@article {pmid33453564,
year = {2021},
author = {Bourdillon, AT and Edwards, HA},
title = {Review of probiotic use in otolaryngology.},
journal = {American journal of otolaryngology},
volume = {42},
number = {2},
pages = {102883},
doi = {10.1016/j.amjoto.2020.102883},
pmid = {33453564},
issn = {1532-818X},
abstract = {OBJECTIVE: Probiotics have garnered considerable attention as an intervention for various conditions common to otolaryngology. The purpose of this review is to evaluate the current literature to offer recommendations about the safety and efficacy of probiotic management in otolaryngologic conditions.

STUDY DESIGN: Narrative review.

METHODS: PubMed and Google Scholar were queried using pertinent keywords to retrieve relevant studies with particular focus in the recent 5 years. All abstracts were assessed and studies, reviews and meta-analyses achieving evaluation of probiotic therapies or characterization of microbiome changes were included for further review. Studies were categorized by condition or anatomic region across various subspecialties. Key data parameters were extracted and evaluated across studies and treatment types.

RESULTS: Strong evidence exists for the use probiotic agents to improve symptoms for allergic rhinitis, chronic rhinosinusitis and certain dental conditions. Despite promising results, further investigation is needed to evaluate and optimize probiotic delivery for mitigating otitis media, oropharyngeal inflammation and upper respiratory tract infections. Preclinical studies suggest that probiotics may potentially offer benefit for voice prosthesis maintenance, wound healing and mitigation of oral dysplasia.

CONCLUSION: Probiotic therapies may offer clinical benefit in a variety of contexts within the field of otolaryngology, especially for short-term relief of certain inflammatory conditions of the oral cavity, auditory and nasal cavities. Further investigation is warranted for evaluation of long-term outcomes and pathogenic deterrence.},
}

@article {pmid33453422,
year = {2021},
author = {Tao, S and Wang, Z and Quan, C and Ge, Y and Qian, Q},
title = {The effects of ALA-PDT on microbiota in pilosebaceous units of patients with severe acne: A metagenomic study.},
journal = {Photodiagnosis and photodynamic therapy},
volume = {},
number = {},
pages = {102050},
doi = {10.1016/j.pdpdt.2020.102050},
pmid = {33453422},
issn = {1873-1597},
abstract = {BACKGROUND: 5-aminolevulinic acid mediated photodynamic therapy (ALA-PDT) is increasingly used to control severe acne. However, its impact on skin microbiota remains uncertain.

OBJECTIVES: We aimed to compare the makeup, diversity, and function of the microbiota in pilosebaceous units of patients with severe acne before and after ALA-PDT.

METHODS: A longitudinal cohort study was performed on 11 participants with severe facial acne. All patients were given 5%ALA-PDT every two weeks for three sessions in total. The contents of lesions were sampled for metagenomic sequencing at baseline and two weeks after of the first ALA-PDT.

RESULTS: Cutibacterium acnes was the most dominant species followed by Staphylococcus epidermidis and Pseudomonas fluorescens. Treatment with ALA-PDT led to clinical improvements in acne severity concurrent with a significant reduction in the relative abundance of C. acnes, while P. fluorescens increased significantly after ALA-PDT. No significant change was identified in other species. ALA-PDT administration was associated with an increased microbiota diversity and reductions in the relative abundance of the functional genes involved in energy metabolism and DNA replication.

CONCLUSIONS: ALA-PDT plays a therapeutic role by killingC. acnes, increasing P. fluorescens and the microbiome diversity, while inhibiting the function of microbiota in pilosebaceous units of severe acne.},
}

@article {pmid33453153,
year = {2021},
author = {Stacy, A and Andrade-Oliveira, V and McCulloch, JA and Hild, B and Oh, JH and Perez-Chaparro, PJ and Sim, CK and Lim, AI and Link, VM and Enamorado, M and Trinchieri, G and Segre, JA and Rehermann, B and Belkaid, Y},
title = {Infection trains the host for microbiota-enhanced resistance to pathogens.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2020.12.011},
pmid = {33453153},
issn = {1097-4172},
abstract = {The microbiota shields the host against infections in a process known as colonization resistance. How infections themselves shape this fundamental process remains largely unknown. Here, we show that gut microbiota from previously infected hosts display enhanced resistance to infection. This long-term functional remodeling is associated with altered bile acid metabolism leading to the expansion of taxa that utilize the sulfonic acid taurine. Notably, supplying exogenous taurine alone is sufficient to induce this alteration in microbiota function and enhance resistance. Mechanistically, taurine potentiates the microbiota's production of sulfide, an inhibitor of cellular respiration, which is key to host invasion by numerous pathogens. As such, pharmaceutical sequestration of sulfide perturbs the microbiota's composition and promotes pathogen invasion. Together, this work reveals a process by which the host, triggered by infection, can deploy taurine as a nutrient to nourish and train the microbiota, promoting its resistance to subsequent infection.},
}

@article {pmid33452946,
year = {2021},
author = {Xiaoming, W and Jing, L and Yuchen, P and Huili, L and Miao, Z and Jing, S},
title = {Characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {33452946},
issn = {1435-4373},
support = {2017YFC1703205//National Key R&D Program of China/ ; },
abstract = {The present study focused on the characteristics of the vaginal microbiomes in prepubertal girls with and without vulvovaginitis. We collected 24 vaginal samples and 16 fecal samples from 10 girls aged 3-9 years with vulvovaginitis and 16 healthy girls of the same age. The samples were divided into three groups: fecal swabs from healthy controls (HF), vaginal swabs from healthy controls (HVS), and vaginal swabs from girls with vulvovaginitis (VVS). Sequencing of the V3-V4 region of the 16S rDNA gene was performed with the NovaSeq PE250 platform to reveal the vaginal microbial community structure in healthy prepubertal girls and vulvovaginitis-associated microbiota. The intestinal microbiomes of healthy children were also analyzed for comparison. This study revealed that the healthy vaginal tract in prepubertal girls was dominated by Prevotella, Porphyromonas, Ezakiella, and Peptoniphilus species, with a high diversity of microbiota. The vulvovaginitis-associated microbiota were dominated by Streptococcus, Prevotella, Haemophilus, and Granulicatella, with lower diversity than that in healthy girls. Furthermore, the compositions of the vaginal and intestinal microbiomes were completely different. ANOSIM, MRPP, Adonis, and AMOVA were used to analyze the beta diversity, and the results showed that there were significant differences in the microbial communities among the three groups. Lactobacillus deficiency and high bacterial diversity were characteristics of the vaginal microbiome in healthy prepubertal girls; this is inconsistent with that in reproductive-age women. The vulvovaginitis-associated vaginal microbiota differed dramatically from normal microbiota, and the main causative agents were not fecal in origin.},
}

@article {pmid33452896,
year = {2021},
author = {Bergo, NM and Bendia, AG and Ferreira, JCN and Murton, BJ and Brandini, FP and Pellizari, VH},
title = {Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33452896},
issn = {1432-184X},
support = {14/50820-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.},
}

@article {pmid33452882,
year = {2021},
author = {Varsadiya, M and Urich, T and Hugelius, G and Bárta, J},
title = {Microbiome structure and functional potential in permafrost soils of the Western Canadian Arctic.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiab008},
pmid = {33452882},
issn = {1574-6941},
abstract = {Substantial amounts of topsoil organic matter (OM) in Arctic Cryosols have been translocated by the process of cryoturbation into deeper soil horizons (cryoOM), reducing its decomposition. Recent Arctic warming deepens the Cryosols´ active layer, making more topsoil and cryoOM carbon accessible for microbial transformation. To quantify bacteria, archaea, and selected microbial groups (methanogens- mcrA gene and diazotrophs- nifH gene) and to investigate bacterial and archaeal diversity, we collected 83 soil samples from four different soil horizons of three distinct tundra types located in Qikiqtaruk (Hershel Island, Western Canada). In general, the abundance of bacteria and diazotrophs decreased from topsoil to permafrost, but not for cryoOM. No such difference was observed for archaea and methanogens. CryoOM was enriched with oligotrophic (slow-growing microorganism) taxa capable of recalcitrant OM degradation. We found distinct microbial patterns in each tundra type: topsoil from wet-polygonal tundra had the lowest abundance of bacteria and diazotrophs, but the highest abundance of methanogens. Wet-polygonal tundra, therefore, represented a hotspot for methanogenesis. Oligotrophic and copiotrophic (fast-growing microorganism) genera of methanogens and diazotrophs were distinctly distributed in topsoil and cryoOM, resulting in different rates of nitrogen flux into these horizons affecting OM vulnerability and potential CO2 and CH4 release.},
}

@article {pmid33452880,
year = {2021},
author = {Lindsay, EL and Faustoferri, RC and Quivey, RG},
title = {Repression of the TreR transcriptional regulator in Streptococcus mutans by the global regulator, CcpA.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnab004},
pmid = {33452880},
issn = {1574-6968},
abstract = {Streptococcus mutans, the etiologic agent of dental caries in humans, is considered a dominating force in the oral microbiome due to its highly-evolved propensity for survival. The oral pathogen encodes an elaborate array of regulatory elements, including the carbon catabolite-responsive regulator, CcpA, a global regulator key in the control of sugar metabolism and in stress tolerance response mechanisms. The recently characterized trehalose utilization operon, integral for the catabolism of the disaccharide trehalose, is controlled by a local regulator, TreR, which has been implicated in a number of cellular functions outside of trehalose catabolism. Electrophoretic mobility shift assays demonstrated that CcpA bound a putative cre site in the treR promoter. Loss of ccpA resulted in elevated expression of treR in cultures of the organism grown in glucose or trehalose, indicating that CcpA not only acts as a repressor of trehalose catabolism genes, but also the local regulator. The loss of both CcpA and TreR in S. mutans resulted in an impaired growth rate and fitness response, supporting the hypothesis that these regulators are involved in carbon catabolism control and in induction of components of the organism's stress response.},
}

@article {pmid33452801,
year = {2021},
author = {Ta, AD and Ollberding, NJ and Karns, R and Haberman, Y and Alazraki, AL and Hercules, D and Baldassano, R and Markowitz, J and Heyman, MB and Kim, S and Kirschner, B and Shapiro, JM and Noe, J and Oliva-Hemker, M and Otley, A and Pfefferkorn, M and Kellermayer, R and Snapper, S and Rabizadeh, S and Xavier, R and Dubinsky, M and Hyams, J and Kugathasan, S and Jegga, AG and Dillman, JR and Denson, LA},
title = {Association of Baseline Luminal Narrowing With Ileal Microbial Shifts and Gene Expression Programs and Subsequent Transmural Healing in Pediatric Crohn Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaa339},
pmid = {33452801},
issn = {1536-4844},
abstract = {BACKGROUND: Transmural healing (TH) is associated with better long-term outcomes in Crohn disease (CD), whereas pretreatment ileal gene signatures encoding myeloid inflammatory responses and extracellular matrix production are associated with stricturing. We aimed to develop a predictive model for ileal TH and to identify ileal genes and microbes associated with baseline luminal narrowing (LN), a precursor to strictures.

MATERIALS AND METHODS: Baseline small bowel imaging obtained in the RISK pediatric CD cohort study was graded for LN. Ileal gene expression was determined by RNASeq, and the ileal microbial community composition was characterized using 16S rRNA amplicon sequencing. Clinical, demographic, radiologic, and genomic variables were tested for association with baseline LN and future TH.

RESULTS: After controlling for ileal location, baseline ileal LN (odds ratio [OR], 0.3; 95% confidence interval [CI], 0.1-0.8), increasing serum albumin (OR, 4; 95% CI, 1.3-12.3), and anti-Saccharomyces cerevisiae antibodies IgG serology (OR, 0.97; 95% CI, 0.95-1) were associated with subsequent TH. A multivariable regression model including these factors had excellent discriminant power for TH (area under the curve, 0.86; positive predictive value, 80%; negative predictive value, 87%). Patients with baseline LN exhibited increased Enterobacteriaceae and inflammatory and extracellular matrix gene signatures, coupled with reduced levels of butyrate-producing commensals and a respiratory electron transport gene signature. Taxa including Lachnospiraceae and the genus Roseburia were associated with increased respiratory and decreased inflammatory gene signatures, and Aggregatibacter and Blautia bacteria were associated with reduced extracellular matrix gene expression.

CONCLUSIONS: Pediatric patients with CD with LN at diagnosis are less likely to achieve TH. The association between specific microbiota, wound healing gene programs, and LN may suggest future therapeutic targets.},
}

@article {pmid33452800,
year = {2021},
author = {Roy Paladhi, U and Harb, AH and Daniel, SG and Dawwas, GK and Schnellinger, EM and Wollack, C and Aberra, FN and Bewtra, M and Green, JA and Klaproth, JA and Lichtenstein, GR and Saxena, A and Berera, S and Buchner, A and Mehta, SJ and Osterman, MT and Rashid, F and Tomov, V and Caldera, F and Sumona, S and Mahadevan, U and Roy, A and Nessel, L and Wu, GD and Bittinger, K and Lewis, JD},
title = {The Impact of Introducing Patient-Reported Inflammatory Bowel Disease Symptoms via Electronic Survey on Clinic Visit Length, Patient and Provider Satisfaction, and the Environment Microbiome.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaa356},
pmid = {33452800},
issn = {1536-4844},
}

@article {pmid33452691,
year = {2021},
author = {Yan, XT and Ye, ZX and Wang, X and Zhang, CX and Chen, JP and Li, JM and Huang, HJ},
title = {Insight into different host range of three planthoppers by transcriptomic and microbiomic analysis.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12695},
pmid = {33452691},
issn = {1365-2583},
abstract = {Brown planthopper (BPH), white-backed planthopper (WBPH), and small brown planthopper (SBPH), are the closely related rice pests that perform differentially on wheat plants. Using fecundity as a fitness measure, we found that SBPH well-adapted on wheat plants, followed by WBPH, while BPH had the worst performance. The transcriptomic responses of SBPH and BPH to wheat plants have been compared previously. To understand the different fitness mechanisms of three planthoppers, this study firstly investigated the transcriptomic responses of WBPH to rice and wheat plants. Genes involved in detoxification, transportation and proteasome were significantly enriched in WBPH in response to different diets. Moreover, comparative analysis demonstrated that most co-regulated genes in BPH and SBPH showed different expression changes; whereas most co-regulated genes in BPH and WBPH exhibited similar expression changes. Subsequently, this study also investigated the influences of host plants on the bacterial community of three planthoppers. The three planthoppers harbored distant diversity of bacterial communities. However, there was no dramatic change in bacterial diversity or relative abundance in planthoppers colonized on different hosts. This study illustrates generic and species-specific changes of three rice planthoppers in response to different plants, which deepen our understanding towards the host fitness for planthopper species.},
}

@article {pmid33452507,
year = {2021},
author = {},
title = {A case of 'stomach flu' arms the microbiome against invaders.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/d41586-021-00078-z},
pmid = {33452507},
issn = {1476-4687},
}

@article {pmid33452327,
year = {2021},
author = {Yuan, ZS and Liu, F and Liu, ZY and Huang, QL and Zhang, GF and Pan, H},
title = {Structural variability and differentiation of niches in the rhizosphere and endosphere bacterial microbiome of moso bamboo (Phyllostachys edulis).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1574},
pmid = {33452327},
issn = {2045-2322},
support = {MYK19027//the Scientific Research Project of Minjiang University/ ; },
abstract = {The plant microbiota play a key role in plant productivity, nutrient uptake, resistance to stress and flowering. The flowering of moso bamboo has been a focus of study. The mechanism of flowering is related to nutrient uptake, temperature, hormone balance and regulation of key genes. However, the connection between microbiota of moso bamboo and its flowering is unknown. In this study, samples of rhizosphere soil, rhizomes, roots and leaves of flowering and nonflowering plants were collected, and 16S rRNA amplicon Illumina sequencing was utilized to separate the bacterial communities associated with different flowering stages of moso bamboo. We identified 5442 OTUs, and the number of rhizosphere soil OTUs was much higher than those of other samples. Principal component analysis (PCA) and hierarchical clustering (Bray Curtis dis) analysis revealed that the bacterial microorganisms related to rhizosphere soil and endophytic tissues of moso bamboo differed significantly from those in bulk soil and rhizobacterial and endosphere microbiomes. In addition, the PCA analyses of root and rhizosphere soil revealed different structures of microbial communities between bamboo that is flowering and not flowering. Through the analysis of core microorganisms, it was found that Flavobacterium, Bacillus and Stenotrophomonas played an important role in the absorption of N elements, which may affect the flowering time of moso bamboo. Our results delineate the complex host-microbe interactions of this plant. We also discuss the potential influence of bacterial microbiome in flowering, which can provide a basis for the development and utilization of moso bamboo.},
}

@article {pmid33452177,
year = {2021},
author = {Ding, Z and Wang, W and Zhang, K and Ming, F and Yangdai, T and Xu, T and Shi, H and Bao, Y and Yao, H and Peng, H and Han, C and Jiang, W and Liu, J and Hou, X and Lin, R},
title = {Novel scheme for non-invasive gut bioinformation acquisition with a magnetically controlled sampling capsule endoscope.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2020-322465},
pmid = {33452177},
issn = {1468-3288},
abstract = {OBJECTIVE: Intestinal flora and metabolites are associated with multiple systemic diseases. Current approaches for acquiring information regarding microbiota/metabolites have limitations. We aimed to develop a precise magnetically controlled sampling capsule endoscope (MSCE) for the convenient, non-invasive and accurate acquisition of digestive bioinformation for disease diagnosis and evaluation.

DESIGN: The MSCE and surgery were both used for sampling both jejunal and ileal GI content in the control and antibiotic-induced diarrhoea groups. The GI content was then used for microbiome profiling and metabolomics profiling.

RESULTS: Compared with surgery, our data showed that the MSCE precisely acquired data regarding the intestinal flora and metabolites, which was effectively differentiated in different intestinal regions and disease models. Using MSCE, we detected a dramatic decrease in the abundance of Bacteroidetes, Patescibacteria and Actinobacteria and hippuric acid levels, as well as an increase in the abundance of Escherichia-Shigella and the 2-pyrrolidinone levels were detected in the antibiotic-induced diarrhoea model by MSCE. MSCE-mediated sampling revealed specific gut microbiota/metabolites including Enterococcus, Lachnospiraceae, acetyl-L-carnitine and succinic acid, which are related to metabolic diseases, cancers and nervous system disorders. Additionally, the MSCE exhibited good sealing characteristics with no contamination after sampling.

