@article {pmid31323554,
year = {2019},
author = {Chowdhury, B and Lin, L and Dhar, BR and Islam, MN and McCartney, D and Kumar, A},
title = {Enhanced biomethane recovery from fat, oil, and grease through co-digestion with food waste and addition of conductive materials.},
journal = {Chemosphere},
volume = {236},
number = {},
pages = {124362},
doi = {10.1016/j.chemosphere.2019.124362},
pmid = {31323554},
issn = {1879-1298},
abstract = {In this study, the effect of conductive additives on co-digestion of fat, oil, and grease (FOG) and food waste (FW) was evaluated. Initially, biochemical methane potential (BMP) test was conducted for optimization of mixing ratio of FW and FOG. The optimal methane production (800 L (kg VS)-1) was obtained from co-digestion of 70% FW + 30% FOG (w/w), which was 1.2 times and 12 times of that obtained from mono-digestion of FW and FOG, respectively. This optimal mixing ratio was used for subsequent fed-batch studies with the addition of two conductive additives, granular activated carbon (GAC) and magnetite. The addition of GAC significantly shortened the lag phase (from 7 to 3 d), reduced accumulation of various volatile fatty acids (VFAs), and enhanced methane production rate (50-80% increase) compared to the control and magnetite-amended bioreactor. Fourier transformation infrared (FTIR) analysis suggested that the degradation of lipids, protein and carbohydrates was the highest in GAC amended reactor, followed by magnetite and control reactors. GAC addition also enriched more abundant and diverse bacteria and methanogens than control. Magnetite addition also showed similar trends but to a lesser degree. The substantial enrichment of syntrophic LCFA β-oxidizing bacteria (e.g. Syntrophomonas) and methanogenic archaea in the GAC-amended bioreactor likely attributed to the superior methanogenesis kinetics in GAC amended bioreactor. Our findings suggest that the addition of GAC could provide a sustainable strategy to enrich kinetically efficient syntrophic microbiome to favor methanogenesis kinetics in co-digestion of FW and FOG.},
}

@article {pmid31323363,
year = {2019},
author = {Cosentino, M and Comi, C and Marino, F},
title = {The vermiform appendix in Parkinson's disease: At the crossroad of peripheral immunity, the nervous system and the intestinal microbiome.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {102357},
doi = {10.1016/j.autrev.2019.102357},
pmid = {31323363},
issn = {1873-0183},
}

@article {pmid31322970,
year = {2019},
author = {Bhattacharya, N and Ganguli-Indra, G and Indra, AK},
title = {Transcriptional Control and Transcriptomic Analysis of Lipid Metabolism in Skin barrier formation and Atopic Dermatitis (AD).},
journal = {Expert review of proteomics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14789450.2019.1646128},
pmid = {31322970},
issn = {1744-8387},
abstract = {INTRODUCTION- Atopic dermatitis (AD) is a multifactorial ailment associated with barrier breach and intense systemic inflammation. Several studies over the years have shown the complex interplay of a large number of factors in governing the progression and outcome of AD. In addition to the diverse types of AD resulting due to variation in the intrinsic mechanisms giving rise to AD such as single nucleotide polymorphisms (SNPs), epigenetic alterations or transcriptional changes, extrinsic factors such as age, ancestry, ethnicity, immunological background of the subject, the interactions of the subject with environmental stimuli and existing microbiome in the periphery surrounding the subject account for further heterogeneity in the clinical manifestations of the disease. AREAS COVERED- Here we have selectively discussed transcriptional regulation of genes associated with skin lipid metabolism in the context of AD. Transcriptional control and transcriptomic changes are just one face of this multifaceted disease known to affect humans and a detailed study concerning those will enable us to develop targeted therapies to deal with the disease. EXPERT OPINION- Large-scale integration of different omics approaches (genomics, epigenomics, transcriptomics, lipidomics, proteomics, metabolomics, effect of exposome) will help identify the potential candidate gene(s) associated with the development of various endotypes of AD.},
}

@article {pmid31322866,
year = {2019},
author = {Huddleston, JP and Thoden, JB and Dopkins, BJ and Narindoshvili, T and Fose, BJ and Holden, HM and Raushel, FM},
title = {Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.9b00326},
pmid = {31322866},
issn = {1520-4995},
abstract = {The ydj gene cluster is found in 80% of sequenced Escherichia coli genomes and other closely related species found in the human microbiome. Based on the annotations of the enzymes located in this cluster, it is expected that together they catalyze the catabolism of an unknown carbohydrate. The focus of this investigation is on YdjI, which is found in the ydj gene cluster of E. coli K-12. It is predicted to be a class II aldolase of unknown function. Here we describe a structural and functional characterization of this enzyme. YdjI catalyzes the hydrogen/deuterium exchange of the proS hydrogen at C3 of dihydroxyacetone or DHAP. In the presence of DHAP, YdjI catalyzes an aldol condensation with a variety of aldo-sugars. YdjI shows strong preference toward higher-order (seven-, eight- and nine-carbon) monosaccharides with specific hydroxyl stereochemistries and a negatively charged terminus (carboxylate or phosphate). The best substrate is L-arabinuronic acid with an apparent kcat = 3.0 s-1. The product, L-glycero-L-galacto-octuluronate-1-phosphate, has a value of kcat/Km of 2.1 × 103 M-1 s-1 in the retro-aldol reaction with YdjI. This is the first recorded synthesis of L-glycero-L-galacto-octuluronate-1-phosphate and six similar carbohydrates. The crystal structure of YdjI, determined to a nominal resolution of 1.75 Å (PDB code: 6OFU), reveals unusual positions for two arginine residues located near the active site. Computational docking was utilized to distinguish preferable binding orientations for L-glycero-L-galacto-octuluronate-1-phosphate. These results indicate a possible alternative binding orientation for L-glycero-L-galacto-octuluronate-1-phosphate than observed in other class II aldolases, which utilize shorter carbohydrate molecules.},
}

@article {pmid31321880,
year = {2019},
author = {Peters, DL and Wang, W and Zhang, X and Ning, Z and Mayne, J and Figeys, D},
title = {Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e1800363},
doi = {10.1002/pmic.201800363},
pmid = {31321880},
issn = {1615-9861},
abstract = {The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signalling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here we review the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases. This article is protected by copyright. All rights reserved.},
}

@article {pmid31321707,
year = {2019},
author = {Bangert, MK and Hasbun, R},
title = {Neurological and Psychiatric Adverse Effects of Antimicrobials.},
journal = {CNS drugs},
volume = {},
number = {},
pages = {},
doi = {10.1007/s40263-019-00649-9},
pmid = {31321707},
issn = {1179-1934},
abstract = {Antimicrobials are a widely used class of medications, but several of them are associated with neurological and psychiatric side effects. The exact incidence of neurotoxicity with anti-infectives is unknown, although it is estimated to be < 1%. Neurotoxicity occurs with all classes of antimicrobials, such as antibiotics, antimycobacterials, antivirals, antifungals and antiretrovirals, with side effects ranging from headaches, anxiety and depression to confusion, delirium, psychosis, mania and seizures, among others. It is important to consider these possible side effects to prevent misdiagnosis or delayed treatment as drug withdrawal can be associated with reversibility in most cases. This article highlights the different neurotoxic effects of a range of antimicrobials, discusses proposed mechanisms of onset and offers general management recommendations. The effects of antibiotics on the gut microbiome and how they may ultimately affect cognition is also briefly examined.},
}

@article {pmid31321608,
year = {2019},
author = {Serena, G and Lima, R and Fasano, A},
title = {Genetic and Environmental Contributors for Celiac Disease.},
journal = {Current allergy and asthma reports},
volume = {19},
number = {9},
pages = {40},
doi = {10.1007/s11882-019-0871-5},
pmid = {31321608},
issn = {1534-6315},
abstract = {PURPOSE OF REVIEW: Celiac disease (CD) is an autoimmune enteropathy triggered by gluten. The purpose of this review is to examine the major genetic and environmental factors that contribute to CD pathogenesis.

RECENT FINDINGS: We reviewed the current state of knowledge on the genetic and environmental components that play a role in CD onset. A genome-wide association study (GWAS) analysis has highlighted several genes other than HLA involved in CD. Recent studies have shown that HLA haplotype influences the microbiome composition in infants and that dysbiosis in the intestinal microflora, in turn, contributes to loss of tolerance to gluten. Recently, observational studies have discussed the hypothesis stating that breast-feeding had a protective role against CD onset. CD etiology is influenced by genetic and environmental factors. A better understanding of these components would deepen our knowledge on the mechanisms that lead to loss of tolerance and could help in developing a more "personalized medicine."},
}

@article {pmid31321385,
year = {2019},
author = {Getachew, B and Reyes, RE and Davies, DL and Tizabi, Y},
title = {Moxidectin Effects on Gut Microbiota of Wistar-Kyoto Rats: Relevance to Depressive-Like Behavior.},
journal = {Clinical pharmacology and translational medicine},
volume = {3},
number = {1},
pages = {134-142},
pmid = {31321385},
issn = {2572-7656},
abstract = {Background/Aims: The prevalent comorbidity between neuropsychiatric and gastrointestinal (GI) disorders is believed to be significantly influenced by gut microbiota (GM). GM may also play a substantial role in comorbidity between substance abuse (e.g. Alcohol Use Disorder, AUD) and depression. The anti-parasitic drug Moxidectin (MOX) has been reported to reduce alcohol intake in male and female mice. This effect is purported to be centrally mediated with a significant contribution linked to purinergic, P2X4 purinergic receptors. However, MOX's effects on GM in animal models of depression is not known.

Methods: Adult male Wistar Kyoto (WKY) rats (5/group) were injected intraperitoneally (i.p.) once daily for 7 days with MOX (2.5mg/kg), or saline as control group. On day 8, approximately 20 h after the last MOX injection, animals were sacrificed, intestinal stools were collected and stored at -80°C DNA was extracted from the samples for 16S rRNA gene-based GM analysis using 16S Metagenomics application.

Results: At taxa and species level, MOX affected a number of bacteria including a 30-fold increase in Bifidobacterium cholerium, a bacterium with a strong ability to degrade carbohydrates that resist digestion in the small intestine. There was a minimum of 2-fold increase in: five probiotic species of Lactobacillus, butyrate-forming Rosburia Facies and Butyrivibro proteovlasticus. In contrast, MOX depleted 11 species, including 2 species of Ruminoccus, which are positively associated with severity of irritable bowel syndrome, and 4 species of Provettela, which are closely associated with depressive-like behavior.

Conclusion: Thus, MOX enhanced probiotic species, and suppressed the opportunistic pathogens. Since overall effect of MOX appears to be promoting GM associated with mood enhancement (e.g. Bifidobacterium and Lactobacillus) and suppressing GM associated with inflammation (e.g. Ruminoccus), potential antidepressant and anti-inflammatory effects of MOX in suitable animal models should be investigated.},
}

@article {pmid31320727,
year = {2019},
author = {Kolody, BC and McCrow, JP and Allen, LZ and Aylward, FO and Fontanez, KM and Moustafa, A and Moniruzzaman, M and Chavez, FP and Scholin, CA and Allen, EE and Worden, AZ and Delong, EF and Allen, AE},
title = {Diel transcriptional response of a California Current plankton microbiome to light, low iron, and enduring viral infection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41396-019-0472-2},
pmid = {31320727},
issn = {1751-7370},
support = {NSF-OCE-1756884//National Science Foundation (NSF)/ ; DGE-1144086//National Science Foundation (NSF)/ ; NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; GBMF3828//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {Phytoplankton and associated microbial communities provide organic carbon to oceanic food webs and drive ecosystem dynamics. However, capturing those dynamics is challenging. Here, an in situ, semi-Lagrangian, robotic sampler profiled pelagic microbes at 4 h intervals over ~2.6 days in North Pacific high-nutrient, low-chlorophyll waters. We report on the community structure and transcriptional dynamics of microbes in an operationally large size class (>5 μm) predominantly populated by dinoflagellates, ciliates, haptophytes, pelagophytes, diatoms, cyanobacteria (chiefly Synechococcus), prasinophytes (chiefly Ostreococcus), fungi, archaea, and proteobacteria. Apart from fungi and archaea, all groups exhibited 24-h periodicity in some transcripts, but larger portions of the transcriptome oscillated in phototrophs. Periodic photosynthesis-related transcripts exhibited a temporal cascade across the morning hours, conserved across diverse phototrophic lineages. Pronounced silica:nitrate drawdown, a high flavodoxin to ferredoxin transcript ratio, and elevated expression of other Fe-stress markers indicated Fe-limitation. Fe-stress markers peaked during a photoperiodically adaptive time window that could modulate phytoplankton response to seasonal Fe-limitation. Remarkably, we observed viruses that infect the majority of abundant taxa, often with total transcriptional activity synchronized with putative hosts. Taken together, these data reveal a microbial plankton community that is shaped by recycled production and tightly controlled by Fe-limitation and viral activity.},
}

@article {pmid31320411,
year = {2019},
author = {Töpel, M and Pinder, MIM and Johansson, ON and Kourtchenko, O and Godhe, A and Clarke, AK},
title = {Complete Genome Sequence of the Diatom-Associated Bacterium Sphingorhabdus sp. Strain SMR4y.},
journal = {Microbiology resource announcements},
volume = {8},
number = {29},
pages = {},
doi = {10.1128/MRA.00482-19},
pmid = {31320411},
issn = {2576-098X},
abstract = {The bacterial strain SMR4y belongs to the diverse microbiome of the marine diatom Skeletonema marinoi strain R05AC. After assembly of its genome, presented here, and subsequent analyses, we placed it in the genus Sphingorhabdus This strain has a 3,479,724-bp circular chromosome (with 3,340 coding sequences) and no known plasmids.},
}

@article {pmid31320106,
year = {2019},
author = {Hajjar, R and Santos, MM and Dagbert, F and Richard, CS},
title = {Current evidence on the relation between gut microbiota and intestinal anastomotic leak in colorectal surgery.},
journal = {American journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjsurg.2019.07.001},
pmid = {31320106},
issn = {1879-1883},
abstract = {BACKGROUND: Anastomotic leak (AL) is a major complication in colorectal surgery. It worsens morbidity, mortality and oncological outcomes in colorectal cancer. Some evidence suggests a potential effect of the intestinal microbiome on wound healing. This review aims to provide a comprehensive review on historical and current evidence regarding the relation between the gastrointestinal microbiota and AL in colorectal surgery, and the potential microbiota-modifying effect of some perioperative commonly used measures.

DATA SOURCES: A comprehensive search was conducted in Pubmed, Medline and Embase for historical and current clinical and animal studies addressing perioperative intestinal microbiota evaluation, intestinal healing and AL.

CONCLUSIONS: Evidence on microbes' role in AL is mainly derived from animal experiments. The microbiota's composition and implications are poorly understood in surgical patients. Elaborate microbiota sequencing is required in colorectal surgery to identify potentially beneficial microbial profiles that could lead to specific perioperative microbiome-altering measures and improve surgical and oncological outcomes.},
}

@article {pmid31319564,
year = {2019},
author = {Ticinesi, A and Nouvenne, A and Cerundolo, N and Catania, P and Prati, B and Tana, C and Meschi, T},
title = {Gut Microbiota, Muscle Mass and Function in Aging: A Focus on Physical Frailty and Sarcopenia.},
journal = {Nutrients},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/nu11071633},
pmid = {31319564},
issn = {2072-6643},
abstract = {Human gut microbiota is able to influence the host physiology by regulating multiple processes, including nutrient absorption, inflammation, oxidative stress, immune function, and anabolic balance. Aging is associated with reduced microbiota biodiversity, increased inter-individual variability, and over-representation of pathobionts, and these phenomena may have great relevance for skeletal muscle mass and function. For this reason, the presence of a gut-muscle axis regulating the onset and progression of age-related physical frailty and sarcopenia has been recently hypothesized. In this narrative review, we summarize the studies supporting a possible association between gut microbiota-related parameters with measures of muscle mass, muscle function, and physical performance in animal models and humans. Reduced muscle mass has been associated with distinct microbiota composition and reduced fermentative capacity in mice, and the administration of probiotics or butyrate to mouse models of muscle wasting has been associated with improved muscle mass. However, no studies have targeted the human microbiome associated with sarcopenia. Limited evidence from human studies shows an association between microbiota composition, involving key taxa such as Faecalibacterium and Bifidobacterium, and grip strength. Similarly, few studies conducted on patients with parkinsonism showed a trend towards a different microbiota composition in those with reduced gait speed. No studies have assessed the association of fecal microbiota with other measures of physical performance. However, several studies, mainly with a cross-sectional design, suggest an association between microbiota composition and frailty, mostly assessed according to the deficit accumulation model. Namely, frailty was associated with reduced microbiota biodiversity, and lower representation of butyrate-producing bacteria. Therefore, we conclude that the causal link between microbiota and physical fitness is still uncertain due to the lack of targeted studies and the influence of a large number of covariates, including diet, exercise, multimorbidity, and polypharmacy, on both microbiota composition and physical function in older age. However, the relationship between gut microbiota and physical function remains a very promising area of research for the future.},
}

@article {pmid31319545,
year = {2019},
author = {Rodriguez, DM and Benninghoff, AD and Aardema, NDJ and Phatak, S and Hintze, KJ},
title = {Basal Diet Determined Long-Term Composition of the Gut Microbiome and Mouse Phenotype to a Greater Extent than Fecal Microbiome Transfer from Lean or Obese Human Donors.},
journal = {Nutrients},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/nu11071630},
pmid = {31319545},
issn = {2072-6643},
support = {A34029 FY15 UAES Grant//Utah Agricultural Experiment Station/ ; },
abstract = {The Western dietary pattern can alter the gut microbiome and cause obesity and metabolic disorders. To examine the interactions between diet, the microbiome, and obesity, we transplanted gut microbiota from lean or obese human donors into mice fed one of three diets for 22 weeks: (1) a control AIN93G diet; (2) the total Western diet (TWD), which mimics the American diet; or (3) a 45% high-fat diet-induced obesity (DIO) diet. We hypothesized that a fecal microbiome transfer (FMT) from obese donors would lead to an obese phenotype and aberrant glucose metabolism in recipient mice that would be exacerbated by consumption of the TWD or DIO diets. Prior to the FMT, the native microbiome was depleted using an established broad-spectrum antibiotic protocol. Interestingly, the human donor body type microbiome did not significantly affect final body weight or body composition in mice fed any of the experimental diets. Beta diversity analysis and linear discriminant analysis with effect size (LEfSe) showed that mice that received an FMT from obese donors had a significantly different microbiome compared to mice that received an FMT from lean donors. However, after 22 weeks, diet influenced the microbiome composition irrespective of donor body type, suggesting that diet is a key variable in the shaping of the gut microbiome after FMT.},
}

