@article {pmid31412298,
year = {2019},
author = {Mahomoodally, MF and Aumeeruddy, MZ and Rengasamy, KRR and Roshan, S and Hammad, S and Pandohee, J and Hu, X and Zengin, G},
title = {Ginger and its Active Compounds in Cancer Therapy: From Folk uses to Nano-therapeutic Applications.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2019.08.009},
pmid = {31412298},
issn = {1096-3650},
abstract = {Ginger is a spice that is renowned for its characteristic aromatic fragrance and pungent taste, with documented healing properties. Field studies conducted in several Asian and African countries revealed that ginger is used traditionally in the management of cancer. The scientific community has probed into the biological validation of its extracts and isolated compounds including the gingerols, shogaols, zingiberene, and zingerone, through in-vitro and in-vivo studies. Nonetheless, an updated compilation of these data together with a deep mechanistic approach is yet to be provided. Accordingly, this review highlights the mechanisms and therapeutics of ginger and its bioactive compounds focused on a cancer context and these evidence are based on the (i) cytotoxic effect against cancer cell lines, (ii) enzyme inhibitory action, (iii) combination therapy with chemotherapeutic and phenolic compounds, (iv) possible links to the microbiome and (v) the use of nano-formulations of ginger bioactive compounds as a more effective drug delivery strategy in cancer therapy.},
}

@article {pmid31412243,
year = {2019},
author = {Huggins, MA and Sjaastad, FV and Pierson, M and Kucaba, TA and Swanson, W and Staley, C and Weingarden, AR and Jensen, IJ and Danahy, DB and Badovinac, VP and Jameson, SC and Vezys, V and Masopust, D and Khoruts, A and Griffith, TS and Hamilton, SE},
title = {Microbial Exposure Enhances Immunity to Pathogens Recognized by TLR2 but Increases Susceptibility to Cytokine Storm through TLR4 Sensitization.},
journal = {Cell reports},
volume = {28},
number = {7},
pages = {1729-1743.e5},
doi = {10.1016/j.celrep.2019.07.028},
pmid = {31412243},
issn = {2211-1247},
abstract = {Microbial exposures can define an individual's basal immune state. Cohousing specific pathogen-free (SPF) mice with pet store mice, which harbor numerous infectious microbes, results in global changes to the immune system, including increased circulating phagocytes and elevated inflammatory cytokines. How these differences in the basal immune state influence the acute response to systemic infection is unclear. Cohoused mice exhibit enhanced protection from virulent Listeria monocytogenes (LM) infection, but increased morbidity and mortality to polymicrobial sepsis. Cohoused mice have more TLR2+ and TLR4+ phagocytes, enhancing recognition of microbes through pattern-recognition receptors. However, the response to a TLR2 ligand is muted in cohoused mice, whereas the response to a TLR4 ligand is greatly amplified, suggesting a basis for the distinct response to Listeria monocytogenes and sepsis. Our data illustrate how microbial exposure can enhance the immune response to unrelated challenges but also increase the risk of immunopathology from a severe cytokine storm.},
}

@article {pmid31412070,
year = {2019},
author = {Arizza, V and Vecchioni, L and Caracappa, S and Sciurba, G and Berlinghieri, F and Gentile, A and Persichetti, MF and Arculeo, M and Alduina, R},
title = {New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220329},
doi = {10.1371/journal.pone.0220329},
pmid = {31412070},
issn = {1932-6203},
abstract = {Caretta caretta is the most common sea turtle species in the Mediterranean Sea. The species is threatened by anthropomorphic activity that causes thousands of deaths and hundreds of strandings along the Mediterranean coast. Stranded turtles are often cared for in rehabilitation centres until they recover or die. The objective of this study was to characterize the gut microbiome of nine sea turtles stranded along the Sicilian coast of the Mediterranean Sea using high-throughput sequencing analysis targeting V3-V4 regions of the bacterial 16S rRNA gene. Stool samples were collected from eight specimens hosted in the recovery centre after a few days of hospitalization (under 7) and from one hosted for many weeks (78 days). To better explore the role of bacterial communities in loggerhead sea turtles, we compared our data with published fecal microbiomes from specimens stranded along the Tuscan and Ligurian coast. Our results highlight that, despite the different origin, size and health conditions of the animals, Firmicutes, Bacteroidetes and Proteobacteria constitute the main components of the microbiota. This study widens our knowledge on the gut microbiome of sea turtles and could be helpful for the set up of rehabilitation therapies of stranded animals after recovery in specialized centres.},
}

