
title = {Phenyl-lactic acid is an active ingredientin bactericidal supernatants of Lactobacillus crispatus.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {JB0036021},
doi = {10.1128/JB.00360-21},
pmid = {34280003},
issn = {1098-5530},
abstract = {Lactobacillus crispatus is a well-established probiotic, with antimicrobial activity against pathogens across several niches of the human body generally attributed to the production of bacteriostatic molecules, including hydrogen peroxide and lactic acid. Here, we show that the cell-free supernatants of clinical isolates of L. crispatus harbor robust bactericidal activity. We further identify phenyl-lactic acid as a bactericidal compound with properties and susceptibility range near-identical to that of the cell-free supernatant. As such, we hypothesize that phenyl-lactic acid is a key active ingredient in L. crispatus supernatant. IMPORTANCE Although Lactobacillus crispatus is an established commensal microbe frequently used in probiotics, its protective role in the bladder microbiome has not been clarified. We report here that some urinary isolates of L. crispatus exhibit bactericidal activity, primarily due to its ability to excrete phenyl-lactic acid into its environment. Both cell free supernatants of L. crispatus isolates and phenyl-lactic acid exhibit bactericidal activity against a wide range of pathogens, including several that are resistant to multiple antibiotics.},
}

@article {pmid34279746,
year = {2021},
author = {Yue, Q and Cai, M and Xiao, B and Zhan, Q and Zeng, C},
title = {The Microbiota-Gut-Brain Axis and Epilepsy.},
journal = {Cellular and molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {34279746},
issn = {1573-6830},
support = {81601140//the national natural science foundation of china, china/ ; 81501130//the national natural science foundation of china, china/ ; 2020JJ5843//natural science foundation of hunan province, china/ ; },
abstract = {Honoured as the second genome in humans, the gut microbiota is involved in a constellation of physiological and pathological processes, including those related to the central nervous system. The communication between the gut microbiota and the brain is realized by a complex bidirectional connection, known as the "microbiota-gut-brain axis", via neuroendocrine, immunological, and direct neural mechanisms. Recent studies indicate that gut dysfunction/dysbiosis is presumably involved in the pathogenesis of and susceptibility to epilepsy. In addition, the reconstruction of the intestinal microbiome through, for example, faecal microbiota transplantation, probiotic intervention, and a ketogenic diet, has exhibited beneficial effects on drug-resistant epilepsy. The purposes of this review are to provide a brief overview of the microbiota-gut-brain axis and to synthesize what is known about the involvement of the gut microbiota in the pathogenesis and treatment of epilepsy, to bring new insight into the pathophysiology of epilepsy and to present a preliminary discussion of novel therapeutic options for epilepsy based on the gut microbiota.},
}

@article {pmid34279560,
year = {2021},
author = {Butler, AM and Durkin, MJ and Keller, MR and Ma, Y and Powderly, WG and Olsen, MA},
title = {Association of Adverse Events with Antibiotic Treatment for Urinary Tract Infection.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciab637},
pmid = {34279560},
issn = {1537-6591},
abstract = {BACKGROUND: Little is known about the relative harms of different antibiotic regimens prescribed to treat uncomplicated urinary tract infection (UTI). We sought to compare the risk of adverse events associated with commonly-used oral antibiotic regimens for the outpatient treatment of uncomplicated UTI.

METHODS: We identified 1,169,033 otherwise healthy, non-pregnant women aged 18-44 years with uncomplicated UTI who initiated an oral antibiotic with activity against common uropathogens from July 1, 2006 to September 30, 2015. We used propensity score-weighted Kaplan-Meier methods and Cox proportional hazards regression models to estimate the association between antibiotic agent and adverse events.

RESULTS: Of two first-line agents, TMP/SMX (versus nitrofurantoin) was associated with higher risk of several adverse drug events including hypersensitivity reaction (hazard ratio [HR] 2.62, 95% CI 2.30-2.98), acute renal failure (HR 2.56, 95% CI 1.55-4.25), skin rash (HR 2.42, 95% CI 2.13-2.75), urticaria (HR 1.37, 95% CI 1.19-1.57), abdominal pain (HR 1.14, 95% CI 1.09-1.19), and nausea / vomiting (HR 1.18, 95% CI 1.10-1.28), but similar risk of potential microbiome-related adverse events. Compared to nitrofurantoin, non-first-line agents were associated with higher risk of several adverse drug events and potential microbiome-related adverse events including non-C. difficile diarrhea, C. difficile infection, vaginitis / vulvovaginal candidiasis, and pneumonia. Treatment duration modified the risk of potential microbiome-related adverse events.

CONCLUSIONS: The risks of adverse drug events and potential microbiome-related events differ widely by antibiotic agent and duration. These findings underscore the utility of using real-world data to fill evidentiary gaps related to antibiotic safety.},
}

@article {pmid34279176,
year = {2021},
author = {Dunn, KA and Forbrigger, Z and Connors, J and Rahman, M and Cohen, A and Van Limbergen, J and Langille, MGI and Stadnyk, AW and Bielawski, JP and Penny, SL and MacDonald, T and Kulkarni, K},
title = {Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia.},
journal = {Leukemia & lymphoma},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/10428194.2021.1953006},
pmid = {34279176},
issn = {1029-2403},
abstract = {Treatment of pediatric acute lymphoblastic leukemia (ALL) with pegaspargase exploits ALL cells dependency on asparagine. Pegaspargase depletes asparagine, consequentially affecting aspartate, glutamine and glutamate. The gut as a confounding source of these amino acids (AAs) and the role of gut microbiome metabolism of AAs has not been examined. We examined asparagine, aspartate, glutamine and glutamate in stool samples from patients over pegaspargase treatment. Microbial gene-products, which interact with these AAs were identified. Stool asparagine declined significantly, and 31 microbial genes changed over treatment. Changes were complex, and included genes involved in AA metabolism, nutrient sensing, and pathways increased in cancers. While we identified changes in a gene (iaaA) with limited asparaginase activity, it lacked significance after correction leaving open other mechanisms for asparagine decline, possibly including loss from gut to blood. Understanding pathways that change AA availability, including by microbes in the gut, could be useful in optimizing pegaspargase therapy.},
}