CONCLUSIONS: We present a newly developed MSCE that can non-invasively and accurately acquire intestinal bioinformation via direct visualization under magnetic control, which may further aid in disease prevention, diagnosis, prognosis and treatment.},
}

@article {pmid33452033,
year = {2021},
author = {Wolff, BA and Clements, WH and Hall, EK},
title = {Metals alter membership but not diversity of a headwater stream microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02635-20},
pmid = {33452033},
issn = {1098-5336},
abstract = {Metal contamination from mining or natural weathering is a common feature of surface waters in the American west. Advances in microbial analyses have created the potential for routine sampling of aquatic microbiomes as a tool to assess the quality of stream habitat. We sought to determine if microbiome diversity and membership were affected by metal contamination and identify candidate microbial taxa to be used to indicate metal stress in stream ecosystems. We evaluated microbiome membership from sediments at multiple sites within the principal drainage of an EPA superfund site near the headwaters of the Upper Arkansas River, Leadville, CO. From each sample, we extracted DNA and sequenced the 16S rRNA gene amplicon on the Illumina MiSeq platform. We used the remaining sediments to simultaneously evaluate environmental metal concentrations. We also conducted an artificial stream mesocosm experiment using sediments collected from two of the observational study sites. The mesocosm experiment had a 2x2 factorial design: 1) location (upstream or downstream of contaminating tributary), and 2) treatment (metal exposure or control). We found no difference in diversity between upstream and downstream sites in the field. Similarly, diversity changed very little following experimental metal exposure. However, microbiome membership differed between upstream and downstream locations and experimental metal exposure changed microbiome membership in a manner that depended on origin of the sediments used in each mesocosm.Importance Our results suggest that microbiomes can be reliable indicators of ecosystem metal stress even when surface water chemistry and other metrics used to assess ecosystem health do not indicate ecosystem stress. Results presented in this study in combination with previously published work on this same ecosystem are consistent with the idea that a microbial response to metals at the base of the food web may be affecting primary consumers. If effects of metals are mediated through shifts in the microbiome, then microbial metrics, as presented here, may aid in the assessment of stream ecosystem health which currently does not include assessments of the microbiome.},
}

@article {pmid33452027,
year = {2021},
author = {Meziti, A and Rodriguez-R, LM and Hatt, JK and Peña-Gonzalez, A and Levy, K and Konstantinidis, KT},
title = {How reliably do metagenome-assembled genomes (MAGs) represent natural populations? Insights from comparing MAGs against isolate genomes derived from the same fecal sample.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02593-20},
pmid = {33452027},
issn = {1098-5336},
abstract = {The recovery of metagenome-assembled genomes (MAGs) from metagenomic data has recently become a common task for microbial studies. The strengths and limitations of the underlying bioinformatics algorithms are well appreciated by now based on performance tests with mock datasets of known composition. However, these mock datasets do not capture the complexity and diversity often observed within natural populations, since their construction typically relies on only a single genome of a given organism. Further, it remains unclear if MAGs can recover population variable (e.g., shared by >10% but <90% of the members of the population) as efficiently as core genes (e.g., shared by >90% of the members). To address these issues, we compared the gene variability of pathogenic Escherichia coli isolates from eight diarrheal samples, for which the isolate was the causative agent, against their corresponding MAGs recovered from the companion metagenomic dataset. Our analysis revealed that MAGs with completeness estimates near 95% captured only 77% of the population core genes and 50% of the variable genes, on average. Further, about 5% of the genes of these MAG were conservatively identified as missing in the isolate and were of different (non-Enterobacteriaceae) taxonomic origin, suggesting errors at the genome binning step, even though contamination estimates based on commonly used pipelines were only 1.5%. Therefore, the quality of MAGs may oftentimes be worse than estimated, and we offer examples of how to recognize and improve such MAGs to sufficient quality by -for instance- employing only contigs longer than 1,000bp for binning.IMPORTANCE Metagenome assembly and recovery of metagenome-assembled genomes (MAGs) have recently become common tasks for microbiome studies across environmental and clinical settings. However, to what extent MAGs can capture the genes of the population they represent remains speculative. Current approaches to evaluate MAG quality are limited to the recovery and copy number of universal, housekeeping genes but these genes represent a small fraction of the total genome, leaving the majority of the genome essentially inaccessible. If MAG quality in reality is lower than these approaches would estimate, this could have dramatic consequences for all downstream analyses and interpretations. In this study, we evaluated this issue using a novel approach that employs comparisons of MAGs to isolate genomes derived from the same samples. Further, our samples originated from a diarrhea case-control study, and thus our results are relevant for recovering the virulence factors of pathogens from metagenomic datasets.},
}

@article {pmid33452025,
year = {2021},
author = {Fracchia, F and Mangeot-Peter, L and Jacquot, L and Martin, F and Veneault-Fourrey, C and Deveau, A},
title = {Colonization of naïve roots from Populus tremula x alba involves successive waves of fungi and bacteria with different trophic abilities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02541-20},
pmid = {33452025},
issn = {1098-5336},
abstract = {Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher if the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of Gray Poplar obtained from plantlets propagated in axenic conditions in natural poplar stand-soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of fungal rDNA ITS and bacterial 16S rRNA amplicons with Confocal Laser Scanning Microscope observations. The microbial colonisation of poplar roots took place in three stages but the dynamic was different between bacteria and fungi. Root bacterial communities were clearly different from the soil after two days of culture. By contrast, if fungi were also already colonizing roots after two days, the initial communities were very close to the one of the soil and were dominated by saprotrophs. Those were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots along time suggest potential competition effect between microorganisms and/or a selection by the host.IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system which provides a unique nutrient rich-environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped along time, we observed the composition of root-associated microbial communities of naïve plantlets of poplar transferred in natural soil. The composition of the final root microbiome rely on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members along time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.},
}

@article {pmid33452024,
year = {2021},
author = {Zhu, HZ and Zhang, ZF and Zhou, N and Jiang, CY and Wang, BJ and Cai, L and Wang, HM and Liu, SJ},
title = {Intensive Bacterial Cultivation and Genome Assembly Reveal Previously Unknown Bacteria and Metabolic Potential in Karst Caves.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02440-20},
pmid = {33452024},
issn = {1098-5336},
abstract = {Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived hypothesis and to disclose the microbial functions in cave ecosystems. In this study, the microbiomes of two karst caves in Guizhou Province in southwest China were examined. A total of 3,562 bacterial strains were cultivated from rock, water, and sediment samples, and 329 species (including 14 newly described species) of 102 genera were found. We created a cave bacterial genome collection of 218 bacterial genomes from a karst cave microbiome through the extraction of 204 database-derived genomes and de novo sequencing of 14 new bacterial genomes. The cultivated genome collection obtained in this study and the metagenome data from previous studies were used to investigate the bacterial metabolism and potential involvement in the carbon, nitrogen, and sulfur biogeochemical cycles in the cave ecosystem. New N2-fixing Azospirillum and alkane-oxidizing Oleomonas species were documented in the karst cave microbiome. Two pcaIJ clusters of the β-ketoadipate pathway that were abundant in both the cultivated microbiomes and the metagenomic data were identified, and their representatives from the cultivated bacterial genomes were functionally demonstrated. This large-scale cultivation of a cave microbiome represents the most intensive collection of cave bacterial resources to date and provides valuable information and diverse microbial resources for future cave biogeochemical research.IMPORTANCE Karst caves are oligotrophic environments that are dark, humid, and have a relative stable annual temperature. The bacteria diversity and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems. We integrated large-scale bacterial cultivation with metagenomic data-mining to explore the composition and metabolisms of the microbiomes in two karst cave systems. Our results reveal the presence of a highly diversified cave bacterial community, and 14 new bacterial species were described and genome-sequenced. In this study, we obtained the most intensive collection of cultivated microbial resources from karst caves to date and predicted the various important routes for the biogeochemical cycling of elements in cave ecosystems.},
}

@article {pmid33451726,
year = {2020},
author = {Li, L and Figeys, D},
title = {Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface.},
journal = {Molecular & cellular proteomics : MCP},
volume = {19},
number = {9},
pages = {1409-1417},
doi = {10.1074/mcp.R120.002051},
pmid = {33451726},
issn = {1535-9484},
abstract = {Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI.},
}

@article {pmid33451555,
year = {2020},
author = {Doellinger, J and Schneider, A and Hoeller, M and Lasch, P},
title = {Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction.},
journal = {Molecular & cellular proteomics : MCP},
volume = {19},
number = {1},
pages = {209-222},
doi = {10.1074/mcp.TIR119.001616},
pmid = {33451555},
issn = {1535-9484},
abstract = {The main challenge of bottom-up proteomic sample preparation is to extract proteomes in a manner that enables efficient protein digestion for subsequent mass spectrometric analysis. Today's sample preparation strategies are commonly conceptualized around the removal of detergents, which are essential for extraction but strongly interfere with digestion and LC-MS. These multi-step preparations contribute to a lack of reproducibility as they are prone to losses, biases and contaminations, while being time-consuming and labor-intensive. We report a detergent-free method, named Sample Preparation by Easy Extraction and Digestion (SPEED), which consists of three mandatory steps, acidification, neutralization and digestion. SPEED is a universal method for peptide generation from various sources and is easily applicable even for lysis-resistant sample types as pure trifluoroacetic acid (TFA) is used for highly efficient protein extraction by complete sample dissolution. The protocol is highly reproducible, virtually loss-less, enables very rapid sample processing and is superior to the detergent/chaotropic agent-based methods FASP, ISD-Urea and SP3 for quantitative proteomics. SPEED holds the potential to dramatically simplify and standardize sample preparation while improving the depth of proteome coverage especially for challenging samples.},
}

@article {pmid33451015,
year = {2021},
author = {Adam, T and Becker, TM and Chua, W and Bray, V and Roberts, TL},
title = {The Multiple Potential Biomarkers for Predicting Immunotherapy Response-Finding the Needle in the Haystack.},
journal = {Cancers},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/cancers13020277},
pmid = {33451015},
issn = {2072-6694},
abstract = {Immune checkpoint inhibitors (ICIs) are being increasingly utilised in a variety of advanced malignancies. Despite promising outcomes in certain patients, the majority will not derive benefit and are at risk of potentially serious immune-related adverse events (irAEs). The development of predictive biomarkers is therefore critical to personalise treatments and improve outcomes. A number of biomarkers have shown promising results, including from tumour (programmed cell death ligand 1 (PD-L1), tumour mutational burden (TMB), stimulator of interferon genes (STING) and apoptosis-associated speck-like protein containing a CARD (ASC)), from blood (peripheral blood mononuclear cells (PBMCs), circulating tumour DNA (ctDNA), exosomes, cytokines and metal chelators) and finally the microbiome.},
}

@article {pmid33450667,
year = {2020},
author = {Ezzat-Zadeh, Z and Henning, SM and Yang, J and Woo, SL and Lee, RP and Huang, J and Thames, G and Gilbuena, I and Tseng, CH and Heber, D and Li, Z},
title = {California strawberry consumption increased the abundance of gut microorganisms related to lean body weight, health and longevity in healthy subjects.},
journal = {Nutrition research (New York, N.Y.)},
volume = {85},
number = {},
pages = {60-70},
doi = {10.1016/j.nutres.2020.12.006},
pmid = {33450667},
issn = {1879-0739},
abstract = {It was our hypothesis that foods high in polyphenols and fiber have prebiotic activity. This human intervention study aimed to determine if daily consumption of freeze-dried California strawberry powder (SBP) leads to changes in the intestinal microbiota, fecal cholesterol and bile acid (BA) microbial metabolites. Fifteen healthy adults consumed a beige diet+26 g of SBP for 4 weeks, followed by 2 weeks of beige diet only. Stool samples were collected at 0, 4, and 6 weeks. Fecal microbiota was analyzed by 16S rRNA sequencing; fecal cholesterol, BA, and microbial metabolites by gas chromatography. Confirming compliance, urine concentration of pelargonidin, urolithin A glucuronide and dimethylellagic acid glucuronide were present after 4 weeks of SBP consumption. Daily SBP altered the abundance of 24 operational taxonomic units (OTUs). Comparing week 4 to baseline the most significant increases were observed for one OTU from Firmicutes\Clostridia\ Christensenellaceae\NA, one OTU from Firmicutes\ Clostridia\Mogibacteriacea\NA, one OTU from Verrucomicrobia\ Verrucomicrobiaceae\Akkermansia\Muciniphila, one OTU from Actinobacteria\ Bifidobacteriaceae\Bifidobacterium\NA, and one OTU from Bacteroidetes\Bacteroidia\ Bacteroidaceae\Bacteroides and decrease of one OTU from Proteobacteria\ Betaproteobacteria\Alcaligenaceae\Sutterella. Comparing week 4 to 6, we observed a reversal of the same OTUs from C Christensenellaceae, V muciniphilia and C Mogibacteriaceae. Fecal short chain fatty acids and most of the fecal markers including cholesterol, coprostanol, primary and secondary BAs were not changed significantly except for lithocholic acid, which was increased significantly at week 6 compared to baseline. In summary, SBP consumption increased the abundance of gut microorganisms related to lean body weight, health and longevity, and increased fecal lithocholic acid at week 6 in healthy study participants.},
}

@article {pmid33450498,
year = {2021},
author = {Srinivasan, M and Adnane, M and Archunan, G},
title = {Significance of cervico-vaginal microbes in bovine reproduction and pheromone production - A hypothetical review.},
journal = {Research in veterinary science},
volume = {135},
number = {},
pages = {66-71},
doi = {10.1016/j.rvsc.2021.01.003},
pmid = {33450498},
issn = {1532-2661},
abstract = {The vaginal microbiota has been studied in animal reproduction and fertility, in particular little information of vaginal microbes in reference to bovine reproduction and pheromone production is known. The vaginal mucosa in healthy cow is colonized by an equilibrated and dynamic composition of aerobic, facultative anaerobic and obligate anaerobic microbes. Cervico-vaginal mucus (CVM) composition, viscosity and volume vary with the cyclicity and health status of the reproductive tract. In addition, CVM contains pheromones, volatile compounds, and proteins that attract males for coitus. Commensal microbiota plays a key role in protection of the genital tract from pathogenic microbes by competition effect. In the bovine species, the microbial composition, its abundance and diversity in the female gut, vagina, urine, saliva, and feces, and the associated chemical communication remains poorly documented. The impact of microbes in the reproductive tract of cow, buffalo and certain mammals are discussed in this review. Since the microbial population diversity of CVM is modified during estrus phase it presumes that it may have a role for pheromone production in conspecific. Herein, we would like to critically discuss the current state of knowledge on microbially produced signals in animals and the role of genital and CVM microbiota in estrous cycle and pregnancy.},
}

@article {pmid33450310,
year = {2021},
author = {Widyarman, AS and Udawatte, NS and Theodorea, CF and Apriani, A and Richi, M and Astoeti, TE and Seneviratne, CJ},
title = {Casein phosphopeptide-amorphous calcium phosphate fluoride treatment enriches the symbiotic dental plaque microbiome in children.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {103582},
doi = {10.1016/j.jdent.2021.103582},
pmid = {33450310},
issn = {1879-176X},
abstract = {OBJECTIVES: The dysbiotic oral microbiome plays a key role in the pathogenesis of caries in children. Topical application of casein phosphopeptide-amorphous calcium phosphate containing fluoride (CPP-ACP/F) is an effective treatment modality for children with caries (CC). Hitherto the mechanism by which CPP-ACP/F modules the oral microbiome in CC has not been investigated. The study aimed to examine the CPP-ACP/F effect on the dental plaque microbiome of children group with caries.

METHODS: This preliminary prospective clinical cohort included 10 children with caries. The children received topical fluoride CPP-ACP/F once-a-week for one month. Plaque samples were collected before and after treatment and subjected to 16S rDNA-based next-generation-sequencing. Microbial composition, diversity and functional roles were analyzed in comparison to the clinical characteristics of cohort using standard bioinformatics tools.

RESULTS: CPP-ACP/F treatment modulated dysbiotic oral microbiome towards healthier community as the higher proportion of Proteobacteria and certain microbial protective species were enriched following CPP-ACP/F treatment. Despite overall uniformity of community structure in children with caries between the groups, some bacterial species were differentially represented in a statistically significant manner between pre- and post- treatments. Three bacterial species were found to be predictive of strongly sensitive to the CPP-ACP/F treatment, marked by decreased abundance of Lautropia mirabalis and increased abundance of Gemella haemolysans and Schwartzia succinivorans.

CONCLUSION: Within the limits of the current study, it could be concluded that the CPP-ACP/F varnish treatment modulated the microbial composition of the dental plaque microbiome towards symbiosis. These symbiotic changes may demonstrate the potential clinical significance of CPP-ACP/F varnish treatment.},
}

@article {pmid33450288,
year = {2021},
author = {Sibeko, L and Johns, T},
title = {Global survey of medicinal plants during lactation and postpartum recovery: evolutionary perspectives and contemporary health implications.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {113812},
doi = {10.1016/j.jep.2021.113812},
pmid = {33450288},
issn = {1872-7573},
abstract = {Cross-cultural comparison of plants used during lactation and the postpartum period offers insight into a largely overlooked area of ethnopharmacological research. Potential roles of phytochemicals in emerging models of interaction among immunity, inflammation, microbiome and nervous system effects on perinatal development have relevance for the life-long health of individuals and of populations in both traditional and contemporary contexts.

AIM OF THE STUDY: Delineate and interpret patterns of traditional and contemporary global use of medicinal plants ingested by mothers during the postpartum period relative to phytochemical activity on immune development and gastrointestinal microbiome of breastfed infants, and on maternal health.

MATERIALS AND METHODS: Published reviews and surveys on galactagogues and postpartum recovery practices plus ethnobotanical studies from around the world were used to identify and rank plants, and ascertain regional use patterns. Scientific literature for 20 most-cited plants based on frequency of publication was assessed for antimicrobial, antioxidant, anti-inflammatory, immunomodulatory, antidepressant, analgesic, galactagogic and safety properties.

RESULTS: From compilation of 4418 use reports related to 1948 species, 105 plant taxa were recorded ≥ 7 times, with the most frequently cited species, Foeniculum vulgare, Trigonella foenum-graecum, Pimpinella anisum, Euphorbia hirta and Asparagus racemosus, 81, 64, 42, 40 and 38 times, respectively. Species and use vary globally, illustrated by the pattern of aromatic plants of culinary importance versus latex-producing plants utilized in North Africa/Middle East and Sub-Saharan Africa with opposing predominance. For 18/20 of the plants a risk/benefit perspective supports assessment that positive immunomodulation and related potential exceed any safety concerns. Published evidence does not support a lactation-enhancing effect for nearly all the most-cited plants while antidepressant data for the majority of plants are predominately limited to animal studies.

CONCLUSIONS: Within a biocultural context traditional postpartum plant use serves adaptive functions for the mother-infant dyad and contributes phytochemicals absent in most contemporary diets and patterns of ingestion, with potential impacts on allergic, inflammatory and other conditions. Polyphenolics and other phytochemicals are widely immunologically active, present in breast milk and predominately non-toxic. Systematic analysis of phytochemicals in human milk, infant lumen and plasma, and immunomodulatory studies that differentiate maternal ingestion during lactation from pregnancy, are needed. Potential herb-drug interaction and other adverse effects should remain central to obstetric advising, but unless a plant is specifically shown as harmful, considering potential contributions to health of individuals and populations, blanket advisories against postpartum herbal use during lactation appear empirically unwarranted.},
}

@article {pmid33450094,
year = {2021},
author = {Bhat, SF and Pinney, SE and Kennedy, KM and McCourt, CR and Mundy, MA and Surette, MG and Sloboda, DM and Simmons, RA},
title = {Exposure to high fructose corn syrup during adolescence in the mouse alters hepatic metabolism and the microbiome in a sex-specific manner.},
journal = {The Journal of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/JP280034},
pmid = {33450094},
issn = {1469-7793},
abstract = {KEY POINTS: The prevalence of obesity and non-alcoholic fatty liver disease in children is dramatically increasing at the same time as consumption of foods with a high sugar content. Intake of high fructose corn syrup (HFCS) is a possible etiology as it is thought to be more lipogenic than glucose. In a mouse model, HFCS intake during adolescence increased fat mass and hepatic lipid levels in male and female mice. However, only males showed impaired glucose tolerance. Multiple metabolites including lipids, bile acids, carbohydrates, and amino acids were altered in liver in a sex-specific manner at 6 weeks of age. Some of these changes were also present in adulthood even though HFCS exposure ended at 6 weeks. HFCS significantly altered the gut microbiome which was associated with changes in key microbial metabolites. These results suggest that HFCS intake during adolescence has profound metabolic changes that are linked to changes in the microbiome and these changes are sex-specific.

ABSTRACT: The rapid increase in obesity, diabetes and fatty liver disease in children over the past 20 years has been linked to increased high fructose corn syrup (HFCS) consumption making it essential to determine the short and long-term effects of HFCS during this vulnerable developmental window. We hypothesized that HFCS exposure during adolescence significantly impairs hepatic metabolic signaling pathways and alters gut microbial composition contributing to changes in energy metabolism with sex-specific effects. C57bl/6J mice with free access to HFCS during adolescence (3-6 weeks of age) underwent glucose tolerance and body composition testing and hepatic metabolomics, gene expression and triglyceride content analysis at 6 and 30 weeks of age (n = 6-8 per sex). At 6 weeks HFCS-exposed mice had significant increases in fat mass, glucose intolerance, hepatic triglycerides (females) and de novo lipogenesis gene expression (ACC, DGAT, FAS, ChREBP, SCD, SREBP, CPT and PPARα) with sex-specific effects. At 30 weeks HFCS-exposed mice also had abnormalities in glucose tolerance (males) and fat mass (females). HFCS exposure enriched carbohydrate, amino acid, long chain fatty acid and secondary bile acid metabolism at 6 weeks with changes in secondary bile metabolism at 6 and 30 weeks. Microbiome studies performed immediately before and after HFCS exposure identified profound shifts of microbial species in male mice only. In summary, a short-term HFCS exposure during adolescence induces fatty liver, alters important metabolic pathways, some of which continue to be altered in adulthood, and changes the microbiome in a sex-specific manner. This article is protected by copyright. All rights reserved.},
}

@article {pmid33450018,
year = {2020},
author = {Chu, XJ and Cao, NW and Zhou, HY and Meng, X and Guo, B and Zhang, HY and Li, BZ},
title = {The oral and gut microbiome in rheumatoid arthritis patients: a systematic review.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaa835},
pmid = {33450018},
issn = {1462-0332},
abstract = {BACKGROUND: Recently, researchers have proposed a possible relationship between RA and the microbiome of the oral cavity and gut. However, this relation has not been systematically established. Herein, we conducted a comprehensive review of the pertinent literature to describe this possible association.