@article {pmid31412044,
year = {2019},
author = {Hyde, J and Gorham, C and Brackney, DE and Steven, B},
title = {Antibiotic resistant bacteria and commensal fungi are common and conserved in the mosquito microbiome.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0218907},
doi = {10.1371/journal.pone.0218907},
pmid = {31412044},
issn = {1932-6203},
abstract = {The emerging and increasing prevalence of bacterial antibiotic resistance is a significant public health challenge. To begin to tackle this problem, it will be critical to not only understand the origins of this resistance but also document environmental reservoirs of antibiotic resistance. In this study we investigated the possibility that both colony and field caught mosquitoes could harbor antibiotic resistant bacteria. Specifically, we characterized the antibiotic resistant bacterial populations from colony-reared Aedes aegypti larvae and adults and two field caught mosquito species Coquillettidia perturbans and Ochlerotatus canadensis. The cultured bacterial populations were dominated by isolates belonging to the class Gammaproteobacteria. Among the antibiotic resistant populations, we found bacteria resistant to carbenicillin, kanamycin, and tetracycline, including bacteria resistant to a cocktail of all three antibiotics in combination. The antibiotic resistant bacteria were numerically rare, at most 5% of total cell counts. Isolates were characterized by 16S rRNA gene sequencing, and clustering into Operational Taxonomic Units (OTUs; 99% sequence identity). 27 antibiotic resistant OTUs were identified, although members of an OTU did not always share the same resistance profile. This suggests the clustering was either not sensitive enough to distinguish different bacteria taxa or different antibiotic resistant sub-populations exist within an OTU. Finally, the antibiotic selection opened up a niche to culture mosquito-associated fungi, and 10 fungal OTUs (28S rRNA gene sequencing) were identified. Two fungal OTUs both classified to the class Microbotryomycetes were commonly identified in the field-caught mosquitoes. Thus, in this study we demonstrate that antibiotic resistant bacteria and certain fungi are common and conserved mosquito microbiome members. These observations highlight the potential of invertebrates to serve as vehicles for the spread of antibiotic resistance throughout the environment.},
}

@article {pmid31411526,
year = {2019},
author = {Peng, M and Tabashsum, Z and Patel, P and Bernhardt, C and Biswas, C and Meng, J and Biswas, D},
title = {Prevention of enteric bacterial infections and modulation of gut microbiota with conjugated linoleic acids producing Lactobacillus in mice.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/19490976.2019.1638724},
pmid = {31411526},
issn = {1949-0984},
abstract = {Probiotics are recognized for outcompeting pathogenic bacteria by competitive receptor-mediated colonization and secretion of functional metabolites which are antimicrobial against certain microbes as well as improving host's gut health and immunity. Recently, we have constructed a bioactive Lactobacillus casei (LC) strain, LC+mcra, by inserting mcra (myosin cross-reactive antigen) gene, which stimulates the conversion of conjugated linoleic acids. In this study, we evaluated the modulation of gut microbiome and protective roles of LC+mcra against pathogenic Salmonella enterica serovar Typhimurium (ST) and enterohemorrhagic E. coli (EHEC) infections in BALB/cJ mice. We observed that LC+mcra colonized efficiently in mice gut intestine and competitively reduced the infection with ST and EHEC in various locations of small and large intestine, specifically cecum, jejunum, and ileum (p < 0.05). Positive modulation of the cecal microbiota, for example, higher relative abundances of Firmicutes, lower relative abundances of Proteobacteria, and increased bacterial species diversity/richness, was detected in ST-challenged mice pretreated with LC+mcra based on 16S metagenomic sequencing. Cytokine gene expression analysis indicated that mice pretreated with LC+mcra associated with attenuated bacterial pathogen-induced gut inflammation. Furthermore, mice fed daily with LC+mcra for one week could protect themselves from the impairments caused by enteric infections with ST or EHEC. These impairments include weight loss, negative hematological changes, intestinal histological alterations, and potential death. This in vivo study suggests that daily consumption of novel conjugated linoleic acids over-producing probiotic effectively improves intestinal microbiota composition and prevents/combats foodborne enteric bacterial infections with pathogenic Salmonella and diarrheagenic E. coli.},
}

@article {pmid31411007,
year = {2019},
author = {Zhu, YX and Song, ZR and Song, YL and Zhao, DS and Hong, XY},
title = {The microbiota in spider mite faeces potentially reflects intestinal bacterial communities in the host.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.12716},
pmid = {31411007},
issn = {1744-7917},
abstract = {Microorganisms provide many physiological functions to herbivorous hosts. Spider mites (genus Tetranychus) are important agricultural pests throughout the world, however, the composition of spider mite microbial community, especially gut microbiome, remains unclear. Here, we investigated the bacterial community in five spider mite species and their associated faeces by deep sequencing of the 16S rRNA gene. The composition of the bacterial community was significantly different among the five prevalent spider mite species, and some bacterial symbionts showed host-species specificity. Moreover, the abundance of the bacterial community in spider mite faeces was significantly higher than that in the corresponding spider mite samples. However, Flavobacterium was detected in all samples, and represent a "core microbiome". Remarkably, the maternally inherited endosymbiont Wolbachia was detected in both spider mite and faeces. Overall, these results offer insight into the complex community of symbionts in spider mites, and give a new direction for future studies. This article is protected by copyright. All rights reserved.},
}

@article {pmid31410991,
year = {2019},
author = {Reza, MM and Finlay, BB and Pettersson, S},
title = {Gut microbes, ageing & organ function: a chameleon in modern biology?.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {e9872},
doi = {10.15252/emmm.201809872},
pmid = {31410991},
issn = {1757-4684},
support = {//School of Biological Sciences, Nanyang Technological University (NTU), Singapore/ ; //Lee Kong Chian School of Medicine, NTU, Singapore/ ; //Ageing Research Institute for Society and Education (ARISE), NTU, Singapore/ ; //Singapore Centre for Environmental Life Sciences Engineering (SCELSE), NTU, Singapore/ ; //NUHS Centre for Healthy Ageing, Singapore CSIRO, Australia/ ; //Bruker, USA/ ; },
abstract = {All species, including humans, are cohabited by a myriad of microbial species, which massively influences body function in a diet-, exercise- and age-dependent manner. The microbiome composition differs between individuals, partly due to the polymorphic immune system, as well as the environment, making the microbe-host interplay unique in each one of us. Ageing is a gradual loss of function in part due to reduced repair mechanisms and accumulation of tissue damage through mechanisms largely unknown. Accumulating evidence suggests that our indigenous microbes, a known major regulator of human physiology, are also connected to regulate the ageing process through signalling pathways and metabolites though the biological mechanisms are unknown. At an ageing meeting in Singapore in 2018, investigators discussed the current understanding of microbe regulation and its impact on healthy ageing. This review summarizes the highlights from the meeting and conveys some of the new ideas that emerged around gut microbes and the biology of ageing. While highly speculative, an idea emerged in which gut microbes constantly respond and evolve to environmental cues, as part of an ageing process, thus serving as a second messenger to support and attenuate organ decline in a diet-, gender- and age-dependent manner.},
}