@article {pmid34278648,
year = {2021},
author = {Zakrzewski, M and Gannon, OM and Panizza, BJ and Saunders, NA and Antonsson, A},
title = {Human papillomavirus infection and tumor microenvironment are associated with the microbiota in patients with oropharyngeal cancers-pilot study.},
journal = {Head & neck},
volume = {},
number = {},
pages = {},
doi = {10.1002/hed.26821},
pmid = {34278648},
issn = {1097-0347},
support = {//Australian Infectious Disease Research Centre/ ; },
abstract = {BACKGROUND: Previous microbiome studies of oropharyngeal cancer have shown that there are differences in the oral microbiota between human papillomavirus (HPV)-positive and HPV-negative patients.

METHODS: We collected saliva, normal tissue, and tumor biopsies from 13 patients with oropharyngeal cancer (eight HPV-positive, five HPV-negative). We obtained basic clinical data from each patient. Extracted DNA was 16S rRNA gene sequenced. Analysis was based on HPV status and sample site using univariate, multivariate, and mixed effect regression methods.

RESULTS: Multivariate analysis methods separated samples based on HPV status (Adonis, p < 0.001). Comparison of patients showed that there were significant changes in microbial richness across all sites based on HPV status (linear mixed effects regression, p = 0.0002).

CONCLUSIONS: We found significant differences in overall microbial community and bacterial richness between oropharyngeal patients based on HPV status. Our results suggest that there are significant differences in the microbiome in patients with oropharyngeal cancer based on HPV status.},
}

@article {pmid34278392,
year = {2021},
author = {Fu, X and Yuan, Q and Zhu, X and Li, Y and Meng, Y and Hashim, JH and Hashim, Z and Ali, F and Zheng, YW and Lai, XX and Spangfort, MD and Wen, H and Wang, L and Deng, F and Hu, Q and Norbäck, D and Sun, Y},
title = {Associations between the indoor microbiome, environmental characteristics and respiratory infections in junior high school students of Johor Bahru, Malaysia.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d1em00115a},
pmid = {34278392},
issn = {2050-7895},
abstract = {Pathogens are commonly present in the human respiratory tract, but symptoms are varied among individuals. The interactions between pathogens, commensal microorganisms and host immune systems are important in shaping the susceptibility, development and severity of respiratory diseases. Compared to the extensive studies on the human microbiota, few studies reported the association between indoor microbiome exposure and respiratory infections. In this study, 308 students from 21 classrooms were randomly selected to survey the occurrence of respiratory infections in junior high schools of Johor Bahru, Malaysia. Vacuum dust was collected from the floor, chairs and desks of these classrooms, and high-throughput amplicon sequencing (16S rRNA and ITS) and quantitative PCR were conducted to characterize the absolute concentration of the indoor microorganisms. Fifteen bacterial genera in the classes Actinobacteria, Alphaproteobacteria, and Cyanobacteria were protectively associated with respiratory infections (p < 0.01), and these bacteria were mainly derived from the outdoor environment. Previous studies also reported that outdoor environmental bacteria were protectively associated with chronic respiratory diseases, such as asthma, but the genera identified were different between acute and chronic respiratory diseases. Four fungal genera from Ascomycota, including Devriesia, Endocarpon, Sarcinomyces and an unclassified genus from Herpotrichillaceae, were protectively associated with respiratory infections (p < 0.01). House dust mite (HDM) allergens and outdoor NO2 concentration were associated with respiratory infections and infection-related microorganisms. A causal mediation analysis revealed that the health effects of HDM and NO2 were partially or fully mediated by the indoor microorganisms. This is the first study to explore the association between environmental characteristics, microbiome exposure and respiratory infections in a public indoor environment, expanding our understanding of the complex interactions among these factors.},
}

@article {pmid34278304,
year = {2020},
author = {Petrick, HL and Foley, KP and Zlitni, S and Brunetta, HS and Paglialunga, S and Miotto, PM and Politis-Barber, V and O'Dwyer, C and Philbrick, DJ and Fullerton, MD and Schertzer, JD and Holloway, GP},
title = {Adipose Tissue Inflammation Is Directly Linked to Obesity-Induced Insulin Resistance, while Gut Dysbiosis and Mitochondrial Dysfunction Are Not Required.},
journal = {Function (Oxford, England)},
volume = {1},
number = {2},
pages = {zqaa013},
doi = {10.1093/function/zqaa013},
pmid = {34278304},
issn = {2633-8823},
abstract = {Obesity is associated with adipose tissue hypertrophy, systemic inflammation, mitochondrial dysfunction, and intestinal dysbiosis. Rodent models of high-fat diet (HFD)-feeding or genetic deletion of multifunctional proteins involved in immunity and metabolism are often used to probe the etiology of obesity; however, these models make it difficult to divorce the effects of obesity, diet composition, or immunity on endocrine regulation of blood glucose. We, therefore, investigated the importance of adipose inflammation, mitochondrial dysfunction, and gut dysbiosis for obesity-induced insulin resistance using a spontaneously obese mouse model. We examined metabolic changes in skeletal muscle, adipose tissue, liver, the intestinal microbiome, and whole-body glucose control in spontaneously hyperphagic C57Bl/6J mice compared to lean littermates. A separate subset of lean and obese mice was subject to 8 weeks of obesogenic HFD feeding, or to pair feeding of a standard rodent diet. Hyperphagia, obesity, adipose inflammation, and insulin resistance were present in obese mice despite consuming a standard rodent diet, and these effects were blunted with caloric restriction. However, hyperphagic obese mice had normal mitochondrial respiratory function in all tissues tested and no discernable intestinal dysbiosis relative to lean littermates. In contrast, feeding mice an obesogenic HFD altered the composition of the gut microbiome, impaired skeletal muscle mitochondrial bioenergetics, and promoted poor glucose control. These data show that adipose inflammation and redox stress occurred in all models of obesity, but gut dysbiosis and mitochondrial respiratory dysfunction are not always required for obesity-induced insulin resistance. Rather, changes in the intestinal microbiome and mitochondrial bioenergetics may reflect physiological consequences of HFD feeding.},
}