METHODS: We systematically performed searches in databases, namely EMBASE, the Cochrane Library, and PubMed, from inception to 7 June 2020 to identify case-control studies that compared the oral and gut microbiome in adult RA patients with those of controls. The primary outcome was specific bacterial changes between RA and controls. The secondary outcome was microbial diversity changes between RA and controls.

RESULTS: In total, 26 articles were considered eligible for inclusion and reported some differences. Therein, ≥3 articles reported decreased Faecalibacterium in the gut of early-RA (ERA)/RA patients compared with healthy controls (HCs). Also, ≥3 articles reported decreased Streptococcus and Haemophilus and increased Prevotella in the oral cavity of ERA/RA patients compared with HCs. In addition, some Prevotella species, including P. histicola and P. oulorum, showed increased trends in RA patients' oral cavity, compared with HCs. The α-diversity of the microbiome was either increased or not changed in the oral cavity of RA patients, but it was more commonly either decreased or not changed in the gut of RA patients.

CONCLUSIONS: In this systematic review, we identified the microbiome associated with RA patients in comparison with controls. More research is needed in the future to find the deep relationship between RA and the microbiome.},
}

@article {pmid33449810,
year = {2021},
author = {Roshanravan, N and Bastani, S and Tutunchi, H and Kafil, B and Nikpayam, O and Mesri Alamdari, N and Hadi, A and Sotoudeh, S and Ghaffari, S and Ostadrahimi, A},
title = {A comprehensive systematic review of the effectiveness of Akkermansia muciniphila, a member of the gut microbiome, for the management of obesity and associated metabolic disorders.},
journal = {Archives of physiology and biochemistry},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/13813455.2021.1871760},
pmid = {33449810},
issn = {1744-4160},
abstract = {AIMS AND BACKGROUND: Obesity is recognised as a significant public health burden worldwide. Recently the cross-talk between gut microbiota and obesity has attracted much attention. To that end, Akkermansia muciniphila has been proposed as a promising microbe to manage obesity. In the present systematic review, we evaluated evidence on the effectiveness and mechanisms of action of Akkermansia muciniphila supplementation in the management of obesity.

METHODS: Electronic databases of MEDLINE, PubMed, Scopus, Web of Science, and Google Scholar were searched thought March 2020 to identify relevant published articles, and eligible articles were systematically reviewed.

RESULTS AND CONCLUSIONS: Fifteen studies were included in the present study. Findings from the present review, which included human and animal (rodent) models support the effectiveness of Akkermansia supplementation as a novel therapeutic approach for the management of obesity and metabolic complications associated with obesity. However, future clinical trials are warranted to verify these outcomes.},
}

@article {pmid33449574,
year = {2021},
author = {Lemberger, U and Quhal, F and Bruchbacher, A and Shariat, SF and Hiess, M},
title = {The microbiome in urinary tract infections in children - an update.},
journal = {Current opinion in urology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOU.0000000000000858},
pmid = {33449574},
issn = {1473-6586},
abstract = {PURPOSE OF REVIEW: Urinary tract infection (UTI) is one of the most common pediatric infections worldwide. Recently introduced 16S rRNA sequencing allows detailed identification of bacteria involved in UTI on a species-based level. The urogenital microbiome in children is scarcely investigated, with underlying conditions differing from adults. Improvement in diagnostic and therapeutic approaches can help to minimize unnecessary antibiotic treatments, thereby protecting the physiological microbiome.

RECENT FINDINGS: Healthy bladders of children display a distinct microbiome than those of adults. UTI is characterized by changes in bacterial composition, with a high prevalence of Enterobacterales. There is a correlation between bacterial species and the pH of the urine, so a characteristic age-related pathogen pattern can be found due to the acidic urine in infants and more alkaline urine in older children. Recently, new methods were proposed to overcome the suboptimal diagnostic performance of urine cultures and urine dipstick test. This allows precise treatment decisions and helps to prevent chronification of UTI, related voiding dysfunctions and renal scaring, systemic abiosis, and the development of antibiotic resistance.

SUMMARY: Uropathogens involved in UTIs in children should be identified with precision to allow targeted therapeutic decisions. This can also help preventing the destruction of the microbiome homeostasis, which could result in a life-long dysbiosis. New treatment approaches and recolonization with probiotics are necessary due to increasing intrinsic antibiotic resistance of bacteria.},
}

@article {pmid33449409,
year = {2021},
author = {Schmidt, KM and Haddad, EN and Sugino, KY and Vevang, KR and Peterson, LA and Koratkar, R and Gross, MD and Kerver, JM and Comstock, SS},
title = {Dietary and plasma carotenoids are positively associated with alpha diversity in the fecal microbiota of pregnant women.},
journal = {Journal of food science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1750-3841.15586},
pmid = {33449409},
issn = {1750-3841},
support = {CHEAR P&F 2018-PF05//Children's Health Exposure Analysis Resource (CHEAR) Pilot and Feasibility (P&F) Program/ ; 1U2CES026533/NH/NIH HHS/United States ; },
abstract = {Because microbes use carotenoids as an antioxidant for protection, dietary carotenoids could be associated with gut microbiota composition. We aimed to determine associations among reported carotenoid intake, plasma carotenoid concentrations, and fecal bacterial communities in pregnant women. Pregnant women (n = 27) were enrolled in a two-arm study designed to assess feasibility of biospecimen collection and delivery of a practical nutrition intervention. Plasma and fecal samples were collected and women were surveyed with a 24-hr dietary checklist and recalls. Plasma carotenoids were analyzed by HPLC using photodiode array detection. Fecal bacteria were analyzed by 16S rRNA DNA sequencing. Results presented are cross-sectional from the 36-week gestational study visit combined across both study arms due to lack of significant differences between intervention and usual care groups (n = 23 women with complete data). Recent intake of carotenoid-containing foods included carrots, sweet potatoes, mangos, apricots, and/or bell peppers for 48% of women; oranges/orange juice (17%); egg (39%); tomato/tomato-based sauces (52%); fruits (83%); and vegetables (65%). Average plasma carotenoid concentrations were 6.4 µg/dL α-carotene (AC), 17.7 µg/dL β-carotene (BC), 11.4 µg/dL cryptoxanthin, 39.0 µg/dL trans-lycopene, and 29.8 µg/dL zeaxanthin and lutein. AC and BC concentrations were higher in women who recently consumed foods high in carotenoids. CR concentrations were higher in women who consumed oranges/orange juice. Microbiota α-diversity positively correlated with AC and BC. Microbiota β-diversity differed significantly across reported intake of carotenoid containing foods and plasma concentrations of AC. This may reflect an effect of high fiber or improved overall dietary quality, rather than a specific effect of carotenoids. PRACTICAL APPLICATION: Little is known about the association between the gut microbiome and specific dietary microconstituents, such as carotenoids, especially during pregnancy. This research demonstrates that a carotenoid-rich diet during pregnancy supports a diverse microbiota, which could be one mechanism by which carotenoids promote health.},
}

@article {pmid33449153,
year = {2021},
author = {Strickland, AB and Shi, M},
title = {Mechanisms of fungal dissemination.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
pmid = {33449153},
issn = {1420-9071},
support = {AI131219/NH/NIH HHS/United States ; AI131905/NH/NIH HHS/United States ; },
abstract = {Fungal infections are an increasing threat to global public health. There are more than six million fungal species worldwide, but less than 1% are known to infect humans. Most of these fungal infections are superficial, affecting the hair, skin and nails, but some species are capable of causing life-threatening diseases. The most common of these include Cryptococcus neoformans, Aspergillus fumigatus and Candida albicans. These fungi are typically innocuous and even constitute a part of the human microbiome, but if these pathogens disseminate throughout the body, they can cause fatal infections which account for more than one million deaths worldwide each year. Thus, systemic dissemination of fungi is a critical step in the development of these deadly infections. In this review, we discuss our current understanding of how fungi disseminate from the initial infection sites to the bloodstream, how immune cells eliminate fungi from circulation and how fungi leave the blood and enter distant organs, highlighting some recent advances and offering some perspectives on future directions.},
}

@article {pmid33449130,
year = {2021},
author = {Zai, X and Luo, W and Bai, W and Li, Y and Xiao, X and Gao, X and Wang, E and Wei, G and Chen, W},
title = {Effect of Root Diameter on the Selection and Network Interactions of Root-Associated Bacterial Microbiomes in Robinia pseudoacacia L.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33449130},
issn = {1432-184X},
support = {31870476//the National Natural Science Foundation of China/ ; 41830755//the National Natural Science Foundation of China/ ; },
abstract = {The high plasticity of root morphology, physiology, and function influences root-associated microbiomes. However, the variation in root-associated microbiome diversity and structures in response to root diameter at different root depths remains poorly understood. Here, we selected black locust (Robinia pseudoacacia L.) as a model plant to investigate the selection and network interactions of rhizospheric and root endophytic bacterial microbiomes associated with roots of different diameters (1, 1-2, and > 2 mm) among root depths of 0-100 cm via the Illumina sequencing of the 16S rRNA gene. The results showed that the alpha diversity of the root-associated bacterial communities decreased with increasing root diameters among different root depths; fewer orders with higher relative abundance, especially in the endosphere, were enriched in association with coarse roots (> 2 mm) than fine roots among root depths. Furthermore, the variation in the enriched bacterial orders associated with different root diameters was explained by bulk soil properties. Higher co-occurrence network complexity and stability emerged in the rhizosphere microbiomes of fine roots than those of coarse roots, in contrast to the situation in the endosphere microbiomes. In particular, the endosphere of roots with a diameter of 1-2 mm exhibited the lowest network complexity and stability and a high proportion of keystone taxa (e.g., Cytophagia, Flavobacteriia, Sphingobacteriia, β-Proteobacteria, and γ-Proteobacteria), suggesting a keystone taxon-reliant strategy in this transitional stage. In summary, this study indicated that root diameter at different root depths differentially affects rhizospheric and endophytic bacterial communities, which implies a close relationship between the bacterial microbiome, root function, and soil properties.},
}

@article {pmid33448927,
year = {2021},
author = {Mortensen, MS and Rasmussen, MA and Stokholm, J and Brejnrod, AD and Balle, C and Thorsen, J and Krogfelt, KA and Bisgaard, H and Sørensen, SJ},
title = {Modeling transfer of vaginal microbiota from mother to infant in early life.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
doi = {10.7554/eLife.57051},
pmid = {33448927},
issn = {2050-084X},
support = {R93-A8944//Lundbeckfonden/ ; R16-A1694//Lundbeckfonden/ ; 903516//Danish Ministry of Health/ ; 0603-00280B//Strategiske Forskningsråd/ ; },
abstract = {Early-life microbiota has been linked to the development of chronic inflammatory diseases. It has been hypothesized that maternal vaginal microbiota is an important initial seeding source and therefore might have lifelong effects on disease risk. To understand maternal vaginal microbiota's role in seeding the child's microbiota and the extent of delivery mode-dependent transmission, we studied 665 mother-child dyads from the COPSAC2010 cohort. The maternal vaginal microbiota was evaluated twice in the third trimester and compared with the children's fecal (at 1 week, 1 month, and 1 year of age) and airway microbiota (at 1 week, 1 month, and 3 months). Based on the concept of weighted transfer ratios (WTRs), we have identified bacterial orders for which the WTR displays patterns indicate persistent or transient transfer from the maternal vaginal microbiome, as well as orders that are shared at later time points independent of delivery mode, indicating a common reservoir.},
}

@article {pmid33448595,
year = {2020},
author = {Dury, GJ and Moczek, AP and Schwab, DB},
title = {Maternal and larval niche construction interact to shape development, survival, and population divergence in the dung beetle Onthophagus taurus.},
journal = {Evolution & development},
volume = {22},
number = {5},
pages = {358-369},
doi = {10.1111/ede.12348},
pmid = {33448595},
issn = {1525-142X},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; 1256689//National Science Foundation, Division of Integrative Organismal Systems/ ; 1901680//National Science Foundation, Division of Integrative Organismal Systems/ ; 61369//John Templeton Foundation/ ; },
abstract = {Through niche construction, organisms modify their environments in ways that can alter how selection acts on themselves and their offspring. However, the role of niche construction in shaping developmental and evolutionary trajectories, and its importance for population divergences and local adaptation, remains largely unclear. In this study, we manipulated both maternal and larval niche construction and measured the effects on fitness-relevant traits in two rapidly diverging populations of the bull-headed dung beetle, Onthophagus taurus. We find that both types of niche construction enhance adult size, peak larval mass, and pupal mass, which when compromised lead to a synergistic decrease in survival. Furthermore, for one measure, duration of larval development, we find that the two populations have diverged in their reliance on niche construction: larval niche construction appears to buffer against compromised maternal niche construction only in beetles from Western Australia, but not in beetles from the Eastern United States. We discuss our results in the context of rapid adaptation to novel conditions and the role of niche construction therein.},
}

@article {pmid33447816,
year = {2020},
author = {Vandeplassche, E and Sass, A and Ostyn, L and Burmølle, M and Kragh, KN and Bjarnsholt, T and Coenye, T and Crabbé, A},
title = {Antibiotic susceptibility of cystic fibrosis lung microbiome members in a multispecies biofilm.},
journal = {Biofilm},
volume = {2},
number = {},
pages = {100031},
pmid = {33447816},
issn = {2590-2075},
abstract = {The lungs of cystic fibrosis (CF) patients are often chronically colonized by multiple microbial species that can form biofilms, including the major CF pathogen Pseudomonas aeruginosa. Herewith, lower microbial diversity in CF airways is typically associated with worse health outcomes. In an attempt to treat CF lung infections patients are frequently exposed to antibiotics, which may affect microbial diversity. This study aimed at understanding if common antibiotics that target P. aeruginosa influence microbial diversity. To this end, a microaerophilic multispecies biofilm model of frequently co-isolated members of the CF lung microbiome (Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus anginosus, Achromobacter xylosoxidans, Rothia mucilaginosa, and Gemella haemolysans) was exposed to antipseudomonal antibiotics. We found that antibiotics that affected several dominant species (i.e. ceftazidime, tobramycin) resulted in higher species evenness compared to colistin, which is only active against P. aeruginosa. Furthermore, susceptibility of individual species in the multispecies biofilm following antibiotic treatment was compared to that of the respective single-species biofilms, showing no differences. Adding three anaerobic species (Prevotella melaninogenica, Veillonella parvula, and Fusobacterium nucleatum) to the multispecies biofilm did not influence antibiotic susceptibility. In conclusion, our study demonstrates antibiotic-dependent effects on microbial community diversity of multispecies biofilms comprised of CF microbiome members.},
}

@article {pmid33447811,
year = {2020},
author = {Zea, L and McLean, RJC and Rook, TA and Angle, G and Carter, DL and Delegard, A and Denvir, A and Gerlach, R and Gorti, S and McIlwaine, D and Nur, M and Peyton, BM and Stewart, PS and Sturman, P and Velez Justiniano, YA},
title = {Potential biofilm control strategies for extended spaceflight missions.},
journal = {Biofilm},
volume = {2},
number = {},
pages = {100026},
pmid = {33447811},
issn = {2590-2075},
support = {80NSSC17K0036/ImNASA/Intramural NASA/United States ; },
abstract = {Biofilms, surface-adherent microbial communities, are associated with microbial fouling and corrosion in terrestrial water-distribution systems. Biofilms are also present in human spaceflight, particularly in the Water Recovery System (WRS) on the International Space Station (ISS). The WRS is comprised of the Urine Processor Assembly (UPA) and the Water Processor Assembly (WPA) which together recycles wastewater from human urine and recovered humidity from the ISS atmosphere. These wastewaters and various process streams are continually inoculated with microorganisms primarily arising from the space crew microbiome. Biofilm-related fouling has been encountered and addressed in spacecraft in low Earth orbit, including ISS and the Russian Mir Space Station. However, planned future missions beyond low Earth orbit to the Moon and Mars present additional challenges, as resupplying spare parts or support materials would be impractical and the mission timeline would be in the order of years in the case of a mission to Mars. In addition, future missions are expected to include a period of dormancy in which the WRS would be unused for an extended duration. The concepts developed in this review arose from a workshop including NASA personnel and representatives with biofilm expertise from a wide range of industrial and academic backgrounds. Here, we address current strategies that are employed on Earth for biofilm control, including antifouling coatings and biocides and mechanisms for mitigating biofilm growth and damage. These ideas are presented in the context of their applicability to spaceflight and identify proposed new topics of biofilm control that need to be addressed in order to facilitate future extended, crewed, spaceflight missions.},
}

@article {pmid33447732,
year = {2021},
author = {Shen, H and Ding, L and Baig, M and Tian, J and Wang, Y and Huang, W},
title = {Improving glucose and lipids metabolism: drug development based on bile acid related targets.},
journal = {Cell stress},
volume = {5},
number = {1},
pages = {1-18},
pmid = {33447732},
issn = {2523-0204},
support = {R01 DK124627/DK/NIDDK NIH HHS/United States ; },
abstract = {Bariatric surgery is one of the most effective treatment options for severe obesity and its comorbidities. However, it is a major surgery that poses several side effects and risks which impede its clinical use. Therefore, it is urgent to develop alternative safer pharmacological approaches to mimic bariatric surgery. Recent studies suggest that bile acids are key players in mediating the metabolic benefits of bariatric surgery. Bile acids can function as signaling molecules by targeting bile acid nuclear receptors and membrane receptors, like FXR and TGR5 respectively. In addition, the composition of bile acids is regulated by either the hepatic sterol enzymes such as CYP8B1 or the gut microbiome. These bile acid related targets all play important roles in regulating metabolism. Drug development based on these targets could provide new hope for patients without the risks of surgery and at a lower cost. In this review, we summarize the most updated progress on bile acid related targets and development of small molecules as drug candidates based on these targets.},
}

@article {pmid33446997,
year = {2020},
author = {Liu, F and Liu, M and Liu, Y and Guo, C and Zhou, Y and Li, F and Xu, R and Liu, Z and Deng, Q and Li, X and Zhang, C and Pan, Y and Ning, T and Dong, X and Hu, Z and Bao, H and Cai, H and Silva, IDS and He, Z and Ke, Y},
title = {Oral microbiome and risk of malignant esophageal lesions in a high-risk area of China: A nested case-control study.},
journal = {Chinese journal of cancer research = Chung-kuo yen cheng yen chiu},
volume = {32},
number = {6},
pages = {742-754},
pmid = {33446997},
issn = {1000-9604},
abstract = {Objective: We aimed to prospectively evaluate the association of oral microbiome with malignant esophageal lesions and its predictive potential as a biomarker of risk.

Methods: We conducted a case-control study nested within a population-based cohort with up to 8 visits of oral swab collection for each subject over an 11-year period in a high-risk area for esophageal cancer in China. The oral microbiome was evaluated with 16S ribosomal RNA (rRNA) gene sequencing in 428 pre-diagnostic oral specimens from 84 cases with esophageal lesions of severe squamous dysplasia and above (SDA) and 168 matched healthy controls. DESeq analysis was performed to identify taxa of differential abundance. Differential oral species together with subject characteristics were evaluated for their potential in predicting SDA risk by constructing conditional logistic regression models.

