@article {pmid31981578,
year = {2020},
author = {O'Neill, AM and Nakatsuji, T and Hayachi, A and Williams, MR and Mills, RH and Gonzalez, DJ and Gallo, RL},
title = {Identification of a human skin commensal bacterium that selectively kills Cutibacterium acnes.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2019.12.026},
pmid = {31981578},
issn = {1523-1747},
abstract = {The microbiome represents a vast resource for drug discovery as its members engage in constant conflict to outcompete one another by deploying diverse strategies for survival. Cutibacterium acnes (C. acnes) is one of the most common bacterial species on human skin and can promote the common disease acne vulgaris. By employing a combined strategy of functional screening, genetics and proteomics we discovered a strain of Staphylococcus capitis (S. capitis E12) that selectively inhibited growth of C. acnes with potency greater than antibiotics commonly used in the treatment of acne. Antimicrobial peptides secreted from S. capitis E12 were identified as four distinct phenol soluble modulins acting synergistically. These peptides were not toxic to human keratinocytes and the S. capitis extract did not kill other commensal skin bacteria but was effective against C. acnes on pig skin and on mice. Overall, these data show how a member of the human skin microbiome can be useful as a biotherapy for acne vulgaris.},
}

@article {pmid31981310,
year = {2020},
author = {Brown, TA and Tashiro, H and Kasahara, DI and Cho, Y and Shore, SA},
title = {Early life microbiome perturbation alters pulmonary responses to ozone in male mice.},
journal = {Physiological reports},
volume = {8},
number = {2},
pages = {e14290},
doi = {10.14814/phy2.14290},
pmid = {31981310},
issn = {2051-817X},
support = {HL007118/HL/NHLBI NIH HHS/United States ; ES000002/ES/NIEHS NIH HHS/United States ; ES013307/ES/NIEHS NIH HHS/United States ; ES024032/ES/NIEHS NIH HHS/United States ; },
abstract = {Early life changes in the microbiome contribute to the development of allergic asthma, but little is known about the importance of the microbiome for other forms of asthma. Ozone is a nonatopic asthma trigger that causes airway hyperresponsiveness and neutrophil recruitment to the lungs. The purpose of this study was to test the hypothesis that early life perturbations in the gut microbiome influence subsequent responses to ozone. To that end, we placed weanling mouse pups from The Jackson Laboratories or from Taconic Farms in sex-specific cages either with other mice from the same vendor (same-housed) or with mice from the opposite vendor (cohoused). Mice were maintained with these cagemates until use. The gut microbial community differs in mice from Jackson Labs and Taconic Farms, and cohousing mice transfers fecal microbiota from one mouse to another. Indeed, 16S rRNA sequencing of fecal DNA indicated that differences in the gut microbiomes of Jackson and Taconic same-housed mice were largely abolished when the mice were cohoused. At 10-12 weeks of age, mice were exposed to room air or ozone (2 ppm for 3 hr). Compared to same-housed mice, cohoused male but not female mice had reduced ozone-induced airway hyperresponsiveness and reduced ozone-induced increases in bronchoalveolar lavage neutrophils. Ozone-induced airway hyperresponsiveness was greater in male than in female mice and the sex difference was largely abolished in cohoused mice. The data indicate a role for early life microbial perturbations in pulmonary responses to a nonallergic asthma trigger.},
}

@article {pmid31981026,
year = {2020},
author = {Sauvêtre, A and Węgrzyn, A and Yang, L and Vestergaard, G and Miksch, K and Schröder, P and Radl, V},
title = {Enrichment of endophytic Actinobacteria in roots and rhizomes of Miscanthus × giganteus plants exposed to diclofenac and sulfamethoxazole.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-020-07609-7},
pmid = {31981026},
issn = {1614-7499},
support = {BKM 08/080/BKM16/0039//Politechnika Śląska/ ; UMO-2012/05/B/ST8/02739//Narodowe Centrum Nauki/ ; _//European Cooperation in Science and Technology/ ; },
abstract = {This study investigates how wastewater containing 2 mg l-1 of sulfamethoxazole (SMX) and 2 mg l-1 of diclofenac (DCF) affects the composition of bacterial communities present in the roots and rhizomes of Miscanthus × giganteus plants grown in laboratory-scale constructed wetlands. Bacterial communities in plant roots and rhizomes were identified in treated and control samples by 16S rRNA amplicon sequencing. Moreover, bacterial endophytes were isolated in R2A and 1/10 869 media and screened for their ability to metabolize SMX and DCF in liquid medium by HPLC. Our results show significant changes in the abundance of main genera, namely Sphingobium and Streptomyces between control and treated plants. Around 70% of the strains isolated from exposed plants belonged to the phylum Actinobacteria and were classified as Streptomyces, Microbacterium, and Glycomyces. In non-exposed plants, Proteobacteria represented 43.5% to 63.6% of the total. We identified 17 strains able to remove SMX and DCF in vitro. From those, 76% were isolated from exposed plants. Classified mainly as Streptomyces, they showed the highest SMX (33%) and DCF (41%) removal efficiency. These isolates, alone or in combination, might be used as bio-inoculants in constructed wetlands to enhance the phytoremediation of SMX and DCF during wastewater treatment.},
}

@article {pmid31980337,
year = {2020},
author = {Scherer, HU and Häupl, T and Burmester, GR},
title = {The etiology of rheumatoid arthritis.},
journal = {Journal of autoimmunity},
volume = {},
number = {},
pages = {102400},
doi = {10.1016/j.jaut.2019.102400},
pmid = {31980337},
issn = {1095-9157},
abstract = {Rheumatoid arthritis is a heterogeneous disease, which can be, based on data combining genetic risk factors and autoantibodies, sub-classified into ACPA-positive and -negative RA. Presence of ACPA and RF as well as rising CRP-levels in some patients years before onset of clinical symptoms indicate that relevant immune responses for RA development are initiated very early. ACPA are highly specific for RA, whereas RF can also be found among healthy (elderly) individuals and patients with other autoimmune diseases or infection. The most important genetic risk factor for RA development, the shared epitope alleles, resides in the MHC class II region. Shared epitope alleles, however, only predispose to the development of ACPA-positive RA. Smoking is thus far the most important environmental risk factor associated with the development of RA. Studies on synovitis have shown the importance not only of adaptive but also of innate immune responses. In summary of the various results from immunological changes in blood and synovial tissue, the extension of the immune response from a diffuse myeloid to a lympho-myeloid inflammation appears to be associated with a more successful therapeutic response to biologics. With respect to advances in synovitis research, new targets for treatment against pathological subsets of immune cells or fibroblasts are already on the horizon. However, alternative strategies involving the microbiome may play an important role as well and research in this field is growing rapidly.},
}

@article {pmid31980039,
year = {2020},
author = {Montoya-Ciriaco, N and Gómez-Acata, S and Muñoz-Arenas, LC and Dendooven, L and Estrada-Torres, A and Díaz de la Vega-Pérez, AH and Navarro-Noya, YE},
title = {Dietary effects on gut microbiota of the mesquite lizard Sceloporus grammicus (Wiegmann, 1828) across different altitudes.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {6},
doi = {10.1186/s40168-020-0783-6},
pmid = {31980039},
issn = {2049-2618},
support = {205945//Consejo Nacional de Ciencia y Tecnología/ ; Cátedras Conacyt 883//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {BACKGROUND: High-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts as an adaptation to environmental changes are still largely unknown. We investigated the food ingested and the bacterial, fungal, and protistan communities in feces of the lizard Sceloporus grammicus inhabiting an altitudinal range using metabarcoding approaches.

RESULTS: The bacterial phyla Bacteroidetes and Firmicutes, and the genera Bacteroides and Parabacteroides dominated the core fecal bacteriome, while Zygomycota and Ascomycota, and the species Basidiobolus ranarum and Basidiobolus magnus dominated the core fecal mycobiome. The diet of S. grammicus included 29 invertebrate families belonging to Arachnida, Chilopoda, and Insecta. The diversity and abundance of its diet decreased sharply at high altitudes, while the abundance of plant material and Agaricomycetes was significantly higher at the highest site. The composition of the fecal microbiota of S. grammicus was different at the three altitudes, but not between females and males. Dietary restriction in S. grammicus at 4150 m might explain the high fecal abundance of Akkermansia and Oscillopira, bacteria characteristic of long fasting periods, while low temperature favored B. magnus. A high proportion of bacterial functions were digestive in S. grammicus at 2600 and 3100, while metabolism of aminoacids, vitamins, and key intermediates of metabolic pathways were higher at 4150 m. Different assemblages of fungal species in the lizard reflect differences in the environments at different elevations. Pathogens were more prevalent at high elevations than at the low ones.

CONCLUSIONS: Limiting food resources at high elevations might oblige S. grammicus to exploit other food resources and its intestinal microbiota have degradative and detoxifying capacities. Sceloporus grammicus might have acquired B. ranarum from the insects infected by the fungus, but its commensal relationship might be established by the quitinolytic capacities of B. ranarum. The mycobiome participate mainly in digestive and degradative functions while the bacteriome in digestive and metabolic functions.},
}

@article {pmid31980025,
year = {2020},
author = {Lee, H and Lee, HK and Min, SK and Lee, WH},
title = {16S rDNA microbiome composition pattern analysis as a diagnostic biomarker for biliary tract cancer.},
journal = {World journal of surgical oncology},
volume = {18},
number = {1},
pages = {19},
doi = {10.1186/s12957-020-1793-3},
pmid = {31980025},
issn = {1477-7819},
support = {2017R1C1B5017902//National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning/ ; NRF-2017M3A9F3047497//National Research Foundation of Korea (NRF) funded by the Ministry of Science, ICT & Future Planning/ ; },
abstract = {BACKGROUND: The aim of this study is to investigate the composition of microbiota in biliary tract cancer patients and healthy adults by metagenome analysis and evaluate its potential values as biomarkers for biliary tract cancer.

METHODS: Patients who were diagnosed with biliary tract cancer or benign inflammation were enrolled in this study. The control group consisted of healthy adults who presented with no history of significant medical issues. We isolated bacteria-derived extracellular vesicles in the plasma. The microbiome composition was investigated with 16S rDNA metagenome analysis. We evaluated each microbiome to ensure suitability for the biliary tract cancer prediction model.

RESULTS: A total of 155 patients were included in this study: 24 patients with diagnosed biliary tract cancers, 43 diagnosed with cholecystitis or cholangitis, and 88 healthy adults. The microbiome composition pattern of the biliary tract cancer differed from the microbiome composition pattern seen in healthy adult group in beta diversity analysis. The percent composition of microbiota was found to be different from the phylum to genus level. Differences in the composition of the Bifidobacteriaceae and Pseudomonaceae families and Corynebacteriaceae Corynebacterium, Oxalobacteraceae Ralstonia and Comamonadaceae Comamonas species may be used to develop predictive models for biliary tract cancer.

CONCLUSION: Biliary tract cancer patients have altered microbiome composition, which represents a promising biomarker to differentiate malignant biliary tract disease from normal control group.},
}

@article {pmid31979034,
year = {2020},
author = {Connelly, S and Fanelli, B and Hasan, NA and Colwell, RR and Kaleko, M},
title = {SYN-007, an Orally Administered Beta-Lactamase Enzyme, Protects the Gut Microbiome from Oral Amoxicillin/Clavulanate without Adversely Affecting Antibiotic Systemic Absorption in Dogs.},
journal = {Microorganisms},
volume = {8},
number = {2},
pages = {},
doi = {10.3390/microorganisms8020152},
pmid = {31979034},
issn = {2076-2607},
abstract = {Beta-lactamases, enzymes produced by bacteria to degrade beta-lactam antibiotics, have been harnessed as therapeutics to protect the gut microbiome from damage caused by antibiotics. Proof-of-concept of this approach using SYN-004 (ribaxamase), a beta-lactamase formulated for oral delivery with intravenous (IV) penicillins and cephalosporins, was demonstrated with animal models and in humans. Ribaxamase degraded ceftriaxone in the gastrointestinal tract, protected the gut microbiome, significantly reduced the incidence of Clostridioidesdifficile disease and attenuated emergence of antibiotic resistant organisms. SYN-007 is a delayed release formulation of ribaxamase intended for use with oral beta-lactams. In dogs treated with oral amoxicillin, SYN-007 diminished antibiotic-mediated microbiome disruption and reduced the emergence of antibiotic resistance without altering amoxicillin systemic absorption. Here, SYN-007 function in the presence of clavulanate, a beta-lactamase inhibitor, was investigated. Dogs received amoxicillin (40 mg/kg, orally (PO), three times a day (TID)) or the combined antibiotic/beta-lactamase inhibitor, amoxicillin/clavulanate (40 mg/kg amoxicillin, 5.7 mg/kg clavulanate, PO, TID) +/- SYN-007 (10 mg, PO, TID) for five days. Serum amoxicillin levels were not significantly different +/- SYN-007 compared to amoxicillin alone or amoxicillin/clavulanate alone as controls for both first and last doses, indicating SYN-007 did not interfere with systemic absorption of the antibiotic. Whole genome shotgun metagenomics analyses of the fecal microbiomes demonstrated both amoxicillin and amoxicillin/clavulanate significantly reduced diversity and increased the frequency of antibiotic resistance genes. Microbiome damage appeared more severe with amoxicillin/clavulanate. In contrast, with SYN-007, microbiome diversity was not significantly altered, and frequency of antibiotic resistance genes did not increase. Importantly, SYN-007 functioned in the presence of clavulanate to protect the gut microbiome indicating that SYN-007 activity was not inhibited by clavulanate in the dog gastrointestinal tract. SYN-007 has the potential to expand microbiome protection to beta-lactam/beta-lactamase inhibitor combinations delivered orally or systemically.},
}

@article {pmid31978342,
year = {2020},
author = {Walter, J and Armet, AM and Finlay, BB and Shanahan, F},
title = {Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents.},
journal = {Cell},
volume = {180},
number = {2},
pages = {221-232},
doi = {10.1016/j.cell.2019.12.025},
pmid = {31978342},
issn = {1097-4172},
abstract = {Human diseases are increasingly linked with an altered or "dysbiotic" gut microbiota, but whether such changes are causal, consequential, or bystanders to disease is, for the most part, unresolved. Human microbiota-associated (HMA) rodents have become a cornerstone of microbiome science for addressing causal relationships between altered microbiomes and host pathology. In a systematic review, we found that 95% of published studies (36/38) on HMA rodents reported a transfer of pathological phenotypes to recipient animals, and many extrapolated the findings to make causal inferences to human diseases. We posit that this exceedingly high rate of inter-species transferable pathologies is implausible and overstates the role of the gut microbiome in human disease. We advocate for a more rigorous and critical approach for inferring causality to avoid false concepts and prevent unrealistic expectations that may undermine the credibility of microbiome science and delay its translation.},
}

@article {pmid31978162,
year = {2020},
author = {Chung, YW and Gwak, HJ and Moon, S and Rho, M and Ryu, JH},
title = {Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227886},
doi = {10.1371/journal.pone.0227886},
pmid = {31978162},
issn = {1932-6203},
abstract = {BACKGROUND: Microbial communities of the mouse gut have been extensively studied; however, their functional roles and regulation are yet to be elucidated. Metagenomic and metatranscriptomic analyses may allow us a comprehensive profiling of bacterial composition and functions of the complex gut microbiota. The present study aimed to investigate the active functions of the microbial communities in the murine cecum by analyzing both metagenomic and metatranscriptomic data on specific bacterial species within the microbial communities, in addition to the whole microbiome.

RESULTS: Bacterial composition of the healthy mouse gut microbiome was profiled using the following three different approaches: 16S rRNA-based profiling based on amplicon and shotgun sequencing data, and genome-based profiling based on shotgun sequencing data. Consistently, Bacteroidetes, Firmicutes, and Deferribacteres emerged as the major phyla. Based on NCBI taxonomy, Muribaculaceae, Lachnospiraceae, and Deferribacteraceae were the predominant families identified in each phylum. The genes for carbohydrate metabolism were upregulated in Muribaculaceae, while genes for cofactors and vitamin metabolism and amino acid metabolism were upregulated in Deferribacteraceae. The genes for translation were commonly enhanced in all three families. Notably, combined analysis of metagenomic and metatranscriptomic sequencing data revealed that the functions of translation and metabolism were largely upregulated in all three families in the mouse gut environment. The ratio of the genes in the metagenome and their expression in the metatranscriptome indicated higher expression of carbohydrate metabolism in Muribaculum, Duncaniella, and Mucispirillum.

CONCLUSIONS: We demonstrated a fundamental methodology for linking genomic and transcriptomic datasets to examine functional activities of specific bacterial species in a complicated microbial environment. We investigated the normal flora of the mouse gut using three different approaches and identified Muribaculaceae, Lachnospiraceae, and Deferribacteraceae as the predominant families. The functional distribution of these families was reflected in the entire microbiome. By comparing the metagenomic and metatranscriptomic data, we found that the expression rates differed for different functional categories in the mouse gut environment. Application of these methods to track microbial transcription in individuals over time, or before and after administration of a specific stimulus will significantly facilitate future development of diagnostics and treatments.},
}

@article {pmid31978143,
year = {2020},
author = {De Cesare, A and Sala, C and Castellani, G and Astolfi, A and Indio, V and Giardini, A and Manfreda, G},
title = {Effect of Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in drinking water on chicken crop and caeca microbiome.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0228338},
doi = {10.1371/journal.pone.0228338},
pmid = {31978143},
issn = {1932-6203},
abstract = {In this study we gained insights into the effects of the supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) in the chicken drinking water on crop and caeca microbiomes. The probiotic was supplemented at the concentrations of 0.2 g Lactobacillus acidophilus/day/bird and 0.02 g Lactobacillus acidophilus/day/bird and its effect on the crop and caeca microbiomes was assessed at 14 and 35 days of rearing. The results showed that mean relative abundance of Lactobacillus acidophilus in the caeca did not show significative differences in the treated and control birds, although Lactobacillus acidophilus as well as Faecalibacterium prausnitzii, Lactobacillus crispatus and Lactobacillus reuteri significantly increased over time. Moreover, the treatment with the high dose of probiotic significantly increased the abundance of Clostridium asparagiforme, Clostridium hathewayi and Clostridium saccharolyticum producing butyrate and other organic acids supporting the chicken health. Finally, at 35 days, the Cell division protein FtsH (EC 3.4.24.-) and the Site-specific recombinase genes were significantly increased in the caeca of birds treated with the high dose of probiotic in comparison to the control group. The results of this study showed that Lactobacillus acidophilus D2/CSL (CECT 4529) supplementation in the drinking water at the concentrations of 0.2 and 0.02 g Lactobacillus acidophilus/day/bird improved beneficial microbes and functional genes in broiler crops and caeca. Nevertheless, the main site of action of the probiotic is the crop, at least in the early stage of the chicken life. Indeed, at 14 days Lactobacillus acidophilus was significantly higher in the crops of chickens treated with the high dose of LA in comparison to the control (14.094 vs 1.741%, p = 0.036).},
}

@article {pmid31978078,
year = {2020},
author = {Angoa-Pérez, M and Zagorac, B and Winters, AD and Greenberg, JM and Ahmad, M and Theis, KR and Kuhn, DM},
title = {Differential effects of synthetic psychoactive cathinones and amphetamine stimulants on the gut microbiome in mice.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227774},
doi = {10.1371/journal.pone.0227774},
pmid = {31978078},
issn = {1932-6203},
abstract = {The list of pharmacological agents that can modify the gut microbiome or be modified by it continues to grow at a high rate. The greatest amount of attention on drug-gut microbiome interactions has been directed primarily at pharmaceuticals used to treat infection, diabetes, cardiovascular conditions and cancer. By comparison, drugs of abuse and addiction, which can powerfully and chronically worsen human health, have received relatively little attention in this regard. Therefore, the main objective of this study was to characterize how selected synthetic psychoactive cathinones (aka "Bath Salts") and amphetamine stimulants modify the gut microbiome. Mice were treated with mephedrone (40 mg/kg), methcathinone (80 mg/kg), methamphetamine (5 mg/kg) or 4-methyl-methamphetamine (40 mg/kg), following a binge regimen consisting of 4 injections at 2h intervals. These drugs were selected for study because they are structural analogs that contain a β-keto substituent (methcathinone), a 4-methyl group (4-methyl-methamphetamine), both substituents (mephedrone) or neither (methamphetamine). Mice were sacrificed 1, 2 or 7 days after treatment and DNA from caecum contents was subjected to 16S rRNA sequencing. We found that all drugs caused significant time- and structure-dependent alterations in the diversity and taxonomic structure of the gut microbiome. The two phyla most changed by drug treatments were Firmicutes (methcathinone, 4-methyl-methamphetamine) and Bacteriodetes (methcathinone, 4-methyl-methamphetamine, methamphetamine, mephedrone). Across time, broad microbiome changes from the phylum to genus levels were characteristic of all drugs. The present results signify that these selected psychoactive drugs, which are thought to exert their primary effects within the CNS, can have profound effects on the gut microbiome. They also suggest new avenues of investigation into the possibility that gut-derived signals could modulate drug abuse and addiction via altered communication along the gut-brain axis.},
}