@article {pmid31318902,
year = {2019},
author = {Frost, F and Storck, LJ and Kacprowski, T and Gärtner, S and Rühlemann, M and Bang, C and Franke, A and Völker, U and Aghdassi, AA and Steveling, A and Mayerle, J and Weiss, FU and Homuth, G and Lerch, MM},
title = {A structured weight loss program increases gut microbiota phylogenetic diversity and reduces levels of Collinsella in obese type 2 diabetics: A pilot study.},
journal = {PloS one},
volume = {14},
number = {7},
pages = {e0219489},
doi = {10.1371/journal.pone.0219489},
pmid = {31318902},
issn = {1932-6203},
abstract = {The global obesity epidemic constitutes a major cause of morbidity and mortality challenging public health care systems worldwide. Thus, a better understanding of its pathophysiology and the development of novel therapeutic options are urgently needed. Recently, alterations of the intestinal microbiome in the obese have been discussed as a promoting factor in the pathophysiology of obesity and as a contributing factor to related diseases such as type 2 diabetes and metabolic syndrome. The present pilot study investigated the effect of a structured weight loss program on fecal microbiota in obese type 2 diabetics. Twelve study subjects received a low-calorie formula diet for six weeks, followed by a nine week food reintroduction and stabilization period. Fecal microbiota were determined by 16S rRNA gene sequencing of stool samples at baseline, after six weeks and at the end of the study after fifteen weeks. All study subjects lost weight continuously throughout the program. Changes in fecal microbiota were most pronounced after six weeks of low-calorie formula diet, but reverted partially until the end of the study. However, the gut microbiota phylogenetic diversity increased persistently. The abundance of Collinsella, which has previously been associated with atherosclerosis, decreased significantly during the weight loss program. This study underlines the impact of dietary changes on the intestinal microbiome and further demonstrates the beneficial effects of weight loss on gut microbiota. Trial registration: ClinicalTrials.gov NCT02970838.},
}

@article {pmid31318704,
year = {2019},
author = {Seerangaiyan, K and Maruthamuthu, M and van Winkelhoff, AJ and Winkel, EG},
title = {Untargeted metabolomics of the bacterial tongue coating of intra-oral halitosis patients.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/ab334e},
pmid = {31318704},
issn = {1752-7163},
abstract = {Intra-oral halitosis (IOH) refers to an unpleasant odour from the oral cavity that is mainly caused by the tongue coating. Although the tongue coating microbiome is thought to play an essential role in IOH, the exact aetiology of IOH remains unclear. Here we investigated and compared the metabolic profiles of the tongue coating microbiomes of patients with IOH versus healthy control. The metabolic profiles were significantly different in IOH patients than in healthy controls. Healthy controls showed higher selenoamino acid and nicotinamide metabolism; these metabolic pathways are mainly involved in maintaining the oxidation-reduction potential and redox state. A total of 39 putative metabolites were associated with IOH. Remarkably, 3 of the metabolites, branched-chain fatty acids (BCFA), 3-fumaryl pyruvate, and acetyl phosphate, are potential key players in IOH. Interestingly, the predominant metabolite in IOH is BCFAs, which might underlie tongue coat formation. In addition, the key metabolite acetyl phosphate has a clear association with the hydrogen sulfide- (H2S-) producing metabolic pathway and anaerobic fermentation. These novel metabolomic findings provide insights into the formation of the tongue coating and the production of H2S, which causes bad breath. Keywords: Intra-oral halitosis, Tongue coating, Microbiome, Metabolites, Hydrogen sulfide (H2S)&#13.},
}

@article {pmid31317505,
year = {2019},
author = {Lee, JY and Tuazon, JP and Corey, S and Bonsack, B and Acosta, S and Ehrhart, J and Sanberg, PR and Borlongan, CV},
title = {A Gutsy Move for Cell-Based Regenerative Medicine in Parkinson's Disease: Targeting the Gut Microbiome to Sequester Inflammation and Neurotoxicity.},
journal = {Stem cell reviews},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12015-019-09906-2},
pmid = {31317505},
issn = {1558-6804},
abstract = {Pharmaceuticals and cell-based regenerative medicine for Parkinson's disease (PD) offer palliative relief but do not arrest the disease progression. Cell therapy has emerged as an experimental treatment, but current cell sources such as human umbilical cord blood (hUCB) stem cells display only partial recapitulation of mature dopaminergic neuron phenotype and function. Nonetheless, stem cell grafts ameliorate PD-associated histological and behavioral deficits likely through stem cell graft-secreted therapeutic substances. We recently demonstrated the potential of hUCB-derived plasma in enhancing motor capabilities and gastrointestinal function, as well as preventing dopaminergic neuronal cell loss, in an 1-methyl-4-phenyl-1,2,3,6-tetrahydro-pyridine (MPTP) rodent model of PD. Recognizing the translational need to test in another PD model, we now examined here the effects of an intravenously transplanted combination of hUCB and plasma into the 6-hydroxydopamine (6-OHDA) lesioned adult rats. Animals received three separate doses of 4 × 106 hUCB cells with plasma beginning at 7 days after stereotaxic 6-OHDA lesion, then behaviorally and immunohistochemically evaluated over 56 days post-lesion. Whereas vehicle-treated lesioned animals exhibited the typical 6-OHDA neurobehavioral symptoms, hUCB and plasma-treated lesioned animals showed significant attenuation of motor function, gut motility, and nigral dopaminergic neuronal survival, combined with diminished pro-inflammatory microbiomes not only in the nigra, but also in the gut. Altogether these data support a regenerative medicine approach for PD by sequestering inflammation and neurotoxicity through correction of gut dysbiosis.},
}

@article {pmid31317313,
year = {2019},
author = {Emmi, G and Prisco, D},
title = {Behçet's syndrome: focus on pathogenetic background, clinical phenotypes and specific treatments.},
journal = {Internal and emergency medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11739-019-02154-9},
pmid = {31317313},
issn = {1970-9366},
}

@article {pmid31317208,
year = {2019},
author = {Bos, LDJ and Kalil, AC},
title = {Changes in lung microbiome do not explain the development of ventilator-associated pneumonia.},
journal = {Intensive care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00134-019-05691-1},
pmid = {31317208},
issn = {1432-1238},
}

@article {pmid31317039,
year = {2019},
author = {Li, S and Fu, C and Zhao, Y and He, J},
title = {Intervention with α-Ketoglutarate Ameliorates Colitis-Related Colorectal Carcinoma via Modulation of the Gut Microbiome.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {8020785},
doi = {10.1155/2019/8020785},
pmid = {31317039},
issn = {2314-6141},
abstract = {The intestinal microbiome plays a crucial role in promoting intestinal health, and perturbations to its constitution may result in chronic intestinal inflammation and lead to colorectal cancer (CRC). α-Ketoglutarate is an important intermediary in the NF-κB-mediated inflammatory pathway that maintains intestinal homeostasis and prevents initiation of intestinal inflammation, a known precursor to carcinoma development. The objective of this study was to assess the potential protective effects of α-ketoglutarate intervention against CRC development, which may arise due to its known anti-inflammatory and antitumour effects. CRC was induced in C57BL/6 mice using azoxymethane (AOM) and dextran sulfate sodium (DSS). Tumour frequency, histological rating, and colonic microbiota were assessed in colonic samples. The findings demonstrated that α-ketoglutarate offered significant protection against CRC development in mice. Furthermore, α-ketoglutarate also exhibited immunomodulatory effects mediated via downregulation of interleukin (IL)-6, IL-22, tumour necrosis factor (TNF)-α, and IL-1β cytokines. Finally, intervention with α-ketoglutarate tended to minimise the frequency of opportunistic pathogens (Escherichia and Enterococcus) while increasing the populations of Akkermansia, Butyricicoccus, Clostridium, and Ruminococcus. Taken together, our findings show that dietary α-ketoglutarate intervention may protect against inflammation-related CRC.},
}

@article {pmid31317029,
year = {2019},
author = {Wiese, M and Bashmakov, Y and Chalyk, N and Nielsen, DS and Krych, Ł and Kot, W and Klochkov, V and Pristensky, D and Bandaletova, T and Chernyshova, M and Kyle, N and Petyaev, I},
title = {Prebiotic Effect of Lycopene and Dark Chocolate on Gut Microbiome with Systemic Changes in Liver Metabolism, Skeletal Muscles and Skin in Moderately Obese Persons.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {4625279},
doi = {10.1155/2019/4625279},
pmid = {31317029},
issn = {2314-6141},
abstract = {Lycopene rich food and dark chocolate are among the best-documented products with a broad health benefit. This study explored the systemic effect of lycopene and dark chocolate (DC) on gut microbiota, blood, liver metabolism, skeletal muscle tissue oxygenation and skin. 30 volunteers were recruited for this trial, 15 women and 15 men with a mean age of 55 ± 5.7 years and with moderate obesity, 30 < BMI < 35 kg/m2. They were randomized and divided into five equal interventional groups: three received different formulations of lycopene, one of them with a 7 mg daily dose and two with 30 mg; another group was given 10 g of DC with 7 mg lycopene embedded into its matrix, and the last group received 10 g DC. The trial was double-blinded for the three lycopene groups and separately for the 2 DC groups; the trial lasted for 1 month. By the end of the trial there were dose-dependent changes in the gut microbiota profile in all three lycopene groups with an increase of relative abundance of, e.g., Bifidobacterium adolescentis and Bifidobacterium longum. This was also accompanied by dose-dependent changes in the blood, liver metabolism, skeletal muscle and skin parameters. Consumption of DC resulted in increased relative abundance of, e.g., Lactobacillus and a reduction of corneocyte exfoliation. This is the first study which reports the prebiotic potential of lycopene and DC.},
}

@article {pmid31316924,
year = {2019},
author = {Lim, SY and Kwak, YS},
title = {Effect of nutrients and exhaustive exercise on brain function.},
journal = {Journal of exercise rehabilitation},
volume = {15},
number = {3},
pages = {341-345},
doi = {10.12965/jer.1938102.051},
pmid = {31316924},
issn = {2288-176X},
abstract = {Epidemiological evidence suggests that health-oriented eating habits are associated with maintaining optimal cognitive ability. Nutrients are functional bioactive molecules promoting human health and essential components as well. Docosahexaenoic acid (DHA; 22:6n-3), one of polyunsaturated fatty acids (PUFAs) is synthesized through elongation pathway from linolenic acid (81:3n-3) which is recognized as important source of brain function. Endurance physical exercise and energy restriction was also recognized of cardiovascular stress adjustment by enhancing brainstem cholinergic activity as well as brain function. However, we even do not know the exact neuronal mechanisms about the nutrients, β-hydroxybutyrate (β-HB) and myokine impacts on brain-derived neurotropic factor (BDNF) activation. Therefore, this review focuses on recent evidence that explains how nutrients and prolonged exercise can affect nervous system pathways that are associated with improving brain function. The results revealed that frequent consumption of polyphenols and n-3 PUFAs could modify gastrointestinal environment with beneficial microorganisms. It may suggest a new hypothesis that gastrointestinal microbiome could influence cognitive function in addition to the traditional etiological pathway. And moreover, prolonged physical exercise includes open skill sports which is induced by β-oxidation of free fatty acids stimulate BDNF. And also β-HB production which is induced by carbohydrate depletion, hypoglycemia, or fasting stimulate BDNF production that acts an significantly important roles in cognitive function and acting on brain function with brain metabolism.},
}

@article {pmid31316785,
year = {2019},
author = {Gutin, L and Piceno, Y and Fadrosh, D and Lynch, K and Zydek, M and Kassam, Z and LaMere, B and Terdiman, J and Ma, A and Somsouk, M and Lynch, S and El-Nachef, N},
title = {Fecal microbiota transplant for Crohn disease: A study evaluating safety, efficacy, and microbiome profile.},
journal = {United European gastroenterology journal},
volume = {7},
number = {6},
pages = {807-814},
doi = {10.1177/2050640619845986},
pmid = {31316785},
issn = {2050-6406},
abstract = {Background: Emerging trials suggest fecal microbiota transplantation (FMT) is a promising treatment for ulcerative colitis; however, there is a paucity of data in Crohn disease (CD).

Objective: The objectives of this article are to determine whether single-dose FMT improves clinical and endoscopic outcomes in CD patients and to identify meaningful changes in the microbiome in response to FMT.

Methods: We performed a prospective, open-label, single-center study. Ten CD patients underwent FMT and were evaluated for clinical response (defined as decrease in Harvey-Bradshaw Index score ≥3 at one month post-FMT) and microbiome profile (16S ribosomal RNA sequencing) at one month post-FMT.

Results: Three of 10 patients responded to FMT. Two of 10 patients had significant adverse events requiring escalation of therapy. On microbiome analysis, bacterial communities of responders had increased relative abundance of bacteria commonly found in donor gut microbiota.

Conclusions: Single-dose FMT in this cohort of CD patients showed modest effect and potential for harm. Responders tended to have lower baseline alpha diversity, suggesting baseline perturbation of microbiota may be an indicator of potential responders to FMT in this patient population. Controlled trials are needed to further assess the efficacy and safety of FMT in CD and determine whether FMT is a viable option in this patient population.Clinicaltrials.gov number: NCT02460705.},
}

@article {pmid31316751,
year = {2019},
author = {Lin, DM and Lin, HC},
title = {A theoretical model of temperate phages as mediators of gut microbiome dysbiosis.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {},
doi = {10.12688/f1000research.18480.1},
pmid = {31316751},
issn = {2046-1402},
abstract = {Bacteriophages are the most prominent members of the gut microbiome, outnumbering their bacterial hosts by a factor of 10. Phages are bacteria-specific viruses that are gaining attention as highly influential regulators of the gut bacterial community. Dysregulation of the gut bacterial community contributes to dysbiosis, a microbiome disorder characterized by compositional and functional changes that contribute to disease. A role for phages in gut microbiome dysbiosis is emerging with evidence that the gut phage community is altered in dysbiosis-associated disorders such as colorectal cancer and inflammatory bowel disease. Several recent studies have linked successful fecal microbiota transplantation to uptake of the donor's gut phage community, offering some insight into why some recipients respond to treatment whereas others do not. Here, we review the literature supporting a role for phages in mediating the gut bacterial community, giving special attention to Western diet dysbiosis as a case study to demonstrate a theoretical phage-based mechanism for the establishment and maintenance of dysbiosis.},
}

@article {pmid31316487,
year = {2019},
author = {Tripathi, BM and Kim, HM and Jung, JY and Nam, S and Ju, HT and Kim, M and Lee, YK},
title = {Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1442},
doi = {10.3389/fmicb.2019.01442},
pmid = {31316487},
issn = {1664-302X},
abstract = {Permafrost-underlain tundra soils in Northern Hemisphere are one of the largest reservoirs of terrestrial carbon, which are highly sensitive to microbial decomposition due to climate warming. However, knowledge about the taxonomy and functions of microbiome residing in different horizons of permafrost-underlain tundra soils is still limited. Here we compared the taxonomic and functional composition of microbiome between different horizons of soil cores from a moist tussock tundra ecosystem in Council, Alaska, using 16S rRNA gene and shotgun metagenomic sequencing. The composition, diversity, and functions of microbiome varied significantly between soil horizons, with top soil horizon harboring more diverse communities than sub-soil horizons. The vertical gradient in soil physico-chemical parameters were strongly associated with composition of microbial communities across permafrost soil horizons; however, a large fraction of the variation in microbial communities remained unexplained. The genes associated with carbon mineralization were more abundant in top soil horizon, while genes involved in acetogenesis, fermentation, methane metabolism (methanogenesis and methanotrophy), and N cycling were dominant in sub-soil horizons. The results of phylogenetic null modeling analysis showed that stochastic processes strongly influenced the composition of the microbiome in different soil horizons, except the bacterial community composition in top soil horizon, which was largely governed by homogeneous selection. Our study expands the knowledge on the structure and functional potential of microbiome associated with different horizons of permafrost soil, which could be useful in understanding the effects of environmental change on microbial responses in tundra ecosystems.},
}

@article {pmid31316485,
year = {2019},
author = {Splivallo, R and Vahdatzadeh, M and Maciá-Vicente, JG and Molinier, V and Peter, M and Egli, S and Uroz, S and Paolocci, F and Deveau, A},
title = {Orchard Conditions and Fruiting Body Characteristics Drive the Microbiome of the Black Truffle Tuber aestivum.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1437},
doi = {10.3389/fmicb.2019.01437},
pmid = {31316485},
issn = {1664-302X},
abstract = {Truffle fungi are well known for their enticing aromas partially emitted by microbes colonizing truffle fruiting bodies. The identity and diversity of these microbes remain poorly investigated, because few studies have determined truffle-associated bacterial communities while considering only a small number of fruiting bodies. Hence, the factors driving the assembly of truffle microbiomes are yet to be elucidated. Here we investigated the bacterial community structure of more than 50 fruiting bodies of the black truffle Tuber aestivum in one French and one Swiss orchard using 16S rRNA gene amplicon high-throughput sequencing. Bacterial communities from truffles collected in both orchards shared their main dominant taxa: while 60% of fruiting bodies were dominated by α-Proteobacteria, in some cases the β-Proteobacteria or the Sphingobacteriia classes were the most abundant, suggesting that specific factors (i.e., truffle maturation and soil properties) shape differently truffle-associated microbiomes. We further attempted to assess the influence in truffle microbiome variation of factors related to collection season, truffle mating type, degree of maturation, and location within the truffle orchards. These factors had differential effects between the two truffle orchards, with season being the strongest predictor of community variation in the French orchard, and spatial location in the Swiss one. Surprisingly, genotype and fruiting body maturation did not have a significant effect on microbial community composition. In summary, our results show, regardless of the geographical location considered, the existence of heterogeneous bacterial communities within T. aestivum fruiting bodies that are dominated by three bacterial classes. They also indicate that factors shaping microbial communities within truffle fruiting bodies differ across local conditions.},
}

@article {pmid31316475,
year = {2019},
author = {Liao, H and Li, Y and Yao, H},
title = {Biochar Amendment Stimulates Utilization of Plant-Derived Carbon by Soil Bacteria in an Intercropping System.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1361},
doi = {10.3389/fmicb.2019.01361},
pmid = {31316475},
issn = {1664-302X},
abstract = {Plant-derived carbon (C) is considered fundamental to understand the interaction between rhizosphere microbes and plants in terrestrial ecosystems. Biochar soil amendment may enhance plant performance via changing soil properties or microbial diversity in the rhizosphere. However, our knowledge of how plant-microbiome associations respond to biochar amendment remains rather limited. Herein, 13CO2 steady-state labeling combined with DNA stable-isotope probing was used to characterize soil bacterial communities in the rhizosphere contributing to the utilization of plant-derived C. The diversity of bacteria active in the utilization of root exudates was determined after biochar amendment in a legume-based intercropping system (Vicia faba L., with Zea mays L.). The results showed the biochar application not only changed the bacterial community structure and diversity in the rhizosphere, but also altered bacterial members actively assimilating plant-derived C. There were more labeled species in the biochar-amended soils than the control soils. Compared with the control, the biochar amendment increased the relative abundances of Firmicutes and Bacteroidetes members (i.e., Bacillus, Clostridium, Sporomusa, Desulfosporosinus, and Alicyclobacillus) while decreasing the abundances of Proteobacteria members (e.g., Methylobacterium and Sphingomonas) utilizing plant-derived C. In contrast, slow-growing species of the phyla Acidobacteria, Planctomycetes, and Gemmatimonadetes were barely labeled. The bacteria found stimulated by the biochar amendment are known for their ability to fix nitrogen, solubilize phosphorus, or reduce iron and sulfur, which may potentially contribute to the "biochar effect" in the rhizosphere. This study is the first to provide empirical evidence that biochar amendment can alter the soil bacterial community assimilating plant-derived C; this may have consequences for nutrient cycling and improving plant performance in intercropping systems.},
}