Results: A total of 125 taxa including 37 named species showed significantly different abundance between SDA cases and controls (all P<0.05 & false discovery rate-adjusted Q<0.10). A multivariate logistic model including 11 SDA lesion-related species and family history of esophageal cancer provided an area under the receiver operating characteristic curve (AUC) of 0.89 (95% CI, 0.84-0.93). Cross-validation and sensitivity analysis, excluding cases diagnosed within 1 year of collection of the baseline specimen and their matched controls, or restriction to screen-endoscopic-detected or clinically diagnosed case-control triads, or using only bacterial data measured at the baseline, yielded AUCs>0.84.

Conclusions: The oral microbiome may play an etiological and predictive role in esophageal cancer, and it holds promise as a non-invasive early warning biomarker for risk stratification for esophageal cancer screening programs.},
}

@article {pmid33446825,
year = {2021},
author = {Corrêa, R and de Oliveira Santos, I and Braz-de-Melo, HA and de Sant'Ana, LP and das Neves Almeida, R and Pasquarelli-do-Nascimento, G and Prado, PS and Kobinger, GP and Maurice, CF and Magalhães, KG},
title = {Gut microbiota modulation induced by Zika virus infection in immunocompetent mice.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1421},
pmid = {33446825},
issn = {2045-2322},
support = {193.001.621/2016//Fundação de Apoio à Pesquisa do Distrito Federal/ ; },
abstract = {Gut microbiota composition can modulate neuroendocrine function, inflammation, and cellular and immunological responses against different pathogens, including viruses. Zika virus (ZIKV) can infect adult immunocompetent individuals and trigger brain damage and antiviral responses. However, it is not known whether ZIKV infection could impact the gut microbiome from adult immunocompetent mice. Here, we investigated modifications induced by ZIKV infection in the gut microbiome of immunocompetent C57BL/6J mice. Adult C57BL/6J mice were infected with ZIKV and the gut microbiota composition was analyzed by next-generation sequencing of the V4 hypervariable region present in the bacterial 16S rDNA gene. Our data showed that ZIKV infection triggered a significant decrease in the bacteria belonging to Actinobacteria and Firmicutes phyla, and increased Deferribacteres and Spirochaetes phyla components compared to uninfected mice. Interestingly, ZIKV infection triggered a significant increase in the abundance of bacteria from the Spirochaetaceae family in the gut microbiota. Lastly, we demonstrated that modulation of microbiota induced by ZIKV infection may lead to intestinal epithelium damage and intense leukocyte recruitment to the intestinal mucosa. Taken together, our data demonstrate that ZIKV infection can impact the gut microbiota composition and colon tissue homeostasis in adult immunocompetent mice.},
}

@article {pmid33446697,
year = {2021},
author = {Marcos-Fernández, R and Ruiz, L and Blanco-Míguez, A and Margolles, A and Sánchez, B},
title = {Precision modification of the human gut microbiota targeting surface-associated proteins.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1270},
pmid = {33446697},
issn = {2045-2322},
support = {AGL2016-78311-R//Agencia Estatal de Investigación/ ; AGL2016-78311-R//Agencia Estatal de Investigación/ ; IDI/2018/000236//Plan Regional de Investigación del Principado de Asturias/ ; IDI/2018/000236//Plan Regional de Investigación del Principado de Asturias/ ; PS-2016//AECC/ ; },
abstract = {This work describes a new procedure that allows the targeted modification of the human gut microbiota by using antibodies raised against bacterial surface-associated proteins specific to the microorganism of interest. To this end, a polyclonal antibody recognising the surface-associated protein Surface Layer Protein A of Lactobacillus acidophilus DSM20079T was developed. By conjugating this antibody with fluorescent probes and magnetic particles, we were able to specifically identify this bacterium both in a synthetic, and in real gut microbiotas by means of a flow cytometry approach. Further, we demonstrated the applicability of this antibody to deplete complex human gut microbiotas from L. acidophilus in a single step. L. acidophilus was found to interact with other bacteria both in synthetic and in real microbiotas, as reflected by its concomitant depletion together with other species. Further optimization of the procedure including a trypsin step enabled to achieve the selective and complete isolation of this species. Depleting a single species from a gut microbiota, using antibodies recognizing specific cell surface elements of the target organism, will open up novel ways to tackle research on the specific immunomodulatory and metabolic contributions of a bacterium of interest in the context of a complex human gut microbiota, including the investigation into therapeutic applications by adding/depleting a key bacterium. This represents the first work in which an antibody/flow-cytometry based application enabled the targeted edition of human gut microbiotas, and represents the basis for the design of precision microbiome-based therapies.},
}

@article {pmid33446688,
year = {2021},
author = {Monteiro, MF and Altabtbaei, K and Kumar, PS and Casati, MZ and Ruiz, KGS and Sallum, EA and Nociti-Junior, FH and Casarin, RCV},
title = {Parents with periodontitis impact the subgingival colonization of their offspring.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1357},
pmid = {33446688},
issn = {2045-2322},
support = {2015/50264-0//Sao Paolo Research Foundation/ ; },
abstract = {Early acquisition of a pathogenic microbiota and the presence of dysbiosis in childhood is associated with susceptibility to and the familial aggregation of periodontitis. This longitudinal interventional case-control study aimed to evaluate the impact of parental periodontal disease on the acquisition of oral pathogens in their offspring. Subgingival plaque and clinical periodontal metrics were collected from 18 parents with a history of generalized aggressive periodontitis and their children (6-12 years of age), and 18 periodontally healthy parents and their parents at baseline and following professional oral prophylaxis. 16S rRNA amplicon sequencing revealed that parents were the primary source of the child's microbiome, affecting their microbial acquisition and diversity. Children of periodontitis parents were preferentially colonized by Filifactor alocis, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, Streptococcus parasanguinis, Fusobacterium nucleatum and several species belonging to the genus Selenomonas even in the absence of periodontitis, and these species controlled inter-bacterial interactions. These pathogens also emerged as robust discriminators of the microbial signatures of children of parents with periodontitis. Plaque control did not modulate this pathogenic pattern, attesting to the microbiome's resistance to change once it has been established. This study highlights the critical role played by parental disease in microbial colonization patterns in their offspring and the early acquisition of periodontitis-related species and underscores the need for greater surveillance and preventive measures in families of periodontitis patients.},
}

@article {pmid33446604,
year = {2021},
author = {Sulaiman, I and Wu, BG and Li, Y and Tsay, JC and Sauthoff, M and Scott, AS and Ji, K and Koralov, SB and Weiden, M and Clemente, J and Jones, D and Huang, YJ and Stringer, KA and Zhang, L and Geber, A and Banakis, S and Tipton, L and Ghedin, E and Segal, LN},
title = {Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism.},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.03434-2020},
pmid = {33446604},
issn = {1399-3003},
abstract = {RATIONALE: Microbiome studies of the lower airway based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary.

METHODS: Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model.

MEASUREMENTS: We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole genome (WGS) and RNA metatranscriptome sequencing. Short chain fatty acids (SCFA) were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed.

MAIN RESULTS: Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFAs levels were compared with WGS and metatranscriptome. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing.

CONCLUSIONS: Functional characterisation of the lower airway microbiota through metatranscriptome identify metabolically active organisms capable of producing metabolites with immunomodulatory capacity such as SCFAs.},
}

@article {pmid33446262,
year = {2021},
author = {Maldonado-Ruiz, LP and Neupane, S and Park, Y and Zurek, L},
title = {The bacterial community of the lone star tick (Amblyomma americanum).},
journal = {Parasites & vectors},
volume = {14},
number = {1},
pages = {49},
pmid = {33446262},
issn = {1756-3305},
support = {GAČR 19-04301S//Grantová Agentura České Republiky/ ; },
abstract = {BACKGROUND: The lone star tick (Amblyomma americanum), an important vector of a wide range of human and animal pathogens, is very common throughout the East and Midwest of the USA. Ticks are known to carry non-pathogenic bacteria that may play a role in their vector competence for pathogens. Several previous studies using the high throughput sequencing (HTS) technologies reported the commensal bacteria in a tick midgut as abundant and diverse. In contrast, in our preliminary survey of the field collected adult lone star ticks, we found the number of culturable/viable bacteria very low.

METHODS: We aimed to analyze the bacterial community of A. americanum by a parallel culture-dependent and a culture-independent approach applied to individual ticks.

RESULTS: We analyzed 94 adult females collected in eastern Kansas and found that 60.8% of ticks had no culturable bacteria and the remaining ticks carried only 67.7 ± 42.8 colony-forming units (CFUs)/tick representing 26 genera. HTS of the 16S rRNA gene resulted in a total of 32 operational taxonomic units (OTUs) with the dominant endosymbiotic genera Coxiella and Rickettsia (> 95%). Remaining OTUs with very low abundance were typical soil bacterial taxa indicating their environmental origin.

CONCLUSIONS: No correlation was found between the CFU abundance and the relative abundance from the culture-independent approach. This suggests that many culturable taxa detected by HTS but not by culture-dependent method were not viable or were not in their culturable state. Overall, our HTS results show that the midgut bacterial community of A. americanum is very poor without a core microbiome and the majority of bacteria are endosymbiotic.},
}

@article {pmid33446094,
year = {2021},
author = {Short, MI and Hudson, R and Besasie, BD and Reveles, KR and Shah, DP and Nicholson, S and Johnson-Pais, TL and Weldon, K and Lai, Z and Leach, RJ and Fongang, B and Liss, MA},
title = {Comparison of rectal swab, glove tip, and participant-collected stool techniques for gut microbiome sampling.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {26},
pmid = {33446094},
issn = {1471-2180},
support = {U01 CA086402/NH/NIH HHS/United States ; P30 CA054174/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Studies of the gut microbiome are becoming increasingly important. Such studies require stool collections that can be processed or frozen in a timely manner so as not to alter the microbial content. Due to the logistical difficulties of home-based stool collection, there has been a challenge in selecting the appropriate sample collection technique and comparing results from different microbiome studies. Thus, we compared stool collection and two alternative clinic-based fecal microbiome collection techniques, including a newer glove-based collection method.

RESULTS: We prospectively enrolled 22 adult men from our prostate cancer screening cohort SABOR (San Antonio Biomarkers of Risk for prostate cancer) in San Antonio, TX, from 8/2018 to 4/2019. A rectal swab and glove tip sample were collected from each participant during a one-time visit to our clinics. A single stool sample was collected at the participant's home. DNA was isolated from the fecal material and 16 s rRNA sequencing of the V1-V2 and V3-V4 regions was performed. We found the gut microbiome to be similar in richness and evenness, noting no differences in alpha diversity among the collection methods. The stool collection method, which remains the gold-standard method for the gut microbiome, proved to have different community composition compared to swab and glove tip techniques (p< 0.001) as measured by Bray-Curtis and unifrac distances. There were no significant differences in between the swab and glove tip samples with regard to beta diversity (p> 0.05). Despite differences between home-based stool and office-based fecal collection methods, we noted that the distance metrics for the three methods cluster by participant indicating within-person similarities. Additionally, no taxa differed among the methods in a Linear Discriminant Analysis Effect Size (LEfSe) analysis comparing all-against-all sampling methods.

CONCLUSION: The glove tip method provides similar gut microbiome results as rectal swab and stool microbiome collection techniques. The addition of a new office-based collection technique could help easy and practical implementation of gut microbiome research studies and clinical practice.},
}

@article {pmid33446027,
year = {2021},
author = {Berard, AR and Miller, C and Araínga, M and Broedlow, CA and Noël-Romas, L and Schifanella, L and Hensley-McBain, T and Roederer, A and Driscoll, C and Coronado, E and Manuzak, J and McKinnon, LR and Villinger, FJ and Hope, TJ and Burgener, AD and Klatt, NR},
title = {SIV susceptibility, immunology and microbiome in the female genital tract of adolescent versus adult pigtail macaques.},
journal = {AIDS research and human retroviruses},
volume = {},
number = {},
pages = {},
doi = {10.1089/AID.2020.0271},
pmid = {33446027},
issn = {1931-8405},
abstract = {In Sub-Saharan Africa, young women aged 15-24 account for nearly 30% of all new HIV infections, however biological and epidemiological factors underlying this disproportionate infection rate are unclear. Here, we assessed biological contributors of SIV/HIV susceptibility in the female genital tract (FGT) using adolescent (n=9) and adult (n=10) pigtail macaques (PTMs) with weekly low-dose intravaginal challenges of SIV. Immunological variables were captured in vaginal tissue of PTMs by flow cytometry and cytokine assays. Vaginal biopsies were profiled by proteomic analysis. The vaginal microbiome was assessed by 16S rRNA sequencing. We were powered to detect a 2.2-fold increase in infection rates between age groups, however we identified no significant differences in susceptibility. This model cannot capture epidemiological factors or may not best represent biological differences of HIV susceptibility. No immune cell subsets measured were significantly different between groups. Inflammatory marker MCP-1 was significantly higher (adj p=0.02), and sCD40L trended higher (adj p=0.06) in vaginal cytobrushes of adults. Proteomic analysis of vaginal biopsies showed no significant (adj p<0.05) protein or pathway differences between groups. Vaginal microbiomes were not significantly different between groups. No differences were observed between age groups in this PTM model, however these animals may not reflect biological factors contributing to HIV risk such as those found in their human counterparts. This model is therefore not appropriate to explore human adolescent differences in HIV risk. Young women remain a key population at risk for HIV infection, and there is still a need for comprehensive assessments and interventions strategies for epidemic control of this uniquely vulnerable population.},
}

@article {pmid33446008,
year = {2021},
author = {DeDecker, L and Coppedge, B and Avelar-Barragan, J and Karnes, W and Whiteson, K},
title = {Microbiome distinctions between the CRC carcinogenic pathways.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/19490976.2020.1854641},
pmid = {33446008},
issn = {1949-0984},
abstract = {Colorectal cancer (CRC) is the third most commonly diagnosed cancer, the third leading cause of cancer-related deaths, and has been on the rise among young adults in the United States. Research has established that the colonic microbiome is different in patients with CRC compared to healthy controls, but few studies have investigated if and how the microbiome may relate to CRC progression through the serrated pathway versus the adenoma-carcinoma sequence. Our view is that progress in CRC microbiome research requires consideration of how the microbiome may contribute to CRC carcinogenesis through the distinct pathways that lead to CRC, which could enable the creation of novel and tailored prevention, screening, and therapeutic interventions. We first highlight the limitations in existing CRC microbiome research and offer corresponding solutions for investigating the microbiome's role in the adenoma-carcinoma sequence and serrated pathway. We then summarize the findings in the select human studies that included data points related to the two major carcinogenic pathways. These studies investigate the microbiome in CRC carcinogenesis and 1) utilize mucosal samples and 2) compare polyps or tumors by histopathologic type, molecular/genetic type, or location in the colon. Key findings from these studies include: 1) Fusobacterium is associated with right-sided, more advanced, and serrated lesions; 2) the colons of people with CRC have bacteria typically associated with normal oral flora; and 3) colons from people with CRC have more biofilms, and these biofilms are predominantly located in the proximal colon (single study).},
}

@article {pmid33445765,
year = {2021},
author = {Wassermann, B and Korsten, L and Berg, G},
title = {Plant Health and Sound Vibration: Analyzing Implications of the Microbiome in Grape Wine Leaves.},
journal = {Pathogens (Basel, Switzerland)},
volume = {10},
number = {1},
pages = {},
doi = {10.3390/pathogens10010063},
pmid = {33445765},
issn = {2076-0817},
support = {ZA 01/2019//Servicestelle für Mobilitätsprogramme des österreichischen Bundesministeriums für Bildung, Wissenschaft und Forschung, KulturKontakt Austria/ ; },
abstract = {Understanding the plant microbiome is a key for plant health and controlling pathogens. Recent studies have shown that plants are responsive towards natural and synthetic sound vibration (SV) by perception and signal transduction, which resulted in resistance towards plant pathogens. However, whether or not native plant microbiomes respond to SV and the underlying mechanism thereof remains unknown. Within the present study we compared grapevine-associated microbiota that was perpetually exposed to classical music with a non-exposed control group from the same vineyard in Stellenbosch, South Africa. By analyzing the 16S rRNA gene and ITS fragment amplicon libraries we found differences between the core microbiome of SV-exposed leaves and the control group. For several of these different genera, e.g., Bacillus, Kocuria and Sphingomonas, a host-beneficial or pathogen-antagonistic effect has been well studied. Moreover, abundances of taxa identified as potential producers of volatile organic compounds that contribute to sensory characteristics of wines, e.g., Methylobacterium, Sphingomonas, Bacillus and Sporobolomyces roseus, were either increased or even unique within the core music-exposed phyllosphere population. Results show an as yet unexplored avenue for improved plant health and the terroir of wine, which are important for environmentally friendly horticulture and consumer appreciation. Although our findings explain one detail of the long-term positive experience to improve grapevine's resilience by this unusual but innovative technique, more mechanistic studies are necessary to understand the whole interplay.},
}

@article {pmid33445571,
year = {2021},
author = {Moore, EK},
title = {Trimethylornithine Membrane Lipids: Discovered in Planctomycetes and Identified in Diverse Environments.},
journal = {Metabolites},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/metabo11010049},
pmid = {33445571},
issn = {2218-1989},
abstract = {Intact polar membrane lipids (IPLs) are the building blocks of all cell membranes. There is a wide range of phosphorus-free IPL structures, including amino acid containing IPLs, that can be taxonomically specific. Trimethylornithine membrane lipids (TMOs) were discovered in northern wetland Planctomycete species that were isolated and described in the last decade. The trimethylated terminal nitrogen moiety of the ornithine amino acid in the TMO structure gives the lipid a charged polar head group, similar to certain phospholipids. Since their discovery, TMOs have been identified in various other recently described northern latitude Planctomycete species, and in diverse environments including tundra soil, a boreal eutrophic lake, meso-oligotrophic lakes, and hot springs. The majority of environments or enrichment cultures in which TMOs have been observed include predominately heterotrophic microbial communities involved in the degradation of recalcitrant material and/or low oxygen methanogenic conditions at primarily northern latitudes. Other ecosystems occupied with microbial communities that possess similar metabolic pathways, such as tropical peatlands or coastal salt marshes, may include TMO producing Planctomycetes as well, further allowing these lipids to potentially be used to understand microbial community responses to environmental change in a wide range of systems. The occurrence of TMOs in hot springs indicates that these unique lipids could have broad environmental distribution with different specialized functions. Opportunities also exist to investigate the application of TMOs in microbiome studies, including forensic necrobiomes. Further environmental and microbiome lipidomics research involving TMOs will help reveal the evolution, functions, and applications of these unique membrane lipids.},
}

@article {pmid33445538,
year = {2021},
author = {Fliegerova, KO and Podmirseg, SM and Vinzelj, J and Grilli, DJ and Kvasnová, S and Schierová, D and Sechovcová, H and Mrázek, J and Siddi, G and Arenas, GN and Moniello, G},
title = {The Effect of a High-Grain Diet on the Rumen Microbiome of Goats with a Special Focus on Anaerobic Fungi.},
journal = {Microorganisms},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/microorganisms9010157},
pmid = {33445538},
issn = {2076-2607},
abstract = {This work investigated the changes of the rumen microbiome of goats switched from a forage to a concentrate diet with special attention to anaerobic fungi (AF). Female goats were fed an alfalfa hay (AH) diet (0% grain; n = 4) for 20 days and were then abruptly shifted to a high-grain (HG) diet (40% corn grain, 60% AH; n = 4) and treated for another 10 days. Rumen content samples were collected from the cannulated animals at the end of each diet period (day 20 and 30). The microbiome structure was studied using high-throughput sequencing for bacteria, archaea (16S rRNA gene) and fungi (ITS2), accompanied by qPCR for each group. To further elucidate unclassified AF, clone library analyses were performed on the ITS1 spacer region. Rumen pH was significantly lower in HG diet fed goats, but did not induce subacute ruminal acidosis. HG diet altered prokaryotic communities, with a significant increase of Bacteroidetes and a decrease of Firmicutes. On the genus level Prevotella 1 was significantly boosted. Methanobrevibacter and Methanosphaera were the most abundant archaea regardless of the diet and HG induced a significant augmentation of unclassified Thermoplasmatales. For anaerobic fungi, HG triggered a considerable rise in Feramyces observed with both ITS markers, while a decline of Tahromyces was detected by ITS2 and decrease of Joblinomyces by ITS1 only. The uncultured BlackRhino group revealed by ITS1 and further elucidated in one sample by LSU analysis, formed a considerable part of the AF community of goats fed both diets. Results strongly indicate that the rumen ecosystem still acts as a source for novel microorganisms and unexplored microbial interactions and that initial rumen microbiota of the host animal considerably influences the reaction pattern upon diet change.},
}

@article {pmid33444573,
year = {2021},
author = {Saha, S and Mara, K and Pardi, DS and Khanna, S},
title = {Long-term Safety of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2021.01.010},
pmid = {33444573},
issn = {1528-0012},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is highly effective for treating recurrent Clostridioides difficile infection (CDI), with emerging data on intermediate and long-term safety.