@article {pmid31978071,
year = {2020},
author = {Min, KR and Galvis, A and Baquerizo Nole, KL and Sinha, R and Clarke, J and Kirsner, RS and Ajdic, D},
title = {Association between baseline abundance of Peptoniphilus, a Gram-positive anaerobic coccus, and wound healing outcomes of DFUs.},
journal = {PloS one},
volume = {15},
number = {1},
pages = {e0227006},
doi = {10.1371/journal.pone.0227006},
pmid = {31978071},
issn = {1932-6203},
abstract = {Diabetic foot ulcers (DFUs) lead to nearly 100,000 lower limb amputations annually in the United States. DFUs are colonized by complex microbial communities, and infection is one of the most common reasons for diabetes-related hospitalizations and amputations. In this study, we examined how DFU microbiomes respond to initial sharp debridement and offloading and how the initial composition associates with 4 week healing outcomes. We employed 16S rRNA next generation sequencing to perform microbial profiling on 50 samples collected from 10 patients with vascularized neuropathic DFUs. Debrided wound samples were obtained at initial visit and after one week from two DFU locations, wound bed and wound edge. Samples of the foot skin outside of the wounds were also collected for comparison. We showed that DFU wound beds are colonized by a greater number of distinct bacterial phylotypes compared to the wound edge or skin outside the wound. However, no significant microbiome diversity changes occurred at the wound sites after one week of standard care. Finally, increased initial abundance of Gram-positive anaerobic cocci (GPAC), especially Peptoniphilus (p < 0.05; n = 5 subjects), was associated with impaired healing; thus, GPAC's abundance could be a predictor of the wound-healing outcome.},
}

@article {pmid31977194,
year = {2020},
author = {Chevrette, MG and Handelsman, J},
title = {From Metagenomes to Molecules: Innovations in Functional Metagenomics Unlock Hidden Chemistry in the Human Microbiome.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.0c00033},
pmid = {31977194},
issn = {1520-4995},
}

@article {pmid31977191,
year = {2020},
author = {Xue, M and Wernke, K and Herzon, SB},
title = {Depurination of colibactin-derived interstrand cross-links.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.9b01070},
pmid = {31977191},
issn = {1520-4995},
abstract = {Colibactin is a genotoxic gut microbiome metabolite long suspected of playing an etiological role in colorectal cancer. Evidence suggests colibactin forms DNA interstrand cross-links (ICLs) in eukaryotic cells and activates ICL repair pathways, leading to the production of ICL-dependent DNA double-strand breaks (DSBs). Here we show that colibactin ICLs can evolve directly to DNA DSBs. Using the topology of supercoiled plasmid DNA as a proxy for alkylation adduct stability, we find that colibactin-derived ICLs are unstable toward depurination and elimination of the 3¢ phosphate. This ICL degradation pathway leads progressively to single strand breaks (SSBs) and subsequently DSBs. The spontaneous conversion of ICLs to DSBs is consistent with the finding that non-homologous end joining repair-deficient cells are sensitized to colibactin-producing bacteria. The results herein further our understanding of colibactin-derived DNA damage and underscore the complexities underlying the DSB phenotype.},
}

@article {pmid31976354,
year = {2020},
author = {Redding, LE and Kelly, BJ and Stefanovski, D and Lautenbach, JK and Tolomeo, P and Cressman, L and Gruber, E and Meily, P and Lautenbach, E},
title = {Pet Ownership Protects Against Recurrence of Clostridioides difficile Infection.},
journal = {Open forum infectious diseases},
volume = {7},
number = {1},
pages = {ofz541},
doi = {10.1093/ofid/ofz541},
pmid = {31976354},
issn = {2328-8957},
abstract = {Background: Clostridioides difficile infection (CDI) is the leading cause of antibiotic-associated and health care-associated diarrhea in humans. Recurrent CDI (R-CDI) occurs in ~20%-30% of patients with CDI and results in increased morbidity, mortality, and hospital costs. Genomic analyses have shown overlap of C. difficile isolates from animals and people, suggesting that a zoonotic reservoir may contribute to recurrence. The objective of this study was to determine whether pet ownership is a risk factor for recurrence of CDI.

Methods: We conducted a case-control study among patients with recurrent CDI (cases; n = 86) and patients with nonrecurrent CDI (controls; n = 146). Multivariable logistic regression modeling was used to determine the association between recurrence of CDI and pet ownership while accounting for patient-level risk factors.

Results: Pet ownership was not significantly associated with recurrence of CDI (odds ratio [OR], 1.02; 95% confidence interval [CI], 0.38-2.72; P = 0.965) among all patients (n = 232). However, among the subset of patients with community-associated or community-onset health care facility-acquired CDI (n = 127), increasing contact with pets was increasingly protective against recurrence: for every point increase in a pet contact score (out of 7 possible points), the odds of recurrence decreased by 14% (OR, 0.86; 95% CI, 0.74-1.00; P = 0.051).

Conclusions: Close interactions with pets appear protective against the recurrence of community-acquired CDI. A potential mechanism may involve beneficial contributions to the microbiota of pet owners afflicted with CDI, as has been observed for other conditions such as atopy, obesity, and food allergies. However, more research is needed to understand the interactions between pets, owners, and their microbiota.},
}

@article {pmid31976311,
year = {2019},
author = {Garza-González, E and Mendoza-Olazarán, S and Morfin-Otero, R and Ramírez-Fontes, A and Rodríguez-Zulueta, P and Flores-Treviño, S and Bocanegra-Ibarias, P and Maldonado-Garza, H and Camacho-Ortiz, A},
title = {Intestinal Microbiome Changes in Fecal Microbiota Transplant (FMT) vs. FMT Enriched with Lactobacillus in the Treatment of Recurrent Clostridioides difficile Infection.},
journal = {Canadian journal of gastroenterology & hepatology},
volume = {2019},
number = {},
pages = {4549298},
doi = {10.1155/2019/4549298},
pmid = {31976311},
issn = {2291-2797},
abstract = {Aim: In this study, we conducted a comparative study to explore the differences in therapeutic efficacy and intestinal microbiome of fecal microbiota transplant (FMT) vs. FMT in addition with Lactobacillus (FMT-L) for treatment of recurrent Clostridioides difficile infection (R-CDI).

Methods: We designed a double-blinded randomized comparative two-arm pilot multicenter study to assess the efficacy and impact in the intestinal microbiome of standard capsules of FMT vs. FMT-L enriched with 3 species of Lactobacillus for patients with R-CDI. A 90-day follow-up of 21 patients was performed, starting at the beginning of the study. From the selected patients, fecal samples were obtained at days 0, 3, 7, and 28 after treatment. Fecal samples and FMT were analyzed by 16S rRNA sequencing.

Results: We included 21 patients (13 in the FMT group and 8 in the FMT-L group). Overall, both groups had a reduction in bowel movements per day, from 8.6 to 3.2 in the first 48 h (62.7% reduction, p=0.001). No severe adverse reactions or recurrences were recorded. Firmicutes were the most abundant phylum in donors. A low relative abundance of Proteobacteria was detected and mostly found in patients even at higher proportions than the donor. The donor's pool also had relatively few Bacteroidetes, and some patients showed a higher abundance of this phylum. Based on the ANOSIM R values, there is a significant difference between the microbial communities of basal samples and samples collected on day 7 (p=0.045) and at day 28 (0.041).

Conclusion: Fecal microbiota transplant by capsules was clinically and genomically similar between traditional FMT and enriched FMT with Lactobacillus spp. Restoration of bacterial diversity and resolution of dysbiosis at days 7 and 28 were observed. Patients with a first episode of recurrence treated with FMT had an excellent response without severe adverse events; FMT should be considered as an early treatment during R-CDI.},
}

@article {pmid31975529,
year = {2020},
author = {Groves, HE and Allen, UD},
title = {Winning with poo? Fecal microbiome transplantation as an emerging strategy for the management of recurrent Clostridioides difficile infection in children.},
journal = {Pediatric transplantation},
volume = {24},
number = {1},
pages = {e13651},
doi = {10.1111/petr.13651},
pmid = {31975529},
issn = {1399-3046},
}

@article {pmid31975449,
year = {2020},
author = {Megrian, D and Taib, N and Witwinowski, J and Beloin, C and Gribaldo, S},
title = {One or two membranes? Diderm Firmicutes challenge the Gram-positive/Gram-negative divide.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.14469},
pmid = {31975449},
issn = {1365-2958},
abstract = {How, when, and why the transition between cell envelopes with one membrane (Gram-positives or monoderms) and two (Gram-negative or diderms) occurred in Bacteria is a key unanswered question in evolutionary biology. Different hypotheses have been put forward, suggesting that either the monoderm or the diderm phenotype is ancestral. The existence of diderm members in the classically monoderm Firmicutes challenges the Gram-positive/Gram-negative divide and provides a great opportunity to tackle the issue. In this review, we present current knowledge on the diversity of bacterial cell envelopes, including these atypical Firmicutes. We discuss how phylogenomic analysis supports the hypothesis that the diderm cell envelope architecture is an ancestral character in the Firmicutes, and that the monoderm phenotype in this phylum arose multiple times independently by loss of the outer membrane. Given the overwhelming distribution of diderm phenotypes with respect to monoderm ones, this scenario likely extends to the ancestor of all bacteria. Finally, we discuss the recent development of genetic tools for Veillonella parvula, a diderm Firmicute member of the human microbiome, which indicates it as an emerging new experimental model to investigate fundamental aspects of the diderm/monoderm transition.},
}

@article {pmid31974531,
year = {2020},
author = {Deane, C},
title = {Spying on the microbiome.},
journal = {Nature chemical biology},
volume = {16},
number = {2},
pages = {106},
doi = {10.1038/s41589-020-0463-7},
pmid = {31974531},
issn = {1552-4469},
}

@article {pmid31974429,
year = {2020},
author = {Radjabzadeh, D and Boer, CG and Beth, SA and van der Wal, P and Kiefte-De Jong, JC and Jansen, MAE and Konstantinov, SR and Peppelenbosch, MP and Hays, JP and Jaddoe, VWV and Ikram, MA and Rivadeneira, F and van Meurs, JBJ and Uitterlinden, AG and Medina-Gomez, C and Moll, HA and Kraaij, R},
title = {Diversity, compositional and functional differences between gut microbiota of children and adults.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {1040},
doi = {10.1038/s41598-020-57734-z},
pmid = {31974429},
issn = {2045-2322},
abstract = {The gut microbiota has been shown to play diverse roles in human health and disease although the underlying mechanisms have not yet been fully elucidated. Large cohort studies can provide further understanding into inter-individual differences, with more precise characterization of the pathways by which the gut microbiota influences human physiology and disease processes. Here, we aimed to profile the stool microbiome of children and adults from two population-based cohort studies, comprising 2,111 children in the age-range of 9 to 12 years (the Generation R Study) and 1,427 adult individuals in the range of 46 to 88 years of age (the Rotterdam Study). For the two cohorts, 16S rRNA gene profile datasets derived from the Dutch population were generated. The comparison of the two cohorts showed that children had significantly lower gut microbiome diversity. Furthermore, we observed higher relative abundances of genus Bacteroides in children and higher relative abundances of genus Blautia in adults. Predicted functional metagenome analysis showed an overrepresentation of the glycan degradation pathways, riboflavin (vitamin B2), pyridoxine (vitamin B6) and folate (vitamin B9) biosynthesis pathways in children. In contrast, the gut microbiome of adults showed higher abundances of carbohydrate metabolism pathways, beta-lactam resistance, thiamine (vitamin B1) and pantothenic (vitamin B5) biosynthesis pathways. A predominance of catabolic pathways in children (valine, leucine and isoleucine degradation) as compared to biosynthetic pathways in adults (valine, leucine and isoleucine biosynthesis) suggests a functional microbiome switch to the latter in adult individuals. Overall, we identified compositional and functional differences in gut microbiome between children and adults in a population-based setting. These microbiome profiles can serve as reference for future studies on specific human disease susceptibility in childhood, adulthood and specific diseased populations.},
}

@article {pmid31974147,
year = {2020},
author = {Hedblom, GA and Dev, K and Bowden, SD and Weber, B and Noll, S and Baumler, DJ and Johnson, TJ},
title = {Draft Genome Sequence of "Candidatus Arthromitus" UMNCA01, a Suspected Commensal Isolated from the Gut Microbiome of Commercial Turkey.},
journal = {Microbiology resource announcements},
volume = {9},
number = {4},
pages = {},
doi = {10.1128/MRA.01143-19},
pmid = {31974147},
issn = {2576-098X},
abstract = {"Candidatus Arthromitus" UMNCA01 was recovered from ileal samples of commercial turkey poults and may have probiotic capabilities. The complete genome was determined using the Illumina MiSeq and HiSeq sequencing platforms. The complete genome consists of 1,631,326 bp and has a G+C content of 26.14%, 1,540 coding sequences (CDS), and 37 RNA coding genes.},
}

@article {pmid31974108,
year = {2020},
author = {Naikawadi, RP},
title = {Is the microbiome-induced glycolytic pathway a harbinger of acute exacerbation of idiopathic pulmonary fibrosis?.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thoraxjnl-2019-214374},
pmid = {31974108},
issn = {1468-3296},
}

@article {pmid31973575,
year = {2020},
author = {Dickson, RP and Schultz, MJ and van der Poll, T and Schouten, LR and Falkowski, NR and Luth, JE and Sjoding, MW and Brown, CA and Chanderraj, R and Huffnagle, GB and Bos, LDJ and , },
title = {Lung Microbiota Predict Clinical Outcomes in Critically Ill Patients.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.201907-1487OC},
pmid = {31973575},
issn = {1535-4970},
abstract = {RATIONALE: Recent studies have revealed that in critically ill patients, lung microbiota are altered and correlate with alveolar inflammation. The clinical significance of altered lung bacteria in critical illness is unknown.

OBJECTIVES: To determine if clinical outcomes of critically ill patients are predicted by features of the lung microbiome at the time of admission.

METHODS: We performed a prospective observational cohort study in an intensive care unit (ICU) at a university hospital. Lung microbiota were quantified and characterized using droplet digital PCR and bacterial 16S rRNA gene sequencing. Primary predictors were the bacterial burden, community diversity, and community composition of lung microbiota. The primary outcome was ventilator-free days, determined at 28 days post admission.

MEASUREMENTS AND MAIN RESULTS: Lungs of 91 critically ill patients were sampled using miniature-bronchoalveolar lavage within 24 hours of ICU admission. Patients with increased bacterial lung bacterial burden had fewer ventilator-free days (HR 0.43, CI 0.21-0.88), which remained significant when controlled for pneumonia and severity of illness. The community composition of lung bacteria predicted ventilator-free days (P=0.003), driven by the presence of gut-associated bacteria (e.g. Lachnospiraceae and Enterobacteriaceae spp.). Detection of gut-associated bacteria was also associated with the presence of the acute respiratory distress syndrome.

CONCLUSIONS: Key features of the lung microbiome (bacterial burden, enrichment with gut-associated bacteria) predict outcomes in critically ill patients. The lung microbiome is an understudied source of clinical variation in critical illness, and represents a novel therapeutic target for the prevention and treatment of acute respiratory failure.},
}

@article {pmid31973241,
year = {2020},
author = {Cao, L and Lee, SG and Melough, MM and Sakaki, JR and Maas, KR and Koo, SI and Chun, OK},
title = {Long-Term Blackcurrant Supplementation Modified Gut Microbiome Profiles in Mice in an Age-Dependent Manner: An Exploratory Study.},
journal = {Nutrients},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/nu12020290},
pmid = {31973241},
issn = {2072-6643},
support = {#2016-67018-24492//USDA NIFA Seed Grant/ ; },
abstract = {Recent studies have suggested that blackcurrant (BC) anthocyanins have promising health benefits, possibly through regulating gut microbiome. Three- and eighteen-month old female mice were fed standard mouse diets for 4 months, each with or without BC (1% w/w) supplementation (n = 3 in each treatment group, 12 in total). We then assessed gut microbiome profiles using 16S sequencing of their feces. Old mice had a less diverse microbiome community compared to young mice and there was a remarkable age-related difference in microbiome composition in the beta diversity analysis. BC supplementation did not significantly affect alpha or beta diversity. The relative abundance of several phyla, including Firmicutes, Bacteroidetes, Proteobacteria and Tenericutes, was lower in old mice. BC downregulated Firmicutes abundance in young mice and upregulated Bacteroidetes in both age groups, leading to a decreased Firmicutes/Bacteroidetes ratio. There were age-specific differences in the effect of BC supplementation on the microbiome. Twenty-four operational taxonomic units showed a significant interaction between age and BC supplementation (p < 0.01), which suggests that the ecosystem and the host health status affect the functions and efficiency of BC intake. These results indicate that BC supplementation favorably modulates gut microbiome, but there are distinct age-specific differences. Studies with human hosts are needed to better understand BC's regulatory effects on the gut microbiome.},
}

@article {pmid31973214,
year = {2020},
author = {Safari, Z and Bruneau, A and Monnoye, M and Mariadassou, M and Philippe, C and Zatloukal, K and Gérard, P},
title = {Murine Genetic Background Overcomes Gut Microbiota Changes to Explain Metabolic Response to High-Fat Diet.},
journal = {Nutrients},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/nu12020287},
pmid = {31973214},
issn = {2072-6643},
support = {W1226//FWF/ ; },
abstract = {Interactions of diet, gut microbiota, and host genetics play essential roles in the development of metabolic diseases. A/J and C57BL/6J (C57) are two mouse strains known to display different susceptibilities to metabolic disorders. In this context, we analyzed gut microbiota composition in A/J and C57 mice, and assessed its responses to high-fat diet (HFD) and antibiotic (AB) treatment. We also exchanged the gut microbiota between the two strains following AB treatment to evaluate its impact on the metabolism. We showed that A/J and C57 mice have different microbiome structure and composition at baseline. Moreover, A/J and C57 microbiomes responded differently to HFD and AB treatments. Exchange of the gut microbiota between the two strains was successful as recipients' microbiota resembled donor-strain microbiota. Seven weeks after inoculation, the differences between recipients persisted and were still closer from the donor-strain microbiota. Despite effective microbiota transplants, the response to HFD was not markedly modified in C57 and A/J mice. Particularly, body weight gain and glucose intolerance in response to HFD remained different in the two mouse strains whatever the changes in microbiome composition. This indicated that genetic background has a much stronger impact on metabolic responses to HFD than gut microbiome composition.},
}

@article {pmid31973090,
year = {2020},
author = {Rodríguez-Rabassa, M and López, P and Sánchez, R and Hernández, C and Rodríguez, C and Rodríguez-Santiago, RE and Orengo, JC and Green, V and Yamamura, Y and Rivera-Amill, V},
title = {Inflammatory Biomarkers, Microbiome, Depression, and Executive Dysfunction in Alcohol Users.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/ijerph17030689},
pmid = {31973090},
issn = {1660-4601},
support = {G12MD007579, U54MD007579, and U54MD007587/NH/NIH HHS/United States ; },
abstract = {Alcohol-related disorders (ARD) are highly prevalent among Latin American-Caribbean countries. Mental disorders are common comorbidities in individuals with ARD. However, the etiology of the association between ARD and mental disorders remains unclear. We examined the association of inflammatory cytokines, microbiome, and other biomakers with measures of depression, social anxiety, and executive functions. We observed a significant increase in cytokine and chemokine expression levels in saliva and plasma in the alcohol group (AG) samples. Also, the salivary bacterial composition in the AG revealed an abundance of Prevotella. Depression symptomatology was markedly higher in the AG, but social anxiety levels were negligible. AG also exhibited executive dysfunctions, which negatively correlated with increased plasma levels of pro-inflammatory cytokines and increased salivary concentrations of Prevotella bacteria. Our study suggests that chronic alcohol use correlates with executive dysfunction, immune system dysregulation, and dysbiosis of the salivary microbiota. Additional studies are needed to understand the role of the microbiome and inflammation in alcohol use and mental comorbidities.},
}

@article {pmid31972620,
year = {2020},
author = {Ekekezie, C and Perler, BK and Wexler, A and Duff, C and Lillis, CJ and Kelly, CR},
title = {Understanding the Scope of Do-It-Yourself Fecal Microbiota Transplant.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000000499},
pmid = {31972620},
issn = {1572-0241},
abstract = {OBJECTIVES: Fecal microbiota transplantation (FMT) has emerged as an effective treatment option for Clostridioides difficile infection (CDI) and is considered an investigational therapy for a number of other diseases. Social media has facilitated widespread exposure of the public to the gut microbiome and FMT, ultimately acting as a catalyst for the Do-It-Yourself (DIY)-FMT movement. The aims of this study were to identify factors that influenced willingness to pursue DIY-FMT including common indications, screening processes, sample preparation, and self-reported efficacy and safety outcomes.