@article {pmid31316473,
year = {2019},
author = {Schlatter, DC and Reardon, CL and Johnson-Maynard, J and Brooks, E and Kahl, K and Norby, J and Huggins, D and Paulitz, TC},
title = {Mining the Drilosphere: Bacterial Communities and Denitrifier Abundance in a No-Till Wheat Cropping System.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1339},
doi = {10.3389/fmicb.2019.01339},
pmid = {31316473},
issn = {1664-302X},
abstract = {Earthworms play important roles in no-till cropping systems by redistributing crop residue to lower soil horizons, providing macropores for root growth, increasing water infiltration, enhancing soil quality and organic matter, and stimulating nitrogen cycling. The soil impacted by earthworm activity, including burrows, casts, and middens, is termed the drilosphere. The objective of this study was to determine the effect of earthworms on soil microbial community composition in the drilosphere at different landscape slope positions. Soil cores (50 cm depth) were extracted from three landscape locations (top, middle, and bottom slope positions) on a sloping aspect of a no-till wheat farm. Soil was sampled at the bottom of the soil core from inside multiple earthworm (Lumbricus terrestris) channels (drilosphere) and from adjacent bulk soil. Bacterial communities were characterized for 16S rRNA gene diversity using high-throughput sequencing and functional denitrifier gene abundance (nirK, nirS, and nosZ) by quantitative PCR. Bacterial communities were structured primarily by the landscape slope position of the soil core followed by source (bulk versus drilosphere soil), with a significant interaction between core position and source. The families AKIW874, Chitinophagaceae, and Comamonadaceae and the genera Amycolatopsis, Caulobacter, Nocardioides, and Variovorax were more abundant in the drilosphere compared to the bulk soil. Most of the individual bacterial taxa enriched in the drilosphere versus bulk soil were members of Actinobacteria, including Micrococcales, Gaiellaceae, Solirubrobacterales, and Mycobacterium. In general, the greatest differences in communities were observed in comparisons of the top and bottom slope positions in which the bottom slope communities had significantly greater richness, diversity, and denitrifier abundance than the top slope position. Populations of denitrifiers (i.e., ratio of nirK+nirS to 16S rRNA) were more abundant in earthworm-impacted soils and there was a significant impact of L. terrestris on soil community composition which was observed only in the top landscape position. There were significant correlations between the abundance of nirK and nirS and taxa within Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, suggesting a broad diversity of denitrifying bacteria. Earthworms influence the soil microbial communities, but the impact depends on the slope location in a variable landscape, which likely reflects different soil characteristics.},
}

@article {pmid31316403,
year = {2019},
author = {Conway, F and Brown, AS},
title = {Maternal Immune Activation and Related Factors in the Risk of Offspring Psychiatric Disorders.},
journal = {Frontiers in psychiatry},
volume = {10},
number = {},
pages = {430},
doi = {10.3389/fpsyt.2019.00430},
pmid = {31316403},
issn = {1664-0640},
abstract = {Maternal immune activation (MIA) at the time of gestation has been linked to increased risk of neurodevelopmental psychiatric disorders. Animal and human models have been used to evaluate the relationship between MIA and these outcomes. Given that each of these two disciplines of study have their benefits and limitations, a translational perspective is expected to illuminate more than by the use of any single approach. In this article, we discuss this translational framework and explore how it may be enhanced by the utilization of epigenetic studies and by investigating the microbiome. In this perspectives piece, we focus on the impact of epidemiologic studies, animal models, and preclinical studies in the literature on MIA as well as the potential for greater integration between fields.},
}

@article {pmid31316375,
year = {2019},
author = {Novotný, M and Klimova, B and Valis, M},
title = {Microbiome and Cognitive Impairment: Can Any Diets Influence Learning Processes in a Positive Way?.},
journal = {Frontiers in aging neuroscience},
volume = {11},
number = {},
pages = {170},
doi = {10.3389/fnagi.2019.00170},
pmid = {31316375},
issn = {1663-4365},
abstract = {The aim of this review is to summarize the effect of human intestinal microbiome on cognitive impairments and to focus primarily on the impact of diet and eating habits on learning processes. Better understanding of the microbiome could revolutionize the possibilities of therapy for many diseases. The authors performed a literature review of available studies on the research topic describing the influence of human microbiome and diet on cognitive impairment or learning processes found in the world's acknowledged databases Web of Science, PubMed, Springer, and Scopus. The digestive tube is populated by billions of living microorganisms including viruses, bacteria, protozoa, helminths, and microscopic fungi. In adulthood, under physiological conditions, the intestinal microbiome appears to be relatively steady. However, it is not true that it would not be influenced, both in the positive sense of the word and in the negative one. The basic pillars that maintain a steady microbiome are genetics, lifestyle, diet and eating habits, geography, and age. It is reported that the gastrointestinal tract and the brain communicate with each other through several pathways and one can speak about gut-brain axis. New evidence is published every year about the association of intestinal dysbiosis and neurological/psychiatric diseases. On the other hand, specific diets and eating habits can have a positive effect on a balanced microbiota composition and thus contribute to the enhancement of cognitive functions, which are important for any learning process.},
}

@article {pmid31316085,
year = {2019},
author = {Walker, JN and Hanson, BM and Pinkner, CL and Simar, SR and Pinkner, JS and Parikh, R and Clemens, MW and Hultgren, SJ and Myckatyn, TM},
title = {Insights into the Microbiome of Breast Implants and Periprosthetic Tissue in Breast Implant-Associated Anaplastic Large Cell Lymphoma.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10393},
doi = {10.1038/s41598-019-46535-8},
pmid = {31316085},
issn = {2045-2322},
support = {509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; 509789//Plastic Surgery Foundation (PSF)/ ; },
abstract = {Though rare, breast implant-associated anaplastic large cell lymphoma (BIA-ALCL), a CD30+ T-cell lymphoma associated with textured breast implants, has adversely impacted our perception of the safety of breast implants. Its etiology unknown, one hypothesis suggests an initiating inflammatory stimulus, possibly infectious, triggers BIA-ALCL. We analyzed microbiota of breast, skin, implant and capsule in BIA-ALCL patients (n = 7), and controls via culturing methods, 16S rRNA microbiome sequencing, and immunohistochemistry. Alpha and beta diversity metrics and relative abundance of Gram-negative bacteria were calculated, and phylogenetic trees constructed. Staphylococcus spp., the most commonly cultured microbes, were identified in both the BIA-ALCL and contralateral control breast. The diversity of bacterial microbiota did not differ significantly between BIA-ALCL and controls for any material analyzed. Further, there were no significant differences in the relative abundance of Gram-negative bacteria between BIA-ALCL and control specimens. Heat maps suggested substantial diversity in the composition of the bacterial microbiota of the skin, breast, implant and capsule between patients with no clear trend to distinguish BIA-ALCL from controls. While we identified no consistent differences between patients with BIA-ALCL-affected and contralateral control breasts, this study provides insights into the composition of the breast microbiota in this population.},
}

@article {pmid31316056,
year = {2019},
author = {Mallick, H and Franzosa, EA and Mclver, LJ and Banerjee, S and Sirota-Madi, A and Kostic, AD and Clish, CB and Vlamakis, H and Xavier, RJ and Huttenhower, C},
title = {Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3136},
doi = {10.1038/s41467-019-10927-1},
pmid = {31316056},
issn = {2041-1723},
abstract = {Microbial community metabolomics, particularly in the human gut, are beginning to provide a new route to identify functions and ecology disrupted in disease. However, these data can be costly and difficult to obtain at scale, while amplicon or shotgun metagenomic sequencing data are readily available for populations of many thousands. Here, we describe a computational approach to predict potentially unobserved metabolites in new microbial communities, given a model trained on paired metabolomes and metagenomes from the environment of interest. Focusing on two independent human gut microbiome datasets, we demonstrate that our framework successfully recovers community metabolic trends for more than 50% of associated metabolites. Similar accuracy is maintained using amplicon profiles of coral-associated, murine gut, and human vaginal microbiomes. We also provide an expected performance score to guide application of the model in new samples. Our results thus demonstrate that this 'predictive metabolomic' approach can aid in experimental design and provide useful insights into the thousands of community profiles for which only metagenomes are currently available.},
}

@article {pmid31315951,
year = {2019},
author = {Lynch, T and Peirano, G and Lloyd, T and Read, R and Carter, J and Chu, A and Shaman, JA and Jarvis, JP and Diamond, E and Ijaz, UZ and Church, D},
title = {Molecular diagnosis of vaginitis: comparing qPCR and microbiome profiling approaches to current microscopy scoring.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JCM.00300-19},
pmid = {31315951},
issn = {1098-660X},
abstract = {INTRODUCTION: Vaginitis is often diagnosed by microscopy and limited to testing for bacterial vaginosis (BV), vulvovaginal candidiasis and trichomoniasis. Approximately 10% of vaginal swabs are negative, but designated 'altered flora' by BV Nugent score, leaving clinicians unsure how to treat patients. Accurate and comprehensive vaginitis diagnostics are needed to direct treatment and reduce risks of recurrent or more severe infections.METHOD: Vaginal swabs were collected from 93 women (mean age: 23.53 yrs, range: 18 - 42 yrs) in a cross-sectional study. Microscopy results for BV and Candida were compared to two molecular approaches, (a) comprehensive qPCR assay including aerobic vaginitis (AV), Candida, STI and BV (Applied Biosystems) with an accompanying BV interpretive algorithm (Coriell Life Sciences) and (b) microbiome profiling of the 16S rRNA gene (Illumina).RESULTS: Microscopy + BV Nugent score had 76% overall agreement with the qPCR + BV interpretive algorithm method (24 positive, 47 negative). Nine samples designated 'altered flora' by Nugent were categorized into 5 BV positive and 4 BV negative by the qPCR method. Although BV negative, 3/4 of the latter samples had positive AV targets with one also STI positive. Microscopic identification of Candida vs. qPCR had 94% agreement (9 positive, 78 negative). The comprehensive qPCR assay revealed alternative etiologies summarized as 38% BV, 10% AV, 5% Candida, 2% STI, 10% mixed infection (positive targets in multiple panels) and 35% negative for all targets. 16S microbiome analysis confirmed the bacterial qPCR results and identified differentiating patterns between AV, BV and Lactobacilli-dominated vaginal microbiomes.},
}

@article {pmid31315786,
year = {2019},
author = {Zhou, H and Suo, J and Zhu, J},
title = {[Therapeutic Relevance of Human Microbiota and Lung Cancer].},
journal = {Zhongguo fei ai za zhi = Chinese journal of lung cancer},
volume = {22},
number = {7},
pages = {464-469},
doi = {10.3779/j.issn.1009-3419.2019.07.09},
pmid = {31315786},
issn = {1999-6187},
abstract = {The human microbiome is closely related to human health status. Disruption of the symbiotic balance of the human microbiome is commonly found in systematic diseases such as diabetes, obesity, and chronic gastric diseases. The human microbiome confers benefits or disease susceptibility to the human body through multiple pathways, associated with approximately 20% of malignancies. The incidence and mortality of lung cancer (LC) in men in China are the highest among all malignancies, which is a serious threat to human health. Emerging evidence has suggested that the human microbiota may be closely related to lung cancer at multiple levels, e.g., by affecting metabolic, inflammatory, or immune pathways. At the same time, the human microbiota affects the efficacy of lung cancer on chemoradiotherapy, gene therapy, immunotherapy and other treatments. Immunotherapy is a promising method for the treatment of malignancies such as lung cancer, but the efficacy of immune checkpoint inhibitors in patients is heterogeneous. Preclinical studies based on lung cancer cell lines suggest that the intestinal microbiota can modulate responses to anti--PD-1 therapy through interactions with the host immune system. But for lung cancer patients, whether the intestinal flora can still regulate immunotherapy remains controversial. In this mini-review, we summarize current research findings describing therapeutic relevance of human microbiota and lung cancer. A better knowledge of the interplay between the human microbiome and lung cancer may promote the development of innovative strategies for prevention and personalized treatment in lung cancer.},
}

@article {pmid31315667,
year = {2019},
author = {Pan, H and Guo, R and Ju, Y and Wang, Q and Zhu, J and Xie, Y and Zheng, Y and Li, T and Liu, Z and Lu, L and Li, F and Tong, B and Xiao, L and Xu, X and Leung, EL and Li, R and Yang, H and Wang, J and Zhou, H and Jia, H and Liu, L},
title = {A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {107},
doi = {10.1186/s40168-019-0719-1},
pmid = {31315667},
issn = {2049-2618},
support = {102/2016/A3//Macau Science and Technology Development Fund/ ; JSGG20160229172752028, JCYJ20160229172757249//Shenzhen Municipal Government of China/ ; },
abstract = {BACKGROUND: Early treatment is key for optimizing the therapeutic success of drugs, and the current initiating treatment that blocks the progression of bone destruction during the pre-arthritic stages remains unsatisfactory. The microbial disorder in rheumatoid arthritis (RA) patients is significantly reversed with effective treatment. Modulating aberrant gut microbiomes into a healthy state is a potential therapeutic approach for preventing bone damage.

RESULTS: By using metagenomic shotgun sequencing and a metagenome-wide association study, we assessed the effect of Lactobacillus casei (L. casei) on the induction of arthritis as well as on the associated gut microbiota and immune disorders in adjuvant-induced arthritis (AIA) rats. Treatment of AIA rats with L. casei inhibited joint swelling, lowered arthritis scores, and prevented bone destruction. Along with the relief of arthritis symptoms, dysbiosis in the microbiome of arthritic rats was significantly reduced after L. casei intervention. The relative abundance of AIA-decreased Lactobacillus strains, including Lactobacillus hominis, Lactobacillus reuteri, and Lactobacillus vaginalis, were restored to normal and Lactobacillus acidophilus was upregulated by the administration of L. casei to the AIA rats. Moreover, L. casei downregulated the expression of pro-inflammatory cytokines, which are closely linked to the effect of the L. casei treatment-associated microbes. Functionally, the maintenance of the redox balance of oxidative stress was involved in the improvement in the L. casei-treated AIA rats.

CONCLUSION: A single bacterium, L. casei (ATCC334), was able to significantly suppress the induction of AIA and protect bones from destruction in AIA rats by restoring the microbiome dysbiosis in the gut, indicating that using probiotics may be a promising strategy for treating RA, especially in the early stage of the disease.},
}

@article {pmid31315634,
year = {2019},
author = {Li, Y and Su, X and Zhang, L and Liu, Y and Shi, M and Lv, C and Gao, Y and Xu, D and Wang, Z},
title = {Dysbiosis of the gut microbiome is associated with CKD5 and correlated with clinical indices of the disease: a case-controlled study.},
journal = {Journal of translational medicine},
volume = {17},
number = {1},
pages = {228},
doi = {10.1186/s12967-019-1969-1},
pmid = {31315634},
issn = {1479-5876},
abstract = {BACKGROUND: Chronic kidney disease (CKD) is a universal chronic disease in China. The balance of the gut microbiome is highly crucial for a healthy human body, especially for the immune system. However, the relationship between the gut microbiome and CKD has not yet been clarified.

METHODS: A total of 122 patients were recruited for this study. Among them, 24 patients were diagnosed with CKD5 but did not receive hemodialysis therapy, 29 patients were diagnosed with CKD5 and received hemodialysis therapy and 69 were matched healthy controls. The gut microbiome composition was analyzed by a 16S rRNA (16S ribosomal RNA) gene-based sequencing protocol. High-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC/ESI-MS/MS) technology was used to evaluate the levels of microbiome-related protein-binding uremic toxins level, indoxyl sulfate (IS) and p-cresyl sulfate (PCS), in the patients.

RESULTS: We compared the gut microbiome results of 122 subjects and established a correlation between the gut microbiome and IS and PCS levels. The results indicated that alpha and beta diversity were different in patients with CKD5 than in the healthy controls (p < 0.01). In comparison to healthy controls, CKD5 patients exhibited a significantly higher relative abundance of Neisseria (p < 0.001), Lachnoclostridium (p < 0.001) and Bifidobacterium (p < 0.001). Faecalibacterium (p < 0.001) displayed a notably lower relative abundance for CKD5 patients both with and without hemodialysis than for controls. It was also found that the concentrations of IS and PCS were correlated with the gut microbiome.

CONCLUSIONS: Our results indicate that CKD5 patients both with and without hemodialysis had dysbiosis of the gut microbiome and that this dysbiosis was associated with an accumulation of IS and PCS. These results may support further clinical diagnosis to a great extent and help in developing potential probiotics to facilitate the treatment of CKD5.},
}

@article {pmid31315576,
year = {2019},
author = {Schnorr, SL and Hofman, CA and Netshifhefhe, SR and Duncan, FD and Honap, TP and Lesnik, J and Lewis, CM},
title = {Taxonomic features and comparisons of the gut microbiome from two edible fungus-farming termites (Macrotermes falciger; M. natalensis) harvested in the Vhembe district of Limpopo, South Africa.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {164},
doi = {10.1186/s12866-019-1540-5},
pmid = {31315576},
issn = {1471-2180},
support = {5R01GM089886-06/GF/NIH HHS/United States ; },
abstract = {BACKGROUND: Termites are an important food resource for many human populations around the world, and are a good supply of nutrients. The fungus-farming 'higher' termite members of Macrotermitinae are also consumed by modern great apes and are implicated as critical dietary resources for early hominins. While the chemical nutritional composition of edible termites is well known, their microbiomes are unexplored in the context of human health. Here we sequenced the V4 region of the 16S rRNA gene of gut microbiota extracted from the whole intestinal tract of two Macrotermes sp. soldiers collected from the Limpopo region of South Africa.

RESULTS: Major and minor soldier subcastes of M. falciger exhibit consistent differences in taxonomic representation, and are variable in microbial presence and abundance patterns when compared to another edible but less preferred species, M. natalensis. Subcaste differences include alternate patterns in sulfate-reducing bacteria and methanogenic Euryarchaeota abundance, and differences in abundance between Alistipes and Ruminococcaceae. M. falciger minor soldiers and M. natalensis soldiers have similar microbial profiles, likely from close proximity to the termite worker castes, particularly during foraging and fungus garden cultivation. Compared with previously published termite and cockroach gut microbiome data, the taxonomic representation was generally split between termites that directly digest lignocellulose and humic substrates and those that consume a more distilled form of nutrition as with the omnivorous cockroaches and fungus-farming termites. Lastly, to determine if edible termites may point to a shared reservoir for rare bacterial taxa found in the gut microbiome of humans, we focused on the genus Treponema. The majority of Treponema sequences from edible termite gut microbiota most closely relate to species recovered from other termites or from environmental samples, except for one novel OTU strain, which clustered separately with Treponema found in hunter-gatherer human groups.