@article {pmid31410749,
year = {2019},
author = {Zhang, F and Wang, M and Yang, J and Xu, Q and Liang, C and Chen, B and Zhang, J and Yang, Y and Wang, H and Shang, Y and Wang, Y and Mu, X and Zhu, D and Zhang, C and Yao, M and Zhang, L},
title = {Response of gut microbiota in type 2 diabetes to hypoglycemic agents.},
journal = {Endocrine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12020-019-02041-5},
pmid = {31410749},
issn = {1559-0100},
abstract = {PURPOSE: Accumulated evidence has indicated that the gut microbiome affected the pharmacology of anti-diabetic agents, and their metabolic products induced by the agents transformed the structure of gastrointestinal microbiota in return. However, the studies around heredity, ethnicity, or living condition, referring to human microbiome were mostly represented by an occidental pattern partial and rare studies that focused on the effect of several first-line hypoglycemic agents on the gut flora in a single medical center. Therefore, we aimed to explore the interaction between gut microbiome and type 2 diabetes (T2D) or hypoglycemics in Chinese population.

METHODS: A total of 130 T2D patients with a specific hypoglycemic treatment and 50 healthy volunteers were enrolled in this study. Gut microbiome compositons were analyzed by 16S ribosomal RNA gene-based sequencing protocol.

RESULTS: Hypoglycemic agents contributed to the alteration of specific species in gut bacteria rather than its total diversity. Metformin increased the abundance of Spirochaete, Turicibacter, and Fusobacterium. Insulin also increased Fusobacterium, and α-glucosidase inhibitors (α-GIs) contributed to the plentitude of Bifidobacterium and Lactobacillus. Both metformin and insulin improved taurine and hypotaurine metabolism, and α-GI promoted several amino acid pathways. Although the community of gut microbiota with metformin and insulin showed similarity, significant differences were available in each diabetic group with hypoglycemia.

CONCLUSIONS: Gut microbiota is significantly associated with anti-diabetic agents. The gut microbiome and metabolism have shown respective characteristics in different T2D groups, which were also significantly different from the healthy group. This study provides some new insights for identification and exploration of the pathogenesis of T2D.},
}

@article {pmid31410046,
year = {2019},
author = {Ribaldone, DG and Pellicano, R and Actis, GC},
title = {Inflammation in gastrointestinal disorders: prevalent socioeconomic factors.},
journal = {Clinical and experimental gastroenterology},
volume = {12},
number = {},
pages = {321-329},
doi = {10.2147/CEG.S210844},
pmid = {31410046},
issn = {1178-7023},
abstract = {Western populations harbor a chronic inflammation pattern that lacks organ cardinal signs (edema, increased temperature, pain, and impaired function), releases increased levels of C-reactive protein, and often runs a creeping clinical course with generalized debilitating disease superimposed on system-specific involvement, mostly including nervous tissue (multiple sclerosis, Parkinson's syndromes), joints (arthritis), and skin (psoriasis). A finalistic interpretation may apply to the consideration of the gut as the source of inflammation. In fact, these kind of local events as well as the remote manifestations named above, could be conditioned by the microbiome, the huge cell population indwelling the gut which is under growing scrutiny. The role of the gut as a barrier organ justifies lingering submucosal inflammation as a patrolling activity to maintain bodily integrity; the microbiome, launching inflammogenic signals in response to abrupt diet changes, confers to gut inflammation a socioeconomic vector calling for hitherto unrecognized multi-disciplinary interventions.},
}

@article {pmid31409870,
year = {2019},
author = {Swe, PM and Zakrzewski, M and Waddell, R and Sriprakash, KS and Fischer, K},
title = {High-throughput metagenome analysis of the Sarcoptes scabiei internal microbiota and in-situ identification of intestinal Streptomyces sp.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11744},
doi = {10.1038/s41598-019-47892-0},
pmid = {31409870},
issn = {2045-2322},
support = {1098804//Department of Health | National Health and Medical Research Council (NHMRC)/ ; FT130101875//Centre of Excellence for Electromaterials Science, Australian Research Council (ARC Centre of Excellence for Electromaterials Science)/ ; },
abstract = {Multiple parasitic arthropods of medical importance depend on symbiotic bacteria. While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of Sarcoptes scabiei. Here we analyze adult female mite and egg metagenome datasets. The majority of adult mite bacterial reads matched with Enterobacteriaceae (phylum Proteobacteria), followed by Corynebacteriaceae (phylum Actinobacteria). Klebsiella was the most dominant genus (78%) and Corynebacterium constituted 9% of the assigned sequences. Scabies mite eggs had a more diverse microbial composition with sequences from Proteobacteria being the most dominant (75%), while Actinobacteria, Bacteroidetes and Firmicutes accounted for 23% of the egg microbiome sequences. DNA sequences of a potential endosymbiont, namely Streptomyces, were identified in the metagenome sequence data of both life stages. The presence of Streptomyces was confirmed by conventional PCR. Digital droplet PCR indicated higher Streptomyces numbers in adult mites compared to eggs. Streptomyces were localized histologically in the scabies mite gut and faecal pellets by Fluorescent In Situ Hybridization (FISH). Streptomyces may have essential symbiotic roles in the scabies parasite intestinal system requiring further investigation.},
}