METHODS: A twenty-five-point cross-sectional survey was posted online through the websites and social media pages of the Peggy Lillis Foundation, The Fecal Transplant Foundation, and The Power of Poop. Responses were cataloged through the Research Electronic Data Capture tool, and descriptive analyses were performed.

RESULTS: Eighty-four respondents completed the survey between January 2018 and February 2019. The majority were female (71%) and white (92%). Most (80%) reported performing FMT on themselves; 87% used Internet resources to assist in the process, and 92% knew their stool donor. Inflammatory bowel disease (35%) and irritable bowel syndrome (29%) were the 2 most common conditions that respondents attempted to treat. Only 12% reported adverse events, whereas 82% reported improvement in their condition.

DISCUSSION: DIY-FMT is being used for many indications, including those for which there is little evidence. There was a high self-reported success rate among respondents with few adverse events. There is a need for increased awareness around DIY-FMT and research around this phenomenon, which may impact public health.},
}

@article {pmid31972462,
year = {2020},
author = {Frankiensztajn, LM and Elliott, E and Koren, O},
title = {The microbiota and the hypothalamus-pituitary-adrenocortical (HPA) axis, implications for anxiety and stress disorders.},
journal = {Current opinion in neurobiology},
volume = {62},
number = {},
pages = {76-82},
doi = {10.1016/j.conb.2019.12.003},
pmid = {31972462},
issn = {1873-6882},
abstract = {There is growing evidence for the involvement of the gut-microbiota in the regulation of emotions, behavior, and higher cognitive functions through the 'microbiome-gut-brain axis'. This relationship between the gut microbiota and the brain is pivotal for the development of the newborn, which receives its commensal microbiota at birth; dysbiosis may result in altered neurodevelopment. The hypothalamus-pituitary-adrenocortical (HPA) axis is actively involved in the stress response but is undeveloped in the newborn. Here, we describe how changes in the commensal microbiota influence the normal development of the HPA axis and review recent findings describing the essential crosstalk between the gut microbiota and the HPA axis and suggesting a role for the maternal and commensal microbiota in the development of the HPA axis and of the stress response.},
}

@article {pmid31972182,
year = {2020},
author = {Mok, SW and Wong, VK and Lo, HH and de Seabra Rodrigues Dias, IR and Leung, EL and Law, BY and Liu, L},
title = {Natural products-based polypharmacological modulation of the peripheral immune system for the treatment of neuropsychiatric disorders.},
journal = {Pharmacology & therapeutics},
volume = {},
number = {},
pages = {107480},
doi = {10.1016/j.pharmthera.2020.107480},
pmid = {31972182},
issn = {1879-016X},
abstract = {Chronic inflammation of the central nervous system (CNS) is critical to the pathogenesis of neuropsychiatric disorders (NPDs) that affect the global population. Current therapeutics for NPDs are limited to relieving symptoms and induce many adverse effects. Therefore, the discovery of novel therapeutic agents from natural sources is urgently needed. Intriguingly, the immune responses of peripheral organs are closely linked through the molecular communication between resident and blood-borne cellular components, which shape the neuroinflammatory phenotypes of NPDs. Since the gut and spleen are the two largest immunological organs of the body, the brain-gut microbiome and brain-spleen axes have been implicated in the connection between the CNS and the peripheral immune system. Accordingly, it has been proposed that the local CNS inflammation observed in NPDs is regulated via the manipulation of the systemic immune system by targeting the gut and spleen. Additionally, the complexity of the signalling network underlying the communication between the CNS and the systemic immune system suggests a strong potential for treating NPDs through a polypharmacological approach. The close association between systemic immunity and the homeostasis of the CNS points to the concept of repurposing interventions for systemic immune disorders to treat NPDs. Notably, natural products represent a promising source of such effective compounds due to both their pharmacological potency and safety. This review discusses the complex implications of dysregulated systemic immunity mediated by the brain-spleen and brain-gut microbiome axes in NPDs, such as Alzheimer's disease, Parkinson's disease, schizophrenia and major depressive disorder. In addition, the potential of repurposing natural product-based bioactive compounds for treating NPDs via modulating systemic immune disorders is intensively discussed.},
}

@article {pmid31971861,
year = {2020},
author = {Yang, J and Li, D and Yang, Z and Dai, W and Feng, X and Liu, Y and Jiang, Y and Li, P and Li, Y and Tang, B and Zhou, Q and Qiu, C and Zhang, C and Xu, X and Feng, S and Wang, D and Wang, H and Wang, W and Zheng, Y and Zhang, L and Wang, W and Zhou, K and Li, S and Yu, P},
title = {Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/19490976.2020.1712986},
pmid = {31971861},
issn = {1949-0984},
abstract = {Colorectal cancer (CRC) causes high morbidity and mortality worldwide, and noninvasive gut microbiome (GM) biomarkers are promising for early CRC diagnosis. However, the GM varies significantly based on ethnicity, diet and living environment, suggesting varied GM biomarker performance in different regions. We performed a metagenomic association analysis on stools from 52 patients and 55 corresponding healthy family members who lived together to identify GM biomarkers for CRC in Chongqing, China. The GM of patients differed significantly from that of healthy controls. A total of 22 microbial genes were included as screening biomarkers with high accuracy in additional 46 cases and 40 randomly selected healthy adults in Chongqing (area under the receive-operation curve (AUC) = 0.905, 95% CI 0.832-0.977). The classifier based on the identified 22 biomarkers also performed well in the cohort from Hong Kong (AUC = 0.811, 95% CI 0.715-0.907) and French (AUC = 0.859, 95% CI 0.773-0.944) populations. Quantitative PCR was applied for measuring three selected biomarkers in the classification of CRC patients in independent Chongqing population containing 30 cases and 30 controls and the best biomarker from Coprobacillus performed well with high AUC (0.930, 95% CI 0.904-0.955). This study revealed increased sensitivity and applicability of our GM biomarkers compared with previous biomarkers significantly promoting the early diagnosis of CRC.},
}

@article {pmid31971855,
year = {2020},
author = {Ramsteijn, AS and Jašarević, E and Houwing, DJ and Bale, TL and Olivier, JD},
title = {Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/19490976.2019.1705728},
pmid = {31971855},
issn = {1949-0984},
abstract = {Up to 10% of women use selective serotonin reuptake inhibitor (SSRI) antidepressants during pregnancy and postpartum. Recent evidence suggests that SSRIs are capable of altering the gut microbiota. However, the interaction between maternal depression and SSRI use on bacterial community composition and the availability of microbiota-derived metabolites during pregnancy and lactation is not clear.We studied this using a rat model relevant to depression, where adult females with a genetic vulnerability and stressed as pups show depressive-like behaviors. Throughout pregnancy and lactation, females received the SSRI fluoxetine or vehicle. High-resolution 16S ribosomal RNA marker gene sequencing and targeted metabolomic analysis were used to assess the fecal microbiome and metabolite availability, respectively.Not surprisingly, we found that pregnancy and lactation segregate in terms of fecal microbiome diversity and composition, accompanied by changes in metabolite availability. However, we also showed that fluoxetine treatment altered important features of this transition from pregnancy to lactation most clearly in previously stressed dams, with lower fecal amino acid concentrations. Amino acid concentrations, in turn, correlated negatively with the relative abundance of bacterial taxa such as Prevotella and Bacteroides.Our study demonstrates an important relationship between antidepressant use during the perinatal period and maternal fecal metabolite availability in a rat model relevant to depression, possibly through parallel changes in the gut microbiome. Since microbial metabolites contribute to homeostasis and development, insults to the maternal microbiome by SSRIs might have health consequences for mother and offspring.},
}

@article {pmid31970561,
year = {2020},
author = {Szczepaniak, A and Fichna, J and Zielińska, M},
title = {Opioids in Cancer Development, Progression and Metastasis: Focus on Colorectal Cancer.},
journal = {Current treatment options in oncology},
volume = {21},
number = {1},
pages = {6},
doi = {10.1007/s11864-019-0699-1},
pmid = {31970561},
issn = {1534-6277},
abstract = {OPINION STATEMENT: So far, opioids have been successfully used to reduce cancer pain in patients in order to improve their quality of life. However, the use of opioids leads to numerous side effects such as constipation, drowsiness, nausea, itching, increased sweating and hormonal changes. In this review, we described the action of opioids in several molecular pathways significant for maintenance of the intestinal homeostasis including the impact on the intestinal epithelium integrity, changes in microbiome composition, modulation of the immune system or induction of apoptosis and inhibition of angiogenesis. We summed up the role of individual opioids in the processes involved in the growth and development of cancer and elucidated if targeting opioid receptors may constitute novel therapeutic option in colon cancer.},
}

@article {pmid31969875,
year = {2019},
author = {Bardos, J and Fiorentino, D and Longman, RE and Paidas, M},
title = {Immunological Role of the Maternal Uterine Microbiome in Pregnancy: Pregnancies Pathologies and Alterated Microbiota.},
journal = {Frontiers in immunology},
volume = {10},
number = {},
pages = {2823},
doi = {10.3389/fimmu.2019.02823},
pmid = {31969875},
issn = {1664-3224},
abstract = {Understanding what happens at the time of embryo implantation has been the subject of significant research. Investigators from many differing fields including maternal fetal medicine, microbiology, genetics, reproductive endocrinology and immunology have all been studying the moment the embryo interacts with the maternal endometrium. A perfect relationship between the uterus and the embryo, mediated by a tightly controlled interaction between the embryo and the endometrium, is required for successful implantation. Any factors affecting this communication, such as altered microbiome may lead to poor reproductive outcomes. Current theories suggest that altered microbiota may trigger an inflammatory response in the endometrium that affects the success of embryo implantation, as inflammatory mediators are tightly regulated during the adhesion of the blastocyst to the epithelial endometrial wall. In this review, we will highlight the various microbiome found during the periconceptual period, the microbiomes interaction with immunological responses surrounding the time of implantation, its effect on implantation, placentation and ultimately maternal and neonatal outcomes.},
}

@article {pmid31969866,
year = {2019},
author = {Hao, X and Zhu, YG and Nybroe, O and Nicolaisen, MH},
title = {The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2951},
doi = {10.3389/fmicb.2019.02951},
pmid = {31969866},
issn = {1664-302X},
abstract = {Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.},
}

@article {pmid31969613,
year = {2020},
author = {Schöps, R and Goldmann, K and Korell, L and Bruelheide, H and Wubet, T and Buscot, F},
title = {Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {919},
doi = {10.1038/s41598-020-57760-x},
pmid = {31969613},
issn = {2045-2322},
support = {BR 1698/11-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WU 614/2-2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Plants are known to modulate their own rhizosphere mycobiome. However, field studies that use resident plants to relate the microbiome assemblage to environmental factors such as land-use suffer from the problem that confounding factors such as plant age and performance may override the targeted effects. In contrast, the use of even-aged phytometer plants pre-cultivated under uniform conditions helps to reduce such random variation. We investigated the rhizosphere mycobiomes of phytometer and resident plants of two common grassland species, Dactylis glomerata L. s. str. and Plantago lanceolata L. along a land-use intensity gradient using ITS rRNA Illumina amplicon sequencing. Remarkably, we did not detect effects of the plant types (resident vs. phytometer plant, even though some fungal taxa exhibited plant species specificity), indicating that phytometer plants hosted a comparable rhizosphere mycobiome as resident plants. Our data indicate that the plant species harbor distinct fungal communities, with fungal richness in the rhizosphere of P. lanceolata being substantially higher than that of D. glomerata. Land-use intensity had a clear impact on the mycobiome of both plant species, with specific fungal genera showing differential tolerance to high intensities. Overall, the phytometer approach has a high potential to reveal environmental impacts on rhizosphere communities.},
}

@article {pmid31969575,
year = {2020},
author = {Álvarez-Narváez, S and Berghaus, LJ and Morris, ERA and Willingham-Lane, JM and Slovis, NM and Giguere, S and Cohen, ND},
title = {A Common Practice of Widespread Antimicrobial Use in Horse Production Promotes Multi-Drug Resistance.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {911},
doi = {10.1038/s41598-020-57479-9},
pmid = {31969575},
issn = {2045-2322},
abstract = {The practice of prophylactic administration of a macrolide antimicrobial with rifampin (MaR) to apparently healthy foals with pulmonary lesions identified by thoracic ultrasonography (i.e., subclinically pneumonic foals) is common in the United States. The practice has been associated epidemiologically with emergence of R. equi resistant to MaR. Here, we report direct evidence of multi-drug resistance among foals treated with MaR. In silico and in vitro analysis of the fecal microbiome and resistome of 38 subclinically pneumonic foals treated with either MaR (n = 19) or gallium maltolate (GaM; n = 19) and 19 untreated controls was performed. Treatment with MaR, but not GaM, significantly decreased fecal microbiota abundance and diversity, and expanded the abundance and diversity of antimicrobial resistance genes in feces. Soil plots experimentally infected with Rhodococcus equi (R. equi) and treated with MaR selected for MaR-resistant R. equi, whereas MaR-susceptible R. equi out-competed resistant isolates in GaM-treated or untreated plots. Our results indicate that MaR use promotes multi-drug resistance in R. equi and commensals that are shed into their environment where they can persist and potentially infect or colonize horses and other animals.},
}

@article {pmid31969452,
year = {2020},
author = {Feng, L and Raman, AS and Hibberd, MC and Cheng, J and Griffin, NW and Peng, Y and Leyn, SA and Rodionov, DA and Osterman, AL and Gordon, JI},
title = {Identifying determinants of bacterial fitness in a model of human gut microbial succession.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1918951117},
pmid = {31969452},
issn = {1091-6490},
abstract = {Human gut microbiota development has been associated with healthy growth but understanding the determinants of community assembly and composition is a formidable challenge. We cultured bacteria from serially collected fecal samples from a healthy infant; 34 sequenced strains containing 103,102 genes were divided into two consortia representing earlier and later stages in community assembly during the first six postnatal months. The two consortia were introduced alone (singly), or sequentially in different order, or simultaneously into young germ-free mice fed human infant formula. The pattern of fitness of bacterial strains observed across the different colonization conditions indicated that later-phase strains substantially outcompete earlier-phase strains, although four early-phase members persist. Persistence was not determined by order of introduction, suggesting that priority effects are not prominent in this model. To characterize succession in the context of the metabolic potential of consortium members, we performed in silico reconstructions of metabolic pathways involved in carbohydrate utilization and amino acid and B-vitamin biosynthesis, then quantified the fitness (abundance) of strains in serially collected fecal samples and their transcriptional responses to different histories of colonization. Applying feature-reduction methods disclosed a set of metabolic pathways whose presence and/or expression correlates with strain fitness and that enable early-stage colonizers to survive during introduction of later colonizers. The approach described can be used to test the magnitude of the contribution of identified metabolic pathways to fitness in different community contexts, study various ecological processes thought to govern community assembly, and facilitate development of microbiota-directed therapeutics.},
}

@article {pmid31969191,
year = {2020},
author = {Chijiiwa, R and Hosokawa, M and Kogawa, M and Nishikawa, Y and Ide, K and Sakanashi, C and Takahashi, K and Takeyama, H},
title = {Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {5},
doi = {10.1186/s40168-019-0779-2},
pmid = {31969191},
issn = {2049-2618},
support = {JPMJPR15FA//Japan Science and Technology Agency/ ; 18H01801//Ministry of Education, Culture, Sports, Science and Technology/ ; 17H06158//Ministry of Education, Culture, Sports, Science and Technology/ ; Cross-ministerial Strategic Innovation Promotion Program (SIP), "Technologies for creating next-generation agriculture, forestry and fisheries"//Bio-oriented Technology Research Advancement Institution/ ; },
abstract = {BACKGROUND: The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota. In this study, we describe a novel single-cell genomic sequencing technique that can identify metabolic responders at the species level without the need for reference genomes, and apply this method to identify bacterial responders to an inulin-based diet in the mouse gut microbiota.

RESULTS: Inulin-feeding changed the mouse fecal microbiome composition to increase Bacteroides spp., resulting in the production of abundant succinate in the mouse intestine. Using our massively parallel single-cell genome sequencing technique, named SAG-gel platform, we obtained 346 single-amplified genomes (SAGs) from mouse gut microbes before and after dietary inulin supplementation. After quality control, the SAGs were classified as 267 bacteria, spanning 2 phyla, 4 classes, 7 orders, and 14 families, and 31 different strains of SAGs were graded as high- and medium-quality draft genomes. From these, we have successfully obtained the genomes of the dominant inulin-responders, Bacteroides spp., and identified their polysaccharide utilization loci and their specific metabolic pathways for succinate production.

CONCLUSIONS: Our single-cell genomics approach generated a massive amount of SAGs, enabling a functional analysis of uncultured bacteria in the intestinal microbiome. This enabled us to estimate metabolic lineages involved in the bacterial fermentation of dietary fiber and metabolic outcomes such as short-chain fatty acid production in the intestinal environment based on the fibers ingested. The technique allows the in-depth isolation and characterization of uncultured bacteria with specific functions in the microbiota and could be exploited to improve human and animal health. Video abstract.},
}

@article {pmid31969090,
year = {2020},
author = {Rodriguez-Gonzalez, A and Orio, L},
title = {Microbiota and alcohol use disorder: are psychobiotics a novel therapeutic strategy?.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/1381612826666200122153541},
pmid = {31969090},
issn = {1873-4286},
abstract = {In recent years, there has been an exciting focus of research attempting to understand neuropsychiatric disorders from a holistic perspective in order to determine the role of gut microbiota in the aetiology and pathogenesis of such disorders. Thus, the possible therapeutic benefits of targeting gut microbiota are being explored for conditions such as stress, depression or schizophrenia. Growing evidence indicates that there is a bidirectional communication between gut microbiota and the brain that has an effect on normal CNS functioning and behavioural responses. Alcohol abuse damages the gastrointestinal tract, alters gut microbiota and induces neuroinflammation and cognitive decline. The relationship between alcohol abuse and hypothalamic-pituitary-adrenal axis activation, inflammation and immune regulation has been well documented. In this review we explore the connection between microbiota, brain function and behaviour, as well as the mechanisms through which alcohol induces microbiota dysbiosis and intestinal barrier dysfunction. Finally, we propose the study of psychobiotics as a novel pharmaceutical strategy to treat alcohol use disorders.},
}

@article {pmid31968300,
year = {2019},
author = {Greenfield, SR and Tighe, SW and Bai, Y and Goerlitz, DS and Von Turkovich, M and Taatjes, DJ and Dragon, JA and Johnson, SS},
title = {Life and its traces in Antarctica's McMurdo Dry Valley paleolakes: a survey of preservation.},
journal = {Micron (Oxford, England : 1993)},
volume = {131},
number = {},
pages = {102818},
doi = {10.1016/j.micron.2019.102818},
pmid = {31968300},
issn = {1878-4291},
abstract = {The extremely cold and arid conditions of Antarctica make it uniquely positioned to investigate fundamental questions regarding the persistence of life in extreme environments. Within the McMurdo Dry Valleys and surrounding mountain ranges are multiple ancient relict lakes, paleolakes, with lacustrine deposits spanning from thousands to millions of years in age. Here we present data from light microscopy, scanning electron microscopy, electron dispersive x-ray spectroscopy, and radiocarbon dating to catalog the remarkable range of life preserved within these deposits. This includes intact microbes and nanobacteria-sized cocci, CaCO3 precipitations consistent with biogenic calcium, previously undescribed net-like structures, possible dormant spores, and long-extinct yet exquisitely preserved non-vascular plants. These images provide an important reference for further microbiome investigations of Antarctic paleolake samples. In addition, these findings may provide a visual reference for the use of subsurface groundwater microbial communities as an analog for paleolake subsurface water on planets such as Mars.},
}

@article {pmid31968071,
year = {2020},
author = {Schmid, D and Song, M and Zhang, X and Willett, WC and Vaidya, R and Giovannucci, EL and Michels, KB},
title = {Yogurt consumption in relation to mortality from cardiovascular disease, cancer, and all causes: a prospective investigation in 2 cohorts of US women and men.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajcn/nqz345},
pmid = {31968071},
issn = {1938-3207},
abstract = {BACKGROUND: Although a link between regular yogurt consumption and mortality appears plausible, data are sparse and have yielded inconsistent results.