@article {pmid34278148,
year = {2021},
author = {Suresh, AP and Kalarikkal, SP and Pullareddy, B and Sundaram, GM},
title = {Low pH-Based Method to Increase the Yield of Plant-Derived Nanoparticles from Fresh Ginger Rhizomes.},
journal = {ACS omega},
volume = {6},
number = {27},
pages = {17635-17641},
doi = {10.1021/acsomega.1c02162},
pmid = {34278148},
issn = {2470-1343},
abstract = {Plant-derived nanoparticles (PDNPs) are naturally occurring exosome-like nanovesicles derived from dietary plants containing key plant bioactives. Ginger-derived PDNPs have a therapeutic effect on alcohol-induced liver injury, inflammatory bowel disease, and colon cancer. PDNPs are conventionally purified by differential ultracentrifugation, a technique not amenable for scale up. We have recently developed a polyethylene glycol (PEG) 6000-based method for cost-effective purification of ginger PDNPs, with comparable efficiency to differential ultracentrifugation (Sci. Rep. 2020, 10 (1), 4456.). Herein, we report a 4-5-fold higher ginger PDNP recovery when PEG precipitation was carried out in low pH conditions (pH 4 and 5). Low pH-derived ginger PDNPs were smaller in size without an overt change in zeta potential. The spontaneous intracellular entry and protection against oxidative stress in A431 cells were similar between ginger PDNPs purified under low, neutral, and alkaline pH. Low-pH purified ginger PDNPs had higher levels of total polyphenolic content compared to PDNPs purified under neutral and alkaline pH. Recently, ginger PDNP-derived microRNAs have been shown to exhibit cross-kingdom regulation by targeting human, gut microbiome, and viral transcripts. Using qRT-PCR, we also verified the presence of miRNAs that were predicted to target SARS-CoV-2 in ginger PDNPs purified under low pH. Thus, we have developed a method to purify ginger PDNPs in high yields by using low-pH conditions without affecting the major bioactive contents of PDNPs.},
}

@article {pmid34278055,
year = {2019},
author = {Di Guglielmo, MD and Franke, K and Cox, C and Crowgey, EL},
title = {Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort.},
journal = {Human microbiome journal},
volume = {12},
number = {},
pages = {},
doi = {10.1016/j.humic.2019.100057},
pmid = {34278055},
issn = {2452-2317},
abstract = {Background: Advancements in sequencing capabilities have enhanced the study of the human microbiome. There are limited studies focused on the gastro-intestinal (gut) microbiome of infants, particularly the impact of diet between breast-fed (BF) versus formula-fed (FF). It is unclear what effect, if any, early feeding has on short-term or long-term composition and function of the gut microbiome.

Results: Using a shotgun metagenomics approach, differences in the gut microbiome between BF (n = 10) and FF (n = 5) infants were detected. A Jaccard distance principle coordinate analysis was able to cluster BF versus FF infants based on the presence or absence of species identified in their gut microbiome. Thirty-two genera were identified as statistically different in the gut microbiome sequenced between BF and FF infants. Furthermore, the computational workflow identified 371 bacterial genes that were statistically different between the BF and FF cohorts in abundance. Only seven genes were lower in abundance (or absent) in the FF cohort compared to the BF cohort, including CRISPR/Cas9; whereas, the remaining candidates, including autotransporter adhesins, were higher in abundance in the FF cohort compared to BF cohort.

Conclusions: These studies demonstrated that FF infants have, at an early age, a significantly different gut microbiome with potential implications for function of the fecal microbiota. Interactions between the fecal microbiota and host hinted at here have been linked to numerous diseases. Determining whether these non-abundant or more abundant genes have biological consequence related to infant feeding may aid in understanding the adult gut microbiome, and the pathogenesis of obesity.},
}

@article {pmid34277834,
year = {2021},
author = {Naqash, AR and Kihn-Alarcón, AJ and Stavraka, C and Kerrigan, K and Maleki Vareki, S and Pinato, DJ and Puri, S},
title = {The role of gut microbiome in modulating response to immune checkpoint inhibitor therapy in cancer.},
journal = {Annals of translational medicine},
volume = {9},
number = {12},
pages = {1034},
doi = {10.21037/atm-20-6427},
pmid = {34277834},
issn = {2305-5839},
abstract = {Immunotherapy has led to a paradigm shift in the treatment of several cancers. There have been significant efforts to identify biomarkers that can predict response and toxicities related to immune checkpoint inhibitor (ICPI) therapy. Despite these advances, it has been challenging to tease out why a subset of patients benefit more than others or why certain patients experience immune-related adverse events (irAEs). Although the immune-modulating properties of the human gut bacterial ecosystem are yet to be fully elucidated, there has been growing interest in evaluating the role of the gut microbiome in shaping the therapeutic response to cancer immunotherapy. Considerable research efforts are currently directed to utilizing metagenomic and metabolic profiling of stool microbiota in patients on ICPI-based therapies. Dysbiosis or loss of microbial diversity has been associated with a poor treatment response to ICPIs and worse survival outcomes in cancer patients. Emerging data have shown that certain bacterial strains, such as Faecalibacterium that confer sensitivity to ICPI, also have a higher propensity to increase the risk of irAEs. Additionally, the microbiome can modulate the local immune response at the intestinal interface and influence the trafficking of bacterial peptide primed T-cells distally, influencing the toxicity patterns to ICPI. Antibiotic or diet induced alterations in composition of the microbiome can also indirectly alter the production of certain bacterial metabolites such as deoxycholate and short chain fatty acids that can influence the anti-tumor tolerogenesis. Gaining sufficient understanding of the exact mechanisms underpinning the interplay between ICPI induced anti-tumor immunity and the immune modulatory role gut microbiome can be vital in identifying potential avenues of improving outcomes to cancer immunotherapy. In the current review, we have summarized and highlighted the key emerging data supporting the role of gut microbiome in regulating response to ICPIs in cancer.},
}