CONCLUSIONS: Macrotermes consumed by humans display special gut microbial arrangements that are atypical for a lignocellulose digesting invertebrate, but are instead suited to the simplified nutrition in the fungus-farmer diet. Our work brings to light the particular termite microbiome features that should be explored further as avenues in human health, agricultural sustainability, and evolutionary research.},
}

@article {pmid31315489,
year = {2019},
author = {Du, Y and Li, X and Su, C and Wang, L and Jiang, J and Hong, B},
title = {The human gut microbiome - a new and exciting avenue in cardiovascular drug discovery.},
journal = {Expert opinion on drug discovery},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/17460441.2019.1638909},
pmid = {31315489},
issn = {1746-045X},
abstract = {Introduction: Over the past decade, numerous research efforts have identified the gut microbiota as a novel regulator of human metabolic syndrome and cardiovascular disease (CVD). With the elucidation of underlying molecular mechanisms of the gut microbiota and its metabolites, the drug-discovery process of CVD therapeutics might be expedited. Areas covered: The authors describe the evidence concerning the impact of gut microbiota on metabolic disorders and CVD and summarize the current knowledge of the gut microbial mechanisms that underlie CVD with a focus on microbial metabolites. In addition, they discuss the potential impact of the gut microbiota on the drug efficacy of available cardiometabolic therapeutic agents. Most importantly, the authors review the role of the gut microbiome as a promising source of potential drug targets and novel therapeutics for the development of new treatment modalities for CVD. This review also presents the various effective strategies to investigate the gut microbiome for CVD drug-discovery approaches. Expert opinion: With the elucidation of its causative role in cardiometabolic disease and atherosclerosis, the human gut microbiome holds promises as a reservoir of novel potential therapeutic targets as well as novel therapeutic agents, paving a new and exciting avenue in cardiovascular drug discovery.},
}

@article {pmid31315377,
year = {2019},
author = {Cai, YL and Cao, Y and Fan, XZ and Luo, XR and Meng, JF and Xue, YM and Gao, F and Zou, MC},
title = {[Microbiome analysis of diabetic foot osteomyelitis by metagenome sequencing technology].},
journal = {Zhonghua yi xue za zhi},
volume = {99},
number = {26},
pages = {2057-2061},
doi = {10.3760/cma.j.issn.0376-2491.2019.26.011},
pmid = {31315377},
issn = {0376-2491},
support = {81600648//National Natural Science Foundation of China for Young Scholars/ ; A2017090//Medicine, Science and Technology Research Foundation of Guangdong/ ; 2016ZC0066//Science and Technology Program of Guangdong/ ; },
abstract = {Objective: To analyze the microbiome of diabetic foot osteomyelitis (DFO) by means of metagenome sequencing and provide evidence for identification of pathogenic bacteria in DFO. Methods: A total of 5 patients (3 males and 2 females) with DFO hospitalized at the Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University were enrolled and infected bone specimens were obtained between September 2016 and April 2017. The mean age was (55.8±9.5) years. Metagenome sequencing was performed to explore the characteristics of microbiome, and compared with the results of 16S rRNA sequencing. Results: The results of metagenome sequencing showed that DFO contained diverse microorganism. Totally, 22 dominant species were obtained, Klebsiella pneumoniae (69.66%) was the most abundant, followed by Veillonella parvula (36.93%) and Prevotella intermedia (34.19%). Compared with the 16S rRNA sequencing, metagenome sequencing could obtain more species information on the basis of fewer samples. At the genus level, both sequencing techniques suggested the most dominant pathogen in DFO was anaerobe. All bone specimens had polymicrobial communities. Conclusions: More microecological diversity and abundance of DFO can be found by using metagenome sequencing. At the species level, more bacteria, even bacterial strains can be identified by metagenome sequencing. At the genus level, the most abundant bacteria is anaerobe, however, at the species level, it is facultative anaerobe.},
}

@article {pmid31315227,
year = {2019},
author = {Hills, RD and Pontefract, BA and Mishcon, HR and Black, CA and Sutton, SC and Theberge, CR},
title = {Gut Microbiome: Profound Implications for Diet and Disease.},
journal = {Nutrients},
volume = {11},
number = {7},
pages = {},
doi = {10.3390/nu11071613},
pmid = {31315227},
issn = {2072-6643},
support = {MCB 1516826//National Science Foundation/ ; Gateway to Research Award//American Foundation for Pharmaceutical Education/ ; },
abstract = {The gut microbiome plays an important role in human health and influences the development of chronic diseases ranging from metabolic disease to gastrointestinal disorders and colorectal cancer. Of increasing prevalence in Western societies, these conditions carry a high burden of care. Dietary patterns and environmental factors have a profound effect on shaping gut microbiota in real time. Diverse populations of intestinal bacteria mediate their beneficial effects through the fermentation of dietary fiber to produce short-chain fatty acids, endogenous signals with important roles in lipid homeostasis and reducing inflammation. Recent progress shows that an individual's starting microbial profile is a key determinant in predicting their response to intervention with live probiotics. The gut microbiota is complex and challenging to characterize. Enterotypes have been proposed using metrics such as alpha species diversity, the ratio of Firmicutes to Bacteroidetes phyla, and the relative abundance of beneficial genera (e.g., Bifidobacterium, Akkermansia) versus facultative anaerobes (E. coli), pro-inflammatory Ruminococcus, or nonbacterial microbes. Microbiota composition and relative populations of bacterial species are linked to physiologic health along different axes. We review the role of diet quality, carbohydrate intake, fermentable FODMAPs, and prebiotic fiber in maintaining healthy gut flora. The implications are discussed for various conditions including obesity, diabetes, irritable bowel syndrome, inflammatory bowel disease, depression, and cardiovascular disease.},
}

@article {pmid31315136,
year = {2019},
author = {Shah, A and Crawford, D and Burger, D and Martin, N and Walker, M and Talley, NJ and Tallis, C and Jones, M and Stuart, K and Keely, S and Lewindon, P and Macdonald, GA and Morrison, M and Holtmann, GJ},
title = {Effects of Antibiotic Therapy in Primary Sclerosing Cholangitis with and without Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis.},
journal = {Seminars in liver disease},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0039-1688501},
pmid = {31315136},
issn = {1098-8971},
abstract = {The authors conducted a systematic review and meta-analysis to assess the effect of antibiotic therapy in primary sclerosing cholangitis (PSC). Effect of antibiotic therapy on Mayo PSC Risk Score (MRS), serum alkaline phosphatase (ALP), total serum bilirubin (TSB), and adverse events (AEs) rates were calculated and expressed as standardized difference of means or proportions. Five studies including 124 PSC patients who received antibiotics were included. Overall, antibiotic treatment was associated with a statistically significant reduction in ALP, MRS, and TSB by 33.2, 36.1, and 28.8%, respectively. ALP reduction was greatest for vancomycin (65.6%, p < 0.002) and smallest with metronidazole (22.7%, p = 0.18). Overall, 8.9% (95% confidence interval: 3.9-13.9) of patients had AEs severe enough to discontinue antibiotic therapy. In PSC patients, antibiotic treatment results in a significant improvement in markers of cholestasis and MRS. Antibiotics, particularly vancomycin, may have a positive effect on PSC either via direct effects on the microbiome or via host-mediated mechanisms.},
}

@article {pmid31314548,
year = {2019},
author = {Lataro, RM and Imori, PFM and Santos, ES and Silva, LEV and Duarte, RTD and Aguiar Silva, CA and Falcão, JP and Paton, JFR and Salgado, HC},
title = {Heart failure developed after myocardial infarction does not affect gut microbiota composition in the rat.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00018.2019},
pmid = {31314548},
issn = {1522-1547},
abstract = {There is a body of evidence that supports that gut dysbiosis plays a role in the pathogenesis of cardiovascular diseases. Decreased cardiac function can reduce intestinal perfusion, resulting in morphological alterations witch may contribute to changes in the gut microbiota composition in heart failure (HF) patients. In this regard, a germane question is whether changes in gut microbiota composition are a cause or consequence of the cardiovascular disturbance. We tested the hypothesis that the development of HF, after myocardial infarction, would cause gut dysbiosis. Faecal samples were collected before and six weeks after myocardial infarction or sham surgery. Gut microbiota was characterized by sequencing the bacterial 16S ribosomal DNA. The composition of bacterial communities in the fecal samples was evaluated by calculating three major ecological parameters: 1) the Chao 1 richness; 2) the Pielou evenness; 3) the Shannon index. None of these indices was changed in either sham or HF rats. The Firmicutes/Bacteroidetes ratio was not altered in HF rats. The number of species in each Phylum was also not different between sham and HF rats. β diversity analysis showed that the composition of gut microbiota was not changed with the development of HF. Bacterial genera were grouped according to their major metabolic end-products (acetate, butyrate, and lactate); but no differences were observed in HF rats. Therefore, we conclude that HF induced by myocardial infarction does not affect gut microbiota composition, at least in rats; indicating that the dysbiosis observed in HF patients may precede cardiovascular disturbance.},
}

@article {pmid31314177,
year = {2019},
author = {Ogunrinde, E and Zhou, Z and Gilkeson, G and Jiang, W},
title = {The limitation and racial difference of the plasma microbiome in SLE disease.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.41044},
pmid = {31314177},
issn = {2326-5205},
abstract = {In a Letter to the Editor, Yang and Liang discuss several possibilities as to why FDRs but not SLE patients displayed reduced diversity in their circulating microbiome in our recent publication in Arthritis & Rheumatology (1). Yang and Liang first mention that differences in the genetic and racial background of the two cohorts may explain the disparity in diversity. This article is protected by copyright. All rights reserved.},
}

@article {pmid31314039,
year = {2019},
author = {Andrade, N and Marques, C and Andrade, S and Silva, C and Rodrigues, I and Guardão, L and Guimarães, JT and Keating, E and Calhau, C and Martel, F},
title = {Effect of chrysin on changes in intestinal environment and microbiome induced by fructose-feeding in rats.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo01142k},
pmid = {31314039},
issn = {2042-650X},
abstract = {Intake of fructose-containing sugars is epidemiological and experimentally linked to metabolic syndrome (MS). We recently verified that the dietary polyphenol chrysin was able to abolish some of the metabolic changes induced by fructose-feeding in the rat. Because the role of the intestine upon fructose-induced MS is poorly understood, we decided to investigate the influence of fructose, in vivo, on the intestinal environment and the ability of chrysin to interfere with the putative observed changes. For this, adult male Sprague-Dawley rats were treated for 18 weeks as follows: (A) tap water (CONT), (B) tap water and chrysin (100 mg kg-1 day-1) (CHRY), (C) 10% fructose in tap water (FRUCT), and (D) 10% fructose in tap water and chrysin (100 mg kg-1 day-1) (FRUCT + CHRY). Our findings show that the relative expression of SGLT1 and GLUT2 mRNA were not affected by fructose-feeding and/or chrysin. In contrast, GLUT5 mRNA expression was markedly increased in fructose-fed animals, and this effect was reduced by chrysin. However, the apparent permeability to 14C-FRUCT was markedly and similarly decreased in FRUCT, CHRY and FRUCT + CHRY rats. Jejunal villus width and crypt depth were significantly higher in FRUCT and FRUCT + CHRYS rats, respectively. Finally, chrysin did not alter gut microbiota composition, but fructose significantly increased Lactobacillus and E. coli. Moreover, FRUCT + CHRY rats had an increase on the Firmicutes to Bacteroidetes ratio. This is the first report showing that chrysin is able to interfere with the effects of fructose at the intestinal level, which may contribute to the fructose-induced MS features.},
}

@article {pmid31313962,
year = {2019},
author = {Moye, ZD and Woolston, J and Abbeele, PVD and Duysburgh, C and Verstrepen, L and DAS, CR and Marzorati, M and Sulakvelidze, A},
title = {A Bacteriophage Cocktail Eliminates Salmonella Typhimurium from the Human Colonic Microbiome while Preserving Cytokine Signaling and Preventing Attachment to and Invasion of Human Cells by Salmonella In Vitro.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {1336-1349},
doi = {10.4315/0362-028X.JFP-18-587},
pmid = {31313962},
issn = {1944-9097},
abstract = {Nontyphoidal Salmonella strains continue to be a major cause of foodborne illness globally. One intriguing approach to reducing the risk of salmonellosis is the direct ingestion of phages targeting Salmonella to enhance natural gut resilience and provide protection during foodborne disease outbreaks. We evaluated the ability of a prophylactically administered bacteriophage cocktail, the foodborne outbreak pill (FOP) targeting Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella, to resolve a Salmonella infection in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME), a simulated gut platform populated by the human intestinal microbiome of healthy donors. The FOP preparation eliminated Salmonella enterica serovar Typhimurium from the colon compartment of the SHIME platform but health-associated metabolites, such as short-chain fatty acids and lactate, remained stable or increased in a donor-dependent manner. In studies of human intestinal cells, pretreatment of Salmonella Typhimurium with the FOP cocktail preserved lipopolysaccharide-stimulated signaling in a Caco-2-THP-1 Transwell system and prevented destruction of the Caco-2 monolayer by Salmonella. Adhesion and invasion of intestinal epithelial cells by Salmonella-a critical factor in Salmonella pathogenesis-was blunted when the bacteria were incubated with the FOP preparation before addition to the monolayer. The FOP phage cocktail was effective for (i) eliminating Salmonella from a simulated human gut without disturbing the indigenous microbiota and (ii) reducing the risk of invasion by Salmonella into the intestinal epithelia. These results suggest that the FOP preparation may be of value for reducing the risk of salmonellosis in humans, e.g., during foodborne disease outbreaks.},
}

@article {pmid31313610,
year = {2019},
author = {Catho, G and Huttner, BD},
title = {Strategies for the eradication of extended-spectrum beta-lactamase or carbapenemase-producing Enterobacteriaceae intestinal carriage.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2019.1645007},
pmid = {31313610},
issn = {1744-8336},
abstract = {Introduction: Among the multidrug resistant pathogens, extended-spectrum beta-lactamase (ESBL-E) or carbapenemase-producing Enterobacteriaceae (CPE) are currently considered the main threat due to the scarcity of therapeutic options and their rapid spread around the globe. In addition to developing new antibiotics and stopping transmission, recent research has focused on "decolonization" strategies to eradicate the carriage of ESBL-E/CPE before infection occurs. Areas covered: In this narrative review, we aim to describe the current evidence of decolonization strategies for ESBL-E or CPE intestinal carriage. We first define decolonization and highlight the issues related to the lack of standardized definition, then we summarize the available data on the natural history of colonization. Finally, we review the strategies assessed over the past 10 years for ESBL and CPE decolonization: oral antibiotics, probiotics and more recently fecal microbiota transplantation. We conclude by presenting the risks and uncertainties associated with these strategies. Expert opinion: The evidence available today is too low to recommend decolonization strategies for ESBL-E or CPE in routine clinical practice. The potential increase of resistance and the impact of microbiome manipulation should not be underestimated. Some of these decolonization strategies may nevertheless be effective, at least in temporarily suppressing colonization, which could be useful for specific populations such as high-risk patients. Effectiveness and long-term effects must be properly assessed through well-designed randomized controlled trials.},
}

@article {pmid31312608,
year = {2019},
author = {Gallon, P and Parekh, M and Ferrari, S and Fasolo, A and Ponzin, D and Borroni, D},
title = {Metagenomics in ophthalmology: Hypothesis or real prospective?.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {e00355},
doi = {10.1016/j.btre.2019.e00355},
pmid = {31312608},
issn = {2215-017X},
abstract = {Metagenomic analysis was originally associated with the studies of genetic material from environmental samples. But, with the advent of the Human Microbiome Project, it has now been applied in clinical practices. The ocular surface (OS) is the most exposed part of the eye, colonized by several microbial communities (both, OS and environmental) that contribute to the maintenance of the physiological state. Limited knowledge has been acquired on these microbes due to the limitations of conventional diagnostic methods. Emerging fields of research are focusing on Next Generation Sequencing (NGS) technologies to obtain reliable information on the OS microbiome. Currently only pre-specified pathogens can be detected by conventional culture-based techniques or Polymerase Chain Reaction (PCR), but there are conditions to state whether metagenomics could revolutionize the diagnosis of ocular diseases. The aim of this review is to provide an updated overview of the studies involving NGS technology for OS microbiome.},
}

@article {pmid31312073,
year = {2019},
author = {Kharrat, N and Assidi, M and Abu-Elmagd, M and Pushparaj, PN and Alkhaldy, A and Arfaoui, L and Naseer, MI and El Omri, A and Messaoudi, S and Buhmeida, A and Rebai, A},
title = {Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset.},
journal = {Bioinformation},
volume = {15},
number = {6},
pages = {372-379},
doi = {10.6026/97320630015372},
pmid = {31312073},
issn = {0973-2063},
abstract = {Gut microbiota and their metabolites play a vital role in colon health and disease. Accumulating evidence suggests that the gut microbiota contributes to the risk of colorectal cancer (CRC). However, the role of a specific microbial community together with their metabolites contributing to the risk, initiation and progression of CRC is still unknown. Hence, we used a Bayesian Networks in combination with the IDA (Intervention calculus when the DAG is absent) to generate a graphical model that allows causal relationships to be inferred from observational data. Results from the analysis of publically available datasets showed that four species: Fusobacteium, Citrobacter, Microbacterium and Slaxkia have estimated non-null lower bounds of causal effects of CRC. These findings support the hypothesis that specific bacterial species (microbial markers) act in concert with locally modified microbiota to cause or influence CRC progression. Additional comprehensive studies are required to validate the potential use of F. nucleatum, Citrobacter as well as Slackia as microbial biomarkers in CRC for prevention, diagnosis, prognosis and/or therapeutics.},
}

@article {pmid31311878,
year = {2019},
author = {van Opstal, EJ and Bordenstein, SR},
title = {Phylosymbiosis Impacts Adaptive Traits in Nasonia Wasps.},
journal = {mBio},
volume = {10},
number = {4},
pages = {},
doi = {10.1128/mBio.00887-19},
pmid = {31311878},
issn = {2150-7511},
abstract = {Phylosymbiosis is defined as microbial community relationships that recapitulate the phylogeny of hosts. As evidence for phylosymbiosis rapidly accumulates in different vertebrate and invertebrate holobionts, a central question is what evolutionary forces cause this pattern. We use intra- and interspecific gut microbiota transplants to test for evidence of selective pressures that contribute to phylosymbiosis. We leverage three closely related species of the parasitoid wasp model Nasonia that recently diverged between 0.4 and 1 million years ago: N. vitripennis, N. giraulti, and N. longicornis Upon exposure of germfree larvae to heat-inactivated microbiota from intra- or interspecific larvae, we measure larval growth, pupation rate, and adult reproductive capacity. We report three key findings: (i) larval growth significantly slows when hosts receive an interspecific versus intraspecific gut microbiota, (ii) marked decreases in pupation and resulting adult survival occur from interspecific gut microbiota exposure, and (iii) adult reproductive capacities including male fertility and longevity are unaffected by early life exposure to an interspecific microbiota. Overall, these findings reveal developmental and survival costs to Nasonia upon larval exposures to interspecific microbiota and provide evidence that selective pressures on phenotypes produced by host-microbiota interactions may underpin phylosymbiosis.IMPORTANCE Phylosymbiosis is an ecoevolutionary hypothesis and emerging pattern in animal-microbiota studies whereby the host phylogenetic relationships parallel the community relationships of the host-associated microbiota. A central prediction of phylosymbiosis is that closely related hosts exhibit a lower microbiota beta diversity than distantly related hosts. While phylosymbiosis has emerged as a widespread trend in a field often challenged to find trends across systems, two critical and understudied questions are whether or not phylosymbiosis is consequential to host biology and if adaptive evolutionary forces underpin the pattern. Here, using germfree rearing in the phylosymbiosis model Nasonia, we demonstrate that early life exposure to heat-inactivated microbiota from more distantly related species poses more severe developmental and survival costs than microbiota from closely related or the same species. This study advances a functional understanding of the consequences and potential selective pressures underpinning phylosymbiosis.},
}

@article {pmid31311863,
year = {2019},
author = {Koprivova, A and Schuck, S and Jacoby, RP and Klinkhammer, I and Welter, B and Leson, L and Martyn, A and Nauen, J and Grabenhorst, N and Mandelkow, JF and Zuccaro, A and Zeier, J and Kopriva, S},
title = {Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1818604116},
pmid = {31311863},
issn = {1091-6490},
abstract = {Plants in their natural ecosystems interact with numerous microorganisms, but how they influence their microbiota is still elusive. We observed that sulfatase activity in soil, which can be used as a measure of rhizosphere microbial activity, is differently affected by Arabidopsis accessions. Following a genome-wide association analysis of the variation in sulfatase activity we identified a candidate gene encoding an uncharacterized cytochrome P450, CYP71A27 Loss of this gene resulted in 2 different and independent microbiota-specific phenotypes: A lower sulfatase activity in the rhizosphere and a loss of plant growth-promoting effect by Pseudomonas sp. CH267. On the other hand, tolerance to leaf pathogens was not affected, which agreed with prevalent expression of CYP71A27 in the root vasculature. The phenotypes of cyp71A27 mutant were similar to those of cyp71A12 and cyp71A13, known mutants in synthesis of camalexin, a sulfur-containing indolic defense compound. Indeed, the cyp71A27 mutant accumulated less camalexin in the roots upon elicitation with silver nitrate or flagellin. Importantly, addition of camalexin complemented both the sulfatase activity and the loss of plant growth promotion by Pseudomonas sp. CH267. Two alleles of CYP71A27 were identified among Arabidopsis accessions, differing by a substitution of Glu373 by Gln, which correlated with the ability to induce camalexin synthesis and to gain fresh weight in response to Pseudomonas sp. CH267. Thus, CYP71A27 is an additional component in the camalexin synthesis pathway, contributing specifically to the control of plant microbe interactions in the root.},
}