OBJECTIVES: We examined the association between regular yogurt consumption and risk of all-cause and cause-specific mortality among US women and men.

METHODS: A total of 82,348 women in the Nurses' Health Study and 40,278 men in the Health Professionals Follow-Up Study without a history of cardiovascular disease (CVD) and cancer in 1980 (women) or 1986 (men) were followed up until 2012. Yogurt consumption was assessed by updated validated FFQs.

RESULTS: During 3,354,957 person-years of follow-up, 20,831 women and 12,397 men died. Compared with no yogurt consumption, the multivariable-adjusted HRs (95% CIs) of mortality were 0.89 (0.86, 0.93), 0.85 (0.81, 0.89), 0.88 (0.84, 0.91), and 0.91 (0.85, 0.98) for ≤1-3 servings/mo, 1 serving/wk, 2-4 servings/wk, and >4 servings/wk in women (P-trend = 0.34), respectively. For men, the corresponding HRs (95% CIs) were 0.99 (0.94, 1.03), 0.98 (0.91, 1.05), 1.04 (0.98, 1.10), and 1.05 (0.95, 1.16), respectively. We further noted inverse associations for cancer mortality (multivariable-adjusted HR comparing extreme categories: 0.87; 95% CI: 0.78, 0.98; P-trend = 0.04) and CVD mortality (HR: 0.92; 95% CI: 0.79, 1.08; P-trend = 0.41) in women, although the latter was attenuated in the multivariable-adjusted model. Replacement of 1 serving/d of yogurt with 1 serving/d of nuts (women and men) or whole grains (women) was associated with a lower risk of all-cause mortality, whereas replacement of yogurt with red meat, processed meat (women and men), and milk or other dairy foods (women) was associated with a greater mortality.

CONCLUSIONS: In our study, regular yogurt consumption was related to lower mortality risk among women. Given that no clear dose-response relation was apparent, this result must be interpreted with caution.},
}

@article {pmid31967848,
year = {2020},
author = {Casado, F and Morty, RE},
title = {The emergence of preclinical studies on the role of the microbiome in lung development and experimental animal models of bronchopulmonary dysplasia.},
journal = {American journal of physiology. Lung cellular and molecular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajplung.00509.2019},
pmid = {31967848},
issn = {1522-1504},
}

@article {pmid31967708,
year = {2020},
author = {Napoli, E and Siracusa, L and Ruberto, G},
title = {New tricks for old guys recent developments in the chemistry, biochemistry, applications and exploitation of selected species from the Lamiaceae family.},
journal = {Chemistry & biodiversity},
volume = {},
number = {},
pages = {},
doi = {10.1002/cbdv.201900677},
pmid = {31967708},
issn = {1612-1880},
abstract = {Lamiaceae is one of the largest families of flowering plants comprising about 250 genera and over 7,000 species. The majority of the plants of this family are aromatic and therefore important source of essential oils. Lamiaceae are widely used as culinary herbs and reported as medicinal plants in several folk traditions. In the Mediterranean area oregano, sage, rosemary, thyme and lavender stand out for geographical diffusion and variety of uses. The aim of this review is to provide recent data dealing with the phytochemical and pharmacological studies, and the more recent applications of the essential oils and the non-volatile phytocomplexes. This literature survey suggests how the deeper understanding of biomolecular processes in the health and food sectors as per as pest control bioremediation of cultural heritage, or interaction with human microbiome, fields, leads to the rediscovery and new potential applications of well-known plants.},
}

@article {pmid31967468,
year = {2020},
author = {Mei, F and Liu, J and Wu, J and Chen, M and Meng, K and Xia, G and Zhao, M},
title = {Collagen peptides isolated from Salmon salar and Tilapia nilotica skin accelerate wound healing by altering cutaneous microbiome colonization via up-regulated NOD2 and BD14.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.9b08002},
pmid = {31967468},
issn = {1520-5118},
abstract = {Collagen peptide can promote wound healing and is closely related to microbiome colonization. We investigated the relationship between collagen peptide, wound healing, and wound microflora colonization by administering the murine wound model with Salmon salar skin collagen peptides (Ss-SCP) and Tilapia nilotica skin collagen peptides (Tn-SCP). We analyzed the vascular endothelial growth factor (VEGF), fibroblast growth factors (β-FGF), pattern recognition receptor (NOD2), antimicrobial peptides β-defence14 (BD14), proinflammatory cytokine (TNF-α, IL-6, IL-8), anti-inflammatory (IL-10), macrophage and neutrophil infiltration levels, and microbial communities in the rat wound. The healing rate of the Ss-SCP and Tn-SCP treated group were significantly accelerated, associated with decreased TNF-α, IL-6, and IL-8, and up-regulated BD14, NOD2, IL-10, VEGF, and β-FGF. Accelerated healing in collagen peptide group shows that the wound microflora such as Leuconostoc, Enterococcus, and Bacillus have a positive effect on wound healing (P<0.01). Other microbiome species such as Stenotrophomonas, Bradyrhizobium, Sphingomonas, and Phyllobacterium had a negative influence was decreased colonization (P<0.01). All together, these studies show that collagen peptide could up-regulate wound NOD2 and BD14, which were implicated in microflora colonization regulation in the wound tissue and promoted wound healing by controlling inflammatory reaction and increasing wound angiogenesis and collagen deposition.},
}

@article {pmid31965894,
year = {2020},
author = {Lee, NY and Yoon, SJ and Han, DH and Gupta, H and Youn, GS and Shin, MJ and Ham, YL and Kwak, MJ and Kim, BY and Yu, JS and Lee, DY and Park, TS and Park, SH and Kim, BK and Joung, HC and Choi, IS and Hong, JT and Kim, DJ and Han, SH and Suk, KT},
title = {Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/19490976.2020.1712984},
pmid = {31965894},
issn = {1949-0984},
abstract = {Targeting the gut-liver axis by modulating the gut-microbiome can be a promising therapeutic approach in nonalcoholic fatty liver disease (NAFLD). The aim of this study was to evaluate the effects of single species and a combination of Lactobacillus and Pediococcus in NAFLD mice model. Six-week male C57BL/6J mice were divided into 9 groups (n = 10/group; normal, Western diet, and 7 Western diet-strains [109 CFU/g, 8 weeks]). The strains used were L. bulgaricus, L. casei, L. helveticus, P. pentosaceus KID7, and three combinations (1: L. casei+L. helveticus, 2: L. casei+L. helveticus+P. pentosaceus KID7, and 3: L. casei+L. helveticus+L. bulgaricus). Liver/Body weight ratio, serum and stool analysis, liver pathology, and metagenomics by 16S rRNA-sequencing were examined. In the liver/body ratio, L. bulgaricus (5.1 ± 0.5), L. helveticus (5.2 ± 0.4), P. pentosaceus KID7 (5.5 ± 0.5), and combination1 and 2 (4.2 ± 0.6 and 4.8 ± 0.7) showed significant reductions compared with Western (6.2 ± 0.6)(p < 0.001). In terms of cholesterol and steatosis/inflammation/NAFLD activity, all groups except for L. casei were associated with an improvement (p < .05). The elevated level of tumor necrosis factor-α/interleukin-1β (pg/ml) in Western (65.8 ± 7.9/163.8 ± 12.2) was found to be significantly reduced in L. bulgaricus (24.2 ± 1.0/58.9 ± 15.3), L. casei (35.6 ± 2.1/62.9 ± 6.0), L. helveticus (43.4 ± 3.2/53.6 ± 7.5), and P. pentosaceus KID7 (22.9 ± 3.4/59.7 ± 12.2)(p < 0.01). Cytokines were improved in the combination groups. In metagenomics, each strains revealed a different composition and elevated Firmicutes/Bacteroidetes ratio in the western (47.1) was decreased in L. bulgaricus (14.5), L. helveticus (3.0), and P. pentosaceus KID7 (13.3). L. bulgaricus, L. casei, L. helveticus, and P. pentosaceus KID7 supplementation can improve NAFLD-progression by modulating gut-microbiome and inflammatory pathway.},
}

@article {pmid31965849,
year = {2019},
author = {Cameron, A and McAllister, TA},
title = {Could probiotics be the panacea alternative to the use of antimicrobials in livestock diets?.},
journal = {Beneficial microbes},
volume = {10},
number = {7},
pages = {773-799},
doi = {10.3920/BM2019.0059},
pmid = {31965849},
issn = {1876-2891},
abstract = {Probiotics are most frequently derived from the natural microbiota of healthy animals. These bacteria and their metabolic products are viewed as nutritional tools for promoting animal health and productivity, disease prevention and therapy, and food safety in an era defined by increasingly widespread antimicrobial resistance in bacterial pathogens. In contemporary livestock production, antimicrobial usage is indispensable for animal welfare, and employed to enhance growth and feed efficiency. Given the importance of antimicrobials in both human and veterinary medicine, their effective replacement with direct-fed microbials or probiotics could help reduce antimicrobial use, perhaps restoring or extending the usefulness of these precious drugs against serious infections. Thus, probiotic research in livestock is rapidly evolving, aspiring to produce local and systemic health benefits on par with antimicrobials. Although many studies have clearly demonstrated the potential of probiotics to positively affect animal health and inhibit pathogens, experimental evidence suggests that probiotics' successes are modest, conditional, strain-dependent, and transient. Here, we explore current understanding, trends, and emerging applications of probiotic research and usage in major livestock species, and highlight successes in animal health and performance.},
}

@article {pmid31965847,
year = {2019},
author = {Shibayama, J and Goto, M and Kuda, T and Fukunaga, M and Takahashi, H and Kimura, B},
title = {Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet.},
journal = {Beneficial microbes},
volume = {10},
number = {7},
pages = {811-821},
doi = {10.3920/BM2019.0072},
pmid = {31965847},
issn = {1876-2891},
abstract = {To clarify the effect of rice bran (RB) and fermented RB (FRB) in a high-sucrose and low-dietary fibre diet on the gut microbiome, the in vitro bile acid-lowering capacity and caecal microbiota of ICR mice fed with 20% RB or FRB diets for two weeks were determined. The caecal microbiome was analysed by 16S rRNA gene amplicon sequencing. The in vitro bile acid-lowering capacity was high for FRB. In mouse experiments, triacylglycerol and total cholesterol were generally lower with FRB, although the faecal frequency was highest in mice fed with RB. The Shannon-Wiener and Simpson's indices for alpha-diversity in the microbiome of mice fed with RB and FRB, were higher than mice fed the control diet. At the phylum level in the caecal microbiome, Firmicutes and Bacteroidetes were high with FRB and RB, respectively. At the operational taxonomic unit level, some bacterial groups related to diabetes and gut toxicity, such as Lachnospiraceae and Enterorhabdus mucosicola, were high for RB but not for FRB diets. These results suggest that FRB, rather than RB, intake improve the intestinal environment and blood lipid condition.},
}

@article {pmid31965839,
year = {2019},
author = {Nealon, NJ and Parker, KD and Lahaie, P and Ibrahim, H and Maurya, AK and Raina, K and Ryan, EP},
title = {Bifidobacterium longum-fermented rice bran and rice bran supplementation affects the gut microbiome and metabolome.},
journal = {Beneficial microbes},
volume = {10},
number = {8},
pages = {823-839},
doi = {10.3920/BM2019.0017},
pmid = {31965839},
issn = {1876-2891},
abstract = {This study investigated gut microbiota composition along with food, host, and microbial derived metabolites in the colon and systemic circulation of healthy mice following dietary rice bran and fermented rice bran intake. Adult male BALB/c mice were fed a control diet or one of two experimental diets containing 10% w/w rice bran fermented by Bifidobacterium longum or 10% w/w non-fermented rice bran for 15 weeks. Metabolomics was performed on the study diets (food), the murine colon and whole blood. These were analysed in concert with 16S rRNA amplicon sequencing of faeces, caecum, and colon microbiomes. Principal components analysis of murine microbiota composition displayed marked separation between control and experimental diets, and between faecal and tissue (caecum and colon) microbiomes. Colon and caecal microbiomes in both experimental diet groups showed enrichment of Roseburia, Lachnospiraceae, and Clostridiales related amplicon sequence variants compared to control. Bacterial composition was largely similar between experimental diets. Metabolite profiling revealed 530 small molecules comprising of 39% amino acids and 21% lipids that had differential abundances across food, colon, and blood matrices, and statistically significant between the control, rice bran, and fermented rice bran groups. The amino acid metabolite, N-delta-acetylornithine, was notably increased by B. longum rice bran fermentation when compared to non-fermented rice bran in food, colon, and blood. These findings support that dietary intake of rice bran fermented with B. longum modulates multiple metabolic pathways important to the gut and overall health.},
}

@article {pmid31965565,
year = {2020},
author = {Dittami, SM and Peters, AF and West, J and Cariou, T and KleinJan, H and Burgunter-Delamare, B and Prechoux, A and Egan, S and Boyen, C},
title = {Revisiting Australian Ectocarpus subulatus (Phaeophyceae) from the Hopkins River: Distribution, abiotic environment, and associated microbiota.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.12970},
pmid = {31965565},
issn = {1529-8817},
abstract = {In 1995 a strain of Ectocarpus was isolated from Hopkins River Falls, Victoria, Australia, constituting one of few available freshwater or nearly freshwater brown algae, and the only one belonging to the genus Ectocarpus. It has since been used as a model to study acclimation and adaptation to low salinities and the role of its microbiota in these processes. To provide more background information on this model, we assessed if Ectocarpus was still present in the Hopkins river twenty-two years after the original finding, estimated its present distribution, described its abiotic environment, and determined its in situ microbial composition. We sampled for Ectocarpus at 15 sites along the Hopkins River as well as 10 neighboring sites and found individuals with ITS and cox1 sequences identical to the original isolate at three sites upstream of Hopkins River Falls. The salinity of the water at these sites ranged from 3.1-6.9, and it was rich in sulfate (1-5 mM). The diversity of bacteria associated with the algae in situ (1312 operational taxonomic units) was one order of magnitude higher than in previous studies of the original laboratory culture, and 95 alga-associated bacterial strains were isolated from algal filaments on site. In particular, species of Planctomycetes were abundant in situ but rare in laboratory-cultures. Our results confirmed that Ectocarpus was still present in the Hopkins River, and the newly isolated algal and bacterial strains offer new possibilities to study the adaptation of Ectocarpus to low salinity and its interactions with its microbiome.},
}

@article {pmid31965103,
year = {2020},
author = {Landhuis, E},
title = {Technologies to watch in 2020.},
journal = {Nature},
volume = {577},
number = {7791},
pages = {585-587},
doi = {10.1038/d41586-020-00114-4},
pmid = {31965103},
issn = {1476-4687},
}

@article {pmid31964997,
year = {2020},
author = {Takakura, W and Oh, SJ and Singer-Englar, T and Mirocha, J and Leite, G and Fridman, A and Pimentel, M and Mathur, R and Pichetshote, N and Rezaie, A},
title = {Comparing the rates of methane production in patients with and without appendectomy: results from a large-scale cohort.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {867},
doi = {10.1038/s41598-020-57662-y},
pmid = {31964997},
issn = {2045-2322},
abstract = {There is no clear study identifying the microbiome of the appendix. However, in other diverticular conditions, such as diverticulosis, methanogens appear important. We investigated whether patients who had undergone appendectomies had decreased levels of exhaled methane (CH4). Consecutive patients who underwent breath testing (BT) from November 2005 to October 2013 were deterministically linked to electronic health records. The numbers of patients with CH4 ≥ 1 ppm (detectable) and ≥ 3 and ≥ 10 ppm (excess) were compared between patients who did and did not undergo appendectomy using a multivariable model adjusted for age and sex. Of the 4977 included patients (48.0 ± 18.4 years, 30.1% male), 1303 (26.2%) had CH4 ≥ 10 ppm, and 193 (3.9%) had undergone appendectomy. Appendectomy was associated with decreased odds of CH4 ≥ 1, ≥ 3, and ≥ 10 ppm (ORs (95% CI) = 0.67 (0.47-0.93), p = 0.02; 0.65 (0.46-0.92), p = 0.01; and 0.66 (0.46-0.93), p = 0.02, respectively). Additionally, the percentage of CH4 producers increased 4-fold from the first to ninth decade of life. This is the first study to report that appendectomy is associated with decreased exhaled CH4. The appendix may play an active physiologic role as a reservoir of methanogens.},
}

@article {pmid31964767,
year = {2020},
author = {Diener, C and Gibbons, SM and Resendis-Antonio, O},
title = {MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota.},
journal = {mSystems},
volume = {5},
number = {1},
pages = {},
doi = {10.1128/mSystems.00606-19},
pmid = {31964767},
issn = {2379-5077},
abstract = {Compositional changes in the gut microbiota have been associated with a variety of medical conditions such as obesity, Crohn's disease, and diabetes. However, connecting microbial community composition to ecosystem function remains a challenge. Here, we introduce MICOM, a customizable metabolic model of the human gut microbiome. By using a heuristic optimization approach based on L2 regularization, we were able to obtain a unique set of realistic growth rates that corresponded well with observed replication rates. We integrated adjustable dietary and taxon abundance constraints to generate personalized metabolic models for individual metagenomic samples. We applied MICOM to a balanced cohort of metagenomes from 186 people, including a metabolically healthy population and individuals with type 1 and type 2 diabetes. Model results showed that individual bacterial genera maintained conserved niche structures across humans, while the community-level production of short-chain fatty acids (SCFAs) was heterogeneous and highly individual specific. Model output revealed complex cross-feeding interactions that would be difficult to measure in vivo Metabolic interaction networks differed somewhat consistently between healthy and diabetic subjects. In particular, MICOM predicted reduced butyrate and propionate production in a diabetic cohort, with restoration of SCFA production profiles found in healthy subjects following metformin treatment. Overall, we found that changes in diet or taxon abundances have highly personalized effects. We believe MICOM can serve as a useful tool for generating mechanistic hypotheses for how diet and microbiome composition influence community function. All methods are implemented in an open-source Python package, which is available at https://github.com/micom-dev/micomIMPORTANCE The bacterial communities that live within the human gut have been linked to health and disease. However, we are still just beginning to understand how those bacteria interact and what potential interventions to our gut microbiome can make us healthier. Here, we present a mathematical modeling framework (named MICOM) that can recapitulate the growth rates of diverse bacterial species in the gut and can simulate metabolic interactions within microbial communities. We show that MICOM can unravel the ecological rules that shape the microbial landscape in our gut and that a given dietary or probiotic intervention can have widely different effects in different people.},
}

@article {pmid31964761,
year = {2020},
author = {Guo, GL and Chiang, JYL},
title = {Is CYP2C70 the key to new mouse models to understand bile acids in humans?.},
journal = {Journal of lipid research},
volume = {},
number = {},
pages = {},
doi = {10.1194/jlr.C120000621},
pmid = {31964761},
issn = {1539-7262},
abstract = {NA.},
}