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

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

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

@article {pmid33444433,
year = {2021},
author = {Kerkhof, LJ},
title = {Is oxford nanopore sequencing ready for analyzing complex microbiomes?.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiab001},
pmid = {33444433},
issn = {1574-6941},
abstract = {This minireview will discuss the improvements in Oxford Nanopore sequencing technology which make the MinION a viable platform for microbial ecology studies. Specific issues being addressed are the increase in sequence accuracy from 65-96.5% during the last 5 years, the ability to obtain a quantifiable/predictive signal from the MinION with respect to target molecule abundance, simple-to-use GUI-based pathways for data analysis, and the modest additional equipment needs for sequencing in the field. Coupling these recent improvements with the low capital costs for equipment and the reasonable per sample cost makes MinION sequencing an attractive option for virtually any laboratory.},
}

@article {pmid33444319,
year = {2021},
author = {McKinney, CA and Bedenice, D and Pacheco, AP and Oliveira, BCM and Paradis, MR and Mazan, M and Widmer, G},
title = {Assessment of clinical and microbiota responses to fecal microbial transplantation in adult horses with diarrhea.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244381},
doi = {10.1371/journal.pone.0244381},
pmid = {33444319},
issn = {1932-6203},
abstract = {BACKGROUND AND AIMS: Fecal microbial transplantation (FMT) is empirically implemented in horses with colitis to facilitate resolution of diarrhea. The purpose of this study was to assess FMT as a clinical treatment and modulator of fecal microbiota in hospitalized horses with colitis.

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

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

@article {pmid33443802,
year = {2021},
author = {Wang, M and Zhao, H and Wen, X and Ho, CT and Li, S},
title = {Citrus flavonoids and the intestinal barrier: Interactions and effects.},
journal = {Comprehensive reviews in food science and food safety},
volume = {20},
number = {1},
pages = {225-251},
doi = {10.1111/1541-4337.12652},
pmid = {33443802},
issn = {1541-4337},
support = {2019ABA100//Hubei Province Technical Innovation Special Project/ ; 81803548//National Natural Science Foundation of China/ ; 19JCQNJC12400//Natural Science Foundation of Tianjin City/ ; TD13-5087//Tianjin Innovative Research Team Grant/ ; },
abstract = {The intestinal barrier plays a central role in sustaining gut homeostasis and, when dysfunctional, may contribute to diseases. Dietary flavonoids derived from Citrus genus represent one of the main naturally occurring phytochemicals with multiple potential benefits for the intestinal barrier function. In the intestine, citrus flavonoids (CFs) undergo ingestion from the lumen, biotransformation in the epithelial cells and/or crosstalk with luminal microbiota to afford various metabolites that may in turn exert protective actions on gut barrier along with their parental compounds. Specifically, the health-promoting properties of CFs and their metabolic bioactives for the intestinal barrier include their capacity to (a) modulate barrier permeability; (b) protect mucus layer; (c) regulate intestinal immune system; (d) fight against oxidative stress; and (e) positively shape microbiome and metabolome. Notably, local effects of CFs can also generate systemic benefits, for instance, improvement of gut microbial dysbiosis helpful to orchestrate gut homeostasis and leading to alleviation of systemic dysmetabolism. Given the important role of the intestinal barrier in overall health, further understanding of underlying action mechanisms and ultimate health effects of CFs as well as their metabolites on the intestine is of great significance to future application of citrus plants and their bioactives as dietary supplements and/or functional ingredients in medical foods.},
}

@article {pmid33443749,
year = {2020},
author = {Hens, K},
title = {[You should exercise a bit more - The ethics of lifestyle and mental health].},
journal = {Tijdschrift voor psychiatrie},
volume = {62},
number = {11},
pages = {976-980},
pmid = {33443749},
issn = {0303-7339},
abstract = {BACKGROUND: The fact that environmental factors and lifestyle play a role in mental health is well known. In the last decades more research has gone into the link between environment and genetics: epigenetics has shown us the molecular link between these two, and the influence of the microbiome on mental health has demonstrated the importance of food. Still, ethical questions remain about how lifestyle advice can be integrated in clinical practice in an ethical way. AIM: To describe the normative import of our view on biology and individual responsibility and the place of lifestyle in the debate. METHOD: A consideration of ethical aspects of lifestyle and lifestyle advice. RESULTS: The normative import of our view on biology and individual responsibility and the place of lifestyle in the debate is described. It is argued that lifestyle has a unique place between biological and psychosocial concepts. Finally, the pitfalls and opportunities of introducing lifestyle in clinical practice are shown. CONCLUSION: Lifestyle is conceptually situated between the biological and the psychosocial, and sheds new light on the importance of certain explanations for recovery, and the relation with specific treatments. Lifestyle advice can only be used optimally in therapy if mental health care professionals also include a dialogue about assumptions and expectations.},
}

@article {pmid33443714,
year = {2021},
author = {Yang, H and Zhang, Y and Chuang, S and Cao, W and Ruan, Z and Xu, X and Jiang, J},
title = {Bioaugmentation of acetamiprid-contaminated soil with Pigmentiphaga sp. strain D-2 and its effect on the soil microbial community.},
journal = {Ecotoxicology (London, England)},
volume = {},
number = {},
pages = {},
pmid = {33443714},
issn = {1573-3017},
support = {2018YFA0901200//National Key R&D Program of china/ ; 2018YFA0901200//National Key R&D Program of china/ ; 2018YFA0901200//National Key R&D Program of china/ ; 41977120//National Natural Science Foundation of China/ ; },
abstract = {Bioaugmentation, a strategy based on microbiome engineering, has been proposed for bioremediation of pollutant-contaminated environments. However, the complex microbiome engineering processes for soil bioaugmentation, involving interactions among the exogenous inoculum, soil environment, and indigenous microbial microbiome, remain largely unknown. Acetamiprid is a widely used neonicotinoid insecticide which has caused environmental contaminations. Here, we used an acetamiprid-degrading strain, Pigmentiphaga sp. D-2, as inoculum to investigate the effects of bioaugmentation on the soil microbial community and the process of microbiome reassembly. The bioaugmentation treatment removed 94.8 and 92.5% of acetamiprid within 40 days from soils contaminated with 50 and 200 mg/kg acetamiprid, respectively. A decrease in bacterial richness and diversity was detected in bioaugmentation treatments, which later recovered with the removal of acetamiprid from soil. Moreover, the bioaugmentation treatment significantly influenced the bacterial community structure, whereas application of acetamiprid alone had little influence on the soil microbial community. Furthermore, the bioaugmentation treatment improved the growth of bacteria associated with acetamiprid degradation, and the inoculated and recruited taxa significantly influenced the keystone taxa of the indigenous microbiome, resulting in reassembly of the bacterial community yielding higher acetamiprid-degrading efficiency than that of the indigenous and acetamiprid-treated communities. Our results provide valuable insights into the mechanisms of microbiome engineering for bioaugmentation of acetamiprid-contaminated soils.},
}

@article {pmid33443222,
year = {2021},
author = {Wang, Q and Kim, SY and Matsushita, H and Wang, Z and Pandyarajan, V and Matsuda, M and Ohashi, K and Tsuchiya, T and Roh, YS and Kiani, C and Zhao, Y and Chan, M and Devkota, S and Lu, SC and Hayashi, T and Carson, DA and Seki, E},
title = {Oral administration of PEGylated TLR7 ligand ameliorates alcohol-associated liver disease via the induction of IL-22.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {1},
pages = {},
doi = {10.1073/pnas.2020868118},
pmid = {33443222},
issn = {1091-6490},
abstract = {Effective therapies for alcohol-associated liver disease (ALD) are limited; therefore, the discovery of new therapeutic agents is greatly warranted. Toll-like receptor 7 (TLR7) is a pattern recognition receptor for single-stranded RNA, and its activation prevents liver fibrosis. We examined liver and intestinal damage in Tlr7-/- mice to determine the role of TLR7 in ALD pathogenesis. In an alcoholic hepatitis (AH) mouse model, hepatic steatosis, injury, and inflammation were induced by chronic binge ethanol feeding in mice, and Tlr7 deficiency exacerbated these effects. Because these results demonstrated that endogenous TLR7 signaling activation is protective in the AH mouse model, we hypothesized that TLR7 activation may be an effective therapeutic strategy for ALD. Therefore, we investigated the therapeutic effect of TLR7 agonistic agent, 1Z1, in the AH mouse model. Oral administration of 1Z1 was well tolerated and prevented intestinal barrier disruption and bacterial translocation, which thus suppressed ethanol-induced hepatic injury, steatosis, and inflammation. Furthermore, 1Z1 treatment up-regulated the expression of antimicrobial peptides, Reg3b and Reg3g, in the intestinal epithelium, which modulated the microbiome by decreasing and increasing the amount of Bacteroides and Lactobacillus, respectively. Additionally, 1Z1 up-regulated intestinal interleukin (IL)-22 expression. IL-22 deficiency abolished the protective effects of 1Z1 in ethanol-induced liver and intestinal damage, suggesting intestinal IL-22 as a crucial mediator for 1Z1-mediated protection in the AH mouse model. Collectively, our results indicate that TLR7 signaling exerts protective effects in the AH mouse model and that a TLR7 ligand, 1Z1, holds therapeutic potential for the treatment of AH.},
}

@article {pmid33442763,
year = {2021},
author = {Mutnale, MC and Reddy, GS and Vasudevan, K},
title = {Bacterial Community in the Skin Microbiome of Frogs in a Coldspot of Chytridiomycosis Infection.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33442763},
issn = {1432-184X},
support = {BSC0207//Council of Scientific and Industrial Research, India/ ; },
abstract = {Chytridiomycosis is a fungal disease caused by the pathogens, Batrachochytrium dendrobatidis (Bd) and B. salamandrivorans (Bsal), which has caused declines in amphibian populations worldwide. Asia is considered as a coldspot of infection, since adult frogs are less susceptible to Bd-induced mortality or morbidity. Using the next-generation sequencing approach, we assessed the cutaneous bacterial community composition and presence of anti-Bd bacteria in six frog species from India using DNA isolated from skin swabs. All the six frog species sampled were tested using nested PCR and found Bd negative. We found a total of 551 OTUs on frog skin, of which the bacterial phyla such as Proteobacteria (56.15% average relative abundance) was dominated followed by Actinobacteria (21.98% average relative abundance) and Firmicutes (13.7% average relative abundance). The contribution of Proteobacteria in the anti-Bd community was highest and represented by 175 OTUs. Overall, the anti-Bd bacterial community dominated (51.7% anti-Bd OTUs) the skin microbiome of the frogs. The study highlights the putative role of frog skin microbiome in affording resistance to Bd infections in coldspots of infection.},
}

@article {pmid33442705,
year = {2021},
author = {Romano-Keeler, J and Fiszbein, D and Zhang, J and Horowitz, J and Hayani, K and Buhimschi, I and Lopez, C and Kadhem, Z and Berman, J and Rasamimari, P and Raghavan, A and Pillers, DM and Sun, J},
title = {Center-Based Experiences Implementing Strategies to Reduce Risk of Horizontal Transmission of SARS-Cov-2: Potential for Compromise of Neonatal Microbiome Assemblage.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2021.01.07.21249418},
pmid = {33442705},
abstract = {Perinatal transmission of COVID-19 is poorly understood and many neonatal intensive care units' (NICU) policies minimize mother-infant contact to prevent transmission. We present our unit's approach and ways it may impact neonatal microbiome acquisition. We attended COVID-19 positive mothers' deliveries from March-August 2020. Delayed cord clamping and skin-to-skin were avoided and infants were admitted to the NICU. No parents' visits were allowed and discharge was arranged with COVID-19 negative family members. Maternal breast milk was restricted in the NICU. All twenty-one infants tested negative at 24 and 48 hours and had average hospital stays of nine days. 40% of mothers expressed breastmilk and 30% of infants were discharged with COVID-19 negative caregivers. Extended hospital stays, no skin-to-skin contact, limited maternal milk use, and discharge to caregivers outside primary residences, potentially affect the neonatal microbiome. Future studies are warranted to explore how ours and other centers' similar policies influence this outcome.},
}

@article {pmid33442401,
year = {2021},
author = {Nie, S and Wang, A and Yuan, Y},
title = {Comparison of clinicopathological parameters, prognosis, micro-ecological environment and metabolic function of Gastric Cancer with or without Fusobacterium sp. Infection.},
journal = {Journal of Cancer},
volume = {12},
number = {4},
pages = {1023-1032},
pmid = {33442401},
issn = {1837-9664},
abstract = {Background: Fusobacterium sp. plays a crucial role in the tumorigenesis and development of gastrointestinal tumors. Our research group previously disclosed that Fusobacterium sp. was more abundant in gastric cancer (GC) tissues than adjacent non-cancerous (NC) tissues. However, Fusobacterium sp. did not exist in all GC tissues and the differentiated features of GC with or without Fusobacterium sp. infection is not clear. Methods: The expression data of 61 GC tissues came from 16S rRNA gene sequencing. Comparison groups were defined based on sOTU at the genus level of Fusobacterium sp., which was performed by the Qiime2 microbiome bioinformatics platform. We used Chi-square and Fisher's exact test to compare clinicopathological parameters, and used Kaplan-Meier analysis, Cox univariate and multivariate analysis to compare prognosis. Micro-ecological environment comparison was characterized by 16S rRNA gene sequencing, and the metabolic function prediction was applied by PICRUSt2. Results of microbial diversity, differential enrichment genus and metabolic function in GC with or without Fusobacterium sp. infection was validated with 229 GC tissues downloaded from an independent cohort in ENA database (PRJNA428883). Results: The infection rate of Fusobacterium sp. in 61 GC tissues was 52.46% and elderly GC patients were more prone to Fusobacterium sp. infection. GC patients infected with Fusobacterium sp. were more likely to have tumor-infiltrating lymphocytes and p53 expression. The microbial diversity and microbial structure showed significant differences between two GC tissue groups with 42 differential enrichment genera. The metabolic function of Fusobacterium sp.-positive GC tissues was related to the biosynthesis of lysine, peptidoglycan, and tRNA. The differences in microbial structure, the existence of some differential enrichment genera and the metabolic function of Fusobacterium sp.-positive GC tissues, were then validated by 229 GC tissues of an independent cohort. Conclusions: Fusobacterium sp. infection can affect the phenotypic characteristics, micro-ecological environment, and metabolic functions of GC, which may provide a basis for further exploring the relationship between Fusobacterium sp. infection and carcinogenesis of GC.},
}

@article {pmid33442384,
year = {2020},
author = {Xu, H and Cao, J and Li, X and Lu, X and Xia, Y and Fan, D and Zhao, H and Ju, D and Xiao, C},
title = {Regional Differences in the Gut Microbiota and Gut-Associated Immunologic Factors in the Ileum and Cecum of Rats With Collagen-Induced Arthritis.},
journal = {Frontiers in pharmacology},
volume = {11},
number = {},
pages = {587534},
pmid = {33442384},
issn = {1663-9812},
abstract = {Rheumatoid arthritis (RA) is a common autoimmune disease characterized by chronic inflammation and a multifactorial etiology. We previously showed that gut microbiota dysbiosis in the rat ileum is involved in the development of collagen-induced arthritis (CIA). The gut microbiota in the distinct gastrointestinal tract (GIT) plays region-specific roles, but information on the different roles of the microbiota in distinct GIT compartments of CIA rats is limited. This study aimed to evaluate the region-specific differences in the gut microbial communities and certain gut-associated immunologic factors in the ileum and cecum of CIA rats. Ileal and cecal digesta were collected from CIA and control rats for microbiome analysis. We determined the microbial richness, diversity and taxa as well as the expression of interleukin (IL)-1β and IL-17A in the epithelium and lamina propria of the ileum and cecum mucosal layers. The CIA-induced microbiota alterations in the ileum differed from those in the cecum. The ileal microbiota were more markedly influenced in CIA, as revealed by sharp reductions in the abundances of the families Enterococcaceae, Lactobacillaceae and Streptococcaceae and the genera Lactobacillus and Lactococcus. Moreover, significant increases in IL-1β, and IL-17A mRNA expression were detected in only the ileal epithelium and lamina propria of the mucosal layer. Therefore, the microbial characteristics in the ileum were consistent with the immune-mediated inflammatory features of CIA, suggesting that the ileal microbiota might better represent the CIA-induced inflammatory responses than the cecal microbiota and that these responses might partially impact the progression of RA by regulating intestinal mucosal immunity.},
}

@article {pmid33442010,
year = {2021},
author = {Stower, H},
title = {Microbiome transplant-induced response to immunotherapy.},
journal = {Nature medicine},
volume = {27},
number = {1},
pages = {21},
doi = {10.1038/s41591-020-01220-6},
pmid = {33442010},
issn = {1546-170X},
}

@article {pmid33441939,
year = {2021},
author = {Gopinath, D and Menon, RK and Wie, CC and Banerjee, M and Panda, S and Mandal, D and Behera, PK and Roychoudhury, S and Kheur, S and Botelho, MG and Johnson, NW},
title = {Differences in the bacteriome of swab, saliva, and tissue biopsies in oral cancer.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1181},
pmid = {33441939},
issn = {2045-2322},
abstract = {Microbial dysbiosis has been implicated in the pathogenesis of oral cancer. We analyzed the compositional and metabolic profile of the bacteriome in three specific niches in oral cancer patients along with controls using 16SrRNA sequencing (Illumina Miseq) and DADA2 software. We found major differences between patients and control subjects. Bacterial communities associated with the tumor surface and deep paired tumor tissue differed significantly. Tumor surfaces carried elevated abundances of taxa belonging to genera Porphyromonas, Enterobacteriae, Neisseria, Streptococcus and Fusobacteria, whereas Prevotella, Treponema, Sphingomonas, Meiothermus and Mycoplasma genera were significantly more abundant in deep tissue. The most abundant microbial metabolic pathways were those related to fatty-acid biosynthesis, carbon metabolism and amino-acid metabolism on the tumor surface: carbohydrate metabolism and organic polymer degradation were elevated in tumor tissues. The bacteriome of saliva from patients with oral cancer differed significantly from paired tumor tissue in terms of community structure, however remained similar at taxonomic and metabolic levels except for elevated abundances of Streptococcus, Lactobacillus and Bacteroides, and acetoin-biosynthesis, respectively. These shifts to a pro-inflammatory profile are consistent with other studies suggesting oncogenic properties. Importantly, selection of the principal source of microbial DNA is key to ensure reliable, reproducible and comparable results in microbiome studies.},
}

@article {pmid33441919,
year = {2021},
author = {Al Kawas, S and Al-Marzooq, F and Rahman, B and Shearston, JA and Saad, H and Benzina, D and Weitzman, M},
title = {The impact of smoking different tobacco types on the subgingival microbiome and periodontal health: a pilot study.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1113},
pmid = {33441919},
issn = {2045-2322},
support = {AJF2018014//Al Jalila Foundation/ ; NIH/NIEHS 1R21ES026996-01A1/NH/NIH HHS/United States ; },
abstract = {Smoking is a risk factor for periodontal disease, and a cause of oral microbiome dysbiosis. While this has been evaluated for traditional cigarette smoking, there is limited research on the effect of other tobacco types on the oral microbiome. This study investigates subgingival microbiome composition in smokers of different tobacco types and their effect on periodontal health. Subgingival plaques were collected from 40 individuals, including smokers of either cigarettes, medwakh, or shisha, and non-smokers seeking dental treatment at the University Dental Hospital in Sharjah, United Arab Emirates. The entire (~ 1500 bp) 16S rRNA bacterial gene was fully amplified and sequenced using Oxford Nanopore technology. Subjects were compared for the relative abundance and diversity of subgingival microbiota, considering smoking and periodontal condition. The relative abundances of several pathogens were significantly higher among smokers, such as Prevotella denticola and Treponema sp. OMZ 838 in medwakh smokers, Streptococcus mutans and Veillonella dispar in cigarette smokers, Streptococcus sanguinis and Tannerella forsythia in shisha smokers. Subgingival microbiome of smokers was altered even in subjects with no or mild periodontitis, probably making them more prone to severe periodontal diseases. Microbiome profiling can be a useful tool for periodontal risk assessment. Further studies are recommended to investigate the impact of tobacco cessation on periodontal disease progression and oral microbiome.},
}