@article {pmid31311843,
year = {2019},
author = {Gutiérrez, N and Garrido, D},
title = {Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00185-19},
pmid = {31311843},
issn = {2379-5077},
abstract = {The gut microbiome is a complex microbial community that plays a key role in human health. Diet is an important factor dictating gut microbiome composition. This is mediated by multiple microbe-microbe interactions that result in the fermentation of nondigestible carbohydrates and the production of short-chain fatty acids. Certain species play key metabolic roles in the microbiome, and their disappearance could result in dysbiosis. In this work, a synthetic consortium of 14 gut microbes was studied during the utilization of prebiotic inulin in batch bioreactors. Fermentations were repeated leaving one species out every time, in order to evaluate the impact of their elimination on the system. Substrate consumption, microbial composition, and metabolite production were determined. Single deletions never resulted in a complete loss of bacterial growth or inulin consumption, suggesting functional redundancy. Deletions of Bacteroides dorei and Lachnoclostridium clostridioforme resulted in lower biomass and higher residual inulin. The absence of B. dorei impacted the abundance of the other 10 species negatively. Lachnoclostridium symbiosum, a butyrate producer, appeared to be the most sensitive species to deletions, being stimulated by the presence of Escherichia coli, Bifidobacterium adolescentis, B. dorei, and Lactobacillus plantarum Conversely, bioreactors without these species did not show butyrate production. L. clostridioforme was observed to be essential for propionate production, and B. dorei for lactate production. Our analysis identified specific members that were essential for the function of the consortium. In conclusion, species deletions from microbial consortia could be a useful approach to identify relevant interactions between microorganisms and defining metabolic roles in the gut microbiome.IMPORTANCE Gut microbes associate, compete for, and specialize in specific metabolic tasks. These interactions are dictated by the cross-feeding of degradation or fermentation products. However, the individual contribution of microbes to the function of the gut microbiome is difficult to evaluate. It is essential to understand the complexity of microbial interactions and how the presence or absence of specific microorganisms affects the stability and functioning of the gut microbiome. The experimental approach of this study could be used for identifying keystone species, in addition to redundant functions and conditions that contribute to community stability. Redundancy is an important feature of the microbiome, and its reduction could be useful for the design of microbial consortia with desired metabolic properties enhancing the tasks of the keystone species.},
}

@article {pmid31311405,
year = {2019},
author = {Guzmán-Castañeda, SJ and Ortega-Vega, EL and de la Cuesta-Zuluaga, J and Velásquez-Mejía, EP and Rojas, W and Bedoya, G and Escobar, JS},
title = {Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/19490976.2019.1634416},
pmid = {31311405},
issn = {1949-0984},
abstract = {Cardiometabolic affections greatly contribute to the global burden of disease. The susceptibility to obesity, cardiovascular disease, and type-2 diabetes, conditions that add to the cardiometabolic syndrome (CMS), was associated with the ancestral genetic composition and gut microbiota. Studies explicitly testing associations between genetic ancestry and gut microbes are growing. We here examined whether the host genetic ancestry was associated with gut microbiota composition, and distinguished the effects of genetic ancestry and non-genetic factors on human cardiometabolic health. We performed a cross-sectional study with 441 community-dwelling Colombian mestizos from five cities spanning the Andes, Pacific, and Caribbean coasts. We characterized the host genetic ancestry by genotyping 40 ancestry informative markers; characterized gut microbiota through 16S rRNA gene sequencing; assessed diet intake, physical activity, cigarette, and medicament consumption; and measured cardiometabolic outcomes that allowed calculating a CMS risk scale. On average, each individual of our cohort was 67 ± 6% European, 21 ± 5% Native American and 12 ± 5% African. Multivariable-adjusted generalized linear models showed that individuals with higher Native American and African ancestries had increased fasting insulin, body mass index and CMS risk, as assessed by the CMS risk scale. Furthermore, we identified 21 OTUs associated to the host genetic ancestry and 20 to cardiometabolic health. While we highlight novel associations between genetic ancestry and gut microbiota, we found that the effect of intestinal microbes was more likely to explain the variance in CMS risk scale than the contributions of European, Native American and African genetic backgrounds.},
}

@article {pmid31311141,
year = {2019},
author = {Paoli, A and Mancin, L and Bianco, A and Thomas, E and Mota, JF and Piccini, F},
title = {Ketogenic Diet and Microbiota: Friends or Enemies?.},
journal = {Genes},
volume = {10},
number = {7},
pages = {},
doi = {10.3390/genes10070534},
pmid = {31311141},
issn = {2073-4425},
abstract = {Over the last years, a growing body of evidence suggests that gut microbial communities play a fundamental role in many aspects of human health and diseases. The gut microbiota is a very dynamic entity influenced by environment and nutritional behaviors. Considering the influence of such a microbial community on human health and its multiple mechanisms of action as the production of bioactive compounds, pathogens protection, energy homeostasis, nutrients metabolism and regulation of immunity, establishing the influences of different nutritional approach is of pivotal importance. The very low carbohydrate ketogenic diet is a very popular dietary approach used for different aims: from weight loss to neurological diseases. The aim of this review is to dissect the complex interactions between ketogenic diet and gut microbiota and how this large network may influence human health.},
}

@article {pmid31311045,
year = {2019},
author = {Steffen, HM and Demir, M},
title = {[Gut Microbiome and Cardiovascular Disease].},
journal = {Deutsche medizinische Wochenschrift (1946)},
volume = {144},
number = {14},
pages = {957-963},
doi = {10.1055/a-0746-4002},
pmid = {31311045},
issn = {1439-4413},
abstract = {Aging, physical activity, bodyweight and diet are well established risk factors for cardiovascular disease. For all of these factors a great impact on the intestinal microbiome has been described. The current review will discuss available data regarding the role of the gut microbiome in regulating blood pressure, vascular function and its possible contribution to atherosclerosis and heart failure.},
}

@article {pmid31311044,
year = {2019},
author = {Siegel, J and Andresen, V and Layer, P},
title = {[Microbiome And Gastrointestinal Diseases].},
journal = {Deutsche medizinische Wochenschrift (1946)},
volume = {144},
number = {14},
pages = {949-956},
doi = {10.1055/a-0899-8759},
pmid = {31311044},
issn = {1439-4413},
abstract = {For some years, microbiome research has become a thriving topic. The most diverse and hitherto poorly understood connections of interactions of the microbiome with the host body (human) seem to play an important role in the genesis of a wide variety of diseases. This article focuses on the importance of the microbiome in gastrointestinal diseases and presents therapeutic approaches.The intestinal microbiome will not be understood completely for a long time due to the highly complex relationships and variety of different microorganisms. The intestinal microbiome is critically involved in the development of diseases, especially in the development of inflammatory bowel disease. Helicobacter pylori infection is a major risk factor for gastric carcinoma. Esophageal microbiome alterations can cause inflammation and decrease the tone of the lower esophageal sphincter. Inflammation is a crucial pathway for tumorigenesis, it can be caused by the "normal" flora and by pathogenic agents. In the microbiome of the colon, interactions of bacteria, viruses and fungi have a very special status. Good oral/dental status protects against pancreatic carcinoma. Fecal microbiome transfer has become more important in the American guideline. Understanding the processes in the intestinal microbiome provides approaches to new therapies that are likely to exceed our current imagination.},
}

@article {pmid31311043,
year = {2019},
author = {Bischoff, SC},
title = {[Optimization of Digestion - How Nutrition and Microbiome Affect Each Other].},
journal = {Deutsche medizinische Wochenschrift (1946)},
volume = {144},
number = {14},
pages = {943-948},
doi = {10.1055/a-0826-1977},
pmid = {31311043},
issn = {1439-4413},
abstract = {Nutrition affects intestinal bacteria by stimulating the expansion of bacteria that can metabolize the nutrient components offered. Conversely, gut bacteria help to optimize food digestion and increase energy intake. Thus, the intestinal microbiome is regulated primarily by nourishment: it determines the composition, function and diversity of the microbiome. As a result, the intestinal microbiome helps to optimize energy and substrate production from food. This is beneficial in cases of imminent malnutrition, but can be detrimental in case of overeating and obesity.},
}

@article {pmid31311041,
year = {2019},
author = {Hintze, G},
title = {[Microbiome - growing importance in medicine].},
journal = {Deutsche medizinische Wochenschrift (1946)},
volume = {144},
number = {14},
pages = {929},
doi = {10.1055/a-0762-3043},
pmid = {31311041},
issn = {1439-4413},
}

@article {pmid31310764,
year = {2019},
author = {Javitt, G and Calvo, MLG and Albert, L and Reznik, N and Ilani, T and Diskin, R and Fass, D},
title = {Intestinal Gel-Forming Mucins Polymerize by Disulfide-Mediated Dimerization of D3 Domains.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmb.2019.07.018},
pmid = {31310764},
issn = {1089-8638},
abstract = {The mucin 2 glycoprotein assembles into a complex hydrogel that protects intestinal epithelia and houses the gut microbiome. A major step in mucin 2 assembly is further multimerization of preformed mucin dimers, thought to produce a honeycomb-like arrangement upon hydrogel expansion. Important open questions are how multiple mucin 2 dimers become covalently linked to one another and how mucin 2 multimerization compares with analogous processes in related polymers such as respiratory tract mucins and the hemostasis protein von Willebrand factor. Here we report the X-ray crystal structure of the mucin 2 multimerization module, found to form a dimer linked by two intersubunit disulfide bonds. The dimer structure calls into question the current model for intestinal mucin assembly, which proposes disulfide-mediated trimerization of the same module. Key residues making interactions across the dimer interface are highly conserved in intestinal mucin orthologs, supporting the physiological relevance of the observed quaternary structure. With knowledge of the interface residues, it can be demonstrated that many of these amino acids are also present in other mucins and in von Willebrand factor, further indicating that the stable dimer arrangement reported herein is likely to be shared across this functionally broad protein family. The mucin 2 module structure thus reveals the manner by which both mucins and von Willebrand factor polymerize, drawing deep structural parallels between macromolecular assemblies critical to mucosal epithelia and the vasculature.},
}

@article {pmid31310736,
year = {2019},
author = {Anderson, G},
title = {Breast Cancer: Occluded Role of Mitochondria N-acetylserotonin/Melatonin Ratio in Co-ordinating Pathophysiology.},
journal = {Biochemical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bcp.2019.07.014},
pmid = {31310736},
issn = {1873-2968},
abstract = {A plethora of factors contribute to the biochemical underpinnings of breast cancer, in the absence of any clear, integrative framework. This article proposes that melatonergic pathway regulation within mitochondria provides an integrative framework for the wide array of data driving breast cancer pathophysiology. As melatonin is toxic to breast cancer cells, its production within mitochondria poses a significant challenge to breast cancer cell survival. Consequently, the diverse plasticity in breast cancer cells may arise from a requirement to decrease mitochondria melatonin synthesis. The aryl hydrocarbon receptor role in breast cancer pathophysiology may be mediated by an increase in cytochrome P450 (CYP)1b1 in mitochondria, leading to the backward conversion of melatonin to N-acetylserotonin (NAS). NAS has distinct effects to melatonin, including its activation of the tyrosine receptor kinase B (TrkB) receptor. TrkB activation significantly contributes to breast cancer cell survival and migration. However, the most important aspect of NAS induction by CYP1b1 in breast cancer cells is the prevention of melatonin effects in mitochondria. Many of the changes occurring in breast cancer cells arise from the need to regulate this pathway in mitochondria, allowing this to provide a framework that integrates a host of previously disparate data, including: microRNAs, estrogen, 14-3-3 proteins, sirtuins, glycolysis, oxidative phosphorylation, indoleamine 2,3-dioxygenase and the kynurenine pathways. It is also proposed that this framework provides a pathoetiological model incorporating the early developmental regulation of the gut microbiome that integrates breast cancer risk factors, including obesity. This has significant treatment, prevention and research implications.},
}

@article {pmid31309868,
year = {2019},
author = {Pantoja-Feliciano, IG and Soares, JW and Doherty, LA and Karl, JP and McClung, HL and Armstrong, NJ and Branck, TA and Arcidiacono, S},
title = {Acute stressor alters inter-species microbial competition for resistant starch-supplemented medium.},
journal = {Gut microbes},
volume = {10},
number = {4},
pages = {439-446},
doi = {10.1080/19490976.2018.1554962},
pmid = {31309868},
issn = {1949-0984},
abstract = {Gut microbiome community dynamics are maintained by complex microbe-microbe and microbe-host interactions, which can be disturbed by stress. In vivo studies on the dynamics and manipulation of those interactions are costly and slow, but can be accelerated using in vitro fermentation. Herein, in vitro fermentation was used to determine how an acute stressor, a sudden change in diet, impacts inter-bacterial species competition for resistant starch-supplemented medium (RSM). Fermentation vessels were seeded with fecal samples collected from 10 individuals consuming a habitual diet or U.S. military rations for 21 days. Lactobacillus spp. growth in response to RSM was attenuated following ration consumption, whereas growth of Ruminococcus bromii was enhanced. These differences were not evident in the pre-fermentation samples. Findings demonstrate how incorporating in vitro fermentation into clinical studies can increase understanding of stress-induced changes in nutrient-microbiome dynamics, and suggest that sudden changes in diet may impact inter-species competition for substrates.},
}

@article {pmid31309394,
year = {2019},
author = {Szari, S and Quinn, JA},
title = {Supporting a Healthy Microbiome for the Primary Prevention of Eczema.},
journal = {Clinical reviews in allergy & immunology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12016-019-08758-5},
pmid = {31309394},
issn = {1559-0267},
abstract = {Eczema is increasing worldwide with associated increases in health costs and decreases in quality of life. There are many factors that are speculated to interact in the development of eczema including genetics and environmental exposures. Prevention of the development of eczema may prevent the further development of food allergies and asthma. This concept has prompted a variety of research into the area of primary prevention of eczema in infants. This exploration includes a growing body of research examining infants supplemented with probiotics, prebiotics, or both (synbiotics) often compared with their breastfed counterparts. The goal of this paper is to examine the evidence for manipulating the microbiome in the prevention of eczema. Several strains of probiotics, compositions of prebiotics, and varied combinations of both are commercially available. Evidence supports altering the microbiome in infants at high risk of atopy who are not able to breastfeed with Lactobacillus strains when given both prenatally followed by prolonged use (greater than 6 months) postnatally for the primary prevention of eczema. Prebiotics have also been shown beneficial for primary prevention of eczema in formula-fed infants with prolonged use greater than 6 months. These findings are in keeping with the World Allergy Organization (WAO) recommendations that support interventions to manipulate the microbiome with both probiotics and prebiotics.},
}

@article {pmid31309109,
year = {2019},
author = {Wang, S and Li, N and Li, N and Zou, H and Wu, M},
title = {A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans.},
journal = {BioMed research international},
volume = {2019},
number = {},
pages = {6361320},
doi = {10.1155/2019/6361320},
pmid = {31309109},
issn = {2314-6141},
abstract = {Obesity is intrinsically linked with the gut microbiome, and studies have identified several obesity-associated microbes. The microbe-microbe interactions can alter the composition of the microbial community and influence host health by producing secondary metabolites (SMs). However, the contribution of these SMs in the prevention and treatment of obesity has been largely ignored. We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. In addition, the mean abundance of BGCs was positively correlated with obesity, consistent with the lower taxonomic diversity in the gut microbiota of obese individuals. By comparing the BGCs of known SM between obese and nonobese samples, we found that menaquinone produced by Enterobacter cloacae showed the highest correlation with BMI, in agreement with a recent study on human adipose tissue composition. Furthermore, an obesity-related nonribosomal peptide synthetase (NRPS) was negatively associated with Bacteroidetes, indicating that the SMs produced by intestinal microbes in obese individuals can change the microbiome structure. This is the first systemic study of the association between gut microbiome BGCs and obesity and provides new insights into the causes of obesity.},
}

@article {pmid31309006,
year = {2019},
author = {Li, C and Tan, X and Bai, J and Xu, Q and Liu, S and Guo, W and Yu, C and Fan, G and Lu, Y and Zhang, H and Yang, H and Chen, J and Liu, X},
title = {A survey of the sperm whale (Physeter catodon) commensal microbiome.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7257},
doi = {10.7717/peerj.7257},
pmid = {31309006},
issn = {2167-8359},
abstract = {Background: Mammalian commensal microbiota play important roles in the health of its host. In comparison to terrestrial mammals, commensal microbiota of marine mammals is mainly focused on the composition and function of skin and gut microbiota, with less attention paid to the health impact of bacteria and viruses. Previous studies on sperm whales (Physeter catodon) have affirmed their important phylogenetic position; however, studies on their commensal microbiota have not been published, due to difficulty in sample collection.

Methods: Here, we sequenced the metagenomes of blood, muscle and fecal samples from a stranded sperm whale using the BGISEQ-500 platform. We compared the diversity and abundance of microbiomes from three different tissues and tried to search pathogenic bacterial and virulence genes probably related to the health of the sperm whale. We also performed 16S rDNA sequencing of the fecal sample to compare to published gut metagenome data from other marine mammals.