@article {pmid31964729,
year = {2020},
author = {Flannery, JE and Stagaman, K and Burns, AR and Hickey, RJ and Roos, LE and Giuliano, RJ and Fisher, PA and Sharpton, TJ},
title = {Gut Feelings Begin in Childhood: the Gut Metagenome Correlates with Early Environment, Caregiving, and Behavior.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
doi = {10.1128/mBio.02780-19},
pmid = {31964729},
issn = {2150-7511},
abstract = {Psychosocial environments impact normative behavioral development in children, increasing the risk of problem behaviors and psychiatric disorders across the life span. Converging evidence demonstrates that early normative development is affected by the gut microbiome, which itself can be altered by early psychosocial environments. However, much of our understanding of the gut microbiome's role in early development stems from nonhuman animal models and predominately focuses on the first years of life, during peri- and postnatal microbial colonization. As a first step to identify if these findings translate to humans and the extent to which these relationships are maintained after initial microbial colonization, we conducted a metagenomic investigation among a cross-sectional sample of early school-aged children with a range of adverse experiences and caregiver stressors and relationships. Our results indicate that the taxonomic and functional composition of the gut microbiome correlates with behavior during a critical period of child development. Furthermore, our analysis reveals that both socioeconomic risk exposure and child behaviors associate with the relative abundances of specific taxa (e.g., Bacteroides and Bifidobacterium species) as well as functional modules encoded in their genomes (e.g., monoamine metabolism) that have been linked to cognition and health. While we cannot infer causality within this study, these findings suggest that caregivers may moderate the gut microbiome's link to environment and behaviors beyond the first few years of life.IMPORTANCE Childhood is a formative period of behavioral and biological development that can be modified, for better or worse, by the psychosocial environment that is in part determined by caregivers. Not only do our own genes and the external environment influence such developmental trajectories, but the community of microbes living in, on, and around our bodies-the microbiome-plays an important role as well. By surveying the gut microbiomes of a cross-sectional cohort of early school-aged children with a range of psychosocial environments and subclinical mental health symptoms, we demonstrated that caregiving behaviors modified the child gut microbiome's association to socioeconomic risk and behavioral dysregulation.},
}

@article {pmid31964728,
year = {2020},
author = {Carini, P and Delgado-Baquerizo, M and Hinckley, ES and Holland-Moritz, H and Brewer, TE and Rue, G and Vanderburgh, C and McKnight, D and Fierer, N},
title = {Effects of Spatial Variability and Relic DNA Removal on the Detection of Temporal Dynamics in Soil Microbial Communities.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
doi = {10.1128/mBio.02776-19},
pmid = {31964728},
issn = {2150-7511},
abstract = {Few studies have comprehensively investigated the temporal variability in soil microbial communities despite widespread recognition that the belowground environment is dynamic. In part, this stems from the challenges associated with the high degree of spatial heterogeneity in soil microbial communities and because the presence of relic DNA (DNA from dead cells or secreted extracellular DNA) may dampen temporal signals. Here, we disentangle the relationships among spatial, temporal, and relic DNA effects on prokaryotic and fungal communities in soils collected from contrasting hillslopes in Colorado, USA. We intensively sampled plots on each hillslope over 6 months to discriminate between temporal variability, intraplot spatial heterogeneity, and relic DNA effects on the soil prokaryotic and fungal communities. We show that the intraplot spatial variability in microbial community composition was strong and independent of relic DNA effects and that these spatial patterns persisted throughout the study. When controlling for intraplot spatial variability, we identified significant temporal variability in both plots over the 6-month study. These microbial communities were more dissimilar over time after relic DNA was removed, suggesting that relic DNA hinders the detection of important temporal dynamics in belowground microbial communities. We identified microbial taxa that exhibited shared temporal responses and show that these responses were often predictable from temporal changes in soil conditions. Our findings highlight approaches that can be used to better characterize temporal shifts in soil microbial communities, information that is critical for predicting the environmental preferences of individual soil microbial taxa and identifying linkages between soil microbial community composition and belowground processes.IMPORTANCE Nearly all microbial communities are dynamic in time. Understanding how temporal dynamics in microbial community structure affect soil biogeochemistry and fertility are key to being able to predict the responses of the soil microbiome to environmental perturbations. Here, we explain the effects of soil spatial structure and relic DNA on the determination of microbial community fluctuations over time. We found that intensive spatial sampling was required to identify temporal effects in microbial communities because of the high degree of spatial heterogeneity in soil and that DNA from nonliving sources masks important temporal patterns. We identified groups of microbes with shared temporal responses and show that these patterns were predictable from changes in soil characteristics. These results provide insight into the environmental preferences and temporal relationships between individual microbial taxa and highlight the importance of considering relic DNA when trying to detect temporal dynamics in belowground communities.},
}

@article {pmid31964727,
year = {2020},
author = {Jackrel, SL and Schmidt, KC and Cardinale, BJ and Denef, VJ},
title = {Microbiomes Reduce Their Host's Sensitivity to Interspecific Interactions.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
doi = {10.1128/mBio.02657-19},
pmid = {31964727},
issn = {2150-7511},
abstract = {Bacteria associated with eukaryotic hosts can affect host fitness and trophic interactions between eukaryotes, but the extent to which bacteria influence the eukaryotic species interactions within trophic levels that modulate biodiversity and species coexistence is mostly unknown. Here, we used phytoplankton, which are a classic model for evaluating interactions between species, grown with and without associated bacteria to test whether the bacteria alter the strength and type of species interactions within a trophic level. We demonstrate that host-associated bacteria alter host growth rates and carrying capacity. This did not change the type but frequently changed the strength of host interspecific interactions by facilitating host growth in the presence of an established species. These findings indicate that microbiomes can regulate their host species' interspecific interactions. As between-species interaction strength impacts their ability to coexist, our findings show that microbiomes have the potential to modulate eukaryotic species diversity and community composition.IMPORTANCE Description of the Earth's microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.},
}

@article {pmid31964724,
year = {2020},
author = {Motone, K and Takagi, T and Aburaya, S and Miura, N and Aoki, W and Ueda, M},
title = {A Zeaxanthin-Producing Bacterium Isolated from the Algal Phycosphere Protects Coral Endosymbionts from Environmental Stress.},
journal = {mBio},
volume = {11},
number = {1},
pages = {},
doi = {10.1128/mBio.01019-19},
pmid = {31964724},
issn = {2150-7511},
abstract = {Reef-building corals form a complex consortium with photosynthetic algae in the family Symbiodiniaceae and bacteria, collectively termed the coral holobiont. These bacteria are hypothesized to be involved in the stress resistance of the coral holobiont, but their functional roles remain largely elusive. Here, we show that cultured Symbiodiniaceae algae isolated from the reef-building coral Galaxea fascicularis are associated with novel bacteria affiliated with the family Flavobacteriaceae Antibiotic treatment eliminated the bacteria from cultured Symbiodiniaceae, resulting in a decreased maximum quantum yield of PSII (variable fluorescence divided by maximum fluorescence [Fv/Fm]) and an increased production of reactive oxygen species (ROS) under thermal and light stresses. We then isolated this bacterial strain, named GF1. GF1 inoculation in the antibiotic-treated Symbiodiniaceae cultures restored the Fv/Fm and reduced the ROS production. Furthermore, we found that GF1 produces the carotenoid zeaxanthin, which possesses potent antioxidant activity. Zeaxanthin supplementation to cultured Symbiodiniaceae ameliorated the Fv/Fm and ROS production, suggesting that GF1 mitigates thermal and light stresses in cultured Symbiodiniaceae via zeaxanthin production. These findings could advance our understanding of the roles of bacteria in Symbiodiniaceae and the coral holobiont, thereby contributing to the development of novel approaches toward coral protection through the use of symbiotic bacteria and their metabolites.IMPORTANCE Occupying less than 1% of the seas, coral reefs are estimated to harbor ∼25% of all marine species. However, the destruction of coral reefs has intensified in the face of global climate changes, such as rising seawater temperatures, which induce the overproduction of reactive oxygen species harmful to corals. Although reef-building corals form complex consortia with bacteria and photosynthetic endosymbiotic algae of the family Symbiodiniaceae, the functional roles of coral-associated bacteria remain largely elusive. By manipulating the Symbiodiniaceae bacterial community, we demonstrated that a bacterium that produces an antioxidant carotenoid could mitigate thermal and light stresses in cultured Symbiodiniaceae isolated from a reef-building coral. Therefore, this study illuminates the unexplored roles of coral-associated bacteria under stressful conditions.},
}

@article {pmid31964404,
year = {2020},
author = {Pollet, T and Sprong, H and Lejal, E and Krawczyk, AI and Moutailler, S and Cosson, JF and Vayssier-Taussat, M and Estrada-Peña, A},
title = {The scale affects our view on the identification and distribution of microbial communities in ticks.},
journal = {Parasites & vectors},
volume = {13},
number = {1},
pages = {36},
doi = {10.1186/s13071-020-3908-7},
pmid = {31964404},
issn = {1756-3305},
abstract = {Ticks transmit the highest variety of pathogens impacting human and animal health worldwide. It is now well established that ticks also harbour a microbial complex of coexisting symbionts, commensals and pathogens. With the development of high throughput sequencing technologies, studies dealing with such diverse bacterial composition in tick considerably increased in the past years and revealed an unexpected microbial diversity. These data on diversity and composition of the tick microbes are increasingly available, giving crucial details on microbial communities in ticks and improving our knowledge on the tick microbial community. However, consensus is currently lacking as to which scales (tick organs, individual specimens or species, communities of ticks, populations adapted to particular environmental conditions, spatial and temporal scales) best facilitate characterizing microbial community composition of ticks and understanding the diverse relationships among tick-borne bacteria. Temporal or spatial scales have a clear influence on how we conduct ecological studies, interpret results, and understand interactions between organisms that build the microbiome. We consider that patterns apparent at one scale can collapse into noise when viewed from other scales, indicating that processes shaping tick microbiome have a continuum of variability that has not yet been captured. Based on available reports, this review demonstrates how much the concept of scale is crucial to be considered in tick microbial community studies to improve our knowledge on tick microbe ecology and pathogen/microbiota interactions.},
}

@article {pmid31964338,
year = {2020},
author = {Bahrndorff, S and Ruiz-González, A and de Jonge, N and Nielsen, JL and Skovgård, H and Pertoldi, C},
title = {Integrated genome-wide investigations of the housefly, a global vector of diseases reveal unique dispersal patterns and bacterial communities across farms.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {66},
doi = {10.1186/s12864-020-6445-z},
pmid = {31964338},
issn = {1471-2164},
support = {11-116256//Teknologi og Produktion, Det Frie Forskningsråd/ ; },
abstract = {BACKGROUND: Houseflies (Musca domestica L.) live in intimate association with numerous microorganisms and is a vector of human pathogens. In temperate areas, houseflies will overwinter in environments constructed by humans and recolonize surrounding areas in early summer. However, the dispersal patterns and associated bacteria across season and location are unclear. We used genotyping-by-sequencing (GBS) for the simultaneous identification and genotyping of thousands of Single Nucleotide Polymorphisms (SNPs) to establish dispersal patterns of houseflies across farms. Secondly, we used 16S rRNA gene amplicon sequencing to establish the variation and association between bacterial communities and the housefly across farms.

RESULTS: Using GBS we identified 18,000 SNPs across 400 individuals sampled within and between 11 dairy farms in Denmark. There was evidence for sub-structuring of Danish housefly populations and with genetic structure that differed across season and sex. Further, there was a strong isolation by distance (IBD) effect, but with large variation suggesting that other hidden geographic barriers are important. Large individual variations were observed in the community structure of the microbiome and it was found to be dependent on location, sex, and collection time. Furthermore, the relative prevalence of putative pathogens was highly dependent on location and collection time.

CONCLUSION: We were able to identify SNPs for the determination of the spatiotemporal housefly genetic structure, and to establish the variation and association between bacterial communities and the housefly across farms using novel next-generation sequencing (NGS) techniques. These results are important for disease prevention given the fine-scale population structure and IBD for the housefly, and that individual houseflies carry location specific bacteria including putative pathogens.},
}

@article {pmid31964179,
year = {2020},
author = {Barr, RD and Ladas, EJ},
title = {The role of nutrition in pediatric oncology.},
journal = {Expert review of anticancer therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737140.2020.1719834},
pmid = {31964179},
issn = {1744-8328},
abstract = {Introduction: Obesity compromises survival in children with cancer in high-income countries (HICs) and is accompanied often by sarcopenia. In low and middle-income countries (LMICs), where the great majority of children live, the prevalence of under-nutrition is as high as 95% in those with cancer. Nutritional support improves clinical outcomes, including survival.Areas covered: This narrative review describes the evolution of attention to nutrition in children with cancer and the increasing understanding of this relationship. An initial focus on obesity in children with acute leukemias in HICs has been matched more recently by a recognition of the negative effect of under-nutrition on survival in children with cancer in LMICs. These observations have stimulated explorations of underlying mechanisms, including dysbiosis of the gut microbiome, and structured nutritional interventions to redress adverse outcomes.Expert opinion: Studies of the gut microbiome and metabolome have yielded important information on the pathogenesis of malnutrition in children, providing new avenues for interventions. Combinations of plant products that are inexpensive and readily available in LMICs have been shown to "mature" the microbiome and the corresponding plasma proteome in children with acute malnutrition, offering the prospect of cost-effective remedies that are tested in children with cancer.},
}

@article {pmid31963808,
year = {2020},
author = {Park, YE and Kim, MS and Shim, KW and Kim, YI and Chu, J and Kim, BK and Choi, IS and Kim, JY},
title = {Effects of Lactobacillus plantarum Q180 on Postprandial Lipid Levels and Intestinal Environment: A Double-Blind, Randomized, Placebo-Controlled, Parallel Trial.},
journal = {Nutrients},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/nu12010255},
pmid = {31963808},
issn = {2072-6643},
support = {G0090100-08//63,508,338/ ; },
abstract = {Probiotics can improve the intestinal environment by enhancing beneficial bacteria to potentially regulate lipid levels; however, the underlying mechanisms remain unclear. The aim of this study was to investigate the effect of Lactobacillus plantarum Q180 (LPQ180) on postprandial lipid metabolism and the intestinal microbiome environment from a clinical perspective. A double-blind, randomized, placebo-controlled study was conducted including 70 participants of both sexes, 20 years of age and older, with healthy blood triacylglyceride (TG) levels below 200 mg/dL. Treatment with LPQ180 for 12 weeks significantly decreased LDL-cholesterol (p = 0.042) and apolipoprotein (Apo)B-100 (p = 0.003) levels, and decreased postprandial maximum concentrations (Cmax) and areas under the curve (AUC) of TG, chylomicron TG, ApoB-48, and ApoB-100. LPQ180 treatment significantly decreased total indole and phenol levels (p = 0.019). In addition, there was a negative correlation between baseline microbiota abundance and lipid marker change, which was negatively correlated with metabolites. This study suggests that LPQ180 might be developed as a functional ingredient to help maintain healthy postprandial lipid levels through modulating gut environment.},
}

@article {pmid31963616,
year = {2020},
author = {Mariani, J and Favero, C and Carugno, M and Pergoli, L and Ferrari, L and Bonzini, M and Cattaneo, A and Pesatori, AC and Bollati, V},
title = {Nasal Microbiota Modifies the Effects of Particulate Air Pollution on Plasma Extracellular Vesicles.},
journal = {International journal of environmental research and public health},
volume = {17},
number = {2},
pages = {},
doi = {10.3390/ijerph17020611},
pmid = {31963616},
issn = {1660-4601},
support = {ERC-2011-StG 282413/ERC_/European Research Council/International ; },
abstract = {Air pollution exposure has been linked to modifications of both extracellular vesicle (EV) concentration and nasal microbiota structure (NMB), which might act as the respiratory health gatekeeper. This study aimed to assess whether an unbalanced NMB could modify the effect of particulate matter (PM) exposure on plasmatic EV levels. Due to two different NMB taxonomical profiles characterized by a widely different relative abundance of the Moraxella genus, the enrolled population was stratified into Mor- (balanced NMB) and Mor+ (unbalanced NMB) groups (Moraxella genus's cut-off ≤25% and >25%, respectively). EV features were assessed by nanoparticle tracking analysis (NTA) and flow-cytometry (FC). Multivariable analyses were applied on EV outcomes to evaluate a possible association between PM10 and PM2.5 and plasmatic EV levels. The Mor- group revealed positive associations between PM levels and plasmatic CD105+ EVs (GMR = 4.39 p = 0.02) as for total EV count (GMR = 1.92 p = 0.02). Conversely, the Mor+ group showed a negative association between exposure and EV outcomes (CD66+ GMR = 0.004 p = 0.01; EpCAM+ GMR = 0.005 p = 0.01). Our findings provide an insight regarding how a balanced NMB may help to counteract PM exposure effects in terms of plasmatic EV concentration. Further research is necessary to understand the relationship between the host and the NMB to disentangle the mechanism exerted by inhaled pollutants in modulating EVs and NMB.},
}

@article {pmid31963315,
year = {2020},
author = {Guirro, M and Gual-Grau, A and Gibert-Ramos, A and Alcaide-Hidalgo, JM and Canela, N and Arola, L and Mayneris-Perxachs, J},
title = {Metabolomics Elucidates Dose-Dependent Molecular Beneficial Effects of Hesperidin Supplementation in Rats Fed an Obesogenic Diet.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {9},
number = {1},
pages = {},
doi = {10.3390/antiox9010079},
pmid = {31963315},
issn = {2076-3921},
support = {TECSPR14-2-0001//Agència per a la Competitivitat de l'Empresa/ ; },
abstract = {Metabolic syndrome (MetS) is a global epidemic concern. Polyphenols are proposed as good candidates for its prevention, although their mechanisms are not fully understood. The gut microbiota seems to play a key role in polyphenol beneficial effects. Here, we assessed the effects of the citrus polyphenol hesperidin combining an untargeted metabolomics approach, which has an inherent potential to elucidate the host-microbiome interplay, with extensive anthropometric and biochemical characterizations and integrating metabolomics results with our previous 16S rRNA bacterial sequencing data. The rats were fed either a standard or an obesogenic cafeteria diet (CAF) for 17 weeks. After nine weeks, rats were supplemented with vehicle; low- (H1), or high- (H2) hesperidin doses. CAF animals developed MetS features. Hesperidin supplementation in CAF rats decreased the total cholesterol, LDL-C, and free fatty acids. The highest hesperidin dose also ameliorated blood pressure, insulin sensitivity, and decreased markers of arterial stiffness and inflammation. Metabolomics revealed an improvement of the lipidomic profile, decreases in circulating amino acids, and lower excretions of inflammation- and oxidative stress-related metabolites. Bacteroidaceae increases in the CAF-H2 group paralleled higher excretions of microbial-derived metabolites. Overall, our results provide detailed insights into the molecular effects of hesperidin on MetS and suggest that it is a promising prebiotic for the treatment of MetS and related conditions.},
}

@article {pmid31961914,
year = {2020},
author = {Meeker, SM and Mears, KS and Sangwan, N and Brittnacher, MJ and Weiss, EJ and Treuting, PM and Tolley, N and Pope, CE and Hager, KR and Vo, AT and Paik, J and Frevert, CW and Hayden, HS and Hoffman, LR and Miller, SI and Hajjar, AM},
title = {CFTR dysregulation drives active selection of the gut microbiome.},
journal = {PLoS pathogens},
volume = {16},
number = {1},
pages = {e1008251},
doi = {10.1371/journal.ppat.1008251},
pmid = {31961914},
issn = {1553-7374},
abstract = {Patients with cystic fibrosis (CF) have altered fecal microbiomes compared to those of healthy controls. The magnitude of this dysbiosis correlates with measures of CF gastrointestinal (GI) disease, including GI inflammation and nutrient malabsorption. However, whether this dysbiosis is caused by mutations in the CFTR gene, the underlying defect in CF, or whether CF-associated dysbiosis augments GI disease was not clear. To test the relationships between CFTR dysfunction, microbes, and intestinal health, we established a germ-free (GF) CF mouse model and demonstrated that CFTR gene mutations are sufficient to alter the GI microbiome. Furthermore, flow cytometric analysis demonstrated that colonized CF mice have increased mesenteric lymph node and spleen TH17+ cells compared with non-CF mice, suggesting that CFTR defects alter adaptive immune responses. Our findings demonstrate that CFTR mutations modulate both the host adaptive immune response and the intestinal microbiome.},
}