@article {pmid31409863,
year = {2019},
author = {Pereira, EM and de Mattos, CS and Dos Santos, OC and Ferreira, DC and de Oliveira, TLR and Laport, MS and de Oliveira Ferreira, E and Dos Santos, KRN},
title = {Staphylococcus hominis subspecies can be identified by SDS-PAGE or MALDI-TOF MS profiles.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11736},
doi = {10.1038/s41598-019-48248-4},
pmid = {31409863},
issn = {2045-2322},
abstract = {Staphylococcus hominis is part of the normal human microbiome. Two subspecies, S. hominis hominis (Shh) and S. hominis novobiosepticus (Shn), have clinical significance. Forty-nine S. hominis isolates were analyzed by the MicroScan automated system, SDS-PAGE and MALDI-TOF methods, followed by partial sequencing of the 16S rDNA gene. The trehalose fermentation test, disk diffusion and broth microdilution tests were used to identify (novobiocin test) and access the susceptibility to oxacillin and vancomycin of isolates. The SCCmec elements and genomic diversity were evaluated by PCR and PFGE methods, respectively. Profiles of 28 (57%; 8 Shh and 20 Shn) isolates corroborated with the results found in all the applied methods of identification. The remaining 21 (43%) isolates were phenotypically identified as Shh by MicroScan; however, they were identified as Shn by SDS-PAGE and mass spectral, and confirmed by 16S rDNA sequencing. Among 41 isolates identified as Shn by the molecular and mass spectrometry methods, 19 (41%) were novobiocin-sensitive, and the trehalose test indicated 11 positive isolates, which are considered atypical phenotypic results for this subspecies. In addition, 92.7% of the isolates identified as Shn by these methods carried mecA gene, while only 12.5% of the Shh isolates were positive. Together, the results highlighted the SDS-PAGE and MALDI-TOF MS methods as promising tools for discriminating S. hominis subspecies.},
}

@article {pmid31409776,
year = {2019},
author = {Luck, H and Khan, S and Kim, JH and Copeland, JK and Revelo, XS and Tsai, S and Chakraborty, M and Cheng, K and Tao Chan, Y and Nøhr, MK and Clemente-Casares, X and Perry, MC and Ghazarian, M and Lei, H and Lin, YH and Coburn, B and Okrainec, A and Jackson, T and Poutanen, S and Gaisano, H and Allard, JP and Guttman, DS and Conner, ME and Winer, S and Winer, DA},
title = {Gut-associated IgA+ immune cells regulate obesity-related insulin resistance.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3650},
doi = {10.1038/s41467-019-11370-y},
pmid = {31409776},
issn = {2041-1723},
support = {119414//Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)/ ; 142708//Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)/ ; 148385//Gouvernement du Canada | Instituts de Recherche en Santé du Canada | CIHR Skin Research Training Centre (Skin Research Training Centre)/ ; OG-3-15-5014//Diabetes Canada (DC)/ ; },
abstract = {The intestinal immune system is emerging as an important contributor to obesity-related insulin resistance, but the role of intestinal B cells in this context is unclear. Here, we show that high fat diet (HFD) feeding alters intestinal IgA+ immune cells and that IgA is a critical immune regulator of glucose homeostasis. Obese mice have fewer IgA+ immune cells and less secretory IgA and IgA-promoting immune mediators. HFD-fed IgA-deficient mice have dysfunctional glucose metabolism, a phenotype that can be recapitulated by adoptive transfer of intestinal-associated pan-B cells. Mechanistically, IgA is a crucial link that controls intestinal and adipose tissue inflammation, intestinal permeability, microbial encroachment and the composition of the intestinal microbiome during HFD. Current glucose-lowering therapies, including metformin, affect intestinal-related IgA+ B cell populations in mice, while bariatric surgery regimen alters the level of fecal secretory IgA in humans. These findings identify intestinal IgA+ immune cells as mucosal mediators of whole-body glucose regulation in diet-induced metabolic disease.},
}