@article {pmid34277753,
year = {2021},
author = {Guo, L and Zhang, D and Fu, S and Zhang, J and Zhang, X and He, J and Peng, C and Zhang, Y and Qiu, Y and Ye, C and Liu, Y and Wu, Z and Hu, CA},
title = {Metagenomic Sequencing Analysis of the Effects of Colistin Sulfate on the Pig Gut Microbiome.},
journal = {Frontiers in veterinary science},
volume = {8},
number = {},
pages = {663820},
doi = {10.3389/fvets.2021.663820},
pmid = {34277753},
issn = {2297-1769},
abstract = {The gut microbiome plays important roles in maintaining host health, and inappropriate use of antibiotics can cause imbalance, which may contribute to serious disease. However, despite its promise, using metagenomic sequencing to explore the effects of colistin on gut microbiome composition in pig has not been reported. Herein, we evaluated the roles of colistin in gut microbiome modulation in pigs. Metagenomic analysis demonstrated that overall microbial diversity was higher in the colistin group compared with the control group. Antibiotic Resistance Genes Database analysis demonstrated that following colistin treatment, expression levels of tsnr, ant6ia, tetq, oleb, norm, ant3ia, and mexh were significantly upregulated, indicating that colistin may induce transformation of antibiotic resistance genes. Colistin also affected the microbiome distribution patterns at both genus and phylum levels. In addition, at the species level, colistin significantly reduced the abundance of Prevotella copri, Phascolarctobacterium succinatutens, and Prevotella stercorea and enhanced the abundance of Treponema succinifaciens and Acidaminococcus fermentans compared to the control group. Gene Ontology analysis demonstrated that following treatment with colistin, metabolic process, cellular process, and single-organism process were the dominant affected terms. Kyoto Encyclopedia of Genes and Genomes analysis showed that oxidative phosphorylation, protein processing in endoplasmic reticulum, various types of N-glycan biosynthesis, protein processing in endoplasmic reticulum, pathogenic Escherichia coli infection, and mitogen-activated protein kinase signaling pathway-yeast were the dominant signaling pathways in the colistin group. Overall, our results suggested that colistin affects microbial diversity and may modulate gut microbiome composition in pig, potentially providing novel strategy or antibiotic rationalization pertinent to human and animal health.},
}

@article {pmid34277679,
year = {2021},
author = {Lu, CS and Chang, HC and Weng, YH and Chen, CC and Kuo, YS and Tsai, YC},
title = {The Add-On Effect of Lactobacillus plantarum PS128 in Patients With Parkinson's Disease: A Pilot Study.},
journal = {Frontiers in nutrition},
volume = {8},
number = {},
pages = {650053},
doi = {10.3389/fnut.2021.650053},
pmid = {34277679},
issn = {2296-861X},
abstract = {Background: Lactobacillus plantarum PS128 (PS128) is a specific probiotic, known as a psychobiotic, which has been demonstrated to alleviate motor deficits and inhibit neurodegenerative processes in Parkinson's disease (PD)-model mice. We hypothesize that it may also be beneficial to patients with PD based on the possible mechanism via the microbiome-gut-brain axis. Methods: This is an open-label, single-arm, baseline-controlled trial. The eligible participants were scheduled to take 60 billion colony-forming units of PS128 once per night for 12 weeks. Clinical assessments were conducted using the Unified Parkinson's Disease Rating Scale (UPDRS), modified Hoehn and Yahr scale, and change in patient "ON-OFF" diary recording as primary outcome measures. The non-motor symptoms questionnaire, Beck depression inventory-II, patient assessment of constipation symptom, 39-item Parkinson's Disease Questionnaire (PDQ-39), and Patient Global Impression of Change (PGI-C) were assessed as secondary outcome measures. Results: Twenty-five eligible patients (32% women) completed the study. The mean age was 61.84 ± 5.74 years (range, 52-72), mean disease duration was 10.12 ± 2.3 years (range, 5-14), and levodopa equivalent daily dosage was 1063.4 ± 209.5 mg/daily (range, 675-1,560). All patients remained on the same dosage of anti-parkinsonian and other drugs throughout the study. After 12 weeks of PS128 supplementation, the UPDRS motor scores improved significantly in both the OFF and ON states (p = 0.004 and p = 0.007, respectively). In addition, PS128 intervention significantly improved the duration of the ON period and OFF period as well as PDQ-39 values. However, no obvious effect of PS128 on non-motor symptoms of patients with PD was observed. Notably, the PGI-C scores improved in 17 patients (68%). PS128 intervention was also found to significantly reduce plasma myeloperoxidase and urine creatinine levels. Conclusion: The present study demonstrated that PS128 supplementation for 12 weeks with constant anti-parkinsonian medication improved the UPDRS motor score and quality of life of PD patients. We suggest that PS128 could serve as a therapeutic adjuvant for the treatment of PD. In the future, placebo-controlled studies are needed to further support the efficacy of PS128 supplementation. Clinical Trial Registration: https://clinicaltrials.gov/, identifier: NCT04389762.},
}