@article {pmid33441848,
year = {2021},
author = {Góngora, E and Elliott, KH and Whyte, L},
title = {Gut microbiome is affected by inter-sexual and inter-seasonal variation in diet for thick-billed murres (Uria lomvia).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1200},
pmid = {33441848},
issn = {2045-2322},
support = {Discovery Grant 241061//Natural Sciences and Engineering Research Council of Canada/ ; Discovery Grant 74221//Natural Sciences and Engineering Research Council of Canada/ ; Arctic Ecology//Canada Research Chairs/ ; Polar Microbiology//Canada Research Chairs/ ; Northern Contaminants Program//Indigenous and Northern Affairs Canada/ ; },
abstract = {The role of the gut microbiome is increasingly being recognized by health scientists and veterinarians, yet its role in wild animals remains understudied. Variations in the gut microbiome could be the result of differential diets among individuals, such as variation between sexes, across seasons, or across reproductive stages. We evaluated the hypothesis that diet alters the avian gut microbiome using stable isotope analysis (SIA) and 16S rRNA gene sequencing. We present the first description of the thick-billed murre (Uria lomvia) fecal microbiome. The murre microbiome was dominated by bacteria from the genus Catellicoccus, ubiquitous in the guts of many seabirds. Microbiome variation was explained by murre diet in terms of proportion of littoral carbon, trophic position, and sulfur isotopes, especially for the classes Actinobacteria, Bacilli, Bacteroidia, Clostridia, Alphaproteobacteria, and Gammaproteobacteria. We also observed differences in the abundance of bacterial genera such as Catellicoccus and Cetobacterium between sexes and reproductive stages. These results are in accordance with behavioural observations of changes in diet between sexes and across the reproductive season. We concluded that the observed variation in the gut microbiome may be caused by individual prey specialization and may also be reinforced by sexual and reproductive stage differences in diet.},
}

@article {pmid33441819,
year = {2021},
author = {Zarantoniello, M and Randazzo, B and Nozzi, V and Truzzi, C and Giorgini, E and Cardinaletti, G and Freddi, L and Ratti, S and Girolametti, F and Osimani, A and Notarstefano, V and Milanović, V and Riolo, P and Isidoro, N and Tulli, F and Gioacchini, G and Olivotto, I},
title = {Physiological responses of Siberian sturgeon (Acipenser baerii) juveniles fed on full-fat insect-based diet in an aquaponic system.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1057},
pmid = {33441819},
issn = {2045-2322},
support = {NUTRIFISH project N° 2017.0571//Fondazione Cassa di Risparmio di Verona Vicenza Belluno e Ancona/ ; },
abstract = {Over the last years, the potential use of Black Soldier Fly meal (BSF) as a new and sustainable aquafeed ingredient has been largely explored in several fish species. However, only fragmentary information is available about the use of BSF meal-based diets in sturgeon nutrition. In consideration of a circular economy concept and a more sustainable aquaculture development, the present research represents the first comprehensive multidisciplinary study on the physiological effects of a BSF diet during sturgeon culture in an aquaponic system. Siberian sturgeon (Acipenser baerii) juveniles were fed over a 60-days feeding trial on a control diet (Hi0) and a diet containing 50% of full-fat BSF meal respect to fish meal (Hi50). Physiological responses of fish were investigated using several analytical approaches, such as gas chromatography-mass spectrometry, histology, Fourier Transformed Infrared Spectroscopy (FTIR), microbiome sequencing and Real-time PCR. While aquaponic systems performed optimally during the trial, Hi50 group fish showed lower diet acceptance that resulted in growth and survival reduction, a decrease in hepatic lipids and glycogen content (FTIR), a higher hepatic hsp70.1 gene expression and a worsening in gut histological morphometric parameters. The low feed acceptance showed by Hi50 group sturgeon highlighted the necessity to improve the palatability of BSF-based diet designed for sturgeon culture.},
}

@article {pmid33441754,
year = {2021},
author = {Imahashi, M and Ode, H and Kobayashi, A and Nemoto, M and Matsuda, M and Hashiba, C and Hamano, A and Nakata, Y and Mori, M and Seko, K and Nakahata, M and Kogure, A and Tanaka, Y and Sugiura, W and Yokomaku, Y and Iwatani, Y},
title = {Impact of long-term antiretroviral therapy on gut and oral microbiotas in HIV-1-infected patients.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {960},
pmid = {33441754},
issn = {2045-2322},
support = {18kk0205011h0203//Japan Agency for Medical Research and Development/ ; },
abstract = {In HIV-1-infected patients, antiretroviral therapy (ART) is a key factor that may impact commensal microbiota and cause the emergence of side effects. However, it is not fully understood how long-term ART regimens have diverse impacts on the microbial compositions over time. Here, we performed 16S ribosomal RNA gene sequencing of the fecal and salivary microbiomes in patients under different long-term ART. We found that ART, especially conventional nucleotide/nucleoside reverse transcriptase inhibitor (NRTI)-based ART, has remarkable impacts on fecal microbial diversity: decreased α-diversity and increased ß-diversity over time. In contrast, dynamic diversity changes in the salivary microbiome were not observed. Comparative analysis of bacterial genus compositions showed a propensity for Prevotella-enriched and Bacteroides-poor gut microbiotas in patients with ART over time. In addition, we observed a gradual reduction in Bacteroides but drastic increases in Succinivibrio and/or Megasphaera under conventional ART. These results suggest that ART, especially NRTI-based ART, has more suppressive impacts on microbiota composition and diversity in the gut than in the mouth, which potentially causes intestinal dysbiosis in patients. Therefore, NRTI-sparing ART, especially integrase strand transfer inhibitor (INSTI)- and/or non-nucleotide reverse transcriptase inhibitor (NNRTI)-containing regimens, might alleviate the burden of intestinal dysbiosis in HIV-1-infected patients under long-term ART.},
}

@article {pmid33441710,
year = {2021},
author = {Relvas, M and Regueira-Iglesias, A and Balsa-Castro, C and Salazar, F and Pacheco, JJ and Cabral, C and Henriques, C and Tomás, I},
title = {Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {929},
pmid = {33441710},
issn = {2045-2322},
support = {MVOS2016//CESPU, Gandra, Paredes, Portugal/ ; MVOS-PT-IINFACTS-2019//CESPU, Gandra, Paredes, Portugal/ ; ISCIII/PI17/01722//Instituto de Salud Carlos III and co-financed by FEDER, Madrid, Spain/ ; },
abstract = {The present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota's abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.},
}

@article {pmid33441592,
year = {2021},
author = {Jo, R and Yama, K and Aita, Y and Tsutsumi, K and Ishihara, C and Maruyama, M and Takeda, K and Nishinaga, E and Shibasaki, KI and Morishima, S},
title = {Comparison of oral microbiome profiles in 18-month-old infants and their parents.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {861},
pmid = {33441592},
issn = {2045-2322},
abstract = {The onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.},
}

@article {pmid33441409,
year = {2021},
author = {Fishbein, SRS and Hink, T and Reske, KA and Cass, C and Struttmann, E and Iqbal, ZH and Seiler, S and Kwon, JH and Burnham, CA and Dantas, G and Dubberke, ER},
title = {Randomized Controlled Trial of Oral Vancomycin Treatment in Clostridioides difficile-Colonized Patients.},
journal = {mSphere},
volume = {6},
number = {1},
pages = {},
pmid = {33441409},
issn = {2379-5042},
abstract = {Clostridioides difficile infection (CDI) is most commonly diagnosed using nucleic acid amplification tests (NAAT); the low positive predictive value of these assays results in patients colonized with C. difficile unnecessarily receiving CDI treatment antibiotics. The risks and benefits of antibiotic treatment in individuals with such cases are unknown. Fecal samples of NAAT-positive, toxin enzyme immunoassay (EIA)-negative patients were collected before, during, and after randomization to vancomycin (n = 8) or placebo (n = 7). C. difficile and antibiotic-resistant organisms (AROs) were selectively cultured from fecal and environmental samples. Shotgun metagenomics and comparative isolate genomics were used to understand the impact of oral vancomycin on the microbiome and environmental contamination. Overall, 80% of placebo patients and 71% of vancomycin patients were colonized with C. difficile posttreatment. One person randomized to placebo subsequently received treatment for CDI. In the vancomycin-treated group, beta-diversity (P = 0.0059) and macrolide-lincosamide-streptogramin (MLS) resistance genes (P = 0.037) increased after treatment; C. difficile and vancomycin-resistant enterococci (VRE) environmental contamination was found in 53% of patients and 26% of patients, respectively. We found that vancomycin alters the gut microbiota, does not permanently clear C. difficile, and is associated with VRE colonization/environmental contamination. (This study has been registered at ClinicalTrials.gov under registration no. NCT03388268.)IMPORTANCE A gold standard diagnostic for Clostridioides difficile infection (CDI) does not exist. An area of controversy is how to manage patients whose stool tests positive by nucleic acid amplification tests but negative by toxin enzyme immunoassay. Existing data suggest most of these patients do not have CDI, but most are treated with oral vancomycin. Potential benefits to treatment include a decreased risk for adverse outcomes if the patient does have CDI and the potential to decrease C. difficile shedding/transmission. However, oral vancomycin perturbs the intestinal microbiota and promotes antibiotic-resistant organism colonization/transmission. We conducted a double-blinded randomized controlled trial to assess the risk-benefit of oral vancomycin treatment in this population. Oral vancomycin did not result in long-term clearance of C. difficile, perturbed the microbiota, and was associated with colonization/shedding of vancomycin-resistant enterococci. This work underscores the need to better understand this population of patients in the context of C. difficile/ARO-related outcomes and transmission.},
}

@article {pmid33441186,
year = {2021},
author = {Yoshimatsu, Y and Mikami, Y and Kanai, T},
title = {Bacteriotherapy for inflammatory bowel disease.},
journal = {Inflammation and regeneration},
volume = {41},
number = {1},
pages = {3},
pmid = {33441186},
issn = {1880-9693},
support = {16gm1010003h0001//Japan Agency for Medical Research and Development/ ; 20gm1210001h0002//Japan Agency for Medical Research and Development/ ; NA//the Takeda Science Foundation/ ; NA//the Kanae Foundation for The Promotion of Medical Science/ ; 20H03666//Japan Society for the Promotion of Science/ ; 15H02534//Japan Society for the Promotion of Science/ ; 20H00536//Japan Society for the Promotion of Science/ ; NA//Mishima Kaiun Memorial Foundation/ ; NA//School of Medicine, Keio University/ ; },
abstract = {The number of patients with inflammatory bowel disease is rapidly increasing in developed countries. The main cause of this increase is thought not to be genetic, but secondary to rapidly modernized environmental change. Changes in the environment have been detrimental to enteric probiotics useful for fermentation, inducing an increase in pathobionts that survive by means other than fermentation. This dysregulated microbiota composition, the so-called dysbiosis, is believed to have increased the incidence of inflammatory bowel disease. Bacteriotherapy, a treatment that prophylactically and therapeutically corrects the composition of disturbed intestinal microbiota, is a promising recent development. In fact, fecal microbiome transplantation for recurrent Clostridioides difficile infection in 2013 was a significant contribution for bacteriotherapy. In this paper, we comprehensively review bacteriotherapy in an easy-to-understand format.},
}

@article {pmid33441125,
year = {2021},
author = {Rafeeq, M and Murad, HAS and Abdallah, HM and El-Halawany, AM},
title = {Protective effect of 6-paradol in acetic acid-induced ulcerative colitis in rats.},
journal = {BMC complementary medicine and therapies},
volume = {21},
number = {1},
pages = {28},
pmid = {33441125},
issn = {2662-7671},
support = {G-128-828-1438//Deanship of Scientific Research, King Abdulaziz University (SA)/ ; },
abstract = {BACKGROUND: Ulcerative colitis is a gut inflammatory disorder due to altered immune response to gut microbiome, with interplay of environmental and genetic factors. TNF-α activates inflammatory response through a cascade of immune responses, augmenting pro-inflammatory mediators and proteases, activating chemotaxis, and infiltration of inflammatory cells, leading to ulceration and haemorrhage through cytotoxic reactive oxygen species. 6-Paradol, a dietary component in several plants belonging to the Zingiberaceae family, has shown anti-inflammatory and antioxidant activities. Current study evaluates the effect of 6-paradol in amelioration of ulcerative colitis in rats for the first time.

METHODS: 6-Paradol (95% purity) was obtained from seeds of Aframomum melegueta. Rats were divided randomly into six groups (n = 8). Group one was administered normal saline; group two was treated with the vehicle only; group three, sulfasalazine 500 mg/kg; and groups four, five, and six, were given 6-paradol (50, 100, 200, respectively) mg/kg orally through gastric gavage for 7 days. Colitis was induced on 4th day by intrarectal administration of 2 ml acetic acid (3%), approximately 3 cm from anal verge. On 8th day, rats were sacrificed, and distal one-third of the colon extending proximally up to 4 cm from anal orifice was taken for biochemical and gross examination. Two centimetres of injured mucosal portion was taken for histopathological investigations. SPSS (ver.26) was used for statistical analysis.

RESULTS: Colonic and serum glutathione (GSH) levels decreased, while colonic and serum malondialdehyde (MDA), colonic myeloperoxidase (MPO) activity, serum interleukin-6 (IL-6), serum tumour necrosis factor-α (TNF-α) levels, and colon weight to length ratio were increased significantly in the colitis untreated group compared to normal control. Treatment with 6-paradol considerably improved all these parameters, especially at a dose of 200 mg/kg (p < 0.001), revealing non-significant differences with sulfasalazine 500 mg/kg and normal control (p = 0.998). Sulfasalazine and 6-paradol in a dose dependent manner also markedly reversed mucosal oedema, atrophy and inflammation, cryptic damage, haemorrhage, and ulceration. There were non-significant differences between low and medium doses and between medium and high doses of 6-paradol for IL-6 and serum MDA levels.

CONCLUSION: 6-Paradol demonstrated protection against acetic acid-induced ulcerative colitis, probably by anti-inflammatory and antioxidant actions.},
}

@article {pmid33440387,
year = {2021},
author = {Maghfour, J and Olson, J and Conic, RRZ and Mesinkovska, NA},
title = {The Association between Alopecia and Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-14},
doi = {10.1159/000512747},
pmid = {33440387},
issn = {1421-9832},
abstract = {IMPORTANCE: The link between autoimmune gut disorders and different types of hair loss conditions has been recently investigated with an increased interest. With acknowledgement of the connection between immune dysregulation and the gut microbiome, this pathway is now becoming recognized as playing an important role in hair growth. The inflammatory cascade that results from the disruption of gut integrity such as seen in inflammatory bowel diseases (IBD) has been associated with certain types of alopecia.

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

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

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

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

@article {pmid33440172,
year = {2021},
author = {Nayak, RR and Alexander, M and Deshpande, I and Stapleton-Gray, K and Rimal, B and Patterson, AD and Ubeda, C and Scher, JU and Turnbaugh, PJ},
title = {Methotrexate impacts conserved pathways in diverse human gut bacteria leading to decreased host immune activation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2020.12.008},
pmid = {33440172},
issn = {1934-6069},
abstract = {Immunomodulatory drugs can inhibit bacterial growth, yet their mechanism of action, spectrum, and clinical relevance remain unknown. Methotrexate (MTX), a first-line rheumatoid arthritis (RA) treatment, inhibits mammalian dihydrofolate reductase (DHFR), but whether it directly impacts gut bacteria is unclear. We show that MTX broadly alters the human gut microbiota. Drug sensitivity varied across strains, but the mechanism of action against DHFR appears conserved between mammalian and bacterial cells. RA patient microbiotas were sensitive to MTX, and changes in gut bacterial taxa and gene family abundance were distinct between responders and non-responders. Transplantation of post-treatment samples into germ-free mice given an inflammatory trigger led to reduced immune activation relative to pre-treatment controls, enabling identification of MTX-modulated bacterial taxa associated with intestinal and splenic immune cells. Thus, conservation in cellular pathways across domains of life can result in broad off-target drug effects on the human gut microbiota with consequences for immune function.},
}

@article {pmid33440171,
year = {2021},
author = {Tanes, C and Bittinger, K and Gao, Y and Friedman, ES and Nessel, L and Paladhi, UR and Chau, L and Panfen, E and Fischbach, MA and Braun, J and Xavier, RJ and Clish, CB and Li, H and Bushman, FD and Lewis, JD and Wu, GD},
title = {Role of dietary fiber in the recovery of the human gut microbiome and its metabolome.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2020.12.012},
pmid = {33440171},
issn = {1934-6069},
abstract = {Gut microbiota metabolites may be important for host health, yet few studies investigate the correlation between human gut microbiome and production of fecal metabolites and their impact on the plasma metabolome. Since gut microbiota metabolites are influenced by diet, we performed a longitudinal analysis of the impact of three divergent diets, vegan, omnivore, and a synthetic enteral nutrition (EEN) diet lacking fiber, on the human gut microbiome and its metabolome, including after a microbiota depletion intervention. Omnivore and vegan, but not EEN, diets altered fecal amino acid levels by supporting the growth of Firmicutes capable of amino acid metabolism. This correlated with relative abundance of a sizable number of fecal amino acid metabolites, some not previously associated with the gut microbiota. The effect on the plasma metabolome, in contrast, were modest. The impact of diet, particularly fiber, on the human microbiome influences broad classes of metabolites that may modify health.},
}

@article {pmid33439976,
year = {2021},
author = {Fabusoro, OK and Mejia, LA},
title = {Nutrition in HIV-Infected Infants and Children: Current Knowledge, Existing Challenges, and New Dietary Management Opportunities.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/advances/nmaa163},
pmid = {33439976},
issn = {2156-5376},
abstract = {HIV infection and undernutrition remain significant public health concerns for infants and children. In infants and children under these conditions, undernutrition is one of the leading causes of death. Proper management of nutrition and related nutrition complications in these groups with increased nutrition needs are prominent challenges, particularly in HIV-prevalent poor-resource environments. Several studies support the complexity of the relation between HIV infection, nutrition, and the immune system. These elements interact and create a vicious circle of poor health outcomes. Recent studies on the use of probiotics as a novel approach to manage microbiome imbalance and gut-mucosal impairment in HIV infection are gaining attention. This new strategy could help to manage dysbiosis and gut-mucosal impairment by reducing immune activation, thereby potentially forestalling unwanted health outcomes in children with HIV. However, existing trials on HIV-infected children are still insufficient. There are also conflicting reports on the dosage and effectiveness of single or multiple micronutrient supplementation in the survival of HIV-infected children with severe acute malnutrition. The WHO has published guidelines that include time of initiation of antiretroviral therapy for HIV-pregnant mothers and their HIV-exposed or HIV-infected children, micronutrient supplementation, dietary formulations, prevention, and management of HIV therapy. However, such guidelines need to be reviewed owing to recent advances in the field of nutrition. There is a need for new intervention studies, practical strategies, and evidence-based guidelines to reduce the disease burden, improve adherence to treatment regimen, and enhance the nutrition, health, and well-being of HIV-infected infants and children. This review provides up-to-date scientific information on current knowledge and existing challenges for nutrition therapy in HIV-infected infants and children. Moreover, it presents new research findings that could be incorporated into current guidelines.},
}

@article {pmid33439913,
year = {2021},
author = {Lee, YT and Mohd Ismail, NI and Wei, LK},
title = {Microbiome and ischemic stroke: A systematic review.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0245038},
doi = {10.1371/journal.pone.0245038},
pmid = {33439913},
issn = {1932-6203},
abstract = {BACKGROUND: Ischemic stroke is one of the non-communicable diseases that contribute to the significant number of deaths worldwide. However, the relationship between microbiome and ischemic stroke remained unknown. Hence, the objective of this study was to perform systematic review on the relationship between human microbiome and ischemic stroke.