@article {pmid31409765,
year = {2019},
author = {Jang, HR and Park, HJ and Kang, D and Chung, H and Nam, MH and Lee, Y and Park, JH and Lee, HY},
title = {A protective mechanism of probiotic Lactobacillus against hepatic steatosis via reducing host intestinal fatty acid absorption.},
journal = {Experimental & molecular medicine},
volume = {51},
number = {8},
pages = {95},
doi = {10.1038/s12276-019-0293-4},
pmid = {31409765},
issn = {2092-6413},
support = {HI14C1135//Korea Health Industry Development Institute (KHIDI)/ ; NRF-2014M3A9D5A01073886//National Research Foundation of Korea (NRF)/ ; NRF-2017R1A2B4009936//National Research Foundation of Korea (NRF)/ ; NRF-2018M3A9F3056405//National Research Foundation of Korea (NRF)/ ; NRF-2018M3A9F3056405//National Research Foundation of Korea (NRF)/ ; },
abstract = {The gut microbiome has been known to contribute up to ~30% of the energy absorption of the host. Although various beneficial mechanisms of probiotics have been suggested for non-alcoholic fatty liver disease (NAFLD), whether and which probiotics impact the host's intestinal energy absorption have not yet been quantitatively studied. Here, we suggest a novel mechanism of probiotics against NAFLD, in which Lactobacillus rhamnosus GG, the most common probiotic, shares intestinal fatty acids and prevents the development of diet-induced hepatic steatosis. By using quantitative methods (radioactive tracers and LC-MS) under both in vitro and in vivo conditions, we found that bacteria and hosts competed for fatty acid absorption in the intestine, resulting in decreased weight gain, body fat mass, and hepatic lipid accumulation without differences in calorie intake and excretion in mice fed the probiotic bacteria.},
}

@article {pmid31409678,
year = {2019},
author = {Edwards, VL and Smith, SB and McComb, EJ and Tamarelle, J and Ma, B and Humphrys, MS and Gajer, P and Gwilliam, K and Schaefer, AM and Lai, SK and Terplan, M and Mark, KS and Brotman, RM and Forney, LJ and Bavoil, PM and Ravel, J},
title = {The Cervicovaginal Microbiota-Host Interaction Modulates Chlamydia trachomatis Infection.},
journal = {mBio},
volume = {10},
number = {4},
pages = {},
doi = {10.1128/mBio.01548-19},
pmid = {31409678},
issn = {2150-7511},
abstract = {The mechanism(s) by which Lactobacillus-dominated cervicovaginal microbiota provide a barrier to Chlamydia trachomatis infection remain(s) unknown. Here we evaluate the impact of different Lactobacillus spp. identified via culture-independent metataxonomic analysis of C. trachomatis-infected women on C. trachomatis infection in a three-dimensional (3D) cervical epithelium model. Lactobacillus spp. that specifically produce d(-) lactic acid were associated with long-term protection against C. trachomatis infection, consistent with reduced protection associated with Lactobacillus iners, which does not produce this isoform, and with decreased epithelial cell proliferation, consistent with the observed prolonged protective effect. Transcriptomic analysis revealed that epigenetic modifications involving histone deacetylase-controlled pathways are integral to the cross talk between host and microbiota. These results highlight a fundamental mechanism whereby the cervicovaginal microbiota modulates host functions to protect against C. trachomatis infection.IMPORTANCE The vaginal microbiota is believed to protect women against Chlamydia trachomatis, the etiologic agent of the most prevalent sexually transmitted infection (STI) in developed countries. The mechanism underlying this protection has remained elusive. Here, we reveal the comprehensive strategy by which the cervicovaginal microbiota modulates host functions to protect against chlamydial infection, thereby providing a novel conceptual mechanistic understanding. Major implications of this work are that (i) the impact of the vaginal microbiota on the epithelium should be considered in future studies of chlamydial infection and other STIs and (ii) a fundamental understanding of the cervicovaginal microbiota's role in protection against STIs may enable the development of novel microbiome-based therapeutic strategies to protect women from infection and improve vaginal and cervical health.},
}

@article {pmid31409661,
year = {2019},
author = {Small, CM and Currey, M and Beck, EA and Bassham, S and Cresko, WA},
title = {Highly Reproducible 16S Sequencing Facilitates Measurement of Host Genetic Influences on the Stickleback Gut Microbiome.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00331-19},
pmid = {31409661},
issn = {2379-5077},
abstract = {Multicellular organisms interact with resident microbes in important ways, and a better understanding of host-microbe interactions is aided by tools such as high-throughput 16S sequencing. However, rigorous evaluation of the veracity of these tools in a different context from which they were developed has often lagged behind. Our goal was to perform one such critical test by examining how variation in tissue preparation and DNA isolation could affect inferences about gut microbiome variation between two genetically divergent lines of threespine stickleback fish maintained in the same laboratory environment. Using careful experimental design and intensive sampling of individuals, we addressed technical and biological sources of variation in 16S-based estimates of microbial diversity. After employing a two-tiered bead beating approach that comprised tissue homogenization followed by microbial lysis in subsamples, we found an extremely minor effect of DNA isolation protocol relative to among-host microbial diversity differences. Abundance estimates for rare operational taxonomic units (OTUs), however, showed much lower reproducibility. Gut microbiome composition was highly variable across fish-even among cohoused siblings-relative to technical replicates, but a subtle effect of host genotype (stickleback line) was nevertheless detected for some microbial taxa.IMPORTANCE Our findings demonstrate the importance of appropriately quantifying biological and technical variance components when attempting to understand major influences on high-throughput microbiome data. Our focus was on understanding among-host (biological) variance in community metrics and its magnitude in relation to within-host (technical) variance, because meaningful comparisons among individuals are necessary in addressing major questions in host-microbe ecology and evolution, such as heritability of the microbiome. Our study design and insights should provide a useful example for others desiring to quantify microbiome variation at biological levels in the face of various technical factors in a variety of systems.},
}