@article {pmid34277527,
year = {2021},
author = {Larroya, A and Pantoja, J and Codoñer-Franch, P and Cenit, MC},
title = {Towards Tailored Gut Microbiome-Based and Dietary Interventions for Promoting the Development and Maintenance of a Healthy Brain.},
journal = {Frontiers in pediatrics},
volume = {9},
number = {},
pages = {705859},
doi = {10.3389/fped.2021.705859},
pmid = {34277527},
issn = {2296-2360},
abstract = {Mental health is determined by a complex interplay between the Neurological Exposome and the Human Genome. Multiple genetic and non-genetic (exposome) factors interact early in life, modulating the risk of developing the most common complex neurodevelopmental disorders (NDDs), with potential long-term consequences on health. To date, the understating of the precise etiology underpinning these neurological alterations, and their clinical management pose a challenge. The crucial role played by diet and gut microbiota in brain development and functioning would indicate that modulating the gut-brain axis may help protect against the onset and progression of mental-health disorders. Some nutritional deficiencies and gut microbiota alterations have been linked to NDDs, suggesting their potential pathogenic implications. In addition, certain dietary interventions have emerged as promising alternatives or adjuvant strategies for improving the management of particular NDDs, at least in particular subsets of subjects. The gut microbiota can be a key to mediating the effects of other exposome factors such as diet on mental health, and ongoing research in Psychiatry and Neuropediatrics is developing Precision Nutrition Models to classify subjects according to a diet response prediction based on specific individual features, including microbiome signatures. Here, we review current scientific evidence for the impact of early life environmental factors, including diet, on gut microbiota and neuro-development, emphasizing the potential long-term consequences on health; and also summarize the state of the art regarding the mechanisms underlying diet and gut microbiota influence on the brain-gut axis. Furthermore, we describe the evidence supporting the key role played by gut microbiota, diet and nutrition in neurodevelopment, as well as the effectiveness of certain dietary and microbiome-based interventions aimed at preventing or treating NDDs. Finally, we emphasize the need for further research to gain greater insight into the complex interplay between diet, gut microbiome and brain development. Such knowledge would help towards achieving tailored integrative treatments, including personalized nutrition.},
}

@article {pmid34277478,
year = {2021},
author = {Senn, V and Bassler, D and Choudhury, R and Scholkmann, F and Righini-Grunder, F and Vuille-Dit-Bille, RN and Restin, T},
title = {Corrigendum: Microbial Colonization From the Fetus to Early Childhood-A Comprehensive Review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {715671},
doi = {10.3389/fcimb.2021.715671},
pmid = {34277478},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2020.573735.].},
}

@article {pmid34277471,
year = {2021},
author = {Redanz, U and Redanz, S and Treerat, P and Prakasam, S and Lin, LJ and Merritt, J and Kreth, J},
title = {Differential Response of Oral Mucosal and Gingival Cells to Corynebacterium durum, Streptococcus sanguinis, and Porphyromonas gingivalis Multispecies Biofilms.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {686479},
doi = {10.3389/fcimb.2021.686479},
pmid = {34277471},
issn = {2235-2988},
abstract = {Polymicrobial interactions with oral mucosal surfaces determine the health status of the host. While a homeostatic balance provides protection from oral disease, a dysbiotic polymicrobial community promotes tissue destruction and chronic oral diseases. How polymicrobial communities transition from a homeostatic to a dysbiotic state is an understudied process. Thus, we were interested to investigate this ecological transition by focusing on biofilm communities containing high abundance commensal species and low abundance pathobionts to characterize the host-microbiome interactions occurring during oral health. To this end, a multispecies biofilm model was examined using the commensal species Corynebacterium durum and Streptococcus sanguinis and the pathobiont Porphyromonas gingivalis. We compared how both single and multispecies biofilms interact with different oral mucosal and gingival cell types, including the well-studied oral keratinocyte cell lines OKF4/TERT-1and hTERT TIGKs as well as human primary periodontal ligament cells. While single species biofilms of C. durum, S. sanguinis, and P. gingivalis are all characterized by unique cytokine responses for each species, multispecies biofilms elicited a response resembling S. sanguinis single species biofilms. One notable exception is the influence of P. gingivalis upon TNF-α and Gro-α production in hTERT TIGKs cells, which was not affected by the presence of other species. This study is also the first to examine the host response to C. durum. Interestingly, C. durum yielded no notable inflammatory responses from any of the tested host cells, suggesting it functions as a true commensal species. Conversely, S. sanguinis was able to induce expression and secretion of the proinflammatory cytokines IL-6 and IL-8, demonstrating a much greater inflammatory potential, despite being health associated. Our study also demonstrates the variability of host cell responses between different cell lines, highlighting the importance of developing relevant in vitro models to study oral microbiome-host interactions.},
}

@article {pmid34277468,
year = {2021},
author = {Xu, Y and Liu, X and Liu, X and Chen, D and Wang, M and Jiang, X and Xiong, Z},
title = {The Roles of the Gut Microbiota and Chronic Low-Grade Inflammation in Older Adults With Frailty.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {675414},
doi = {10.3389/fcimb.2021.675414},
pmid = {34277468},
issn = {2235-2988},
abstract = {Frailty is a major public issue that affects the physical health and quality of life of older adults, especially as the population ages. Chronic low-grade inflammation has been speculated to accelerate the aging process as well as the development of age-related diseases such as frailty. Intestinal homeostasis plays a crucial role in healthy aging. The interaction between the microbiome and the host regulates the inflammatory response. Emerging evidence indicates that in older adults with frailty, the diversity and composition structure of gut microbiota are altered. Age-associated changes in gut microbiota composition and in their metabolites contribute to increased gut permeability and imbalances in immune function. In this review, we aim to: identify gut microbiota changes in the aging and frail populations; summarize the role of chronic low-grade inflammation in the development of frailty; and outline how gut microbiota may be related to the pathogenesis of frailty, more specifically, in the regulation of gut-derived chronic inflammation. Although additional research is needed, the regulation of gut microbiota may represent a safe, easy, and inexpensive intervention to counteract the chronic inflammation leading to frailty.},
}