@article {pmid31961718,
year = {2020},
author = {Racine Miousse, I and Ewing, LE and Skinner, CM and Pathak, R and Garg, S and Kutanzi, KR and Melnyk, S and Hauer-Jensen, M and Koturbash, I},
title = {Methionine dietary supplementation potentiates ionizing radiation-induced gastrointestinal syndrome.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00351.2019},
pmid = {31961718},
issn = {1522-1547},
abstract = {Methionine is an essential amino acid needed for a variety of processes in living organisms. Ionizing radiation (IR) depletes tissue methionine concentrations and leads to the loss of DNA methylation and decreased synthesis of glutathione. In this study, we aimed to investigate the effects of methionine dietary supplementation in CBA/CaJ mice after exposure to doses ranging from 3 to 8.5 Gy 137Cs of total body irradiation. We report that mice fed a methionine-supplemented diet (MSD) (19.5 g/kg vs 6.5 mg/kg in a methionine-adequate diet, MAD) developed acute radiation toxicity at doses as low as 3 Gy. Partial body irradiation performed with hind-limb shielding resulted in a 50% mortality rate in MSD-fed mice exposed to 8.5 Gy, suggesting prevalence of radiation-induced gastrointestinal syndrome in the development of acute radiation toxicity. Analysis of the intestinal microbiome demonstrated shifts in the gut ecology, observed along with the development of leaky gut syndrome and bacterial translocation into the liver. Normal gut physiology impairment was facilitated by alterations in the one-carbon metabolism pathway and was exhibited as decreases in the circulating citrulline levels mirrored by decreased intestinal mucosal surface area and the number of surviving crypts. In conclusion, we demonstrate that a relevant excess of methionine dietary intake exacerbates the detrimental effects of exposure to IR in the small intestine.},
}

@article {pmid31961674,
year = {2020},
author = {Chang, PT and Rao, K and Longo, LO and Lawton, ES and Scherer, G and Van Arnam, EB},
title = {Thiopeptide Defense by an Ant's Bacterial Symbiont.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.9b00897},
pmid = {31961674},
issn = {1520-6025},
abstract = {Fungus-growing ants and their microbial symbionts have emerged as a model system for understanding antibiotic deployment in an ecological context. Here we establish that bacterial symbionts of the ant Trachymyrmex septentrionalis antagonize their most likely competitors, other strains of ant-associated bacteria, using the thiopeptide antibiotic GE37468. Genomic analysis suggests that these symbionts acquired the GE37468 gene cluster from soil bacteria. This antibiotic, with known activity against human pathogens, was previously identified in a biochemical screen but had no known ecological role. GE37468's host-associated defense role in this insect niche intriguingly parallels the function of similar thiopeptides in the human microbiome.},
}

@article {pmid31961657,
year = {2020},
author = {Hu, B and Yu, S and Shi, C and Gu, J and Shao, Y and Chen, Q and Li, Y and Mezzenga, R},
title = {Amyloid-Polyphenol Hybrid Nanofilaments Mitigate Colitis and Regulate Gut Microbial Dysbiosis.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.9b09125},
pmid = {31961657},
issn = {1936-086X},
abstract = {It is a desirable and powerful strategy to precisely fabricate functional soft matter through self-assembly of molecular building blocks across a range of length scales. Proteins, nucleic acids, and polyphenols are the self-assemblers ubiquitous in nature. Assembly of proteins into flexible biocolloids, amyloid fibrils with high aspect ratio, has emerged as an unchallenged templating strategy for high-end technological materials and bio-nanotechnologies. We demonstrate the ability of these fibrils to support the deposition and self-assembly of polyphenols into hybrid nanofilaments and functional macroscopic hydrogels made thereof. The length scale of the substance that amyloid fibrils can attach with acting as the building templates was extended from nanometer down to sub-nanometer. Significantly increased loading capacities of polyphenols (up to 4.0 wt%) compared with other delivery systems and improved stability were realized. After oral administration, the hydrogels could transport from stomach, to the small intestine and finally to the gut (cecum, colon, rectum), with a long-time retaining in the colon. Oral administration of the hydrogels significantly ameliorated colitis in a mouse model, promoted intestinal barrier function, suppressed the pro-inflammatory mRNA expression, and very significantly (P < 0.01) regulated gut microbial dysbiosis. Specifically, it reduced the abundances of normally enriched OTUs related to colitis, especially targeting facultative anaerobes of the phylum Proteobacteria, such as Aestuariispira and Escherichia. The short-chain fatty acids (SCFA) metabolites were enriched. Combined with their non-toxic nature observed in this long-term study in mice, the obtained amyloid-polyphenol gels have high application potentials for gastrointestinal diseases by "drugging the microbiome".},
}

@article {pmid31961458,
year = {2020},
author = {Fritz-Wallace, K and Engelmann, B and Krause, JL and Schäpe, SS and Pöppe, J and Herberth, G and Rösler, U and Jehmlich, N and von Bergen, M and Rolle-Kampczyk, U},
title = {Quantification of glyphosate and AMPA from microbiome reactor fluids.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {},
number = {},
pages = {},
doi = {10.1002/rcm.8668},
pmid = {31961458},
issn = {1097-0231},
abstract = {RATIONALE: Glyphosate is one of the most widely used herbicides and it is suspected to affect the intestinal microbiota through inhibition of aromatic amino acid synthesis via the shikimate pathway. In vitro microbiome bioreactors are increasingly used as model systems to investigate effects on the intestinal microbiota and consequently methods for the quantitation of glyphosate and its degradation product AMPA in microbiome model systems are required.

METHODS: An optimized protocol enables the analysis of both glyphosate and AMPA by simple extraction with methanol:acetonitrile:water (2:3:1) without further enrichment steps. Glyphosate and AMPA are separated by liquid chromatography on an amide column and identified and quantified with a targeted MS/MS method on a QTRAP 5500 system (AB Sciex).

RESULTS: Our method has a limit of detection (LOD) in extracted water samples of < 2 ng/mL for both glyphosate and AMPA. In complex intestinal medium the LOD is 2 ng/mL and 5 ng/mL for glyphosate and AMPA, respectively. These LODs allow for measurement at exposure-relevant concentrations. Glyphosate levels in a bioreactor model of porcine colon were determined and consequently it was verified whether AMPA was produced by porcine gut microbiota.

CONCLUSIONS: The method presented here allows quantitation of glyphosate and AMPA in complex bioreactor fluids and thus enables studies on the impact of glyphosate and its metabolism on the intestinal microbiota. In addition, the extraction protocol is compatible with an untargeted metabolomics analysis, thus allowing other perturbations caused by glyphosate in the same sample to be looked for.},
}

@article {pmid31961432,
year = {2020},
author = {Jones, CMA and Connors, J and Dunn, KA and Bielawski, JP and Comeau, AM and Langille, MGI and Van Limbergen, J},
title = {Bacterial Taxa and Functions Are Predictive of Sustained Remission Following Exclusive Enteral Nutrition in Pediatric Crohn's Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaa001},
pmid = {31961432},
issn = {1536-4844},
abstract = {BACKGROUND: The gut microbiome is extensively involved in induction of remission in pediatric Crohn's disease (CD) patients by exclusive enteral nutrition (EEN). In this follow-up study of pediatric CD patients undergoing treatment with EEN, we employ machine learning models trained on baseline gut microbiome data to distinguish patients who achieved and sustained remission (SR) from those who did not achieve remission nor relapse (non-SR) by 24 weeks.

METHODS: A total of 139 fecal samples were obtained from 22 patients (8-15 years of age) for up to 96 weeks. Gut microbiome taxonomy was assessed by 16S rRNA gene sequencing, and functional capacity was assessed by metagenomic sequencing. We used standard metrics of diversity and taxonomy to quantify differences between SR and non-SR patients and to associate gut microbial shifts with fecal calprotectin (FCP), and disease severity as defined by weighted Pediatric Crohn's Disease Activity Index. We used microbial data sets in addition to clinical metadata in random forests (RFs) models to classify treatment response and predict FCP levels.

RESULTS: Microbial diversity did not change after EEN, but species richness was lower in low-FCP samples (<250 µg/g). An RF model using microbial abundances, species richness, and Paris disease classification was the best at classifying treatment response (area under the curve [AUC] = 0.9). KEGG Pathways also significantly classified treatment response with the addition of the same clinical data (AUC = 0.8). Top features of the RF model are consistent with previously identified IBD taxa, such as Ruminococcaceae and Ruminococcus gnavus.

CONCLUSIONS: Our machine learning approach is able to distinguish SR and non-SR samples using baseline microbiome and clinical data.},
}

@article {pmid31961431,
year = {2020},
author = {Chang, Y and Chen, Y and Zhou, Q and Wang, C and Chen, L and Di, W and Zhang, Y},
title = {Short-chain fatty acids accompanying changes in the gut microbiome contribute to the development of hypertension in patients with preeclampsia.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20191253},
pmid = {31961431},
issn = {1470-8736},
abstract = {Preeclampsia (PE) is regarded as a pregnancy-associated hypertension disorder that is related to excessive inflammatory responses. Although the gut microbiota (GM) and short-chain fatty acids (SCFA) have been related to hypertension, their effects on PE remain unknown. We determined the GM abundance and faecal SCFA levels by 16S ribosomal RNA sequencing and gas chromatography, respectively, using faecal samples from 27 patients with severe PE and 36 healthy, pregnant control ubjects. We found that patients with PE had significantly decreased GM diversity and altered GM abundance. At the phylum level, patients with PE exhibited decreased abundance of Firmicutes albeit increased abundance of Proteobacteria; at the genus level, patients with PE had lower abundance of Blautia, Eubacterium_rectale, Eubacterium_hallii, Streptococcus, Bifidobacterium, Collinsella, Alistipes, and Subdoligranulum, albeit higher abundance of Enterobacter and Escherichia_Shigella. The faecal levels of butyric and valeric acid were significantly decreased in patients with PE and significantly correlated with the above-mentioned differential GM abundance. We predicted significantly increased abundance of the lipopolysaccharide (LPS)-synthesis pathway and significantly decreased abundance of the G protein-coupled receptor pathway in patients with PE, based on phylogenetic reconstruction of unobserved states. Finally, we evaluated the effects of oral butyrate on LPS-induced hypertension in pregnant rats. We found that butyrate significantly reduced the BP in these rats. In summary, we provide the first evidence linking GM dysbiosis and reduced faecal SCFA to PE and demonstrate that butyrate can directly regulate BP in vivo, suggesting its potential as a therapeutic agent for PE.},
}

@article {pmid31960913,
year = {2020},
author = {Grisnik, M and Bowers, O and Moore, AJ and Jones, BF and Campbell, JR and Walker, DM},
title = {The cutaneous microbiota of bats has in vitro antifungal activity against the white nose pathogen.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz193},
pmid = {31960913},
issn = {1574-6941},
abstract = {Since its introduction into the USA, Pseudogymnoascus destructans (Pd), the fungal pathogen of white-nose syndrome, has killed millions of bats. Recently, bacteria capable of inhibiting the growth of Pd have been identified within bat microbial assemblages, leading to increased interest in elucidating bacterial assemblage-pathogen interactions. Our objectives were to determine if bat cutaneous bacteria have antifungal activity against Pd, and correlate differences in the bat cutaneous microbiota with the presence/absence of Pd. We hypothesized that the cutaneous microbiota of bats is enriched with antifungal bacteria, and that the skin assemblage will correlate with Pd status. To test this, we sampled bat microbiota, adjacent roost surfaces, and soil from Pd positive caves to infer possible overlap of antifungal taxa, we tested these bacteria for bioactivity in vitro, and lastly compared bacterial assemblages using both amplicon and shotgun high-throughput DNA sequencing. Results suggest that the presence of Pd has an inconsistent influence on the bat cutaneous microbial assemblage across sites. Operational taxonomic units (OTUs) that corresponded with cultured antifungal bacteria were present within all sample types but were significantly more abundant on bat skin relative to the environment. Additionally, the microbial assemblage of Pd negative bats was found to have more OTUs that corresponded to antifungal taxa than positive bats, suggesting an interaction between fungal pathogens and the cutaneous microbial assemblage.},
}

@article {pmid31960901,
year = {2020},
author = {Rubin, RL and Jones, AN and Hayer, M and Shuman-Goodier, ME and Andrews, LV and Hungate, BA},
title = {Opposing effects of bacterial endophytes on biomass allocation of a wild donor and agricultural recipient.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaa012},
pmid = {31960901},
issn = {1574-6941},
abstract = {Root endophytes are a promising tool for increasing plant growth, but it is unclear whether they perform consistently across plant hosts. We characterized the blue grama (Bouteloua gracilis) root microbiome using two sequencing methods, quantified the effects of root endophytes in the original host (blue grama) and an agricultural recipient, corn (Zea mays) under drought and well-watered conditions, and examined in-vitro mechanisms for plant growth promotion. 16S rRNA amplicon sequencing revealed that the blue grama root microbiome was similar across an elevation gradient, with the exception of four genera. Culturing and Sanger sequencing revealed eight unique endophytes belonging to the genera Bacillus, Lysinibacillus, and Pseudomonas. All eight endophytes colonized corn roots, but had opposing effects on aboveground and belowground biomass in each plant species: they increased blue grama shoot mass by 45% (19) (mean +/- SE) while decreasing corn shoot mass by 10% (19), and increased corn root: shoot by 44% (7), while decreasing blue grama root: shoot by 17% (7). Furthermore, contrary to our expectations, endophytes had stronger effects on plant growth under well-watered conditions rather than drought conditions. Collectively, these results suggest that ecological features, including host identity, bacterial traits, climate conditions, and morphological outcomes should be carefully considered in the design and implementation of agricultural inoculum.},
}

@article {pmid31960586,
year = {2020},
author = {Johnston, RA and Belenky, P},
title = {Filling a hole in ozone research: The impacts of early life microbiome alterations on pulmonary responses to a non-atopic asthma trigger.},
journal = {Physiological reports},
volume = {8},
number = {1},
pages = {e14346},
doi = {10.14814/phy2.14346},
pmid = {31960586},
issn = {2051-817X},
support = {P20GM121344/GM/NIGMS NIH HHS/United States ; R21AT010366/NH/NIH HHS/United States ; R21AT010366/AT/NCCIH NIH HHS/United States ; },
}

@article {pmid31960494,
year = {2020},
author = {Broadley, D and McElwee, KJ},
title = {A 'hair-raising' history of alopecia areata.},
journal = {Experimental dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/exd.14073},
pmid = {31960494},
issn = {1600-0625},
abstract = {A 3500 year old papyrus from ancient Egypt provides a list of treatments for many diseases including "bite hair loss"; most likely alopecia areata (AA). The treatment of AA remained largely unchanged for over 1500 years. In 30 CE, Celsus described AA presenting as scalp alopecia in spots or the "windings of a snake", and suggested treatment with caustic compounds and scarification. The first "modern" description of AA came in 1813, though treatment still largely employed caustic agents. From the mid-19th Century onwards, various hypotheses of AA development were put forward including; infectious microbes (1843), nerve defects (1858), physical trauma and psychological stress (1881), focal inflammation (1891), diseased teeth (1902), toxins (1912), and endocrine disorders (1913). The 1950s brought new treatment developments with the first use of corticosteroid compounds (1952), and the first suggestion that AA was an autoimmune disease (1958). Research progressively shifted towards identifying hair follicle specific autoantibodies (1995). The potential role of lymphocytes in AA was made implicit with immunohistological studies (1980s). However, studies confirming their functional role were not published until the development of rodent models (1990s). Genetic studies, particularly genome wide association studies, have now come to the forefront and open up a new era of AA investigation (2000s). Today, AA research is actively focused on genetics, the microbiome, dietary modulators, the role of atopy, immune cell types in AA pathogenesis, primary antigenic targets, mechanisms by which immune cells influence hair growth, and of course the development of new treatments based on these discoveries.},
}

@article {pmid31960273,
year = {2020},
author = {Wan, P and Chen, J},
title = {A Calm, Dispassionate Look at Skin Microbiota in Atopic Dermatitis: An Integrative Literature Review.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13555-020-00352-4},
pmid = {31960273},
issn = {2193-8210},
support = {YJ-SCMC2017-12//Foundation of Shanghai Children's Medical Center, School of Medicine, Shanghai Jiaotong University/ ; },
abstract = {Atopic dermatitis (AD) is a chronic common inflammatory skin disorder with clinical characteristics of pruritic, dry, and recurrent flares that involve the whole body. Recent studies have demonstrated that the skin microbiota, characterized by an overgrowth of Staphylococcus aureus (S. aureus), plays a critical role in the manifestation of AD. There is striking evidence that skin microbiota can modulate the development and progression of AD. Therefore, more and more therapeutic approaches are adopted for modifying skin microbiota. Here we discuss the role of skin microbiota in the etiology and maintenance of AD; furthermore, we summarize the effects of therapeutic treatments on skin microbiota in AD based on published literature. With the help of the theoretical guidance suggested by microbial metagenome analysis, the reconstitution of microbiota should be a promising way to harness the pathogens of AD and could be used as a brand-new therapeutic strategy in clinical trials. We believe that the targeted therapy of dysbiosis in AD may possibly become a unique approach to an integrated treatment program in the near future.},
}

@article {pmid31959989,
year = {2020},
author = {Hayden, HS and Eng, A and Pope, CE and Brittnacher, MJ and Vo, AT and Weiss, EJ and Hager, KR and Martin, BD and Leung, DH and Heltshe, SL and Borenstein, E and Miller, SI and Hoffman, LR},
title = {Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-019-0714-x},
pmid = {31959989},
issn = {1546-170X},
support = {R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K24HL141669//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5P30DK089507//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01DK095869//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; SINGH15R0//Cystic Fibrosis Foundation (CF Foundation)/ ; },
abstract = {Most infants with cystic fibrosis (CF) have pancreatic exocrine insufficiency that results in nutrient malabsorption and requires oral pancreatic enzyme replacement. Newborn screening for CF has enabled earlier diagnosis, nutritional intervention and enzyme replacement for these infants, allowing most infants with CF to achieve their weight goals by 12 months of age1. Nevertheless, most infants with CF continue to have poor linear growth during their first year of life1. Although this early linear growth failure is associated with worse long-term respiratory function and survival2,3, the determinants of body length in infants with CF have not been defined. Several characteristics of the CF gastrointestinal (GI) tract, including inflammation, maldigestion and malabsorption, may promote intestinal dysbiosis4,5. As GI microbiome activities are known to affect endocrine functions6,7, the intestinal microbiome of infants with CF may also impact growth. We identified an early, progressive fecal dysbiosis that distinguished infants with CF and low length from infants with CF and normal length. This dysbiosis included altered abundances of taxa that perform functions that are important for GI health, nutrient harvest and growth hormone signaling, including decreased abundance of Bacteroidetes and increased abundance of Proteobacteria. Thus, the GI microbiota represent a potential therapeutic target for the correction of low linear growth in infants with CF.},
}

@article {pmid31959984,
year = {2020},
author = {Stevens, AJ and Purcell, RV and Darling, KA and Eggleston, MJF and Kennedy, MA and Rucklidge, JJ},
title = {Author Correction: Human gut microbiome changes during a 10 week Randomised Control Trial for micronutrient supplementation in children with attention deficit hyperactivity disorder.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {1180},
doi = {10.1038/s41598-020-58141-0},
pmid = {31959984},
issn = {2045-2322},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid31959912,
year = {2020},
author = {Retchless, AC and Kretz, CB and Rodriguez-Rivera, LD and Chen, A and Soeters, HM and Whaley, MJ and Wang, X},
title = {Oropharyngeal microbiome of a college population following a meningococcal disease outbreak.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {632},
doi = {10.1038/s41598-020-57450-8},
pmid = {31959912},
issn = {2045-2322},
abstract = {Asymptomatic oropharyngeal carriage of Neisseria meningitidis peaks in adolescence and young adulthood. Following a meningococcal disease outbreak at a U.S. college, we profiled the oropharyngeal microbiomes of 158 students to identify associations between bacterial community composition and meningococcal carriage or risk factors for carriage, including male gender, smoking, and frequent social mixing. Metagenomic shotgun sequencing identified 268 bacterial taxa at the genus or species level, with Streptococcus, Veillonella, and Rothia species being most abundant. Microbiome composition showed weak associations with meningococcal carriage and risk factors for carriage. N. meningitidis abundance was positively correlated with that of Fusobacterium nucleatum, consistent with hypothesized propionic acid cross-feeding. Additional species had positive abundance correlations with N. meningitidis, including Aggregatibacter aphrophilus, Campylobacter rectus, Catonella morbi, Haemophilus haemolyticus, and Parvimonas micra. N. meningitidis abundance was negatively correlated with unidentified Veillonella species. Several of these species are commonly found in dental plaque, while N. meningitidis is primarily found in the pharynx, suggesting that ecological interactions extend throughout the oral cavity. Although risk factors for meningococcal carriage do not strongly impact most bacterial species in the oropharynx, variation in the upper respiratory tract microbiome may create conditions that are more or less favorable for N. meningitidis carriage.},
}

@article {pmid31959230,
year = {2020},
author = {Peng, C and Xu, X and Li, Y and Li, X and Yang, X and Chen, H and Zhu, Y and Lu, N and He, C},
title = {Sex-specific association between the gut microbiome and high-fat diet-induced metabolic disorders in mice.},
journal = {Biology of sex differences},
volume = {11},
number = {1},
pages = {5},
doi = {10.1186/s13293-020-0281-3},
pmid = {31959230},
issn = {2042-6410},
support = {81860106//National Natural Science Foundation of China/ ; 700977001//Education Department of Jiangxi Province/ ; 20171BAB215010//Jiangxi Provincial Department of Science and Technology/ ; PY201816//Nanchang University/ ; },
abstract = {BACKGROUND: Accumulating evidence indicates that high-fat diet (HFD)-induced metabolic disorders are associated with dysbiosis of the gut microbiota. However, the sex-specific characteristics of the gut microbiota and its association with a sexually dimorphic response to a HFD remain unclear.