@article {pmid31409660,
year = {2019},
author = {Zhang, S and Song, W and Wemheuer, B and Reveillaud, J and Webster, N and Thomas, T},
title = {Comparative Genomics Reveals Ecological and Evolutionary Insights into Sponge-Associated Thaumarchaeota.},
journal = {mSystems},
volume = {4},
number = {4},
pages = {},
doi = {10.1128/mSystems.00288-19},
pmid = {31409660},
issn = {2379-5077},
abstract = {Thaumarchaeota are frequently reported to associate with marine sponges (phylum Porifera); however, little is known about the features that distinguish them from their free-living thaumarchaeal counterparts. In this study, thaumarchaeal metagenome-assembled genomes (MAGs) were reconstructed from metagenomic data sets derived from the marine sponges Hexadella detritifera, Hexadella cf. detritifera, and Stylissa flabelliformis Phylogenetic and taxonomic analyses revealed that the three thaumarchaeal MAGs represent two new species within the genus Nitrosopumilus and one novel genus, for which we propose the names "CandidatusUNitrosopumilus hexadellus," "CandidatusUNitrosopumilus detritiferus," and "CandidatusUCenporiarchaeum stylissum" (the U superscript indicates that the taxon is uncultured). Comparison of these genomes to data from the Sponge Earth Microbiome Project revealed that "CaUCenporiarchaeum stylissum" has been exclusively detected in sponges and can hence be classified as a specialist, while "CaUNitrosopumilus detritiferus" and "CaUNitrosopumilus hexadellus" are also detected outside the sponge holobiont and likely lead a generalist lifestyle. Comparison of the sponge-associated MAGs to genomes of free-living Thaumarchaeota revealed signatures that indicate functional features of a sponge-associated lifestyle, and these features were related to nutrient transport and metabolism, restriction-modification, defense mechanisms, and host interactions. Each species exhibited distinct functional traits, suggesting that they have reached different stages of evolutionary adaptation and/or occupy distinct ecological niches within their sponge hosts. Our study therefore offers new evolutionary and ecological insights into the symbiosis between sponges and their thaumarchaeal symbionts.IMPORTANCE Sponges represent ecologically important models to understand the evolution of symbiotic interactions of metazoans with microbial symbionts. Thaumarchaeota are commonly found in sponges, but their potential adaptations to a host-associated lifestyle are largely unknown. Here, we present three novel sponge-associated thaumarchaeal species and compare their genomic and predicted functional features with those of closely related free-living counterparts. We found different degrees of specialization of these thaumarchaeal species to the sponge environment that is reflected in their host distribution and their predicted molecular and metabolic properties. Our results indicate that Thaumarchaeota may have reached different stages of evolutionary adaptation in their symbiosis with sponges.},
}

@article {pmid31409249,
year = {2019},
author = {Becker, CG and Bletz, MC and Greenspan, SE and Rodriguez, D and Lambertini, C and Jenkinson, TS and Guimarães, PR and Assis, APA and Geffers, R and Jarek, M and Toledo, LF and Vences, M and Haddad, CFB},
title = {Low-load pathogen spillover predicts shifts in skin microbiome and survival of a terrestrial-breeding amphibian.},
journal = {Proceedings. Biological sciences},
volume = {286},
number = {1908},
pages = {20191114},
doi = {10.1098/rspb.2019.1114},
pmid = {31409249},
issn = {1471-2954},
abstract = {Wildlife disease dynamics are strongly influenced by the structure of host communities and their symbiotic microbiota. Conspicuous amphibian declines associated with the waterborne fungal pathogen Batrachochytrium dendrobatidis (Bd) have been observed in aquatic-breeding frogs globally. However, less attention has been given to cryptic terrestrial-breeding amphibians that have also been declining in tropical regions. By experimentally manipulating multiple tropical amphibian assemblages harbouring natural microbial communities, we tested whether Bd spillover from naturally infected aquatic-breeding frogs could lead to Bd amplification and mortality in our focal terrestrial-breeding host: the pumpkin toadlet Brachycephalus pitanga. We also tested whether the strength of spillover could vary depending on skin bacterial transmission within host assemblages. Terrestrial-breeding toadlets acquired lethal spillover infections from neighbouring aquatic hosts and experienced dramatic but generally non-protective shifts in skin bacterial composition primarily attributable to their Bd infections. By contrast, aquatic-breeding amphibians maintained mild Bd infections and higher survival, with shifts in bacterial microbiomes that were unrelated to Bd infections. Our results indicate that Bd spillover from even mildly infected aquatic-breeding hosts may lead to dysbiosis and mortality in terrestrial-breeding species, underscoring the need to further investigate recent population declines of terrestrial-breeding amphibians in the tropics.},
}

@article {pmid31409048,
year = {2019},
author = {Drago, L and Panelli, S and Bandi, C and Zuccotti, G and Perini, M and D'Auria, E},
title = {What Pediatricians Should Know Before Studying Gut Microbiota.},
journal = {Journal of clinical medicine},
volume = {8},
number = {8},
pages = {},
doi = {10.3390/jcm8081206},
pmid = {31409048},
issn = {2077-0383},
abstract = {Billions of microorganisms, or "microbiota", inhabit the gut and affect its homeostasis, influencing, and sometimes causing if altered, a multitude of diseases. The genomes of the microbes that form the gut ecosystem should be summed to the human genome to form the hologenome due to their influence on human physiology; hence the term "microbiome" is commonly used to refer to the genetic make-up and gene-gene interactions of microbes. This review attempts to provide insight into this recently discovered vital organ of the human body, which has yet to be fully explored. We herein discuss the rhythm and shaping of the microbiome at birth and during the first years leading up to adolescence. Furthermore, important issues to consider for conducting a reliable microbiome study including study design, inclusion/exclusion criteria, sample collection, storage, and variability of different sampling methods as well as the basic terminology of molecular approaches, data analysis, and clinical interpretation of results are addressed. This basic knowledge aims to provide the pediatricians with a key tool to avoid data dispersion and pitfalls during child microbiota study.},
}