Results: Our results demonstrated notable differences in species richness and abundance in the three samples. Extensive bacteria, including Enterococcus faecium, Fusobacterium nucleatum, Pseudomonas aeruginosa, Streptococcus anginosus, Streptococcus pneumoniae, and Streptococcus suis, and five toxigenic Clostridium species usually associated with infection, were found in the three samples. We also found the taxa composition of sperm whale gut microbiota was similar to that of other whales, suggesting co-evolution with its host. This study is the first report of the sperm whale gut microbiome, and provides a foundation for the pathogen detection and health assessment of the sperm whale.},
}

@article {pmid31308831,
year = {2019},
author = {Bose, M and Mukherjee, P},
title = {Role of Microbiome in Modulating Immune Responses in Cancer.},
journal = {Mediators of inflammation},
volume = {2019},
number = {},
pages = {4107917},
doi = {10.1155/2019/4107917},
pmid = {31308831},
issn = {1466-1861},
abstract = {The complex interactions between genes and the environment play important roles in disease susceptibility and progression. One of the chronic diseases that is affected by this gene-environment interplay is cancer. However, our knowledge about these environmental factors remains limited. The microorganisms that inhabit our bodies have recently been acknowledged to play a crucial role as an environmental factor, to which we are constantly exposed. Studies have revealed significant differences in the relative abundance of certain microbes in cancer cases compared with controls. It has been reported that changes in the composition of normal gut microbiota can increase/decrease cancer susceptibility and progression by diverse mechanisms including, but not limited to, inflammation-a well-known hallmark of carcinogenesis. The microbiota can also affect the response to various treatments including immunotherapy. The microbiome-immune-cancer axis will continue to provide insight into the basic mechanisms of carcinogenesis. In this review, we provide a brief understanding of the mechanisms by which microbiota affects cancer development, progression, and treatment.},
}

@article {pmid31308634,
year = {2019},
author = {Zhang, DY and Zhu, L and Liu, HN and Tseng, YJ and Weng, SQ and Liu, TT and Dong, L and Shen, XZ},
title = {The protective effect and mechanism of the FXR agonist obeticholic acid via targeting gut microbiota in non-alcoholic fatty liver disease.},
journal = {Drug design, development and therapy},
volume = {13},
number = {},
pages = {2249-2270},
doi = {10.2147/DDDT.S207277},
pmid = {31308634},
issn = {1177-8881},
abstract = {Background: It is reported that various diseases such as non-alcoholic fatty liver disease (NAFLD) are associated with imbalance of microbiome. And FXR has been well investigated in liver diseases. Purpose: The objective of this study was to identify the role of farnesoid X receptor agonist obeticholic acid via targeting gut microbiota in NAFLD. Patients and methods: Male C57BL/6 mice were fed either a normal-chow diet or a high-fat diet (HFD). Obeticholic acid(30mg/(kg·d)) and/or a combination of antibiotics were administered orally by gavage to mice for 12 weeks. Gut microbiota profiles were established through 16S rRNA amplicon sequencing. The effects of obeticholic acid on liver inflammation, the gut barrier, endotoxemia, gut microbiome and composition of the bile acid were also investigated. Results: Obeticholic acid treatment can significantly improve obesity, circulation metabolism disorders, liver inflammation and fibrosis, and intestinal barrier damage caused by HFD. Removal of normal commensal bacteria can weaken the effect of obeticholic acid. The gut microbial structure was changed, and abundance of Blautia was increased significantly after treated with obeticholic acid. After obeticholic acid treatment, the concentration of taurine-bound bile acid caused by HFD was reduced in the liver. Conclusion: Taken together, these data suggest that obeticholic acid has aprotective effect on NAFLD via changing the components of gut microbiota, specifically increasing the abundance of Blautia.},
}

@article {pmid31308552,
year = {2019},
author = {Ji, BW and Sheth, RU and Dixit, PD and Huang, Y and Kaufman, A and Wang, HH and Vitkup, D},
title = {Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-019-0467-y},
pmid = {31308552},
issn = {1548-7105},
abstract = {Metagenomic sequencing has enabled detailed investigation of diverse microbial communities, but understanding their spatiotemporal variability remains an important challenge. Here, we present decomposition of variance using replicate sampling (DIVERS), a method based on replicate sampling and spike-in sequencing. The method quantifies the contributions of temporal dynamics, spatial sampling variability, and technical noise to the variances and covariances of absolute bacterial abundances. We applied DIVERS to investigate a high-resolution time series of the human gut microbiome and a spatial survey of a soil bacterial community in Manhattan's Central Park. Our analysis showed that in the gut, technical noise dominated the abundance variability for nearly half of the detected taxa. DIVERS also revealed substantial spatial heterogeneity of gut microbiota, and high temporal covariances of taxa within the Bacteroidetes phylum. In the soil community, spatial variability primarily contributed to abundance fluctuations at short time scales (weeks), while temporal variability dominated at longer time scales (several months).},
}

@article {pmid31308384,
year = {2019},
author = {Bang, S and Yoo, D and Kim, SJ and Jhang, S and Cho, S and Kim, H},
title = {Establishment and evaluation of prediction model for multiple disease classification based on gut microbial data.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {10189},
doi = {10.1038/s41598-019-46249-x},
pmid = {31308384},
issn = {2045-2322},
support = {14162MFDS972//Ministry of Food and Drug Safety (MFDS)/ ; },
abstract = {Diseases prediction has been performed by machine learning approaches with various biological data. One of the representative data is the gut microbial community, which interacts with the host's immune system. The abundance of a few microorganisms has been used as markers to predict diverse diseases. In this study, we hypothesized that multi-classification using machine learning approach could distinguish the gut microbiome from following six diseases: multiple sclerosis, juvenile idiopathic arthritis, myalgic encephalomyelitis/chronic fatigue syndrome, acquired immune deficiency syndrome, stroke and colorectal cancer. We used the abundance of microorganisms at five taxonomy levels as features in 696 samples collected from different studies to establish the best prediction model. We built classification models based on four multi-class classifiers and two feature selection methods including a forward selection and a backward elimination. As a result, we found that the performance of classification is improved as we use the lower taxonomy levels of features; the highest performance was observed at the genus level. Among four classifiers, LogitBoost-based prediction model outperformed other classifiers. Also, we suggested the optimal feature subsets at the genus-level obtained by backward elimination. We believe the selected feature subsets could be used as markers to distinguish various diseases simultaneously. The finding in this study suggests the potential use of selected features for the diagnosis of several diseases.},
}

@article {pmid31308358,
year = {2019},
author = {Alsahafi, E and Begg, K and Amelio, I and Raulf, N and Lucarelli, P and Sauter, T and Tavassoli, M},
title = {Clinical update on head and neck cancer: molecular biology and ongoing challenges.},
journal = {Cell death & disease},
volume = {10},
number = {8},
pages = {540},
doi = {10.1038/s41419-019-1769-9},
pmid = {31308358},
issn = {2041-4889},
abstract = {Head and neck squamous cell carcinomas (HNSCCs) are an aggressive, genetically complex and difficult to treat group of cancers. In lieu of truly effective targeted therapies, surgery and radiotherapy represent the primary treatment options for most patients. But these treatments are associated with significant morbidity and a reduction in quality of life. Resistance to both radiotherapy and the only available targeted therapy, and subsequent relapse are common. Research has therefore focussed on identifying biomarkers to stratify patients into clinically meaningful groups and to develop more effective targeted therapies. However, as we are now discovering, the poor response to therapy and aggressive nature of HNSCCs is not only affected by the complex alterations in intracellular signalling pathways but is also heavily influenced by the behaviour of the extracellular microenvironment. The HNSCC tumour landscape is an environment permissive of these tumours' aggressive nature, fostered by the actions of the immune system, the response to tumour hypoxia and the influence of the microbiome. Solving these challenges now rests on expanding our knowledge of these areas, in parallel with a greater understanding of the molecular biology of HNSCC subtypes. This update aims to build on our earlier 2014 review by bringing up to date our understanding of the molecular biology of HNSCCs and provide insights into areas of ongoing research and perspectives for the future.},
}

@article {pmid31308136,
year = {2019},
author = {Ingman, WV},
title = {The Gut Microbiome: A New Player in Breast Cancer Metastasis.},
journal = {Cancer research},
volume = {79},
number = {14},
pages = {3539-3541},
doi = {10.1158/0008-5472.CAN-19-1698},
pmid = {31308136},
issn = {1538-7445},
abstract = {There is increasing interest in the role of the gut microbiome in health and disease, and a number of observational and in vitro studies have suggested it may play a role in breast cancer development and progression. Buchta Rosean and colleagues present the first functional evidence that a preexisting disturbance in the gut microbiome leads to increased breast cancer cell metastasis in a mouse model. This discovery places the gut microbiome as a new player in breast cancer metastasis; however, further studies are required to determine the relevance of the findings in this mouse model to human disease. A better understanding of the relationship between the bacterial ecosystem of the gut and progression of breast cancer has enormous potential for improving treatment outcomes for patients with breast cancer.See related article by Buchta Rosean et al., p. 3662.},
}

@article {pmid31307985,
year = {2019},
author = {Burdet, C and Nguyen, TT and Duval, X and Ferreira, S and Andremont, A and Guedj, J and Mentré, F and , },
title = {Impact of antibiotic gut exposure on the temporal changes in microbiome diversity.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1128/AAC.00820-19},
pmid = {31307985},
issn = {1098-6596},
abstract = {Although the global deleterious impact of antibiotics on the intestinal microbiota is well known, the temporal changes in microbial diversity during and after an antibiotic treatment are still poorly characterized. We used plasma and fecal samples frequently collected during and up to one month after treatment in 22 healthy volunteers assigned to a 5-day treatment by moxifloxacin (N=14) or no intervention (N=8). Moxifloxacin concentrations were measured both in plasma and feces, and bacterial diversity was determined in feces by 16S rRNA gene profiling and quantified using Shannon index and number of operational taxonomic units (OTUs). Nonlinear mixed-effects models were used to relate drug pharmacokinetics and bacterial diversity over time. Moxifloxacin reduced bacterial diversity in a concentration-dependent manner, with a median maximal loss of 27.5% of the Shannon index (min;max: 17.5;27.7) and 47.4% of the OTUs number (30.4;48.3). As a consequence of both the long fecal half-life of moxifloxacin and the susceptibility of the gut microbiota to moxifloxacin, bacterial diversity indices did not return to their pre-treatment levels until days 16 and 21, respectively. Finally, the model characterized the effect of moxifloxacin on bacterial diversity biomarkers, and provides a novel framework for analyzing antibiotic effects on the intestinal microbiome.},
}

@article {pmid31307786,
year = {2019},
author = {Snell, G and Hiho, S and Levvey, B and Sullivan, L and Westall, G},
title = {Consequences of donor-derived passengers (pathogens, cells, biological molecules and proteins) on clinical outcomes.},
journal = {The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.healun.2019.06.019},
pmid = {31307786},
issn = {1557-3117},
abstract = {It is recognized that donor factors contribute to lung transplant outcomes. Recent observations and studies have started to elucidate potential mechanisms behind explaining these observations. This perspective piece summarizes evolving lung transplant literature on the subject, focusing on donor "passenger" organisms, cells, hormones, and proteins transferred to the recipient. Many extrinsic and intrinsic donor features or properties have important consequences for subsequent allograft function in the recipient. Potentially, a better understanding of these features may provide useful novel therapeutic targets to enhance allograft outcomes.},
}

@article {pmid31307536,
year = {2019},
author = {Chen, J and McIlroy, SE and Archana, A and Baker, DM and Panagiotou, G},
title = {A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {104},
doi = {10.1186/s40168-019-0714-6},
pmid = {31307536},
issn = {2049-2618},
support = {2016-67//Environment and Conservation Fund/ ; },
abstract = {BACKGROUND: Coastal marine environments are one of the most productive ecosystems on Earth. However, anthropogenic impacts exert significant pressure on coastal marine biodiversity, contributing to functional shifts in microbial communities and human health risk factors. However, relatively little is known about the impact of eutrophication-human-derived nutrient pollution-on the marine microbial biosphere.

RESULTS: Here, we tested the hypothesis that benthic microbial diversity and function varies along a pollution gradient, with a focus on human pathogens and antibiotic resistance genes. Comprehensive metagenomic analysis including taxonomic investigation, functional detection, and ARG annotation revealed that zinc, lead, total volatile solids, and ammonia nitrogen were correlated with microbial diversity and function. We propose several microbes, including Planctomycetes and sulfate-reducing microbes as candidates to reflect pollution concentration. Annotation of antibiotic resistance genes showed that the highest abundance of efflux pumps was found at the most polluted site, corroborating the relationship between pollution and human health risk factors. This result suggests that sediments at polluted sites harbor microbes with a higher capacity to reduce intracellular levels of antibiotics, heavy metals, or other environmental contaminants.

CONCLUSIONS: Our findings suggest a correlation between pollution and the marine sediment microbiome and provide insight into the role of high-turnover microbial communities as well as potential pathogenic organisms as real-time indicators of water quality, with implications for human health and demonstrate the inner functional shifts contributed by the microcommunities.},
}

@article {pmid31307473,
year = {2019},
author = {Song, J and Ma, W and Gu, X and Zhao, L and Jiang, J and Xu, Y and Zhang, L and Zhou, M and Yang, L},
title = {Metabolomic signatures and microbial community profiling of depressive rat model induced by adrenocorticotrophic hormone.},
journal = {Journal of translational medicine},
volume = {17},
number = {1},
pages = {224},
doi = {10.1186/s12967-019-1970-8},
pmid = {31307473},
issn = {1479-5876},
support = {2019SHUTCM182//Innovation Project for Undergraduates of Shanghai University of Traditional Chinese Medicine/ ; 17XD1403500//Program of Shanghai Academic/Technology Research Leader/ ; 81773927//National Natural Science Foundation of China (CN)/ ; 81573814//National Natural Science Foundation of China (CN)/ ; 2017.10-2020.9 to Jiaye Jiang//Xinglin Young Scholar/ ; },
abstract = {BACKGROUND: Adrenocorticotrophic hormone (ACTH)-treatment rat model has been utilized as a widely accepted model of treatment-resistant depression. Metabolomic signatures represent the pathophysiological phenotype of diseases. Recent studies in gut microbiota and metabolomics analysis revealed the dramatic role of microbiome in psychoneurological system diseases, but still, the mechanisms underlying gut microbiome-host interaction remain unclear.

METHODS: Male Wistar rats were s.c. injection of ACTH fragment 1-24 for 14 days to induce treatment-resistant depression. Depression-related behavioral tests, analysis of serum monoamine neurotransmitters and hypothalamic-pituitary-adrenal (HPA) axis-related hormones were determined for assessment of ACTH-induced depression rat model. A gas chromatography-time-of-flight mass spectrometer based urinary metabolomic signatures integrated 16S rRNA sequence analysis based gut microbial profiling was performed, as well as Spearman's correlation coefficient analysis was used to manifest the covariation between the differential urinary metabolites and gut microbiota of genus level.

RESULTS: Chronic injection of ACTH-induced depression-like phenotype (increased immobility time in forced swimming test and tail suspension test) was accompanied by peripheral serotonin down-regulation and HPA axis overactivation (ACTH and corticosterone up-regulation). Urinary metabolomics analysis indicated that pyruvic acid, L-threonine, mannitol, D-gluconic acid, 4-hydroxybenzoic acid, D-arabitol, myo-inositol and ascorbic acid levels were reduced in ACTH-treated rats' urine, while hippurate level was elevated. In addition, microbial community profiling revealed bacterial enrichment (e.g. Ruminococcus, Klebsiella) and reduction (e.g. Akkermansia, Lactobacillus) in the ACTH-induced depression rat model. Correlation analysis showed that Akkermansia and Lactobacillus were closely relevant to metabolites myo-inositol and hippurate, which were included in host inositol phosphate metabolism, and phenylalanine, tyrosine and tryptophan biosynthesis.

CONCLUSIONS: Depression rat model induced by ACTH is associated with disturbance of pyruvate metabolism, ascorbate and aldarate metabolism, inositol phosphate metabolism, glycine, serine and threonine metabolism, and glycolysis or gluconeogenesis, as well as changes in microbial community structure. Gut microbiota may participate in the mediation of systemic metabolomic changes in ACTH-induced depression model. Therefore, integrated metabolomic signatures and gut microbial community profiling would provide a basis for further studies on the pathogenesis of depression.},
}

@article {pmid31307469,
year = {2019},
author = {Huang, C and Shi, G},
title = {Smoking and microbiome in oral, airway, gut and some systemic diseases.},
journal = {Journal of translational medicine},
volume = {17},
number = {1},
pages = {225},
doi = {10.1186/s12967-019-1971-7},
pmid = {31307469},
issn = {1479-5876},
support = {81770025//National Natural Science Foundation of China/ ; },
abstract = {The human microbiome harbors a diverse array of microbes which establishes a mutually beneficial relation with the host in healthy conditions, however, the dynamic homeostasis is influenced by both host and environmental factors. Smoking contributes to modifications of the oral, lung and gut microbiome, leading to various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn's disease, ulcerative colitis and cancers. However, the exact causal relationship between smoking and microbiome alteration remains to be further explored.},
}

@article {pmid31304250,
year = {2017},
author = {You, X and Einson, JE and Lopez-Pena, CL and Song, M and Xiao, H and McClements, DJ and Sela, DA},
title = {Food-grade cationic antimicrobial ε-polylysine transiently alters the gut microbial community and predicted metagenome function in CD-1 mice.},
journal = {NPJ science of food},
volume = {1},
number = {},
pages = {8},
doi = {10.1038/s41538-017-0006-0},
pmid = {31304250},
issn = {2396-8370},
abstract = {Diet is an important factor influencing the composition and function of the gut microbiome, but the effect of antimicrobial agents present within foods is currently not understood. In this study, we investigated the effect of the food-grade cationic antimicrobial ε-polylysine on the gut microbiome structure and predicted metagenomic function in a mouse model. The relative abundances of predominant phyla and genera, as well as the overall community structure, were perturbed in response to the incorporation of dietary ε-polylysine. Unexpectedly, this modification to the gut microbiome was experienced transiently and resolved to the initial basal composition at the final sampling point. In addition, a differential non-random assembly was observed in the microbiomes characterized from male and female co-housed animals, although their perturbation trajectories in response to diet remain consistent. In conclusion, antimicrobial ε-polylysine incorporated into food systems transiently alters gut microbial communities in mice, as well as their predicted function. This indicates a dynamic but resilient microbiome that adapts to microbial-active dietary components.},
}

@article {pmid31306822,
year = {2019},
author = {Han, L and Cai, L and Zhang, H and Long, Z and Yu, Y and Fang, H},
title = {Development of antibiotic resistance genes in soils with ten successive treatments of chlortetracycline and ciprofloxacin.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {253},
number = {},
pages = {152-160},
doi = {10.1016/j.envpol.2019.07.031},
pmid = {31306822},
issn = {1873-6424},
abstract = {Antibiotic contamination caused by the long-term use of organic manure (OM) in greenhouse agricultural soils poses potential detrimental effects to the soil environment. By applying OM containing chlortetracycline (CTC) and/or ciprofloxacin (CIP) ten times in soil under laboratory conditions, we investigated the dissipation and accumulation characteristics of CTC and CIP in the soil, the changes in the microbial pollution-induced community tolerance (PICT), and the diversity and abundance of antibiotic resistance genes (ARGs) in the soil microbiome. The dissipation of CTC was rapid while CIP was accumulated in repeatedly treated soils; further, CIP could inhibit the dissipation of CTC. Meanwhile, the PICT to CTC and/or CIP significantly increased up to 15.0-fold after ten successive treatments compared to that in the first treatment. As the treatment frequency increased, significant upward trends in the abundances of tetracycline resistance genes tetA(G), tetX2, tetX, tetG, tetA(33), tetA, tetW, and tetA(P), fluoroquinolone resistance gene qnrA6, and multiple resistance gene mexF were revealed by both metagenomic and qPCR analyses. The findings demonstrated that repeated treatments with CTC and/or CIP can alter the dissipation rate, promote an increase in PICT to CTC and/or CIP, and increase the ARGs abundance in steps.},
}

@article {pmid31306584,
year = {2019},
author = {Fay, KT and Klingensmith, NJ and Chen, CW and Zhang, W and Sun, Y and Morrow, KN and Liang, Z and Burd, EM and Ford, ML and Coopersmith, CM},
title = {The gut microbiome alters immunophenotype and survival from sepsis.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {fj201802188R},
doi = {10.1096/fj.201802188R},
pmid = {31306584},
issn = {1530-6860},
abstract = {The microbiome is increasingly implicated in immune regulation and mortality from sepsis. Mice with identical genetic backgrounds but distinct microbiomes were obtained from different vendors and analyzed following cecal ligation and puncture (CLP). β diversity of the microbiome measured from feces demonstrated significant differences between The Jackson Laboratory (Jax; Bar Harbor, ME, USA) and Charles River Laboratories (CR; Wilmington, MA, USA) C57/B6 mice. Jax mice had 7-d mortality of 90% following CLP, whereas CR mice had a mortality of 53%. Differences in vendor were associated with altered immunophenotype with increased splenic IFN-γ+CD4+ T cells, effector memory CD4+ T cells, and central memory CD4+ T cells and increased Peyer's patch effector memory CD4+ T cells in septic CR mice. To determine whether differences in the microbiome were responsible for these differences, Jax and CR mice were cohoused for 3 wk, after which they assumed a similar microbiota composition. Cohoused mice had improved survival following CLP compared to Jax mice and had similar survival regardless of their vendor of origin. All differences in immunophenotype between septic Jax and CR mice disappeared following cohousing. These findings suggest that the microbiome plays a crucial role in survival and the host immune response from sepsis and represents a potential target for therapeutic intervention.-Fay, K. T., Klingensmith, N. J., Chen, C.-W., Zhang, W., Sun, Y., Morrow, K. N., Liang, Z., Burd, E. M., Ford, M. L., Coopersmith, C. M. The gut microbiome alters immunophenotype and survival from sepsis.},
}