@article {pmid34277461,
year = {2021},
author = {Hu, C and Wang, P and Yang, Y and Li, J and Jiao, X and Yu, H and Wei, Y and Li, J and Qin, Y},
title = {Chronic Intermittent Hypoxia Participates in the Pathogenesis of Atherosclerosis and Perturbs the Formation of Intestinal Microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {560201},
doi = {10.3389/fcimb.2021.560201},
pmid = {34277461},
issn = {2235-2988},
abstract = {Chronic intermittent hypoxia (CIH) is the prominent signature of highly prevalent obstructive sleep apnea (OSA) pathophysiology, which leads to increased risk and aggravation of atherosclerotic cardiovascular diseases. However, whether intestinal microbiota is implicated in the mechanisms linking CIH to arteriosclerosis (AS) pathogenesis remains unclear. The association of CIH with the development of altered gut microbiota (GM) may provide the opportunity to develop preventive strategies for atherosclerotic cardiovascular risk reduction. Animal models of apolipoprotein E-deficient (apoE-/-) mice treated with high-fat diet (HFD) and subjected to CIH conditions was applied to mimic the AS observed in patients with OSA. The physiological status and atherosclerotic lesion formation were confirmed by histological analysis. 16S rDNA sequencing of fecal samples was conducted to determine the changes in gut microbial composition. Morphometric analysis demonstrated that CIH caused aggravated atherosclerotic lesions and facilitated AS in apoE-/- mice treated with HFD. The gut bacteria was significantly varied in AS and AS+CIH mice compared with that in the control mice. Significantly perturbed GM profiles were detected in AS mice with and without CIH, with altered microbial α- and β- diversity and shifts in bacterial compositions at phylum and genus levels. While the difference between AS and AS+CIH was observed at different bacteria taxa levels. Aggravation of reduced Sutterella and increased Halomonas, Halomonadaceae and Oceanospirillales was noted in CIH-treated AS mice. The correlation of intestinal bacterial parameters with pathological changes in artery indicated complicated interactions under CIH-induced GM dysbiosis. Furthermore, the gut microbial functions in the potential ability of replication recombination and repair proteins, glycan biosynthesis and metabolism, as well as metabolism of cofactors and vitamins were identified to be further suppressed by CIH. Our findings demonstrated a causal effect of CIH on GM alterations in AS mice and suggested that the disordered GM features in AS development were deteriorated by CIH, which may be associated with AS aggravation. Preventative strategies targeting gut microbiome are highly recommended for intervention of OSA-related AS.},
}

@article {pmid34277168,
year = {2021},
author = {Elsouri, K and Arboleda, V and Heiser, S and Kesselman, MM and Demory Beckler, M},
title = {Microbiome in Rheumatoid Arthritis and Celiac Disease: A Friend or Foe.},
journal = {Cureus},
volume = {13},
number = {6},
pages = {e15543},
doi = {10.7759/cureus.15543},
pmid = {34277168},
issn = {2168-8184},
abstract = {Rheumatoid arthritis (RA) and celiac disease (CD) are both autoimmune diseases with increasing global prevalence. These two diseases have been connected based on similar HLA mutations, serological markers, rheumatological, and gastrointestinal manifestations. In this review, we discuss the role of the oral and gut microbiome in the development and progression of RA and CD. Here, we highlight similar microbial dysbiosis and how these alterations in composition can lead to worsening disease severity in both CD and RA. Additionally, we analyze the role of probiotics in regulating the microbiome and improving symptoms associated with RA and CD.},
}

@article {pmid34277110,
year = {2021},
author = {Gwak, MG and Chang, SY},
title = {Gut-Brain Connection: Microbiome, Gut Barrier, and Environmental Sensors.},
journal = {Immune network},
volume = {21},
number = {3},
pages = {e20},
doi = {10.4110/in.2021.21.e20},
pmid = {34277110},
issn = {1598-2629},
abstract = {The gut is an important organ with digestive and immune regulatory function which consistently harbors microbiome ecosystem. The gut microbiome cooperates with the host to regulate the development and function of the immune, metabolic, and nervous systems. It can influence disease processes in the gut as well as extra-intestinal organs, including the brain. The gut closely connects with the central nervous system through dynamic bidirectional communication along the gut-brain axis. The connection between gut environment and brain may affect host mood and behaviors. Disruptions in microbial communities have been implicated in several neurological disorders. A link between the gut microbiota and the brain has long been described, but recent studies have started to reveal the underlying mechanism of the impact of the gut microbiota and gut barrier integrity on the brain and behavior. Here, we summarized the gut barrier environment and the 4 main gut-brain axis pathways. We focused on the important function of gut barrier on neurological diseases such as stress responses and ischemic stroke. Finally, we described the impact of representative environmental sensors generated by gut bacteria on acute neurological disease via the gut-brain axis.},
}

@article {pmid34277109,
year = {2021},
author = {Losol, P and Choi, JP and Kim, SH and Chang, YS},
title = {The Role of Upper Airway Microbiome in the Development of Adult Asthma.},
journal = {Immune network},
volume = {21},
number = {3},
pages = {e19},
doi = {10.4110/in.2021.21.e19},
pmid = {34277109},
issn = {1598-2629},
abstract = {Clinical and molecular phenotypes of asthma are complex. The main phenotypes of adult asthma are characterized by eosinophil and/or neutrophil cell dominant airway inflammation that represent distinct clinical features. Upper and lower airways constitute a unique system and their interaction shows functional complementarity. Although human upper airway contains various indigenous commensals and opportunistic pathogenic microbiome, imbalance of this interactions lead to pathogen overgrowth and increased inflammation and airway remodeling. Competition for epithelial cell attachment, different susceptibilities to host defense molecules and antimicrobial peptides, and the production of proinflammatory cytokine and pattern recognition receptors possibly determine the pattern of this inflammation. Exposure to environmental factors, including infection, air pollution, smoking is commonly associated with asthma comorbidity, severity, exacerbation and resistance to anti-microbial and steroid treatment, and these effects may also be modulated by host and microbial genetics. Administration of probiotic, antibiotic and corticosteroid treatment for asthma may modify the composition of resident microbiota and clinical features. This review summarizes the effect of some environmental factors on the upper respiratory microbiome, the interaction between host-microbiome, and potential impact of asthma treatment on the composition of the upper airway microbiome.},
}