@article {pmid31408948,
year = {2019},
author = {Hayashi, T and Fujita, K and Matsushita, M and Nonomura, N},
title = {Main Inflammatory Cells and Potentials of Anti-Inflammatory Agents in Prostate Cancer.},
journal = {Cancers},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/cancers11081153},
pmid = {31408948},
issn = {2072-6694},
support = {JP18K16693//Japan Society for the Promotion of Science/ ; },
abstract = {Prostate cancer is the most common type of cancer and the leading cause of cancer deaths among men in many countries. Preventing progression is a major concern for prostate cancer patients on active surveillance, patients with recurrence after radical therapies, and patients who acquired resistance to systemic therapies. Inflammation, which is induced by various factors such as infection, microbiome, obesity, and a high-fat diet, is the major etiology in the development of prostate cancer. Inflammatory cells play important roles in tumor progression. Various immune cells including tumor-associated neutrophils, tumor-infiltrating macrophages, myeloid-derived suppressor cells, and mast cells promote prostate cancer via various intercellular signaling. Further basic studies examining the relationship between the inflammatory process and prostate cancer progression are warranted. Interventions by medications and diets to control systemic and/or local inflammation might be effective therapies for prostate cancer progression. Epidemiological investigations and basic research using human immune cells or mouse models have revealed that non-steroidal anti-inflammatory drugs, metformin, statins, soy isoflavones, and other diets are potential interventions for preventing progression of prostate cancer by suppressing inflammation. It is essential to evaluate appropriate indications and doses of each drug and diet.},
}

@article {pmid31408913,
year = {2019},
author = {Sood, A and Singh, A and Mahajan, R and Midha, V and Mehta, V and Gupta, YK and Narang, V and Kaur, K},
title = {Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study).},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.14829},
pmid = {31408913},
issn = {1440-1746},
abstract = {BACKGROUND: Faecal microbiota transplantation (FMT) targets gut microbiome dysbiosis and is an emerging therapy for ulcerative colitis (UC). Though initial results with FMT in patients with active UC are encouraging, data regarding its acceptability, tolerability and safety are scant.

METHODS: A retrospective analysis of patients with active UC (Mayo clinic score ≥4), who received multisession FMT (at weeks 0, 2, 6, 10, 14, 18 and 22) via colonoscopy between June 2016 and June 2018, was done. Patient acceptability, tolerability and immediate and long term safety of the therapy were assessed.

RESULTS: Of the 129 patients with active UC who were offered FMT, 101 patients consented; giving acceptability of 78.3%. Faecal slurry retention time, improved with each session (3.27 ± 1.06 hours for first session vs 5.12 ± 0.5 hours for seventh session). Abdominal discomfort, flatulence, abdominal distension, borborygmi and low grade fever (30.8%, 15.9%, 9.8%, 7.9% and 7.6% respectively) were the most common post procedural short term adverse events. Long term adverse events included new-onset urticaria (n=2,4.3%), arthritis/arthralgias(n=3, 6.5%), depression (n=1, 2.2%), partial sensorineural hearing loss (n=1, 2.2%), and allergic bronchitis (n=1, 2.2%). Thirteen (12.9%) patients dropped out due to adverse events.

CONCLUSION: FMT appears to be a safe and well tolerated procedure, with good acceptability in patients with active UC.},
}

@article {pmid31408742,
year = {2019},
author = {Ari, O and Karabudak, S and Kalcioglu, MT and Gunduz, AY and Durmaz, R},
title = {The bacteriome of otitis media with effusion: Does it originate from the adenoid?.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {126},
number = {},
pages = {109624},
doi = {10.1016/j.ijporl.2019.109624},
pmid = {31408742},
issn = {1872-8464},
abstract = {OBJECTIVE: The aim of this study was to evaluate the composition and the diversity of bacteriome in middle ear effusion (MEE) and adenoid specimens of pediatric patients having otitis media with effusion (OME).

MATERIALS AND METHODS: Sample collection from children with OME followed by next generation sequencing. Seventeen adenoid and 43 middle ear effusion specimens from 25 children having OME were evaluated. Microbiome analysis was performed via Ion 16S rRNA metagenomics kit.

RESULTS: Twenty-two different bacterial species were identified from all of the samples analyzed. There were variations in the prevalence and relative abundance of the bacteriome observed between adenoid and MEE samples. MEE microbiome was significantly dominated by Alloicoccus otitis (44%), Turicella otitidis (6%), and Staphylococcus auricularis (3%). Whereas, Rothia mucilaginosa (39%), R. dentocariosa (11%), S. aureus (5%), Veillonella rogosae (2%), Granulicatella elegans (2%), Granulicatella adiacens (2%), Eikenella corrodens (1%), and Prevotella nanceiensis (1%) had significantly higher relative abundance in adenoid samples. Overall, there was no statistically significant difference in alpha diversity of MEE and adenoid samples, whereas adenoid samples constituted a cluster in the beta diversity graph.