@article {pmid31306512,
year = {2019},
author = {Xu, Q and Biancalana, M and Grant, JC and Chiu, HJ and Jaroszewski, L and Knuth, MW and Lesley, SA and Godzik, A and Elsliger, MA and Deacon, AM and Wilson, IA},
title = {Structures of single-layer β-sheet proteins evolved from β-hairpin repeats.},
journal = {Protein science : a publication of the Protein Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/pro.3683},
pmid = {31306512},
issn = {1469-896X},
support = {U54 GM094586/GM/NIGMS NIH HHS/United States ; },
abstract = {Free-standing single β-sheets are extremely rare in naturally occurring proteins, even though β-sheet motifs are ubiquitous. Here we report on crystal structures of three homologous, single-layer, anti-parallel β-sheet proteins, comprised of three or four twisted β-hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β-sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent-exposed tyrosine residues, was also identified on the concave surface of the β-sheet. These new modular single-layer β-sheet proteins may serve as a new model system for studying folding and design of β-rich proteins. This article is protected by copyright. All rights reserved.},
}

@article {pmid31306499,
year = {2019},
author = {Seabloom, EW and Condon, B and Kinkel, L and Komatsu, KJ and Lumibao, CY and May, G and McCulley, RL and Borer, ET},
title = {Effects of nutrient supply, herbivory, and host community on fungal endophyte diversity.},
journal = {Ecology},
volume = {},
number = {},
pages = {e02758},
doi = {10.1002/ecy.2758},
pmid = {31306499},
issn = {1939-9170},
support = {//National Science Foundation/ ; //University of Minnesota/ ; },
abstract = {The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across four mesic prairies in the central United States. Composition of fungal endophyte communities differed among sites and among individuals within a site, but was not consistently affected by experimental manipulation of nutrient supply to hosts (A. gerardii) or herbivore reduction via fencing. In contrast, mean fungal diversity was similar among sites but was limited by total plant biomass at the plot scale. Our work demonstrates that distributed experiments motivated by ecological theory are a powerful tool to unravel the multiscale processes governing microbial community composition and diversity.},
}

@article {pmid31305265,
year = {2019},
author = {Zaiss, MM and Jones, RM and Schett, G and Pacifici, R},
title = {The gut-bone axis: how bacterial metabolites bridge the distance.},
journal = {The Journal of clinical investigation},
volume = {130},
number = {},
pages = {},
doi = {10.1172/JCI128521},
pmid = {31305265},
issn = {1558-8238},
abstract = {The gut microbiome is a key regulator of bone health that affects postnatal skeletal development and skeletal involution. Alterations in microbiota composition and host responses to the microbiota contribute to pathological bone loss, while changes in microbiota composition that prevent, or reverse, bone loss may be achieved by nutritional supplements with prebiotics and probiotics. One mechanism whereby microbes influence organs of the body is through the production of metabolites that diffuse from the gut into the systemic circulation. Recently, short-chain fatty acids (SCFAs), which are generated by fermentation of complex carbohydrates, have emerged as key regulatory metabolites produced by the gut microbiota. This Review will focus on the effects of SCFAs on the musculoskeletal system and discuss the mechanisms whereby SCFAs regulate bone cells.},
}

@article {pmid31304222,
year = {2019},
author = {Nafarin, AR and Hegar, B and Sjakti, HA and Vandenplas, Y},
title = {Gut microbiome pattern in adolescents with functional gastrointestinal disease.},
journal = {International journal of pediatrics & adolescent medicine},
volume = {6},
number = {1},
pages = {12-15},
doi = {10.1016/j.ijpam.2019.01.005},
pmid = {31304222},
issn = {2352-6467},
abstract = {Background: Functional gastrointestinal disease (FGID) has a worldwide prevalence of 10-45%, and is one of the most common causes of recurrent abdominal pain in children. FGID is characterized with abdominal discomfort and changes in bowel movement. Alteration in gut microbiota is associated with FGID, but data are limited, and there are no data from Indonesia.

Methods: A case-control study was conducted in 22 FGID children and 28 healthy subjects aged 13-18 years at the junior high school and senior high school in Central Jakarta. FGID was diagnosed using Rome IV criteria. Age, sex, and level of education were recorded. Stool samples were collected and investigated for Bifidobacterium spp. and Enterobacteriaceae.

Results: Most of the FGID subjects were females (17/22), with a median age of 16 years. The median values of Bifidobacterium spp. were 138.95 (range: 0.2-22,735.8) CFU/gram for the FGID subjects and 232.5 (range: 1.9-38,985.6) CFU/gram in healthy subjects, which showed no statistically significant difference (P = .49). The median values of Enterobacteriaceae were 58.9 (range: 2.5-9577.8) CFU/gram in FGID subjects and 85 (range: 12.1-3139.4) CFU/gram in healthy subjects, which showed no statistically significant difference (P = .94). Our findings indicate that the gut microbiome of adolescents with FGIDs is characterized by a huge variability in levels of Bifidobacterium spp. and Enterobacteriaceae.

Conclusion: Because of the wide range detected in the number of Bifidobacterium spp. and Enterobacteriaceae in FGID and healthy subjects, no statistically significant difference was observed. More studies in larger groups of selected patients may be needed.},
}

@article {pmid31304220,
year = {2019},
author = {Almana, Y and Mohammed, R},
title = {Current concepts in pediatric inflammatory bowel disease; IL10/IL10R colitis as a model disease.},
journal = {International journal of pediatrics & adolescent medicine},
volume = {6},
number = {1},
pages = {1-5},
doi = {10.1016/j.ijpam.2019.02.002},
pmid = {31304220},
issn = {2352-6467},
abstract = {Inflammatory bowel disease (IBD) is a heterogeneous group of disorders composed mainly of ulcerative colitis (UC) and Crohn's disease (CD) and undetermined IBD. The peak incidence of occurrence is mainly beyond the pediatric age group. Recent knowledge about genetic factors had been strongly linked to pediatric IBD (PIBD). Recent advances in genomic technologies have prompted the identification of genetic defects underlying rare, very early-onset IBD (VEO-IBD) as a disease subgroup noted especially in populations with higher consanguinity rates. A better understanding of key players in the complex homeostasis of the immune system in the gut and illustrating the relationships between intestinal microbiome, systemic immune dysregulation and primary immunodeficiency have received growing recognition over the years. In this article, we provide a review of the key players of the immunity of the gut, compare between adult and pediatric IBD as an interesting module to investigate the relationship between monogenic and multifactorial/polygenic diseases, list genetic mutations confirmed to be linked to VEO IBD and summarize the scientific work that led to the discovery of one of the monogenic mutations related to infantile colitis, namely IL10 and IL10 receptor defects.},
}

@article {pmid31304012,
year = {2019},
author = {Canibe, N and O'Dea, M and Abraham, S},
title = {Potential relevance of pig gut content transplantation for production and research.},
journal = {Journal of animal science and biotechnology},
volume = {10},
number = {},
pages = {55},
doi = {10.1186/s40104-019-0363-4},
pmid = {31304012},
issn = {1674-9782},
abstract = {It is becoming increasingly evident that the gastrointestinal microbiota has a significant impact on the overall health and production of the pig. This has led to intensified research on the composition of the gastrointestinal microbiota, factors affecting it, and the impact of the microbiota on health, growth performance, and more recently, behavior of the host. Swine production research has been heavily focused on assessing the effects of feed additives and dietary modifications to alter or take advantage of select characteristics of gastrointestinal microbes to improve health and feed conversion efficiency. Research on faecal microbiota transplantation (FMT) as a possible tool to improve outcomes in pigs through manipulation of the gastrointestinal microbiome is very recent and limited data is available. Results on FMT in humans demonstrating the transfer of phenotypic traits from donors to recipients and the high efficacy of FMT to treat Clostridium difficile infections in humans, together with data from pigs relating GI-tract microbiota composition with growth performance has likely played an important role in the interest towards this strategy in pig production. However, several factors can influence the impact of FMT on the recipient, and these need to be identified and optimized before this tool can be applied to pig production. There are obvious inherent biosecurity and regulatory issues in this strategy, since the donor's microbiome can never be completely screened for all possible non-desirable microorganisms. However, considering the success observed in humans, it seems worth investigating this strategy for certain applications in pig production. Further, FMT research may lead to the identification of specific bacterial group(s) essential for a particular outcome, resulting in the development of banks of clones which can be used as targeted therapeutics, rather than the broader approach applied in FMT. This review examines the factors associated with the use of FMT, and its potential application to swine production, and includes research on using the pig as model for human medical purposes.},
}

@article {pmid31303990,
year = {2019},
author = {Thamban Chandrika, N and Fosso, MY and Alimova, Y and May, A and Gonzalez, OA and Garneau-Tsodikova, S},
title = {Novel zafirlukast derivatives exhibit selective antibacterial activity against Porphyromonas gingivalis.},
journal = {MedChemComm},
volume = {10},
number = {6},
pages = {926-933},
doi = {10.1039/c9md00074g},
pmid = {31303990},
issn = {2040-2511},
abstract = {Periodontal disease is an oral chronic immune-inflammatory disease highly prevalent worldwide that is initiated by specific oral bacterial species leading to local and systemic effects. The development of new preventive/therapeutic strategies to specifically target oral periodontopathogens without perturbing oral microbiome species normally colonizing the oral cavity is needed. The fast and affordable strategy of repositioning of already FDA-approved drugs can be an answer to the development of novel treatments against periodontal pathogens such as Porphyromonas gingivalis. Herein, we report the synthesis and antibacterial activity of novel zafirlukast derivatives, their bactericidal effect, and their cytotoxicity against oral epithelial cell lines. Many of these derivatives exhibited superior antibacterial activity against P. gingivalis compared to the parent drug zafirlukast. The most promising compounds were found to be selective against P. gingivalis and they were bactericidal in their activity. Finally, we demonstrated that these potent derivatives of zafirlukast provided a better safety profile against oral epithelial cells compared to zafirlukast.},
}

@article {pmid31303969,
year = {2019},
author = {Chen, T and Olsen, I},
title = {Porphyromonas gingivalis and its CRISPR-Cas system.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1638196},
doi = {10.1080/20002297.2019.1638196},
pmid = {31303969},
issn = {2000-2297},
abstract = {The clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated proteins (Cas) are immune systems in prokaryotes present in most Bacteria and Archaea. They provide adaptive immunity against foreign elements such as bacteriophages/viruses, plasmids and transposons. During immunization a small sequence of foreign DNA, a so-called spacer is integrated into the CRISPR locus in the host cell. Spacers are then transcribed into small RNA guides that direct cleavage of foreign DNA by Cas nucleases. Immunization through spacer acquisition is transferred vertically to the progeny. It is possible that this genetic immune system of bacteria participates in modulating the microbiome of 'chronic' periodontitis, in which Porphyromonas gingivalis has been identified as a keystone pathogen causing microbial dysbiosis. An in-depth review of our current knowledge on the CRISPR-Cas systems in P. gingivalis is given in this paper with the attempt to understand how this anaerobic bacterium may protect itself in the periodontal pocket where bacteriophages are abundant and even out-number bacteria.},
}

@article {pmid31303186,
year = {2019},
author = {Garcia-Mazcorro, JF and Ishaq, SL and Rodriguez-Herrera, MV and Garcia-Hernandez, CA and Kawas, JR and Nagaraja, TG},
title = {Review: Are there indigenous Saccharomyces in the digestive tract of livestock animal species? Implications for health, nutrition and productivity traits.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {1-9},
doi = {10.1017/S1751731119001599},
pmid = {31303186},
issn = {1751-732X},
abstract = {All livestock animal species harbour complex microbial communities throughout their digestive tract that support vital biochemical processes, thus sustaining health and productivity. In part as a consequence of the strong and ancient alliance between the host and its associated microbes, the gut microbiota is also closely related to productivity traits such as feed efficiency. This phenomenon can help researchers and producers develop new and more effective microbiome-based interventions using probiotics, also known as direct-fed microbials (DFMs), in Animal Science. Here, we focus on one type of such beneficial microorganisms, the yeast Saccharomyces. Saccharomyces is one of the most widely used microorganisms as a DFM in livestock operations. Numerous studies have investigated the effects of dietary supplementation with different species, strains and doses of Saccharomyces (mostly Saccharomyces cerevisiae) on gut microbial ecology, health, nutrition and productivity traits of several livestock species. However, the possible existence of Saccharomyces which are indigenous to the animals' digestive tract has received little attention and has never been the subject of a review. We for the first time provide a comprehensive review, with the objective of shedding light into the possible existence of indigenous Saccharomyces of the digestive tract of livestock. Saccharomyces cerevisiae is a nomadic yeast able to survive in a broad range of environments including soil, grass and silages. Therefore, it is very likely that cattle and other animals have been in direct contact with this and other types of Saccharomyces throughout their entire existence. However, to date, the majority of animal scientists seem to agree that the presence of Saccharomyces in any section of the gut only reflects dietary contamination; in other words, these are foreign organisms that are only transiently present in the gut. Importantly, this belief (i.e. that Saccharomyces come solely from the diet) is often not well grounded and does not necessarily hold for all the many other groups of microbes in the gut. In addition to summarizing the current body of literature involving Saccharomyces in the digestive tract, we discuss whether the beneficial effects associated with the consumption of Saccharomyces may be related to its foreign origin, though this concept may not necessarily satisfy the theories that have been proposed to explain probiotic efficacy in vivo. This novel review may prove useful for biomedical scientists and others wishing to improve health and productivity using Saccharomyces and other beneficial microorganisms.},
}

@article {pmid31302808,
year = {2019},
author = {Selvig, D and Piceno, Y and Terdiman, J and Zydek, M and Umetsu, SE and Balitzer, D and Fadrosh, D and Lynch, K and Lamere, B and Leith, T and Kassam, Z and Beck, K and Lewin, S and Ma, A and Somsouk, M and Lynch, SV and El-Nachef, N},
title = {Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-019-05715-2},
pmid = {31302808},
issn = {1573-2568},
abstract = {AIMS: This pilot study assessed the efficacy, safety, and microbiome dynamics of fecal microbiota transplantation (FMT) for patients with chronic pouchitis.

METHODS: A prospective open-label pilot study was performed at an academic center among pouchitis patients undergoing FMT. Patients received a minimum of a single FMT by pouchoscopy from healthy, screened donors. The primary outcome was clinical improvement in pouchitis assessed by patient survey at week 4. Secondary outcomes included decrease in total Pouchitis Disease Activity Index (PDAI) Score ≥ 3 at week 4, bowel movement frequency, ESR, CRP, fecal calprotectin, abdominal pain, and PDAI subscores including endoscopic and histologic changes. Stool samples were collected at baseline and 4 weeks post-FMT to assess bacterial microbiota using V4 16S rRNA sequencing.

RESULTS: Nineteen patients were enrolled; however, 1 patient was lost to follow-up. No patients had a major adverse event or escalation of therapy related to FMT. Total PDAI scores, endoscopic scores, and histologic scores did not decrease significantly post-FMT. However, there was a statistically significant improvement in bowel movement (BM) frequency (9.25-7.25 BM/day, p = 0.03) and trend for improvement in abdominal pain to improve post-FMT (p = 0.05). Bacterial microbiota profiling revealed no distinct community-level changes post-FMT, though a small number of specific bacterial taxa significantly differed in relative abundance.

CONCLUSIONS: A single FMT has a tolerable short-term safety profile and may be associated with a decrease in bowel movements in patients with chronic pouchitis; however, no robust endoscopic or histologic changes were observed.},
}

@article {pmid31302571,
year = {2019},
author = {Sacco, KA and Milner, JD},
title = {Gene-environment interactions in primary atopic disorders.},
journal = {Current opinion in immunology},
volume = {60},
number = {},
pages = {148-155},
doi = {10.1016/j.coi.2019.06.002},
pmid = {31302571},
issn = {1879-0372},
abstract = {Environmental factors modify disease presentation and severity in allergic disorders. Primary atopic disorders (PADs) are a heterogenous group of single gene disorders that lead to significant atopic and allergic disease manifestations. However, a number of these monogenic diseases have variable penetrance suggesting that gene-gene and/or gene-environment interactions could modulate the clinical phenotype. Environmental factors such as diet, the microbiome at the epithelial-environment interface, the presence and/or extent of infection, and psychologic stress can alter disease phenotypic expression of allergic diseases, and PADs provide discrete contexts in which to understand these influences. We outline how gene-environment interactions likely contribute to a variable penetrance and expressivity in PADs. Dietary modifications of both macronutrients and/or micronutrients alter T-cell metabolism and may influence effector T-cell function. The mucosal microbiome may affect local inflammation and may remotely influence regulatory elements, while psychologic stress can affect mast cell and other allergic effector cell function. Understanding gene-environment interactions in PADs can hopefully provide a foundation for interrogating gene-environment interactions to common allergic disorders, and also present opportunities for personalized interventions based on the altered pathways and environmental influences in affected individuals.},
}

@article {pmid31302570,
year = {2019},
author = {Stephen-Victor, E and Chatila, TA},
title = {Regulation of oral immune tolerance by the microbiome in food allergy.},
journal = {Current opinion in immunology},
volume = {60},
number = {},
pages = {141-147},
doi = {10.1016/j.coi.2019.06.001},
pmid = {31302570},
issn = {1879-0372},
support = {R01 AI126915/AI/NIAID NIH HHS/United States ; },
abstract = {The steep rise in the incidence and prevalence of food allergy (FA) in the last few decades have focused attention of environmental mechanisms which act to promote disease, chief among which is the microbiome. Recent studies have now established the presence of pathogenic dysbiosis in FA that could be precipitated by a variety of environmental insults, including among others antibiotic usage and mode of delivery, that act to subvert the immune regulatory response that enforce tolerance to dietary antigens. A key attribute of this dysbiosis is the loss of Clostridial bacterial species that act to promote the formation of food allergen-specific nascent regulatory T cells in the gut. Significantly, different immunoprotective commensal bacteria, including members of the Clostridiales and Bacteroidales orders act to induce the transcription factor RORγt in nascent Treg cells via an upstream MyD88-dependent mechanism to promote tolerance to dietary antigens. Activation of this axis is disrupted by the dysbiosis, and can be restored by treatment with therapeutic microbiota. These findings highlight the potential for novel microbiota-based approaches to the prevention and treatment of the FA epidemic.},
}

@article {pmid31302555,
year = {2019},
author = {Li, PD and Jeewon, R and Aruna, B and Li, HY and Lin, FC and Wang, HK},
title = {Metabarcoding reveals differences in fungal communities between unflooded versus tidal flat soil in coastal saline ecosystem.},
journal = {The Science of the total environment},
volume = {690},
number = {},
pages = {911-922},
doi = {10.1016/j.scitotenv.2019.06.473},
pmid = {31302555},
issn = {1879-1026},
abstract = {In the saline-affected ecosystem, fungi have huge potential to promote growth, induce disease resistance and enhance tolerance against salt-stress of host plants. Since areas of plowland are gradually decreasing, the reclamation of coastal saline lands could play a crucial role in maintaining agricultural productivity and crop security globally. Therefore, it is of great significance to explore the fungal diversity in the coastal saline ecosystem. Here, we collected saline soil samples from unflooded areas and tidal flat areas, the two typical distinct landforms in coastal saline ecosystems, and used ITS metabarcoding to depict the diversity of fungal communities. We found that fungal species evenness had a remarkably higher variation from the tidal flat compared to unflooded soil samples. Furthermore, we also confirmed that the fungal niches differentiation reports in the coastal saline ecosystem. Our ITS based DNA sequencing revealed that both unflooded and tidal flat soil were mainly composed of amplicon sequence variants (ASVs) belonging to Ascomycota (93.43% and 86.91% respectively). Based on our findings, understanding the associations and distinctions of fungal microbiome between unflooded soil and tidal flat could provide the basis for the development of reclamation in coastal saline lands.},
}