@article {pmid34276755,
year = {2021},
author = {Vassilev, N and Malusà, E and Neri, D and Xu, X},
title = {Editorial: Plant Root Interaction With Associated Microbiomes to Improve Plant Resiliency and Crop Biodiversity.},
journal = {Frontiers in plant science},
volume = {12},
number = {},
pages = {715676},
doi = {10.3389/fpls.2021.715676},
pmid = {34276755},
issn = {1664-462X},
}

@article {pmid34276696,
year = {2021},
author = {Runge, S and Rosshart, SP},
title = {The Mammalian Metaorganism: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {702378},
doi = {10.3389/fimmu.2021.702378},
pmid = {34276696},
issn = {1664-3224},
abstract = {The field of microbiome research has developed rapidly over the past decades and has become a topic of major interest to basic, preclinical, and clinical research, the pharmaceutical industry as well as the general public. The microbiome is a complex and diverse ecosystem and defined as the collection of all host-associated microorganisms and their genes. It is acquired through vertical transmission and environmental exposure and includes microbes of all kingdoms: bacteria, archaea, prokaryotic and eukaryotic viruses, fungi, protozoa, and the meiofauna. These microorganisms co-evolved with their respective hosts over millions of years, thereby establishing a mutually beneficial, symbiotic relationship on all epithelial barriers. Thus, the microbiome plays a pivotal role in virtually every aspect of mammalian physiology, particularly in the development, homeostasis, and function of the immune system. Consequently, the combination of the host genome and the microbial genome, together referred to as the metagenome, largely drives the mammalian phenotype. So far, the majority of studies have unilaterally focused on the gastrointestinal bacterial microbiota. However, recent work illustrating the impact of viruses, fungi, and protozoa on host immunity urges us towards a holistic view of the mammalian microbiome and the appreciation for its non-bacterial kingdoms. In addition, the importance of microbiota on epithelial barriers other than the gut as well as their systemic effects via microbially-derived biologically active compounds is increasingly recognized. Here, we want to provide a brief but comprehensive overview of the most important findings and the current knowledge on how microbes of all kingdoms and microbial niches shape local and systemic immunity in health and disease.},
}

@article {pmid34276643,
year = {2021},
author = {Liu, F and Ren, T and Li, X and Zhai, Q and Xu, X and Zhang, N and Jiang, P and Niu, Y and Lv, L and Shi, G and Feng, N},
title = {Distinct Microbiomes of Gut and Saliva in Patients With Systemic Lupus Erythematous and Clinical Associations.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {626217},
doi = {10.3389/fimmu.2021.626217},
pmid = {34276643},
issn = {1664-3224},
abstract = {Alterations in the microbiome of the gut and oral cavity are involved in the etiopathogenesis of systemic lupus erythematosus (SLE). We aimed to assess whether both microbiome compositions in feces and saliva were specific in patients with SLE. A total of 35 patients with SLE, as well as sex- and age-matched asymptomatic subjects as healthy control (HC) group were recruited. Fecal swabs and saliva samples were collected from the participants. 16S ribosomal RNA gene sequencing was performed on the samples. Compared with the HC group, reduced bacterial richness and diversity were detected in the feces of patients with SLE, and increased bacterial diversity in their saliva. Both feces and saliva samples explained the cohort variation. The feces were characterized by enrichment of Lactobacillus, and depletion of an unclassified bacterium in the Ruminococcaceae family and Bifidobacterium. Lack of Bifidobacterium was observed in patients with arthritis. Akkermansia and Ruminococcus negatively correlated with the serum levels of C3. In saliva, Veillonella, Streptococcus, and Prevotella were dominant, and Bacteroides was negatively associated with disease activity. These findings can assist us to comprehensively understand the bacterial profiles of different body niches in SLE patients.},
}

@article {pmid34276639,
year = {2021},
author = {Baldewijns, S and Sillen, M and Palmans, I and Vandecruys, P and Van Dijck, P and Demuyser, L},
title = {The Role of Fatty Acid Metabolites in Vaginal Health and Disease: Application to Candidiasis.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {705779},
doi = {10.3389/fmicb.2021.705779},
pmid = {34276639},
issn = {1664-302X},
abstract = {Although the vast majority of women encounters at least one vaginal infection during their life, the amount of microbiome-related research performed in this area lags behind compared to alternative niches such as the intestinal tract. As a result, effective means of diagnosis and treatment, especially of recurrent infections, are limited. The role of the metabolome in vaginal health is largely elusive. It has been shown that lactate produced by the numerous lactobacilli present promotes health by limiting the chance of infection. Short chain fatty acids (SCFA) have been mainly linked to dysbiosis, although the causality of this relationship is still under debate. In this review, we aim to bring together information on the role of the vaginal metabolome and microbiome in infections caused by Candida. Vulvovaginal candidiasis affects near to 70% of all women at least once in their life with a significant proportion of women suffering from the recurrent variant. We assess the role of fatty acid metabolites, mainly SCFA and lactate, in onset of infection and virulence of the fungal pathogen. In addition, we pinpoint where lack of research limits our understanding of the molecular processes involved and restricts the possibility of developing novel treatment strategies.},
}

@article {pmid34276594,
year = {2021},
author = {Del Frari, G and Ferreira, RB},
title = {Microbial Blends: Terminology Overview and Introduction of the Neologism "Skopobiota".},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {659592},
doi = {10.3389/fmicb.2021.659592},
pmid = {34276594},
issn = {1664-302X},
}