METHODS: Male and female mice were randomly assigned to receive a chow diet (CD) or HFD for 12 weeks. A group of HFD mice were pretreated with antibiotic cocktails for 4 weeks. Body weight, insulin sensitivity and the levels of serum metabolic parameters (blood glucose and insulin) were evaluated. 16S rRNA gene sequencing was performed to analyze the composition of the gut microbiota.

RESULTS: HFD-induced body weight gain (BWG) was higher in male mice than in female mice. While insulin resistance was increased in the HFD group compared to CD group in male mice, there was no difference in insulin resistance among female mice. Antibiotic-pretreatment alleviated HFD-induced insulin resistance in male mice and elevated fasting blood glucose in female mice. The composition of the gut microbiota in male mice was remarkably different from that in female mice independent of diet. A higher abundance of the genera Parabacteroides, Lactobacillus, Bacteroides, and Bifidobacterium was observed in females than inmales. HFD feeding also influenced the structure of the gut microbiota, as it decreased the abundance of short-chain fatty acids-producing bacteria including Roseburia and Lachnospiraceae_NK4A136_group. Alterations in the gut microbiota in response to antibiotics followed by HFD were different between males and females, indicating sex-dependent sensitivity to antibiotics.

CONCLUSIONS: We identified that sex had a greater impact on the composition of gut microbiota than environmental factors (HFD and antibiotics). The enrichment of beneficial microbes in female mice may be associated with the resistance of female mice to HFD-induced metabolic disorders, which was weakened by antibiotic pretreatment.},
}

@article {pmid31958990,
year = {2020},
author = {Bharwani, A and Bala, A and Surette, M and Bienenstock, J and Vigod, SN and Taylor, VH},
title = {Gut Microbiome Patterns Associated With Treatment Response in Patients With Major Depressive Disorder.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {706743719900464},
doi = {10.1177/0706743719900464},
pmid = {31958990},
issn = {1497-0015},
abstract = {OBJECTIVES: Compelling animal data exists examining the impact of the gut microbiome on the brain, but work is required to translate these findings in a clinical population. We sought to do this by exploring the effects of antidepressant medications on the gut microbiota, and establishing a baseline Major Depressive Disorder (MDD) gut phenotype.

METHODS: Participants with a primary diagnosis of MDD (n = 15) who were nonmedicated were recruited and followed over 6 months. Stool samples were collected prior to treatment initiation and 3 and 6 months following treatment. 16S rRNA sequencing was employed in order to analyze the gut microbial community profile. Symptom severity was measured by the Beck Depression Inventory. Alpha diversity metrics revealed no significant difference in the community diversity across any of the time-points.

RESULTS: Comparison of within-group versus between-group distances revealed a lack of clustering of samples based on time-point, suggesting no significant change in the microbiota across treatment duration. When analyzed based on treatment response, however, patients in the responder group exhibited greater phylogenetic diversity than non-responders (Mann-Whitney U = 5, p = 0.026). At 3-months, 35 Operational Taxonomic Units (OTUs) were significantly different between groups and at 6-months, 42 OTUs were significantly different between responders and non-responders.

CONCLUSIONS: These observations indicate that antidepressant medications alter the gut microbiota of patients with MDD, with disparate effects in responders versus non responders. This supports the concept of a microbiota phenotype associate with treatment response in MDD.},
}

@article {pmid31958628,
year = {2020},
author = {Jia, J and Cheng, M and Xue, X and Guan, Y and Wang, Z},
title = {Characterization of tetracycline effects on microbial community, antibiotic resistance genes and antibiotic resistance of Aeromonas spp. in gut of goldfish Carassius auratus Linnaeus.},
journal = {Ecotoxicology and environmental safety},
volume = {191},
number = {},
pages = {110182},
doi = {10.1016/j.ecoenv.2020.110182},
pmid = {31958628},
issn = {1090-2414},
abstract = {The gut of aquatic animals was a significant niche for dissemination of antibiotic resistance genes (ARGs) and direct response of living conditions. In this study, the gut microbiota of goldfish Carassius auratus Linnaeus was sampled at 7 days and 21 days after treatment with tetracycline at 0.285 and 2.85 μg L-1 to investigate the influences on the microbial structure and antibiotic resistance. The proportion of tetracycline resistance bacteria was 1.02% in the control group, while increased to 23.00%, 38.43%, 62.05% in groups of high concentration for 7 days (H7), low concentration for 21 days (L21) and high concentration for 21 days (H21), respectively. Compared to the control group, the diversity of isolated Aeromonas spp. was decreased in the treatment groups and the minimal inhibitory concentration (MIC) of resistant isolates was enhanced from 32 to 256 μg mL-1 with the treatment of tetracycline in time- and dose-dependent manners. Furthermore, the abundance of most genes was increased in treatment groups and efflux genes mainly responded to the stress of tetracycline with an average level of 1.0 × 10-2. After treatment with tetracycline, the predominant species were changed both at phylum and genus levels. The present study explored the impact of tetracycline on gut microbiota of goldfish at environmentally realistic concentrations for the first time and our findings will provide a reference for characterizing the microbiome of fish in the natural environment.},
}

@article {pmid31958431,
year = {2020},
author = {Galazzo, G and van Best, N and Bervoets, L and Dapaah, IO and Savelkoul, PH and Hornef, MW and , and Lau, S and Hamelmann, E and Penders, J and , and Hutton, EK and Morrison, K and Holloway, AC and McDonald, H and Ratcliffe, EM and Stearns, JC and Schertzer, JD and Surette, MG and Thabane, L and Mommers, M},
title = {Development of the Microbiota and Associations With Birth Mode, Diet, and Atopic Disorders in a Longitudinal Analysis of Stool Samples, Collected From Infancy Through Early Childhood.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2020.01.024},
pmid = {31958431},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Establishment of the gastrointestinal microbiota during infancy affects immune system development and oral tolerance induction. Perturbations in the microbiome during this period can contribute to development of immune-mediated diseases. We monitored microbiota maturation and associations with subsequent development of allergies in infants and children.

METHODS: We collected 1453 stool samples, at 5, 13, 21 and 31 weeks post-partum (infants), and once at school-age (6-11 years), from 440 children (49.3% girls, 24.8% born by caesarean section; all children except for 6 were breastfed for varying durations; median 40 weeks; interquartile range, 30-53 weeks). Microbiota were analyzed by amplicon sequencing. Children were followed through 3 years of age for development of atopic dermatitis; data on allergic sensitization and asthma were collected when children were school age.

RESULTS: Diversity of fecal microbiota, assessed by Shannon index, did not differ significantly among children from 5 through 13 weeks after birth, but thereafter gradually increased to 21 and 31 weeks. Most bacteria within the Bacteroidetes and Proteobacteria phyla were already present at 5 weeks after birth, whereas many bacteria of the Firmicutes phylum were acquired at later times in infancy. At school age, many new Actinobacteria, Firmicutes, and Bacteroidetes bacterial taxa emerged. The largest increase in microbial diversity occurred after 31 weeks. Vaginal, compared with cesarean section delivery, was most strongly associated with an enrichment of Bacteroides species at 5 weeks through 31 weeks. From 13 weeks onwards, diet became most important determinant of microbiota composition-cessation of breastfeeding, rather than solid food introduction, was associated with changes. For example, Bifidobacteria, staphylococci, and streptococci significantly decreased upon cessation of breastfeeding, whereas bacteria within the Lachnospiraceae family (Pseudobutyrivibrio, Lachnobacterium, Roseburia, and Blautia) increased. When we adjusted for confounding factors, we found fecal microbiota composition to be associated with development of atopic dermatitis, allergic sensitization, and asthma. Members of the Lachnospiraceae family, as well as the genera Faecalibacterium and Dialister, were associated with a reduced risk of atopy.

CONCLUSIONS: In a longitudinal study of fecal microbiota of children from 5 weeks through 6-11 years, we tracked changes in diversity and composition associated with the development of allergies and asthma.},
}

@article {pmid31958374,
year = {2020},
author = {Agany, DDM and Potts, R and Hernandez, JLG and Gnimpieba, EZ and Pietri, JE},
title = {Microbiome Differences Between Human Head and Body Lice Ecotypes Revealed by 16S RRNA Gene Amplicon Sequencing.},
journal = {The Journal of parasitology},
volume = {106},
number = {1},
pages = {14-24},
pmid = {31958374},
issn = {1937-2345},
abstract = {Human head lice and body lice (Pediculus humanus) are neglected ectoparasites. Head lice continue to be prevalent in children worldwide, and insecticide resistance in these insects has complicated their treatment. Meanwhile, body lice, which are most common in the developing world, are resurging among marginalized populations in developed nations. Today, the microbiome is being increasingly recognized as a key mediator of insect physiology. However, the microbial communities that inhabit human lice have remained unknown beyond only a few species of bacteria. Knowledge of the microbiomes of head and body lice could improve our understanding of the observed physiological differences between the 2 ecotypes and potentially inform the development of novel interventions against lice infestations and louse-borne infectious diseases. Toward these goals, here we performed 16S rRNA gene amplicon sequencing to characterize the microbiomes of both head and body lice and identify patterns of interest among these communities. Our data reveal that head and body lice harbor limited but distinct communities of bacteria that include known intracellular endosymbionts ("Candidatus Riesia pediculicola"), extracellular bacteria that may be horizontally acquired from the host environment, and a number of taxa of known or potential public health significance. Notably, in body lice, the relative abundance of vertically transmitted endosymbionts is lower than in head lice, which is a significant driver of greater alpha diversity. Further, several differentially abundant non-endosymbiont taxa and differences in beta diversity were observed between head lice and body lice. These findings support the hypothesis that microbiome differences could contribute to the divergence between human louse ecotypes and underscore the need for future studies to better comprehend the acquisition and physiological roles of human lice microbiomes.},
}

@article {pmid31958342,
year = {2020},
author = {Ayers, R and Patel, V and Burger, E and Cain, C and Ou-Yang, D and Wessell, N and Kleck, C},
title = {Corrosion of Titanium Spinal Explants Is Similar to That Observed in Oil Field Line Pipe Steel: Evidence of Microbial-Influenced Corrosion In Vivo.},
journal = {Orthopedics},
volume = {43},
number = {1},
pages = {62-67},
doi = {10.3928/01477447-20191213-01},
pmid = {31958342},
issn = {1938-2367},
abstract = {Current explanations of biomedical alloy degradation are focused on the physicochemical mechanisms of galvanic, pitting, crevice, and fretting corrosion. Ultimately, these studies dismiss the corrosion mechanism as a function of the local microbiome. Sixty spine hardware constructs were examined immediately after explantation for biofilm formation. Marked rod sections were imaged using scanning electron microscopy with energy dispersive x-ray spectroscopy. Backscatter mode was employed to better image the topology of the surface. There is clear differentiation between discoloration due to corrosion vs mechanical damage. Under scanning electron microscopy backscatter electron shadow examination, the authors noted that not all biofilm was removed using the surgical wipes. Corrosion pits were noticeably larger and numerous in areas of biofilm. In areas not associated with biofilms, there were few pits even if mechanical wear was evident. There is no evidence that the surface corrosion is modified between clinically diagnosed infected and noninfected patients. The surface damage present on explanted Ti6Al4V spine rods is uniquely similar to damage found in other industries where microbial-influenced corrosion is prevalent. Given that similar anaerobic, sulfur-reducing bacteria reside in and on human tissues, it is most likely that corrosion observed on explanted hardware is the result of microbial-influenced corrosion and not from inflammatory or other processes. Using analysis methods from other industries to characterize the microbiome present on explanted hardware is necessary. In so doing, a new definition of hardware-induced infection will be forthcoming. [Orthopedics. 2020;43(1):62-67.].},
}

@article {pmid31957590,
year = {2019},
author = {Mueller, NT and Hourigan, SK and Hoffmann, DE and Levy, L and von Rosenvinge, EC and Chou, B and Dominguez-Bello, MG},
title = {Bacterial Baptism: Scientific, Medical, and Regulatory Issues Raised by Vaginal Seeding of C-Section-Born Babies.},
journal = {The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics},
volume = {47},
number = {4},
pages = {568-578},
doi = {10.1177/1073110519897732},
pmid = {31957590},
issn = {1748-720X},
abstract = {Several lines of evidence suggest that children born via Cesarean section (C-section) are at greater risk for adverse health outcomes including allergies, asthma and obesity. Vaginal seeding is a medical procedure in which infants born by C-section are swabbed immediately after birth with vaginal secretions from the mother. This procedure has been proposed as a way to transfer the mother's vaginal microbiome to the child, thereby restoring the natural exposure that occurs during vaginal birth that is interrupted in the case of babies born via C-section. Preliminary evidence indicates partial restoration of microbes. However, there is insufficient evidence to determine the health benefits of the procedure. Several studies, including trial, are currently underway. At the same time, in the clinic setting, doctors are increasingly being asked to by expectant mothers to have their babies seeded. This article reports on the current research on this procedure and the issues it raises for regulators, researchers, physicians, and patients.},
}

@article {pmid31957585,
year = {2019},
author = {Hoffmann, DE},
title = {Introduction: The Promise and Challenges of Microbiome-Based Therapies.},
journal = {The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics},
volume = {47},
number = {4},
pages = {476-481},
doi = {10.1177/1073110519897725},
pmid = {31957585},
issn = {1748-720X},
}

@article {pmid31957113,
year = {2020},
author = {O'Toole, PW and Shiels, PG},
title = {The role of the microbiota in sedentary life style disorders and ageing: Lessons from the animal kingdom.},
journal = {Journal of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/joim.13021},
pmid = {31957113},
issn = {1365-2796},
abstract = {A paradox of so-called developed countries is that, as the major historical causes of human mortality are eliminated or mitigated by medical progress, life-style related diseases have become major killers. Furthermore, as life-span is extended by the combined effects of modern medicine, health-span is struggling to keep apace because of the burden of non-communicable diseases linked to diet and sedentary life-style. The gut microbiome is now recognized as a plastic environmental risk factor for many of these diseases, the microbiome being defined as the complex community of co-evolved commensal microbes that breaks down components of a complex diet, modulates innate immunity, and produces signalling molecules and metabolites that can impact on diverse regulatory systems in mammals. Aspects of the so-called "Western" life-style linked to disease risk such as energy dense diet and antibiotic treatment are known to affect the composition and function of the microbiome. Here we review the detailed mechanisms whereby the gut microbiome may modulate risk of diseases linked to sedentary life-style, and ageing related health loss. We focus on the comparative value of natural animal models such as hibernation for studying metabolic regulation, and the challenge of extrapolating from animal models to processes that occur in human ageing.},
}

@article {pmid31957074,
year = {2020},
author = {de Laffolie, J and Sheridan, D and Reinshagen, K and Wessel, L and Zimmermann, C and Stricker, S and Lerch, MM and Weigel, M and Hain, T and Domann, E and Rudloff, S and Nichols, BL and Naim, HY and Zimmer, KP},
title = {Digestive enzyme expression in the large intestine of children with short bowel syndrome in a late stage of adaptation.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {},
doi = {10.1096/fj.201901758RR},
pmid = {31957074},
issn = {1530-6860},
support = {SFB621//German Research Foundation/ ; },
abstract = {BACKGROUND AND AIMS: Intestinal adaptation in short bowel syndrome (SBS) includes morphologic processes and functional mechanisms. This study investigated whether digestive enzyme expression in the duodenum and colon is upregulated in SBS patients.

METHOD: Sucrase-isomaltase (SI), lactase-phlorizin hydrolase (LPH), and neutral Aminopeptidase N (ApN) were analyzed in duodenal and colonic biopsies from nine SBS patients in a late stage of adaptation as well as healthy and disease controls by immunoelectron microscopy (IEM), Western blots, and enzyme activities. Furthermore, proliferation rates and intestinal microbiota were analyzed in the mucosal specimen.

RESULTS: We found significantly increased amounts of SI, LPH, and ApN in colonocytes in most SBS patients with large variation and strongest effect for SI and ApN. Digestive enzyme expression was only partially elevated in duodenal enterocytes due to a low proliferation level measured by Ki-67 staining. Microbiome analysis revealed high amounts of Lactobacillus resp. low amounts of Proteobacteria in SBS patients with preservation of colon and ileocecal valve. Colonic expression was associated with a better clinical course in single cases.