@article {pmid31302481,
year = {2019},
author = {Keerthisinghe, TP and Wang, M and Zhang, Y and Dong, W and Fang, M},
title = {Low-dose tetracycline exposure alters gut bacterial metabolism and host-immune response: "Personalized" effect?.},
journal = {Environment international},
volume = {131},
number = {},
pages = {104989},
doi = {10.1016/j.envint.2019.104989},
pmid = {31302481},
issn = {1873-6750},
abstract = {The human gut microbiome (GM) in healthy people is chronically exposed to tetracycline (TET) via environmental exposure and dietary uptake. However, limited information is available on its effect on the GM metabolome and effect on the host, especially at the dietary exposure level. Here, we investigated how TET at both sub-pharmaceutical and dietary exposure levels affects the metabolome and the secretome-induced host immune response by studying several representative gut bacteria. Interestingly, the metabolome showed a highly species-specific pattern with a distinct dose-response relationship. B. fragilis was highly sensitive to TET and vitamin, nucleotide, and amino acid metabolism pathways were the most vulnerable metabolic pathways at dietary exposure level. For key metabolite short chain fatty acids, TET significantly induced the synthesis of butyrate in B. fragilis, rather than C. sporogenes and E. coli. Furthermore, TET induced the release of lipopolysaccharides (LPS) in E. coli and enhanced the immune response; however, there was no obvious effect on B. fragilis. Interestingly, the overall immune response modulation with TET exposure relied on the ratio between E. coli and B. fragilis, possibly due to the neutralization of active LPS from E. coli by the LPS from B. fragilis. Overall, our results showed that the effect of TET from environmental exposure on the host health would be highly dependent on the GM composition, especially for the gut bacterial metabolome and secretome induced immune response.},
}

@article {pmid31302340,
year = {2019},
author = {Santamaria, F and Montella, S and Stocchero, M and Pirillo, P and Bozzetto, S and Giordano, G and Poeta, M and Baraldi, E},
title = {Effects of pidotimod and bifidobacteria mixture on clinical symptoms and urinary metabolomic profile of children with recurrent respiratory infections: A randomized placebo-controlled trial.},
journal = {Pulmonary pharmacology & therapeutics},
volume = {},
number = {},
pages = {101818},
doi = {10.1016/j.pupt.2019.101818},
pmid = {31302340},
issn = {1522-9629},
abstract = {BACKGROUND: Many preschool children develop recurrent respiratory tract infections (RRI). Strategies to prevent RRI include the use of immunomodulators as pidotimod or probiotics, but there is limited evidence of their efficacy on clinical features or on urine metabolic profile.

OBJECTIVE: To evaluate whether pidotimod and/or bifidobacteria can reduce RRI morbidity and influence the urine metabolic profile in preschool children.

MATERIALS AND METHODS: Children aged 3-6 years with RRI were enrolled in a four-arm, exploratory, prospective, randomized, double-blinded, placebo-controlled trial. Patients were randomly assigned to receive pidotimod plus bifidobacteria, pidotimod plus placebo, bifidobacteria plus placebo or double placebo for the first 10 days of each month over 4 consecutive months. Respiratory symptoms and infections were recorded with a daily diary by parents during the study. Metabolomic analyses on urine samples collected before and after treatment were performed.

RESULTS: Compared to placebo, children receiving pidotimod, alone or with bifidobacteria, had more symptom-free days (69 versus 44, p = 0.003; and 65 versus 44, p = 0.02, respectively) and a lower percentage of days with common cold (17% versus 37%, p = 0.005; and 15% versus 37%, p = 0.004, respectively). The metabolomic analysis showed that children treated with Pidotimod (alone or in combination with bifidobacteria) present, respect to children treated with placebo, a biochemical profile characterized by compounds related to the pathway of steroids hormones, hippuric acid and tryptophan. No significant difference in the metabolic profile was found between children receiving bifidobacteria alone and controls.

CONCLUSIONS: Preschool children with RRI treated with pidotimod have better clinical outcomes and a different urine metabolomic profile than subjects receiving placebo. Further investigations are needed to clarify the connection between pidotimod and gut microbiome.},
}

@article {pmid31302235,
year = {2019},
author = {Wallace, IJ and Bendele, AM and Riew, G and Frank, EH and Hung, HH and Holowka, NB and Bolze, AS and Venable, EM and Yegian, A and Dingwall, HL and Carmody, RN and Grodzinsky, AJ and Lieberman, DE},
title = {Physical inactivity and knee osteoarthritis in guinea pigs.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2019.07.005},
pmid = {31302235},
issn = {1522-9653},
abstract = {OBJECTIVE: To investigate whether and how a sedentary lifestyle contributes to knee osteoarthritis (OA) incidence and severity.

DESIGN: An experiment was conducted using Hartley guinea pigs, an established idiopathic knee OA model. To simulate a sedentary lifestyle, growing animals (n=18) were housed for 22 weeks in small cages that restricted their mobility, while another group of animals (n=17) received daily treadmill exercise to simulate moderate physical activity. After the experiment, histological assessments, biochemical assays, and mechanical testing were conducted to compare tibial articular cartilage structure, strength, and degree of OA degeneration between sedentary and physically active animals. Groups were also compared based on body weight and composition, as well as gut microbial communities assessed using fecal 16S rRNA gene sequencing.

RESULTS: Prevalence of knee OA was similar between sedentary and physically active animals, but severity of the disease (cartilage lesion depth) was substantially greater in the sedentary group (p=0.02). In addition, during the experiment, sedentary animals developed cartilage with lower aggrecan quantity (p=0.03) and accumulated more body weight (p=0.005) and visceral adiposity (p=0.007). Groups did not differ greatly, however, in terms of cartilage thickness, collagen quantity, or stiffness, nor in terms of muscle weight, subcutaneous adiposity, or gut microbiome composition.

CONCLUSIONS: Our findings indicate that a sedentary lifestyle promotes the development of knee OA, particularly by enhancing disease severity rather than risk of onset, and this potentially occurs through multiple pathways including by engendering growth of functionally deficient joint tissues and the accumulation of excess body weight and adiposity.},
}

@article {pmid31302202,
year = {2019},
author = {Ezzy, AC and Hagstrom, AD and George, C and Hamlin, AS and Pereg, L and Murphy, AJ and Winter, G},
title = {Storage and handling of human faecal samples affect the gut microbiome composition: A feasibility study.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {105668},
doi = {10.1016/j.mimet.2019.105668},
pmid = {31302202},
issn = {1872-8359},
abstract = {Human gut microbiome analysis through faecal sampling typically involves five stages: sample collection, storage, DNA extraction, next generation sequencing and bioinformatics analysis. Of these, the first three are considered irreversible. This feasibility study describes an assessment of methodologies used for faecal DNA extraction and sample handling, using the parameters DNA yield, purity and resultant microbial profile. Six DNA extraction techniques, including commercially available kits and manual protocols were compared on human faecal samples (n = 3). Different extraction techniques produced significant variance in DNA yield (range 2.7-164 ng/mg faeces) and microbial diversity profiles, with considerable variation in phyla dominance (Firmicutes (P < 0.001), Bacteroidetes (P = 0.003), Actinobacteria (P = 0.003), One-way ANOVA). The most effective method, with the highest DNA yield, was a simple and inexpensive extraction technique named MetaHIT. Using this method, DNA was extracted from separate faecal samples (n = 3) and had been aliquoted to seven storage conditions including three stabilizing buffers and three temperature conditions, for a period of 120-h, with storage at -80 °C as a control treatment. DNA yield and purity was not statistically different between the control and remaining treatments. 16S rDNA-based diversity profile was largely comparable across the treatments with only minor differences in genera between samples stored at room temperature in air and - 80 °C control. Overall these results suggest that the choice of DNA extraction method has a greater influence on the resultant microbial diversity profile than the short-term storage method.},
}

@article {pmid31301989,
year = {2019},
author = {Becker, F and Gavins, FNE and Fontenot, J and Jordan, P and Yun, JY and Scott, R and Polk, PR and Friday, RE and Boktor, M and Musso, M and Romero, E and Boudreaux, S and Simmons, J and Hasselschwert, DL and Goetzmann, JE and Vanchiere, J and Cvek, U and Trutschl, M and Kilgore, P and Alexander, JS},
title = {Dynamic gut microbiome changes following regional intestinal lymphatic obstruction in primates.},
journal = {Pathophysiology : the official journal of the International Society for Pathophysiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pathophys.2019.06.004},
pmid = {31301989},
issn = {0928-4680},
abstract = {The pathogenesis of inflammatory bowel disease (IBD) has been linked with lymphostasis, but whether and how lymphatic obstruction might disturb the intestinal microbiome in the setting of Crohn's Disease (CD) is currently unknown. We employed a new model of CD in African Green monkeys, termed 'ATLAS' (African green monkey truncation of lymphatics with obstruction and sclerosis), to evaluate how gut lymphatic obstruction alters the intestinal microbiome at 7, 21 and 61 days. Remarkable changes in several microbial sub- groupings within the gut microbiome were observed at 7 days post-ATLAS compared to controls including increased abundance of Prevotellaceae and Bacteroidetes-Prevotella-Porphyromonas (BPP), which may contribute to disease activity in this model of gut injury. To the best of our knowledge, these findings represent the first report linking lymphatic structural/gut functional changes with alterations in the gut microbiome as they may relate to the pathophysiology of CD.},
}

@article {pmid31301692,
year = {2019},
author = {Stanton, DE and Batterman, SA and Von Fischer, J and Hedin, LO},
title = {Rapid nitrogen fixation by canopy microbiome in tropical forest determined by both phosphorus and molybdenum.},
journal = {Ecology},
volume = {},
number = {},
pages = {e02795},
doi = {10.1002/ecy.2795},
pmid = {31301692},
issn = {1939-9170},
abstract = {Biological nitrogen fixation is critical for the nitrogen cycle of tropical forests, yet we know little about the factors that control the microbial nitrogen-fixers that colonize the microbiome of leaves and branches that make up a forest canopy. Forest canopies are especially prone to nutrient limitation because they are (1) disconnected from soil nutrient pools, and (2) often subject to leaching. Earlier studies have suggested a role of phosphorus and molybdenum in controlling biological N-fixation rates, but experimental confirmation has hitherto been unavailable. We here present the results of a manipulation of canopy nutrient availability. Our findings demonstrate a primary role of phosphorus in constraining overall N-fixation by canopy cyanobacteria, but also a secondary role of molybdenum in determining per-cell fixation rates. A conservative evaluation suggests that canopy fixation can contribute to significant N fluxes at the ecosystem level, especially as bursts following atmospheric inputs of nutrient-rich dust. This article is protected by copyright. All rights reserved.},
}

@article {pmid31301494,
year = {2019},
author = {Taboada-Santos, A and Braz, GHR and Fernandez-Gonzalez, N and Carballa, M and Lema, JM},
title = {Thermal hydrolysis of sewage sludge partially removes organic micropollutants but does not enhance their anaerobic biotransformation.},
journal = {The Science of the total environment},
volume = {690},
number = {},
pages = {534-542},
doi = {10.1016/j.scitotenv.2019.06.492},
pmid = {31301494},
issn = {1879-1026},
abstract = {Pretreatment technologies prior to anaerobic digestion (AD) have been developed with the aim of enhancing biogas productivity and reducing the presence of pathogens in digested sludge. Among them, thermal hydrolysis (TH) appears as the most promising one. In wastewater treatment plants (WWTPs) sludge is the end point of many organic micropollutants (OMPs), which was proved to lead to important environmental and human risks since sludge is commonly used in agriculture. The objective of this work is to determine the fate OMPs in TH and subsequent AD. Sewage sludge was pretreated in a TH pilot plant at 170 °C for 20 min. Afterwards, two anaerobic digesters with a working volume of 14 L fed with fresh and pretreated sludge were operated in parallel in mesophilic conditions. TH proved to be an effective technology to partially or totally remove the dissolved fraction of OMPs as well as the fraction sorbed into those suspended solids that are solubilised after this pretreatment. However, it did not affect the OMPs sorbed concentration into solids that are not solubilised. Globally, the OMPs removal efficiency during TH appears to be linked to the solids solubilisation during this process. Afterwards, the OMPs biotransformation efficiency in AD of fresh and pretreated sludge was determined. Noticeable differences between the microbiome of both reactors was determined, but the anaerobic biotransformation was not substantially different for most of the OMPs. However, it affected musk fragrances, which presented considerably lower biotransformation efficiency in the reactor fed with pretreated sludge. Therefore, TH was proved effective in partially removing OMPs but not in enhancing their bioavailability and subsequent anaerobic biotransformation.},
}

@article {pmid31301451,
year = {2019},
author = {Allegretti, JR and Kassam, Z and Mullish, BH and Chiang, A and Carrellas, M and Hurtado, J and Marchesi, JR and McDonald, JAK and Pechlivanis, A and Barker, GF and Blanco, JM and Garcia-Perez, I and Wong, WF and Gerardin, Y and Silverstein, M and Kennedy, K and Thompson, C},
title = {Effects of Fecal Microbiota Transplantation With Oral Capsules in Obese Patients.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2019.07.006},
pmid = {31301451},
issn = {1542-7714},
abstract = {BACKGROUND & AIMS: Studies in mice have shown that the intestinal microbiota can contribute to obesity via the anorexigenic gut hormone glucagon-like peptide 1 (GLP1) and bile acids, which affect lipid metabolism. We performed a randomized, placebo-controlled pilot study of the effects of fecal microbiota transplantation (FMT) in obese, metabolically uncompromised patients.

METHODS: We performed a double-blind study of 22 obese patients (body mass index [BMI] ≥ 35kg/m2) without a diagnosis of diabetes, non-alcoholic steatohepatitis, or metabolic syndrome. Participants were randomly assigned (1:1) to groups that received FMT by capsules (induction dose of 30 capsules at week 4 and maintenance dose of 12 capsules at week 8) or placebo capsules. FMT capsules were derived from a single, lean donor (BMI, 17.5 kg/m2). Patients were followed through week 26; the primary outcome was safety. Stool and serum samples were collected from patients at baseline and at weeks 1, 4, 6, 8 and 12 after administration of the first dose of FMT or placebo and analyzed by 16S RNA gene sequencing. Stool and serum samples were analyzed for metabolomics by liquid chromatography-mass spectrometry. Additional outcomes were change in area under the curve for GLP1 at week 12.

RESULTS: We observed no significant differences in adverse events between patients who received FMT vs placebo. There was no increase in the area under the curve of GLP1 in either group. Patients who received FMT had sustained shifts in microbiomes associated with obesity toward those of the donor (P<.001). Patients who received FMT had a sustained decrease in stool levels of taurocholic acid (P<.05), compared with baseline; bile acid profiles began to more closely resemble those of the donor. We did not observe significant changes in mean BMI at week 12 in either group.

CONCLUSIONS: In a placebo-controlled pilot study, we found that FMT capsules (derived from a lean donor) were safe but did not reduce BMI in obese metabolically uncompromised patients. The FMT capsules were well tolerated and led to sustained changes in the intestinal microbiome and bile acid profiles that were similar to those of the lean donor.},
}

@article {pmid31301372,
year = {2019},
author = {Lowe, AJ and Wang, X and Mueller, JF and Abramson, MJ and Yeh, RY and Erbas, B and Dharmage, SC and Lodge, CJ},
title = {Exposure to breast-milk triclosan and parabens and eczema phenotypes at 12-months: a nested case-control study.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2019.07.001},
pmid = {31301372},
issn = {1097-6825},
abstract = {Levels of butyl-paraben in breastmilk at three months were associated with increased risk of atopic-eczema at 12 months of age, potentially due to altered gut microbiome.},
}

@article {pmid31301059,
year = {2019},
author = {Lew, LC and Hor, YY and Jaafar, MH and Lau, AS and Khoo, BY and Sasidharan, S and Choi, SB and Ong, KL and Kato, T and Nakanishi, Y and Ohno, H and Liong, MT},
title = {Effects of Potential Probiotic Strains on the Fecal Microbiota and Metabolites of D-Galactose-Induced Aging Rats Fed with High-Fat Diet.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12602-019-09545-6},
pmid = {31301059},
issn = {1867-1314},
support = {URICAS grant (1001/ PTEKIND/870030)//Universiti Sains Malaysia/ ; },
abstract = {Both aging and diet play an important role in influencing the gut ecosystem. Using premature senescent rats induced by D-galactose and fed with high-fat diet, this study aims to investigate the effects of different potential probiotic strains on the dynamic changes of fecal microbiome and metabolites. In this study, male Sprague-Dawley rats were fed with high-fat diet and injected with D-galactose for 12 weeks to induce aging. The effect of Lactobacillus plantarum DR7, L. fermentum DR9, and L. reuteri 8513d administration on the fecal microbiota profile, short-chain fatty acids, and water-soluble compounds were analyzed. It was found that the administration of the selected strains altered the gut microbiota diversity and composition, even at the phylum level. The fecal short-chain fatty acid content was also higher in groups that were administered with the potential probiotic strains. Analysis of the fecal water-soluble metabolites revealed that administration of L. plantarum DR7 and L. reuteri 8513d led to higher fecal content of compounds related to amino acid metabolism such as tryptophan, leucine, tyrosine, cysteine, methionine, valine, and lysine; while administration of L. fermentum DR9 led to higher prevalence of compounds related to carbohydrate metabolism such as erythritol, xylitol, and arabitol. In conclusion, it was observed that different strains of lactobacilli can cause difference alteration in the gut microbiota and the metabolites, suggesting the urgency to explore the specific metabolic impact of specific strains on the host.},
}

@article {pmid31301004,
year = {2019},
author = {Li, JKM and Chiu, PKF and Ng, CF},
title = {The impact of microbiome in urological diseases: a systematic review.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11255-019-02225-y},
pmid = {31301004},
issn = {1573-2584},
abstract = {OBJECTIVE: The term microbiome is used to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space, in which there were increasing evidences to suggest that they might have potential roles in various medical conditions. While the study of microbiome in the urinary system is not as robust as the systems included in the Human Microbiome Project, there are still evidences in the literature showing that microbiome may have a role in urological diseases. Therefore, we would like to perform a systematic review on the topic and summarize the available evidence on the impact of microbiome on urological diseases.

METHODOLOGY: This review was performed according to the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) statement. After screening 589 abstracts and including additional studies (such as references from review papers), 76 studies were included for review and discussion.

RESULTS: Studies had suggested that there were correlations of microbiome of different body cavities (e.g., fecal, urinary and seminal fluid) with urological diseases. Also, different diseases would have different microbiome profile in different body cavities. Unfortunately, the studies on the association of microbiome and urological diseases were still either weak or inconsistent.

CONCLUSION: Studies suggested that there might be some relationship between microbiome and various urological diseases. However, further large-scale studies with control of confounding factors should be performed under a standardized methodology in order to have better understanding of the relationship. Also, more standardized reporting protocol for microbiome studies should be considered for better communications in future studies.},
}