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

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

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

@article {pmid33439113,
year = {2021},
author = {Hilgarth, M and Redwitz, J and Ehrmann, MA and Vogel, RF and Jakob, F},
title = {Bombella favorum sp. nov. and Bombella mellum sp. nov., two novel species isolated from the honeycombs of Apis mellifera.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1099/ijsem.0.004633},
pmid = {33439113},
issn = {1466-5034},
abstract = {As part of a study investigating the microbiome of bee hives and honey, two novel strains (TMW 2.1880T and TMW 2.1889T) of acetic acid bacteria were isolated and subsequently taxonomically characterized by a polyphasic approach, which revealed that they cannot be assigned to known species. The isolates are Gram-stain-negative, aerobic, pellicle-forming, catalase-positive and oxidase-negative. Cells of TMW 2.1880T are non-motile, thin/short rods, and cells of TMW 2.1889T are motile and occur as rods and long filaments. Morphological, physiological and phylogenetic analyses revealed a distinct lineage within the genus Bombella. Strain TMW 2.1880T is most closely related to the type strain of Bombella intestini with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 94.16 and 56.3 %, respectively. The genome of TMW 2.1880T has a size of 1.98 Mb and a G+C content of 55.3 mol%. Strain TMW 2.1889T is most closely related to the type strain of Bombella apis with a 16S rRNA gene sequence similarity of 99.5 %, and ANIb and in silico DDH values of 85.12 and 29.5 %, respectively. The genome of TMW 2.1889T has a size of 2.07 Mb and a G+C content of 60.4 mol%. Ubiquinone analysis revealed that both strains contained Q-10 as the main respiratory quinone. Major fatty acids for both strains were C16 : 0, C19 : 0 cyclo ω8c and summed feature 8, respectively, and additionally C14 : 0 2-OH only for TMW 2.1880T and C14 : 0 only for TMW 2.1889T. Based on polyphasic evidence, the two isolates from honeycombs of Apis mellifera represent two novel species of the genus Bombella, for which the names Bombella favorum sp. nov and Bombella mellum sp. nov. are proposed. The designated respective type strains are TMW 2.1880T (=LMG 31882T=CECT 30114T) and TMW 2.1889T (=LMG 31883T=CECT 30113T).},
}

@article {pmid33439104,
year = {2021},
author = {Manandhar, I and Alimadadi, A and Aryal, S and Munroe, PB and Joe, B and Cheng, X},
title = {Gut microbiome-based supervised machine learning for clinical diagnosis of inflammatory bowel diseases.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00360.2020},
pmid = {33439104},
issn = {1522-1547},
support = {Dean's Postdoctoral to Faculty Fellowship//University of Toledo College of Medicine and Life Sciences/ ; P30 Core Center Pilot Grant//NIDA Center of Excellence in Omics, Systems Genetics, and the Addictome/ ; HL143082//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Despite the availability of various diagnostic tests for inflammatory bowel diseases (IBD), misdiagnosis of IBD occurs frequently, and thus there is a clinical need to further improve the diagnosis of IBD. As gut dysbiosis is reported in IBD patients, we hypothesized that supervised machine learning (ML) could be used to analyze gut microbiome data for predictive diagnostics of IBD. To test our hypothesis, fecal 16S metagenomic data of 729 IBD and 700 non-IBD subjects from the American Gut Project were analyzed using five different ML algorithms. Fifty differential bacterial taxa were identified (LEfSe: LDA > 3) between the IBD and non-IBD groups, and ML classifications trained with these taxonomic features using random forest (RF) achieved a testing AUC of ~0.80. Next, we tested if operational taxonomic units (OTUs), instead of bacterial taxa, could be used as ML features for diagnostic classification of IBD. Top 500 high-variance OTUs were used for ML training and an improved testing AUC of ~0.82 (RF) was achieved. Lastly, we tested if supervised ML could be used for differentiating Crohn's disease (CD) and ulcerative colitis (UC). Using 331 CD and 141 UC samples, 117 differential bacterial taxa (LEfSe: LDA > 3) were identified, and the RF model trained with differential taxonomic features or high-variance OTU features achieved a testing AUC > 0.90. In summary, our study demonstrates the promising potential of artificial intelligence via supervised ML modeling for predictive diagnostics of IBD using gut microbiome data.},
}

@article {pmid33439103,
year = {2021},
author = {Cuna, AC and Morowitz, MJ and Ahmed, I and Umar, S and Sampath, V},
title = {Dynamics of the Preterm Gut Microbiome in Health and Disease.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00399.2020},
pmid = {33439103},
issn = {1522-1547},
support = {R01DK117296//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; K08DK125735//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Advances in metagenomics have allowed a detailed study of the gut microbiome, and its role in human health and disease. Infants born prematurely possess a fragile gut microbial ecosystem that is vulnerable to perturbation. Alterations in the developing gut microbiome in preterm infants are linked to life-threatening diseases such as necrotizing enterocolitis (NEC) and late onset sepsis; and may impact future risk of asthma, atopy, obesity, and psychosocial disease. In this mini review, we summarize recent literature on the origins and patterns of development of the preterm gut microbiome in the perinatal period. The host-microbiome-environmental factors that portend development of dysbiotic intestinal microbial patterns associated with NEC and sepsis are reviewed. Strategies to manipulate the microbiome and mitigate dysbiosis, including the use of probiotics and prebiotics will also be discussed. Finally, we explore the challenges and future directions of gut microbiome research in preterm infants.},
}

@article {pmid33438970,
year = {2021},
author = {Kollef, MH and Torres, A and Shorr, AF and Martin-Loeches, I and Micek, ST},
title = {Nosocomial Infection.},
journal = {Critical care medicine},
volume = {49},
number = {2},
pages = {169-187},
doi = {10.1097/CCM.0000000000004783},
pmid = {33438970},
issn = {1530-0293},
abstract = {OBJECTIVE: The first 70 years of critical care can be considered a period of "industrial revolution-like" advancement in terms of progressing the understanding and care of critical illness. Unfortunately, like the industrial revolution's impact on the environment, advancing ICU care of increasingly elderly, immunosuppressed, and debilitated individuals has resulted in a greater overall burden and complexity of nosocomial infections within modern ICUs. Given the rapid evolution of nosocomial infections, the authors provide an updated review.

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

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

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

@article {pmid33438892,
year = {2021},
author = {Peters, BA and Xue, X and Wang, Z and Usyk, M and Santoro, N and Sharma, A and Anastos, K and Tien, PC and Golub, ET and Weber, KM and Gustafson, D and Kaplan, RC and Burk, R and Qi, Q},
title = {Menopausal status and observed differences in the gut microbiome in women with and without HIV infection.},
journal = {Menopause (New York, N.Y.)},
volume = {Publish Ahead of Print},
number = {},
pages = {},
doi = {10.1097/GME.0000000000001730},
pmid = {33438892},
issn = {1530-0374},
abstract = {OBJECTIVE: Gut microbiota respond to host physiological phenomena, yet little is known regarding shifts in the gut microbiome due to menopausal hormonal and metabolic changes in women. HIV infection impacts menopause and may also cause gut dysbiosis. We therefore sought to determine the association between menopausal status and gut microbiome composition in women with and without HIV.

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

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

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

@article {pmid33438345,
year = {2021},
author = {Le Poole, IC},
title = {Myron Gordon Award paper: Microbes, T-cell diversity and pigmentation.},
journal = {Pigment cell & melanoma research},
volume = {},
number = {},
pages = {},
doi = {10.1111/pcmr.12957},
pmid = {33438345},
issn = {1755-148X},
abstract = {Melanocytes are static, minimally proliferative cells. This leaves them vulnerable in vitiligo. Yet upon malignant transformation, they form vicious tumors. This profound switch in physiology is accompanied by genetic change, and is driven by environmental factors. If UV exposure in younger years supports malignant transformation and melanoma formation, it can likewise impart mutations on melanocytes that reduce their viability, to initiate vitiligo. A wide variety of microbes can influence these diametrically opposed outcomes before either disease takes hold. These microbes are vehicles of change that we are only beginning to study. Once a genetic modification occurs, there is a wide variety of immune cells ready to respond. Though it does not act alone, the T cell is among the most decisive responders in this process. The same biochemical process that offered the skin protection by producing melanin can become an Achilles heel for the cell when the T cells target melanosomal enzymes or, on occasion, neoantigens. T cells are precise, determined and consequential when they strike. Here we probe the relationship between the microbiome and its metabolites, epithelial integrity, and the activation of T cells that target benign and malignant melanocytes in vitiligo and melanoma.},
}

@article {pmid33438331,
year = {2021},
author = {Cook, KA and Domissy, A and Simon, RA and White, AA and Modena, BD},
title = {Dysbiosis in aspirin-exacerbated respiratory disease.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.22762},
pmid = {33438331},
issn = {2042-6984},
support = {K23 HL144418/HL/NHLBI NIH HHS/United States ; //Scripps Clinic Medical Group/ ; K23 HL144418/HL/NHLBI NIH HHS/United States ; },
}

@article {pmid33438150,
year = {2021},
author = {Corniello, A and Guida, M and Stellato, L and Trifuoggi, M and Carraturo, F and Del Gaudio, E and Del Giudice, C and Forte, G and Giarra, A and Iorio, M and Marzaioli, F and Toscanesi, M},
title = {Hydrochemical, isotopic and microbiota characterization of telese mineral waters (Southern Italy).},
journal = {Environmental geochemistry and health},
volume = {},
number = {},
pages = {},
pmid = {33438150},
issn = {1573-2983},
abstract = {The study deals with the analyses of springs and wells at the base of Montepugliano Hill that represents the SE edge of the wide carbonate Matese massif (Campania, southern Italy). At the base of the hill, from west to east and for almost one kilometre, cold springs HCO3-Ca type (Grassano springs, ~ 4.5 m3/s; TDS: about 0.45 g/L) pass to hypothermal, HCO3-Ca type, sulphurous and CO2-rich springs (~ 1 m3/s with TDS > 1 g/L). Some of the latter are widely used in Telese Spa and Centro Relax Spa. Chemical and isotopic analyses carried out for this study support the hypothesis that all these waters (mineral and non-mineral) have the same catchment area, which is located in the Matese massif. As regards the sulphurous springs, they receive both meteoric waters infiltration and uprising of deeper waters rich in endogenous CO2 and H2S gases through important faults systems. Far from these faults, the chemistry of groundwater is scarcely (or not at all) affected by these deep fluid enrichment processes. This scheme is very significant; in fact, when very important groundwater resources are present, it is possible to use both mineral waters in Spa and, in areas far from the faults, those not yet mineralized. Finally, at Montepugliano Hill, in the final stage of the flow path, groundwater is also affected by change in the microbiome: this could provide a basis for comparison between various mineral waters.},
}

@article {pmid33438074,
year = {2021},
author = {Shen, J and Wyness, AJ and Claire, MW and Zerkle, AL},
title = {Spatial Variability of Microbial Communities and Salt Distributions Across a Latitudinal Aridity Gradient in the Atacama Desert.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {33438074},
issn = {1432-184X},
support = {678812//H2020 European Research Council/ ; 60501//John Templeton Foundation/ ; 201708060070//Chinese Scholarship Council/ ; },
abstract = {Over the past 150 million years, the Chilean Atacama Desert has been transformed into one of the most inhospitable landscapes by geophysical changes, which makes it an ideal Mars analog that has been explored for decades. However, a heavy rainfall that occurred in the Atacama in 2017 provides a unique opportunity to study the response of resident extremophiles to rapid environmental change associated with excessive water and salt shock. Here we combine mineral/salt composition measurements, amendment cell culture experiments, and next-generation sequencing analyses to study the variations in salts and microbial communities along a latitudinal aridity gradient of the Atacama Desert. In addition, we examine the reshuffling of Atacama microbiomes after the rainfall event. Analysis of microbial community composition revealed that soils within the southern arid desert were consistently dominated by Actinobacteria, Chloroflexi, Proteobacteria, Firmicutes, Bacteroidetes, Gemmatimonadetes, Planctomycetes, and Acidobacteria, and Verrucomicrobia. Intriguingly, the hyperarid microbial consortia exhibited a similar pattern to the more southern desert. Salts at the shallow subsurface were dissolved and leached down to a deeper layer, challenging indigenous microorganisms with the increasing osmotic stress. Microbial viability was found to change with aridity and rainfall events. This study sheds light on the structure of xerotolerant, halotolerant, and radioresistant microbiomes from the hyperarid northern desert to the less arid southern transition region, as well as their response to changes in water availability.},
}

@article {pmid33437992,
year = {2021},
author = {Lim, MY and Hong, S and Kim, JH and Nam, YD},
title = {Association between Gut Microbiome and Frailty in the Older Adult Population in Korea.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/gerona/glaa319},
pmid = {33437992},
issn = {1758-535X},
abstract = {Frailty is a common geriatric syndrome associated with the risk of adverse health outcomes. Recently, two key pathophysiological characteristics of frailty, altered energy metabolism and dysregulated immunity, have been reported to be associated with gut microbiome dysbiosis, indicating that the gut microbiome plays a role in frailty. However, few studies have directly examined the relationship between the gut microbiome and frailty. Here, we investigated the association of frailty measures with the gut microbiome using 16S rRNA gene sequencing data obtained from the fecal samples of 176 Korean older adults. Overall frailty was scored using the Korean Frailty Index (FI). Grip strength and Geriatric Depression Scale (GDS) scores were used as physical and mental frailty measures, respectively. In contrast to age, metabolic, and inflammatory biomarkers, the frailty measures were associated with inter-individual variations in microbial composition (false discovery rate [FDR] < 0.2). Both FI and GDS scores were negatively associated with microbial diversity (FDR < 0.2). Frailty measures showed distinct associations with specific microbial taxa and metabolic functions. Particularly, the Bacteroides enterotype was found only in subjects categorized in the frail group. Moreover, we observed that the abundance of beneficial taxa, such as Prevotella copri and Coprococcus eutactus, was reduced in frailer individuals, whereas that of detrimental taxa, such as Bacteroides fragilis and Clostridium hathewayi, was increased (FDR < 0.2). Our findings suggest that the gut microbiome can be used an indicator of an increased risk of frailty or a target for improving health in frail older adults.},
}

@article {pmid33437563,
year = {2021},
author = {Pabbathi, NPP and Velidandi, A and Tavarna, T and Gupta, S and Raj, RS and Gandam, PK and Baadhe, RR},
title = {Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review.},
journal = {Biomass conversion and biorefinery},
volume = {},
number = {},
pages = {1-28},
pmid = {33437563},
issn = {2190-6815},
abstract = {As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.},
}

@article {pmid33437414,
year = {2021},
author = {Kuthyar, S and Kowalewski, MM and Roellig, DM and Mallott, EK and Zeng, Y and Gillespie, TR and Amato, KR},
title = {Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria.},
journal = {Ecology and evolution},
volume = {11},
number = {1},
pages = {45-57},
pmid = {33437414},
issn = {2045-7758},
abstract = {Habitat disturbance, a common consequence of anthropogenic land use practices, creates human-animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host-microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host-microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.},
}

@article {pmid33437187,
year = {2020},
author = {Siwicka-Gieroba, D and Czarko-Wicha, K},
title = {Lung microbiome - a modern knowledge.},
journal = {Central-European journal of immunology},
volume = {45},
number = {3},
pages = {342-345},
pmid = {33437187},
issn = {1426-3912},
abstract = {Recent studies have reported that commensal microorganisms are not just "passive occupants" but may play a crucial role in the immune system activation. It is well-known that in critically ill patients, the microbiome is modified and may be associated with the development of immunosuppression in sepsis, contributing to the development of acute renal injury, cardiovascular diseases, or more importantly, respiratory system disturbances. The conviction of lung sterility has gone down in history. The presence of characteristic gut microbiome, such as Bacteroidetes and Enterobacteriaceae, was demonstrated in lungs of critically ill patients. This bacteria's translocation, especially in ischemia-reperfusion injury, results in increased concentration of inflammation response markers and may play a pivotal role in the pathogenesis of respiratory system disturbances, including acute respiratory distress syndrome. Recent studies have shown that ischemia-reperfusion injury is often observed in intensive care units (ICUs) and predispose to microbiome disturbances that are strictly connected with immune system activation and epithelial damage. Potential effects of dysbiosis treatment are under highly activated investigation. Therefore, it is possible that microbiota-targeted therapy may constitute the future therapeutic path in ICUs.},
}

@article {pmid33437021,
year = {2021},
author = {de Sousa Lopes, L and Mendes, LW and Antunes, JEL and de Souza Oliveira, LM and Melo, VMM and de Araujo Pereira, AP and da Costa, AF and de Paula Oliveira, J and Martínez, CR and Figueiredo, MDVB and Araujo, ASF},
title = {Distinct bacterial community structure and composition along different cowpea producing ecoregions in Northeastern Brazil.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {831},
pmid = {33437021},
issn = {2045-2322},
abstract = {Soil microbial communities represent the largest biodiversity on Earth, holding an important role in promoting plant growth and productivity. However, the knowledge about how soil factors modulate the bacteria community structure and distribution in tropical regions remain poorly understood, mainly in different cowpea producing ecoregions belonging to Northeastern Brazil. This study addressed the bacterial community along three different ecoregions (Mata, Sertão, and Agreste) through the16S rRNA gene sequencing. The results showed that soil factors, such as Al3+, sand, Na+, cation exchange excel, and total organic C, influenced the bacterial community and could be a predictor of the distinct performance of cowpea production. Also, the bacterial community changed between different ecoregions, and some keystone groups related to plant-growth promotion, such as Bradyrhizobium, Bacillales, Rhizobiales, and Solibacillus, were correlated to cowpea yield, so revealing that the soil microbiome has a primordial role in plant productivity. Here, we provide evidence that bacterial groups related to nutrient cycling can help us to increase cowpea efficiency and we suggest that a better microbiome knowledge can contribute to improving the agricultural performance.},
}

@article {pmid33436896,
year = {2021},
author = {Funosas, G and Triadó-Margarit, X and Castro, F and Villafuerte, R and Delibes-Mateos, M and Rouco, C and Casamayor, EO},
title = {Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {766},
pmid = {33436896},
issn = {2045-2322},
support = {CGL2013-43197-R//Agencia Estatal de Investigación/ ; INTERACTOMA RTI2018-101205-B-I00//Agencia Estatal de Investigación/ ; },
abstract = {Studies connecting microbiome composition and functional performance in wildlife have received little attention and understanding their connections with wildlife physical condition are sorely needed. We studied the variation in gut microbiota (hard fecal pellets) between allopatric subspecies of the European wild rabbit in wild populations and in captured individuals studied under captivity. We evaluated the influence of environmental and host-specific factors. The microbiome of wild rabbit populations reduced its heterogeneity under controlled conditions. None of the host-specific factors tested correlated with the microbiota composition. We only observed significant intra-group dispersion for the age factor. The most diverse microbiomes were rich in Ruminococcaceae potentially holding an enriched functional profile with dominance of cellulases and xylanases, and suggesting higher efficiency in the digestion of fiber-rich food. Conversely, low diversity gut microbiomes showed dominance of Enterobacteriaceae potentially rich in amylases. We preliminary noticed geographical variations in field populations with higher dominance of Ruminococcaceae in south-western than in north-eastern Spain. Spatial differences appeared not to be subspecies driven, since they were lost in captivity, but environmentally driven, although differences in social structure and behavior may also play a role that deserve further investigations. A marginally significant relationship between the Ruminococcaceae/Enterobacteriaceae ratio and potential life expectancy was observed in captive rabbits. We hypothesize that the gut microbiome may determine the efficiency of feeding resource exploitation, and can also be a potential proxy for life expectancy, with potential applications for the management of declining wild herbivorous populations. Such hypotheses remain to be explored in the future.},
}