@article {pmid34276581,
year = {2021},
author = {Diamond, E and Hewlett, K and Penumutchu, S and Belenky, A and Belenky, P},
title = {Coffee Consumption Modulates Amoxicillin-Induced Dysbiosis in the Murine Gut Microbiome.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {637282},
doi = {10.3389/fmicb.2021.637282},
pmid = {34276581},
issn = {1664-302X},
abstract = {The microbiome is essential for host health, and perturbations resulting from antibiotic use can lead to dysbiosis and disease. Diet can be a powerful modulator of microbiome composition and function, with the potential to mitigate the negative effects of antibiotic use. Thus, it is necessary to study the impacts of diet and drug interactions on the gut microbiome. Coffee is a commonly consumed beverage containing many compounds that have the potential to affect the microbiome, including caffeine, polyphenols, and fiber. We supplemented mice with caffeinated and decaffeinated coffee in conjunction with amoxicillin, and used 16S rRNA amplicon sequencing of fecal samples to investigate changes in diversity and composition of the murine fecal microbiome. We found that antibiotics, regardless of coffee supplementation, caused significant disruption to the murine fecal microbiome, enriching for Proteobacteria, Verrucomicrobia, and Bacteroidetes, but reducing Firmicutes. While we found that coffee alone did not have a significant impact on the composition of the fecal microbiome, coffee supplementation did significantly affect relative abundance metrics in mice treated with amoxicillin. After caffeinated coffee supplementation, mice treated with amoxicillin showed a smaller increase in Proteobacteria, specifically of the family Burkholderiaceae. Correspondingly we found that in vitro, Burkholderia cepacia was highly resistant to amoxicillin, and that it was inhibited by concentrations of caffeine and caffeinated coffee comparable to levels of caffeine in murine ceca. Overall, this work shows that coffee, and possibly the caffeine component, can impact both the microbiome and microbiome members during antibiotic exposure.},
}

@article {pmid34276580,
year = {2021},
author = {Gorokhova, E and Motiei, A and El-Shehawy, R},
title = {Understanding Biofilm Formation in Ecotoxicological Assays With Natural and Anthropogenic Particulates.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {632947},
doi = {10.3389/fmicb.2021.632947},
pmid = {34276580},
issn = {1664-302X},
abstract = {Fossil-made polymers harbor unique bacterial assemblages, and concerns have been raised that ingested microplastic may affect the consumer gut microbiota and spread pathogens in animal populations. We hypothesized that in an ecotoxicity assay with a mixture of polystyrene (PS) and clay: (1) microbiome of the test animals inoculates the system with bacteria; (2) relative contribution of PS and the total amount of suspended solids (SS) select for specific bacterial communities; and (3) particle aggregation is affected by biofilm community composition, with concomitant effects on the animal survival. Mixtures of PS and clay at different concentrations of SS (10, 100, and 1000 mg/L) with a varying microplastics contribution (%PS; 0-80%) were incubated with Daphnia magna, whose microbiome served as an inoculum for the biofilms during the exposure. After 4-days of exposure, we examined the biofilm communities by 16S rRNA gene sequencing, particle size distribution, and animal survival. The biofilm communities were significantly different from the Daphnia microbiota used to inoculate the system, with an overrepresentation of predatory, rare, and potentially pathogenic taxa in the biofilms. The biofilm diversity was stimulated by %PS and decreased by predatory bacteria. Particle aggregate size and the biofilm composition were the primary drivers of animal survival, with small particles and predatory bacteria associated with a higher death rate. Thus, in effect studies with solid waste materials, ecological interactions in the biofilm can affect particle aggregation and support potentially harmful microorganisms with concomitant effects on the test animals.},
}

@article {pmid34276574,
year = {2021},
author = {Battey, JND and Szostak, J and Phillips, B and Teng, C and Tung, CK and Lim, WT and Yeo, YS and Ouadi, S and Baumer, K and Thomas, J and Martinis, J and Sierro, N and Ivanov, NV and Vanscheeuwijck, P and Peitsch, MC and Hoeng, J},
title = {Impact of 6-Month Exposure to Aerosols From Potential Modified Risk Tobacco Products Relative to Cigarette Smoke on the Rodent Gastrointestinal Tract.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {587745},
doi = {10.3389/fmicb.2021.587745},
pmid = {34276574},
issn = {1664-302X},
abstract = {Cigarette smoking causes adverse health effects that might occur shortly after smoking initiation and lead to the development of inflammation and cardiorespiratory disease. Emerging studies have demonstrated the role of the intestinal microbiome in disease pathogenesis. The intestinal microbiome is susceptible to the influence of environmental factors such as smoking, and recent studies have indicated microbiome changes in smokers. Candidate modified risk tobacco products (CMRTP) are being developed to provide substitute products to lower smoking-related health risks in smokers who are unable or unwilling to quit. In this study, the ApoE-/- mouse model was used to investigate the impact of cigarette smoke (CS) from the reference cigarette 3R4F and aerosols from two CMRTPs based on the heat-not-burn principle [carbon-heated tobacco product 1.2 (CHTP 1.2) and tobacco heating system 2.2 (THS 2.2)] on the intestinal microbiome over a 6-month period. The effect of cessation or switching to CHTP 1.2 after 3 months of CS exposure was also assessed. Next-generation sequencing was used to evaluate the impact of CMRTP aerosols in comparison to CS on microbiome composition and gene expression in the digestive tract of mice. Our analyses highlighted significant gene dysregulation in response to 3R4F exposure at 4 and 6 months. The findings showed an increase in the abundance of Akkermansiaceae upon CS exposure, which was reversed upon cessation. Cessation resulted in a significant decrease in Akkemansiaceae abundance, whereas switching to CHTP 1.2 resulted in an increase in Lactobacillaceae abundance. These microbial changes could be important for understanding the effect of CS on gut function and its relevance to disease pathogenesis via the microbiome.},
}