CONCLUSION: In SBS patients disaccharidases and peptidases can be upregulated in the colon. Stimulation of this colonic intestinalization process by drugs, nutrients, and pre- or probiotics might offer better therapeutic approaches.},
}

@article {pmid31956606,
year = {2019},
author = {Katagiri, S and Shiba, T and Tohara, H and Yamaguchi, K and Hara, K and Nakagawa, K and Komatsu, K and Watanabe, K and Ohsugi, Y and Maekawa, S and Iwata, T},
title = {Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {434},
doi = {10.3389/fcimb.2019.00434},
pmid = {31956606},
issn = {2235-2988},
abstract = {Stroke is associated with multiple forms of disability, including dysphagia. Post-stroke dysphagia increases the risks of pneumonia and mortality and often results in cessation of oral feeding. However, appropriate rehabilitation methods can eventually lead to resumption of oral food intake. This study tried to clarify that re-initiating oral food intake could modify the composition of oral/gut microbial communities in patients with dysphagia. From 78 patients with sub-acute stage of stroke, 11 complete tube feeding subjects without taking antibiotics were enrolled and received rehabilitation for re-initiation of oral food intake, and 8 subjects were brought back to complete oral feeding. Oral and gut microbiota community profiles were evaluated using 16S rRNA sequencing of the saliva and feces samples before and after re-initiation of oral food intake in patients recovering from enteral nutrition under the same nutrient condition. Standard nutrition in the hospital was 1,840 kcal, including protein = 75 g, fat = 45 g, and carbohydrates = 280 g both for tube and oral feeding subjects. Oral food intake increased oral and gut microbiome diversity and altered the composition of the microbiome. Oral and gut microbiome compositions were drastically different; however, the abundance of family Carnobacteriaceae and genus Granulicatella was increased in both the oral and gut microbiome after re-initiation of oral food intake. Although oral microbiota showed more significant changes than the gut microbiota, metagenome prediction revealed the presence of more differentially enriched pathways in the gut. In addition, simpler co-occurrence networks of oral and gut microbiomes, indicating improved dysbiosis of the microbiome, were observed during oral feeding as compared to that during tube feeding. Oral food intake affects oral and gut microbiomes in patients recovering from enteral nutrition. Rehabilitation for dysphagia can modify systemic health by increasing the diversity and altering the composition and co-occurrence network structure of oral and gut microbial communities.},
}

@article {pmid31956320,
year = {2019},
author = {Harrison, XA and Price, SJ and Hopkins, K and Leung, WTM and Sergeant, C and Garner, TWJ},
title = {Diversity-Stability Dynamics of the Amphibian Skin Microbiome and Susceptibility to a Lethal Viral Pathogen.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2883},
doi = {10.3389/fmicb.2019.02883},
pmid = {31956320},
issn = {1664-302X},
abstract = {Variation among animals in their host-associated microbial communities is increasingly recognized as a key determinant of important life history traits including growth, metabolism, and resistance to disease. Quantitative estimates of the factors shaping the stability of host microbiomes over time at the individual level in non-model organisms are scarce. Addressing this gap in our knowledge is important, as variation among individuals in microbiome stability may represent temporal gain or loss of key microbial species and functions linked to host health and/or fitness. Here we use controlled experiments to investigate how both heterogeneity in microbial species richness of the environment and exposure to the emerging pathogen Ranavirus influence the structure and temporal dynamics of the skin microbiome in a vertebrate host, the European common frog (Rana temporaria). Our evidence suggests that altering the bacterial species richness of the environment drives divergent temporal microbiome dynamics of the amphibian skin. Exposure to ranavirus effects changes in skin microbiome structure irrespective of total microbial diversity, but individuals with higher pre-exposure skin microbiome diversity appeared to exhibit higher survival. Higher diversity skin microbiomes also appear less stable over time compared to lower diversity microbiomes, but stability of the 100 most abundant ("core") community members was similar irrespective of microbiome richness. Our study highlights the importance of extrinsic factors in determining the stability of host microbiomes over time, which may in turn have important consequences for the stability of host-microbe interactions and microbiome-fitness correlations.},
}

@article {pmid31956235,
year = {2019},
author = {Benderli, NC and Ogai, K and Lloyd, YM and Arios, JP and Jiyarom, B and Awanakam, AH and Esemu, LF and Hori, A and Megnekou, R and Leke, RGF and Kuraishi, T and Okamoto, S and Ekali, GL},
title = {Feasibility of microbial sample collection on the skin from people in Yaoundé, Cameroon.},
journal = {Drug discoveries & therapeutics},
volume = {13},
number = {6},
pages = {360-364},
doi = {10.5582/ddt.2019.01075},
pmid = {31956235},
issn = {1881-784X},
abstract = {Characterization of microbial communities in the skin in healthy individuals and diseased patients holds valuable information for understanding pathogenesis of skin diseases and as a source for developing novel therapies. Notably, resources regarding skin microbiome are limited in developing countries where skin disorders from infectious diseases are extremely common. A simple method for sample collection and processing for skin microbiome studies in such countries is crucial. The aim of this study is to confirm the feasibility of collecting skin microbiota from individuals in Yaoundé, a capital city of Cameroon, and subsequent extraction of bacterial DNA in a resource limited setting. Skin swabs from several individuals in Yaoundé were successfully obtained, and sufficient amount of bacterial 16S ribosomal RNA-coding DNA was collected, which was confirmed by quantitative PCR. The median copy number of 16S ribosomal RNA gene varied across participants and collection sites, with significantly more copies in samples collected from the forehead compared to the left and right forearm, or back. This study demonstrated that collecting surface skin microbes using our swabbing method is feasible in a developing country. We further showed that even with limited resources, we could collect sufficient amount of skin microbiota from the inhabitants in Yaoundé where no studies of skin microbiome were reported, which can be passed to further metagenomic analysis such as next generation sequencing.},
}

@article {pmid31955739,
year = {2020},
author = {Jeong, DY and Jeong, SY and Zhang, T and Wu, X and Qiu, JY and Park, S},
title = {Chungkookjang, a soy food, fermented with Bacillus amyloliquefaciens protects gerbils against ishcmeic stroke injury, and post-stroke hyperglycemia.},
journal = {Food research international (Ottawa, Ont.)},
volume = {128},
number = {},
pages = {108769},
doi = {10.1016/j.foodres.2019.108769},
pmid = {31955739},
issn = {1873-7145},
abstract = {Chungkookjang is a traditional Korean fermented soybean food with anti-diabetic and thrombolytic activity. It may also have anti-stroke activity. We determined that chungkookjang made with Sunchang Research Center for Fermentation Microbes 100730 and 100731 strains of Bacillus amyloliquefaciens(SRCM100730; CKJ730) and SRCM100731(CKJ731) protected against ischemic stroke and post-stroke hyperglycemia in Mongolian gerbils with ischemic stroke induced by transient occlusion of the carotid arteries. Gerbil fed 4.5% cooked soybeans (CSB), CKJ730, CKJ731, or cellulose (negative-control) in 40 energy% fat diets for 3 weeks, and then had artery occlusion for 8 min and continued taking the assigned diet for 5 weeks. CKJ730 and CKJ731 had thrombolytic activity and prevented neuronal cell death. Consequently, they improved short-term memory and spontaneous alteration compared to the negative-control. CKJ730 and CKJ731 improved neurological symptoms including drooped eyes, crouched posture, flexor reflex, and walking patterns the most among the stroke-induced gerbils. CKJ730 and CKJ731 increased active time, grip strength, and blood flow measured by Doppler compared to the negative-control. CKJ730 protected against post-stroke glucose dysregulation by restoring β-cell mass in the gerbils with transient artery occlusion. Serum tumor necrosis factor-α and interleukin-1β levels were lower in CKJ730 and CKJ731 than the negative-control. CSB also improved glucose metabolism and suppressed inflammatory cytokines, but less than CKJ730 and CKJ731. Clostridia increased, and Bacteriodia slightly decreased in the negative-control group, compared to the normal-control. CKJ730 and CKJ731 changed the amounts of Bacteriodia and Clostridia to be similar to normal-control. In conclusion, the daily intake of chungkookjang fermented with B. amyloliquefaciens improved the gut microbiome, increased blood flow to the brain, suppressed systemic inflammation, and may reduce the susceptibility to injury from ischemic stroke in gerbils subjected to ischemic injury.},
}

@article {pmid31955643,
year = {2020},
author = {Quinn, L and Sheh, A and Ellis, JL and Smith, DE and Booth, SL and Fu, X and Muthupalani, S and Ge, Z and Puglisi, DA and Wang, TC and Gonda, TA and Holcombe, H and Fox, JG},
title = {Helicobacter pylori antibiotic eradication coupled with a chemically defined diet in INS-GAS mice triggers dysbiosis and vitamin K deficiency resulting in gastric hemorrhage.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/19490976.2019.1710092},
pmid = {31955643},
issn = {1949-0984},
abstract = {Infection with Helicobacter pylori causes chronic inflammation and is a risk factor for gastric cancer. Antibiotic treatment or increased dietary folate prevents gastric carcinogenesis in male INS-GAS mice. To determine potential synergistic effects, H. pylori-infected male INS-GAS mice were fed an amino acid defined (AAD) diet with increased folate and were treated with antibiotics after 18 weeks of H. pylori infection. Antibiotic therapy decreased gastric pathology, but dietary folate had no effect. However, the combination of antibiotics and the AAD diet induced anemia, gastric hemorrhage, and mortality. Clinical presentation suggested hypovitaminosis K potentially caused by dietary deficiency and dysbiosis. Based on current dietary guidelines, the AAD diet was deficient in vitamin K. Phylloquinone administered subcutaneously and via a reformulated diet led to clinical improvement with no subsequent mortalities and increased hepatic vitamin K levels. We characterized the microbiome and menaquinone profiles of antibiotic-treated and antibiotic-free mice. Antibiotic treatment decreased the abundance of menaquinone producers within orders Bacteroidales and Verrucomicrobiales. PICRUSt predicted decreases in canonical menaquinone biosynthesis genes, menA and menD. Reduction of menA from Akkermansia muciniphila, Bacteroides uniformis, and Muribaculum intestinale were confirmed in antibiotic-treated mice. The fecal menaquinone profile of antibiotic-treated mice had reduced MK5 and MK6 and increased MK7 and MK11 compared to antibiotic-free mice. Loss of menaquinone-producing microbes due to antibiotics altered the enteric production of vitamin K. This study highlights the role of diet and the microbiome in maintaining vitamin K homeostasis.},
}

@article {pmid31955527,
year = {2020},
author = {Illiano, P and Brambilla, R and Parolini, C},
title = {The mutual interplay of gut microbiota, diet and human disease.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.15217},
pmid = {31955527},
issn = {1742-4658},
abstract = {The intestinal milieu harbours the gut microbiota, consisting of a complex community of bacteria, archaea, fungi, viruses, and protozoans that bring to the host organism an endowment of cells and genes more numerous than its own. In the last ten years, mounting evidence has highlighted the prominent influence of the gut mutualistic bacterial communities on human health. Microbial colonization occurs alongside with immune system development and plays a role in intestinal physiology. The community of the gut microbiota does not undergo significant fluctuations throughout adult life. However, bacterial infections, antibiotic treatment, lifestyle, surgery, and diet might profoundly affect it. Gut microbiota dysbiosis, defined as marked alterations in the amount and function of the intestinal microorganisms, is correlated with the aetiology of chronic non-communicable diseases, ranging from cardiovascular, neurologic, respiratory, and metabolic illnesses to cancer. In this review, we focus on the interplay among gut microbiota, diet, and host to provide a perspective on the role of microbiota and their unique metabolites in the pathogenesis and/or progression of various human disorders. We discuss interventions based on microbiome studies, i.e. faecal microbiota transplantation, probiotics, and prebiotics, to introduce the concept that correcting gut dysbiosis can ameliorate disease symptoms, thus offering a new approach toward disease treatment.},
}

@article {pmid31954994,
year = {2020},
author = {Ternák, G and Kuti, D and Kovács, KJ},
title = {Dysbiosis in Parkinson's disease might be triggered by certain antibiotics.},
journal = {Medical hypotheses},
volume = {137},
number = {},
pages = {109564},
doi = {10.1016/j.mehy.2020.109564},
pmid = {31954994},
issn = {1532-2777},
abstract = {Parkinson's disease (PD) is a neurodegenerative amyloid disorder with debilitating motor symptoms due to the loss of dopamine-synthesizing, basal ganglia-projecting neurons in the substantia nigra. An interesting feature of the disease is that most of PD patients have gastrointestinal problems and bacterial dysbiosis, years before the full expression of motor symptoms. We hypothesized that antibiotic consumption might be a contributing factor of gut microbiome dysbiosis in PD, favoring curli-producing Enterobacteria. Curli is a bacterial α-synuclein (αSyn) which is deposited first in the enteric nervous system and amyloid deposits are propagated in a prion like manner to the central nervous system. In addition, antibiotics result in a low-grade systemic inflammation, which also contributes to damage of neurons in enteric- and central nervous system. To support our hypothesis, by comparing PD prevalence change with antibiotic consumption data in EU countries, we found significant positive correlation between use narrow spectrum penicillin + penicillinase resistant penicillin and increased prevalence of the disease.},
}

@article {pmid31954979,
year = {2019},
author = {Hagihara, M and Kuroki, Y and Ariyoshi, T and Higashi, S and Fukuda, K and Yamashita, R and Matsumoto, A and Mori, T and Mimura, K and Yamaguchi, N and Okada, S and Nonogaki, T and Ogawa, T and Iwasaki, K and Tomono, S and Asai, N and Koizumi, Y and Oka, K and Yamagishi, Y and Takahashi, M and Mikamo, H},
title = {Clostridium butyricum Modulates the Microbiome to Protect Intestinal Barrier Function in Mice with Antibiotic-Induced Dysbiosis.},
journal = {iScience},
volume = {23},
number = {1},
pages = {100772},
doi = {10.1016/j.isci.2019.100772},
pmid = {31954979},
issn = {2589-0042},
abstract = {Clostridium butyricum MIYAIRI 588 (CBM 588) is a probiotic bacterium that has previously been used to prevent antibiotic-associated diarrhea. However, the underlying mechanism by which CBM 588 protects the gut epithelial barrier remains unclear. Here, we show that CBM 588 increased the abundance of Bifidobacterium, Lactobacillus, and Lactococcus species in the gut microbiome and also enhanced the intestinal barrier function of mice with antibiotic-induced dysbiosis. Additionally, CBM 588 significantly promoted the expansion of IL-17A-producing γδT cells and IL-17A-producing CD4 cells in the colonic lamina propria (cLP), which was closely associated with changes in the intestinal microbial composition. Additionally, CBM 588 plays an important role in controlling antibiotic-induced gut inflammation through upregulation of anti-inflammatory lipid metabolites such as palmitoleic acid, 15d-prostaglandin J2, and protectin D1. This study reveals a previously unrecognized mechanism of CBM 588 and provides new insights into gut epithelial barrier protection with probiotics under conditions of antibiotic-induced dysbiosis.},
}

@article {pmid31954488,
year = {2020},
author = {Schwabe, RF and Greten, TF},
title = {Gut microbiome in HCC - Mechanisms, diagnosis and therapy.},
journal = {Journal of hepatology},
volume = {72},
number = {2},
pages = {230-238},
doi = {10.1016/j.jhep.2019.08.016},
pmid = {31954488},
issn = {1600-0641},
abstract = {The microbiome exerts essential functions in health and disease, modulating key processes in metabolism, inflammation and immunity. Recent evidence has revealed a key role of the microbiome in carcinogenesis as well as anti-cancer immune responses in mouse models and patients. Herein, we will review functions of the gut microbiome in hepatocellular carcinoma (HCC), the third leading cause of worldwide cancer mortality. The majority of HCC develops in patients with chronic liver disease, caused by viral hepatitis, non-alcoholic fatty liver disease (NAFLD) and alcohol-related fatty liver disease. In this review, we will discuss mechanisms by which the gut-liver axis promotes the development of HCC in mouse models and patients, including dysbiosis, the leaky gut and bacterial metabolites, with a particular focus on NAFLD as the fastest growing cause of HCC development. Moreover, we will review recent progress in harnessing the gut microbiome as a potential diagnostic tool and novel therapeutic target in patients with HCC, in particular in the setting of immunotherapy.},
}

@article {pmid31954405,
year = {2020},
author = {Chen, Y and Bonkowski, M and Shen, Y and Griffiths, BS and Jiang, Y and Wang, X and Sun, B},
title = {Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {4},
doi = {10.1186/s40168-019-0775-6},
pmid = {31954405},
issn = {2049-2618},
support = {2016YFD0200309//National Key Research and Development Program/ ; 41977098//National Natural Science Foundation of China/ ; BK20180049//Distinguished Youth Scholar Program of Jiangsu Province/ ; CARS-22-G-14//Modern Agricultural Industry Technology System of the Ministry of Agriculture of China/ ; BK20191510//Basic Research Program of Jiangsu Province/ ; BK20171520//Basic Research Program of Jiangsu Province/ ; },
abstract = {BACKGROUND: Stress-induced hormones are essential for plants to modulate their microbiota and dynamically adjust to the environment. Despite the emphasis of the role of the phytohormone ethylene in the plant physiological response to heterospecific neighbour detection, less is known about how this activated signal mediates focal plant rhizosphere microbiota to enhance plant fitness. Here, using 3 years of peanut (Arachis hypogaea L.), a legume, and cyanide-containing cassava (Manihot esculenta Crantz) intercropping and peanut monocropping field, pot and hydroponic experiments in addition to exogenous ethylene application and soil incubation experiments, we found that ethylene, a cyanide-derived signal, is associated with the chemical identification of neighbouring cassava and the microbial re-assemblage in the peanut rhizosphere.

RESULTS: Ethylene production in peanut roots can be triggered by cyanide production of neighbouring cassava plants. This gaseous signal alters the microbial composition and re-assembles the microbial co-occurrence network of peanut by shifting the abundance of an actinobacterial species, Catenulispora sp., which becomes a keystone in the intercropped peanut rhizosphere. The re-assembled rhizosphere microbiota provide more available nutrients to peanut roots and support seed production.

CONCLUSIONS: Our findings suggest that root ethylene acts as a signal with a dual role. It plays a role in perceiving biochemical cues from interspecific neighbours, and also has a regulatory function in mediating the rhizosphere microbial assembly, thereby enhancing focal plant fitness by improving seed production. This discovery provides a promising direction to develop novel intercropping strategies for targeted manipulations of the rhizosphere microbiome through phytohormone signals. Video abstract.},
}

@article {pmid31954373,
year = {2020},
author = {Duan, C and Kuang, L and Xiang, X and Zhang, J and Zhu, Y and Wu, Y and Yan, Q and Liu, L and Li, T},
title = {Activated Drp1-mediated mitochondrial ROS influence the gut microbiome and intestinal barrier after hemorrhagic shock.},
journal = {Aging},
volume = {12},
number = {},
pages = {},
doi = {10.18632/aging.102690},
pmid = {31954373},
issn = {1945-4589},
abstract = {A role of the mitochondrial dynamin-related protein (Drp1) on gut microbiome composition and intestinal barrier function after hemorrhagic shock has not been identified previously and thus addressed in this study. Here, we used a combination of 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling in WT and Drp1 KO mouse models to examine the functional impact of activated Drp1 on the gut microbiome as well as mitochondrial metabolic regulation after hemorrhagic shock. Our data showed that changes in mitochondrial Drp1 activity participated in the regulation of intestinal barrier function after hemorrhagic shock. Activated Drp1 significantly perturbed gut microbiome composition in the Bacteroidetes phylum. The abundance of short-chain fatty acid (SCFA) producing microbes, such as Bacteroides, Butyricimonas and Odoribacter, was markedly decreased in mice after shock, and was inversely correlated with both the distribution of the tight junction protein ZO1 and intestinal permeability. Together, these data suggest that Drp1 activation perturbs the gut microbiome community and SCFA production in a ROS-specific manner and thereby substantially disturbs tight junctions and intestinal barrier function after hemorrhagic shock. Our findings provide novel insights for targeting Drp1-mediated mitochondrial function as well as the microbiome in the treatment of intestinal barrier dysfunction after shock.},
}

@article {pmid31953982,
year = {2020},
author = {Sonnenberg, A and Turner, KO and Genta, RM},
title = {Associations Between Gastric Histopathology and the Occurrence of Colon Polyps.},
journal = {Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland},
volume = {},
number = {},
pages = {},
doi = {10.1111/codi.14968},
pmid = {31953982},
issn = {1463-1318},
abstract = {BACKGROUND AND AIMS: Compromise of the gastric acid barrier may facilitate bacterial invasion of the lower intestinal tract and promote the development of colonic neoplasia. Our study tested the associations between histopathologic abnormalities of the upper and lower gastrointestinal tract in patients undergoing bidirectional endoscopy.

METHODS: The Inform Diagnostics database is a national electronic repository of histopathologic records of patients distributed throughout the USA. A case-control study of 302,061 patients, of whom 163,168 had colon polyps, evaluated whether the occurrence of colonic polyps was influenced by the presence of the following gastroesophageal diagnoses: gastric H. pylori infection, gastric intestinal metaplasia, fundic gland polyps, and gastric hyperplastic polyps. The influence of individual diagnoses on the occurrence of colonic polyps was expressed as odds ratios with their 95% confidence intervals.

RESULTS: The odds ratio for tubular adenomas being associated with gastric H. pylori was 1.53 (1.49-1.58), with intestinal metaplasia 1.65 (1.59-1.71), with fundic gland polyps 1.49 (1.45-1.54), and with gastric hyperplastic polyps 1.85 (1.75-1.96). The odds ratio for sessile serrated polyps being associated with gastric H. pylori was 1.03 (0.96-1.10), with intestinal metaplasia 1.21 (1.13-1.30), with fundic gland polyps 1.79 (1.69-1.89), and with gastric hyperplastic polyps 1.52 (1.35-1.71.

CONCLUSIONS: A diminished gastric acid barrier function, which occurs in various upper gastrointestinal diseases associated with lowered gastric acid output, may promote the development of colonic neoplasia.},
}