@article {pmid33436882,
year = {2021},
author = {Moustafa, MAM and Chel, HM and Thu, MJ and Bawm, S and Htun, LL and Win, MM and Oo, ZM and Ohsawa, N and Lahdenperä, M and Mohamed, WMA and Ito, K and Nonaka, N and Nakao, R and Katakura, K},
title = {Anthropogenic interferences lead to gut microbiome dysbiosis in Asian elephants and may alter adaptation processes to surrounding environments.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {741},
pmid = {33436882},
issn = {2045-2322},
support = {19F19097//Japan Society for the Promotion of Science/ ; 15H05633//Japan Society for the Promotion of Science/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 16H06431//Japan Society for the Promotion of Science/ ; 19H03118//Japan Society for the Promotion of Science/ ; 19F19097//Japan Society for the Promotion of Science/ ; 17H04638//Japan Society for the Promotion of Science/ ; },
abstract = {Human activities interfere with wild animals and lead to the loss of many animal populations. Therefore, efforts have been made to understand how wildlife can rebound from anthropogenic disturbances. An essential mechanism to adapt to environmental and social changes is the fluctuations in the host gut microbiome. Here we give a comprehensive description of anthropogenically induced microbiome alterations in Asian elephants (n = 30). We detected gut microbial changes due to overseas translocation, captivity and deworming. We found that microbes belonging to Planococcaceae had the highest contribution in the microbiome alterations after translocation, while Clostridiaceae, Spirochaetaceae and Bacteroidia were the most affected after captivity. However, deworming significantly changed the abundance of Flavobacteriaceae, Sphingobacteriaceae, Xanthomonadaceae, Weeksellaceae and Burkholderiaceae. These findings may provide fundamental ideas to help guide the preservation tactics and probiotic replacement therapies of a dysbiosed gut microbiome in Asian elephants. More generally, these results show the severity of anthropogenic activities at the level of gut microbiome, altering the adaptation processes to new environments and the subsequent capability to maintain normal physiological processes in animals.},
}

@article {pmid33436774,
year = {2021},
author = {Likhitrattanapisal, S and Siriarchawatana, P and Seesang, M and Chunhametha, S and Boonsin, W and Phithakrotchanakoon, C and Kitikhun, S and Eurwilaichitr, L and Ingsriswang, S},
title = {Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {582},
pmid = {33436774},
issn = {2045-2322},
abstract = {Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.},
}

@article {pmid33436707,
year = {2021},
author = {Stinson, LF and Ma, J and Rea, A and Dymock, M and Geddes, DT},
title = {Centrifugation does not remove bacteria from the fat fraction of human milk.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {572},
pmid = {33436707},
issn = {2045-2322},
abstract = {Analysis of the human milk microbiome is complicated by the presence of a variable quantity of fat. The fat fraction of human milk is typically discarded prior to analysis. It is assumed that all cells are pelleted out of human milk by high speed centrifugation; however, studies of bovine milk have reported that bacteria may remain trapped within the fat fraction. Here, the bacterial DNA profiles of the fat fraction and cell pellet of human milk (n = 10) were analysed. Human and bacterial DNA was consistently recovered from the fat fraction of human milk (average of 12.4% and 32.7%, respectively). Staphylococcus epidermidis was significantly more abundant in the cell pellet compared to the fat fraction (P = 0.038), and three low-abundance species (< 5% relative abundance) were recovered from one fraction only. However, inclusion of fat reduced the efficiency of DNA extraction by 39%. Culture-based methods were used to quantify the distribution of an exogenously added strain of Staphylococcus aureus in human milk fractions. S. aureus was consistently recovered from the fat fraction (average 28.9%). Bacterial DNA profiles generated from skim milk or cell pellets are not representative of the entire human milk microbiome. These data have critical implications for the design of future work in this field.},
}

@article {pmid33436518,
year = {2021},
author = {Panpetch, W and Kullapanich, C and Dang, CP and Visitchanakun, P and Saisorn, W and Wongphoom, J and Wannigama, DL and Thim-Uam, A and Patarakul, K and Somboonna, N and Tumwasorn, S and Leelahavanichkul, A},
title = {Candida Administration Worsens Uremia-Induced Gut Leakage in Bilateral Nephrectomy Mice, an Impact of Gut Fungi and Organismal Molecules in Uremia.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436518},
issn = {2379-5077},
abstract = {The impact of gut fungi and (1→3)-β-d-glucan (BG), a major fungal cell wall component, on uremia was explored by Candida albicans oral administration in bilateral nephrectomy (BiNx) mice because of the prominence of C. albicans in the human intestine but not in mice. As such, BiNx with Candida administration (BiNx-Candida) enhanced intestinal injury (colon cytokines and apoptosis), gut leakage (fluorescein isothiocyanate [FITC]-dextran assay, endotoxemia, serum BG, and bacteremia), systemic inflammation, and liver injury at 48 h postsurgery compared with non-Candida BiNx mice. Interestingly, uremia-induced enterocyte apoptosis was severe enough for gut translocation of viable bacteria, as indicated by culture positivity for bacteria in blood, mesenteric lymph nodes (MLNs), and other organs, which was more severe in BiNx-Candida than in non-Candida BiNx mice. Candida induced alterations in the gut microbiota of BiNx mice as indicated by (i) the higher fungal burdens in the feces of BiNx-Candida mice than in sham-Candida mice by culture methods and (ii) increased Bacteroides with decreased Firmicutes and reduced bacterial diversity in the feces of BiNx-Candida mice compared with non-Candida BiNx mice by fecal microbiome analysis. In addition, lipopolysaccharide plus BG (LPS+BG), compared with each molecule alone, induced high supernatant cytokine levels, which were enhanced by uremic mouse serum in both hepatocytes (HepG2 cells) and macrophages (RAW264.7 cells). Moreover, LPS+BG, but not each molecule alone, reduced the glycolysis capacity and mitochondrial function in HepG2 cells as determined by extracellular flux analysis. Additionally, a probiotic, Lactobacillus rhamnosus L34 (L34), attenuated disease severity only in BiNx-Candida mice but not in non-Candida BiNx mice, as indicated by liver injury and serum cytokines through the attenuation of gut leakage, the fecal abundance of fungi, and fecal bacterial diversity but not fecal Gram-negative bacteria. In conclusion, Candida enhanced BiNx severity through the worsening of gut leakage and microbiota alterations that resulted in bacteremia, endotoxemia, and glucanemia.IMPORTANCE The impact of fungi in the intestine on acute uremia was demonstrated by the oral administration of Candida albicans in mice with the removal of both kidneys. Because fungi in the mouse intestine are less abundant than in humans, a Candida-administered mouse model has more resemblance to patient conditions. Accordingly, acute uremia, without Candida, induced intestinal mucosal injury, which resulted in the translocation of endotoxin, a major molecule of gut bacteria, from the intestine into blood circulation. In acute uremia with Candida, intestinal injury was more severe due to fungi and the alteration in intestinal bacteria (increased Bacteroides with decreased Firmicutes), leading to the gut translocation of both endotoxin from gut bacteria and (1→3)-β-d-glucan from Candida, which synergistically enhanced systemic inflammation in acute uremia. Both pathogen-associated molecules were delivered to the liver and induced hepatocyte inflammatory responses with a reduced energy production capacity, resulting in acute uremia-induced liver injury. In addition, Lactobacillus rhamnosus attenuated intestinal injury through reduced gut Candida and improved intestinal bacterial conditions.},
}

@article {pmid33436515,
year = {2021},
author = {Tláskal, V and Brabcová, V and Větrovský, T and Jomura, M and López-Mondéjar, R and Oliveira Monteiro, LM and Saraiva, JP and Human, ZR and Cajthaml, T and Nunes da Rocha, U and Baldrian, P},
title = {Complementary Roles of Wood-Inhabiting Fungi and Bacteria Facilitate Deadwood Decomposition.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436515},
issn = {2379-5077},
abstract = {Forests accumulate and store large amounts of carbon (C), and a substantial fraction of this stock is contained in deadwood. This transient pool is subject to decomposition by deadwood-associated organisms, and in this process it contributes to CO2 emissions. Although fungi and bacteria are known to colonize deadwood, little is known about the microbial processes that mediate carbon and nitrogen (N) cycling in deadwood. In this study, using a combination of metagenomics, metatranscriptomics, and nutrient flux measurements, we demonstrate that the decomposition of deadwood reflects the complementary roles played by fungi and bacteria. Fungi were found to dominate the decomposition of deadwood and particularly its recalcitrant fractions, while several bacterial taxa participate in N accumulation in deadwood through N fixation, being dependent on fungal activity with respect to deadwood colonization and C supply. Conversely, bacterial N fixation helps to decrease the constraints of deadwood decomposition for fungi. Both the CO2 efflux and N accumulation that are a result of a joint action of deadwood bacteria and fungi may be significant for nutrient cycling at ecosystem levels. Especially in boreal forests with low N stocks, deadwood retention may help to improve the nutritional status and fertility of soils.IMPORTANCE Wood represents a globally important stock of C, and its mineralization importantly contributes to the global C cycle. Microorganisms play a key role in deadwood decomposition, since they possess enzymatic tools for the degradation of recalcitrant plant polymers. The present paradigm is that fungi accomplish degradation while commensalist bacteria exploit the products of fungal extracellular enzymatic cleavage, but this assumption was never backed by the analysis of microbial roles in deadwood. This study clearly identifies the roles of fungi and bacteria in the microbiome and demonstrates the importance of bacteria and their N fixation for the nutrient balance in deadwood as well as fluxes at the ecosystem level. Deadwood decomposition is shown as a process where fungi and bacteria play defined, complementary roles.},
}

@article {pmid33436514,
year = {2021},
author = {Fagorzi, C and Bacci, G and Huang, R and Cangioli, L and Checcucci, A and Fini, M and Perrin, E and Natali, C and diCenzo, GC and Mengoni, A},
title = {Nonadditive Transcriptomic Signatures of Genotype-by-Genotype Interactions during the Initiation of Plant-Rhizobium Symbiosis.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436514},
issn = {2379-5077},
abstract = {Rhizobia are ecologically important, facultative plant-symbiotic microbes. In nature, there is a large variability in the association of rhizobial strains and host plants of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of a host plant. RNA sequencing of the model rhizobium Sinorhizobium meliloti exposed to root exudates or luteolin (an inducer of nod genes, involved in the early steps of symbiotic interaction) was performed on a combination of three S. meliloti strains and three alfalfa varieties as host plants. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, 35% were influenced by the strain genotype, 16% were influenced by the plant genotype, and 29% were influenced by strain-by-host plant genotype interactions. We also examined the response of a hybrid S. meliloti strain in which the symbiotic megaplasmid (∼20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes were upregulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes are influenced by the genotypes of both symbiotic partners and their interaction, suggesting a wide spectrum of genetic determinants involved in the phenotypic variation of plant-rhizobium symbiosis.IMPORTANCE A sustainable way for meeting the need of an increased global food demand should be based on a holobiont perspective, viewing crop plants as intimately associated with their microbiome, which helps improve plant nutrition, tolerance to pests, and adverse climate conditions. However, the genetic repertoire needed for efficient association with plants by the microbial symbionts is still poorly understood. The rhizobia are an exemplary model of facultative plant symbiotic microbes. Here, we evaluated whether genotype-by-genotype interactions could be identified in the initial transcriptional response of rhizobium perception of a host plant. We performed an RNA sequencing study to analyze the transcriptomes of different rhizobial strains elicited by root exudates of three alfalfa varieties as a proxy of an early step of the symbiotic interaction. The results indicated strain- and plant variety-dependent variability in the observed transcriptional changes, providing fundamentally novel insights into the genetic basis of rhizobium-plant interactions. Our results provide genetic insights and perspective to aid in the exploitation of natural rhizobium variation for improvement of legume growth in agricultural ecosystems.},
}

@article {pmid33436510,
year = {2021},
author = {He, JW and Zhou, XJ and Li, YF and Wang, YN and Liu, LJ and Shi, SF and Xin, XH and Li, RS and Falchi, M and Lv, JC and Zhang, H},
title = {Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy.},
journal = {mSystems},
volume = {6},
number = {1},
pages = {},
pmid = {33436510},
issn = {2379-5077},
abstract = {The gut microbiota has been implicated in immunoglobin A nephropathy (IgAN) because the intestinal immune response is assumed to be one of the disease triggers. Since the microbial composition is heritable, we hypothesize that genetic variants controlling gut microbiota composition may be associated with susceptibility to IgAN or clinical phenotypes. A total of 175 gut-microbiome-associated genetic variants were retrieved from the Genome-Wide Association Study (GWAS) Catalog. Genetic associations were examined in 1,511 patients with IgAN and 4,469 controls. Subphenotype associations and microbiome annotations were undertaken for a better understanding of how genes shaped phenotypes. Likely candidate microbes suggested in genetic associations were validated using 16S rRNA gene sequencing in two independent data sets with 119 patients with IgAN and 45 controls in total. Nine genetic variants were associated with susceptibility to IgAN. Risk genotypes of LYZL1 were associated with higher serum levels of galactose-deficient IgA1 (Gd-IgA1). Other significant findings included the associations between the risk genotype of SIPA1L3 and early age at onset, PLTP and worse kidney function, and AL365503.1 and more severe hematuria. Besides, risk genotypes of LYZL1 and SIPA1L3 were associated with decreased abundances of Dialister and Bacilli, respectively. Risk genotypes of PLTP and AL365503.1 were associated with increased abundances of Erysipelotrichaceae and Lachnobacterium, respectively. 16S data validated a decreased tendency for Dialister and an increased tendency for Erysipelotrichaceae in IgAN. In this pilot study, our results provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics and shed new light on candidate bacteria for future pathogenesis studies.IMPORTANCE The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]). The relationship between host genetics and the microbiota and the role of the microbiota in IgAN are unclear. We retrieved the GWAS Catalog and associated microbiome QTL in IgAN, observing that nine genetic variants were associated with IgAN susceptibility and some clinical phenotypes. In a consistent way, the decreased abundance of Dialister was associated with higher serum levels of Gd-IgA1, and 16S rRNA gene analysis confirmed the decreased abundance of Dialister in IgAN. These data provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics, which is a new strategy for future pathogenesis and intervention studies.},
}

@article {pmid33436440,
year = {2021},
author = {Griesenauer, B and González-Beiras, C and Fortney, KR and Lin, H and Gao, X and Godornes, C and Nelson, DE and Katz, BP and Lukehart, SA and Mitjà, O and Dong, Q and Spinola, SM},
title = {Streptococcus pyogenes Is Associated with Idiopathic Cutaneous Ulcers in Children on a Yaws-Endemic Island.},
journal = {mBio},
volume = {12},
number = {1},
pages = {},
pmid = {33436440},
issn = {2150-7511},
abstract = {Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases are idiopathic (IU). Using mass drug administration (MDA) of azithromycin, a yaws eradication campaign on Lihir Island in Papua New Guinea reduced but failed to eradicate yaws; IU rates remained constant throughout the campaign. To identify potential etiologies of IU, we obtained swabs of CU lesions (n = 279) and of the skin of asymptomatic controls (AC; n = 233) from the Lihir Island cohort and characterized their microbiomes using a metagenomics approach. CU bacterial communities were less diverse than those of the AC. Using real-time multiplex PCR with pathogen-specific primers, we separated CU specimens into HD-positive (HD+), TP+, HD+TP+, and IU groups. Each CU subgroup formed a distinct bacterial community, defined by the species detected and/or the relative abundances of species within each group. Streptococcus pyogenes was the most abundant organism in IU (22.65%) and was enriched in IU compared to other ulcer groups. Follow-up samples (n = 31) were obtained from nonhealed ulcers; the average relative abundance of S. pyogenes was 30.11% in not improved ulcers and 0.88% in improved ulcers, suggesting that S. pyogenes in the not improved ulcers may be azithromycin resistant. Catonella morbi was enriched in IU that lacked S. pyogenes As some S. pyogenes and TP strains are macrolide resistant, penicillin may be the drug of choice for CU azithromycin treatment failures. Our study will aid in the design of diagnostic tests and selective therapies for CU.IMPORTANCE Cutaneous ulcers (CU) affect approximately 100,000 children in the tropics each year. While two-thirds of CU are caused by Treponema pallidum subspecies pertenue and Haemophilus ducreyi, the cause(s) of the remaining one-third is unknown. Given the failure of mass drug administration of azithromycin to eradicate CU, the World Health Organization recently proposed an integrated disease management strategy to control CU. Success of this strategy requires determining the unknown cause(s) of CU. By using 16S rRNA gene sequencing of swabs obtained from CU and the skin of asymptomatic children, we identified another possible cause of skin ulcers, Streptococcus pyogenes Although S. pyogenes is known to cause impetigo and cellulitis, this is the first report implicating the organism as a causal agent of CU. Inclusion of S. pyogenes into the integrated disease management plan will improve diagnostic testing and treatment of this painful and debilitating disease of children and strengthen elimination efforts.},
}

@article {pmid33436437,
year = {2021},
author = {Amenyogbe, N and Dimitriu, P and Smolen, KK and Brown, EM and Shannon, CP and Tebbutt, SJ and Cooper, PJ and Marchant, A and Goetghebuer, T and Esser, M and Finlay, BB and Kollmann, TR and Mohn, WW},
title = {Biogeography of the Relationship between the Child Gut Microbiome and Innate Immune System.},
journal = {mBio},
volume = {12},
number = {1},
pages = {},
pmid = {33436437},
issn = {2150-7511},
abstract = {The gut microbiome is a well-recognized modulator of host immunity, and its compositions differ between geographically separated human populations. Systemic innate immune responses to microbial derivatives also differ between geographically distinct human populations. However, the potential role of the microbiome in mediating geographically varied immune responses is unexplored. We here applied 16S amplicon sequencing to profile the stool microbiome and, in parallel, measured whole-blood innate immune cytokine responses to several pattern recognition receptor (PRR) agonists among 2-year-old children across biogeographically diverse settings. Microbiomes differed mainly between high- and low-resource environments and were not strongly associated with other demographic factors. We found strong correlations between responses to Toll-like receptor 2 (TLR2) and relative abundances of Bacteroides and Prevotella populations, shared among Canadian and Ecuadorean children. Additional correlations between responses to TLR2 and bacterial populations were specific to individual geographic cohorts. As a proof of concept, we gavaged germfree mice with human donor stools and found murine splenocyte responses to TLR stimulation were consistent with responses of the corresponding human donor populations. This study identified differences in immune responses correlating to gut microbiomes across biogeographically diverse settings and evaluated biological plausibility using a mouse model. This insight paves the way to guide optimization of population-specific interventions aimed to improve child health outcomes.IMPORTANCE Both the gut microbiome and innate immunity are known to differ across biogeographically diverse human populations. The gut microbiome has been shown to directly influence systemic immunity in animal models. With this, modulation of the gut microbiome represents an attractive avenue to improve child health outcomes associated with altered immunity using population-specific approaches. However, there are very scarce data available to determine which members of the gut microbiome are associated with specific immune responses and how these differ around the world, creating a substantial barrier to rationally designing such interventions. This study addressed this knowledge gap by identifying relationships between distinct bacterial taxa and cytokine responses to specific microbial agonists across highly diverse settings. Furthermore, we provide evidence that immunomodulatory effects of region-specific stool microbiomes can be partially recapitulated in germfree mice. This is an important contribution toward improving global child health by targeting the gut microbiome.},
}

@article {pmid33436328,
year = {2021},
author = {Hussein, AA and Elsayed, AS and Durrani, M and Jing, Z and Iqbal, U and Gomez, EC and Singh, PK and Liu, S and Smith, G and Tang, L and Guru, KA},
title = {Investigating the association between the urinary microbiome and bladder cancer: An exploratory study.},
journal = {Urologic oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urolonc.2020.12.011},
pmid = {33436328},
issn = {1873-2496},
abstract = {INTRODUCTION: We sought to investigate the association between the urinary microbiome and bladder cancer, including the difference between nonmuscle-invasive (NMIBC) and muscle-invasive (MIBC) bladder cancer, and Bacillus Calmette Guerin (BCG) responsive vs. BCG-refractory NMIBC.

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

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

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