CONCLUSION: Bacteriome of MEE is mostly dominated by A. otitis yet accompanied by other bacteria with lower relative abundances suggests that OME is likely to be a polymicrobial process. Despite similarities, significant differences in relative abundances of several predominant species between bacteriome in the MEE and adenoid put the theory that OME in children is originated from the adenoids under question.},
}

@article {pmid31408679,
year = {2019},
author = {Thumann, TA and Pferschy-Wenzig, EM and Moissl-Eichinger, C and Bauer, R},
title = {The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {112153},
doi = {10.1016/j.jep.2019.112153},
pmid = {31408679},
issn = {1872-7573},
abstract = {. Many medicinal plants have been traditionally used for the treatment of gastrointestinal disorders. According to the monographs published by the Committee on Herbal Medicinal Products (HMPC) at the European Medicines Agency, currently 44 medicinal plants are recommended in the European Union for the treatment of gastrointestinal disorders based on traditional use. The main indications are functional and chronic gastrointestinal disorders, such as functional dyspepsia and irritable bowel syndrome (IBS), and typical effects of these plants are stimulation of gastric secretion, spasmolytic and carminative effects, soothing effects on the gastrointestinal mucosa, laxative effects, adstringent or antidiarrheal activities, and anti-inflammatory effects. A possible interaction with human gut microbiota has hardly been considered so far, although it is quite likely.

AIM OF THE STUDY: . In this review, we aimed to identify and evaluate published studies which have investigated interactions of these plants with the gut microbiome.

RESULTS: . According to this survey, only a minor portion of the 44 medicinal plants considered in EMA monographs for the treatment of gastrointestinal diseases has been studied so far with regard to potential interactions with gut microbiota. We could identify eight relevant in vitro studies that have been performed with six of these medicinal plants, 17 in vivo studies performed in experimental animals involving seven of the medicinal plants, and three trials in humans performed with two of the plants. The most robust evidence exists for the use of inulin as a prebiotic, and in this context also the prebiotic activity of chicory root has been investigated quite intensively. Flaxseed dietary fibers are also known to be fermented by gut microbiota to short chain fatty acids, leading to prebiotic effects. This could cause a health-beneficial modulation of gut microbiota by flaxseed supplementation. In flaxseed, also other compound classes like lignans and polyunsaturated fatty acids are present, that also have been shown to interact with gut microbiota. Drugs rich in tannins and anthocyanins also interact intensively with gut microbiota, since these compounds reach the colon at high levels in unchanged forms. Tannins and anthocyanins are intensively metabolized by certain gut bacteria, leading to the generation of small, bioavailable and potentially bioactive metabolites. Moreover, interaction with these compounds may exert a prebiotic-like effect on gut microbiota. Gut microbial metabolization has also been shown for certain licorice constituents, but their potential effects on gut microbiota still need to be investigated in detail. Only a limited amount of studies investigated the interactions of essential oil- and secoiridoid-containing drugs with human gut microbiota. However, other constituents present in some of these drugs, like curcumin (curcuma), shogaol (ginger), and rosmarinic acid have been shown to be metabolized by human gut microbiota, and preliminary data also indicate potential gut microbiome modulatory effects. To conclude, the interaction with gut microbiota is still not fully investigated for many herbal drugs traditionally used for gastrointestinal disorders, which offers a vast field for future research.},
}

@article {pmid31408588,
year = {2019},
author = {Husson, J and Mongodin, EF and Bromberg, JS},
title = {Invited Editorial re: Vendor-Specific Microbiome Controls both Acute and Chronic Murine Lung Allograft Rejection by Altering CD4+Foxp3+ Regulatory T Cell Levels.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1111/ajt.15563},
pmid = {31408588},
issn = {1600-6143},
abstract = {Despite advances in immunosuppressive management in lung transplantation, acute and chronic rejection remain challenging. One under-studied area of research is the role of the microbiota and its effects on alloimmunity and allograft rejection. Prior work has shown that the microbiota modulates innate and adaptive immunity through pathways such as the induction of suppressive Foxp3+ CD4+ regulatory T cells (Treg). Guo et al in this issue of the AJT demonstrate vendor-specific differences in lung allograft rejection in a minor histocompatibility mismatch murine model, and these differences are ameliorated by antibiotics. The authors thus focused on the microbiota and investigated whether the association between microbiota and lung allograft rejection may be related to microbiota-induced alterations in Treg responses. This article is protected by copyright. All rights reserved.},
}

@article {pmid31408370,
year = {2019},
author = {Lechner, K and von Schacky, C and McKenzie, AL and Worm, N and Nixdorff, U and Lechner, B and Kränkel, N and Halle, M and Krauss, RM and Scherr, J},
title = {Lifestyle factors and high-risk atherosclerosis: Pathways and mechanisms beyond traditional risk factors.},
journal = {European journal of preventive cardiology},
volume = {},
number = {},
pages = {2047487319869400},
doi = {10.1177/2047487319869400},
pmid = {31408370},
issn = {2047-4881},
abstract = {Despite major efforts to reduce atherosclerotic cardiovascular disease (ASCVD) burden with conventional risk factor control, significant residual risk remains. Recent evidence on non-traditional determinants of cardiometabolic health has advanced our understanding of lifestyle-disease interactions. Chronic exposure to environmental stressors like poor diet quality, sedentarism, ambient air pollution and noise, sleep deprivation and psychosocial stress affect numerous traditional and non-traditional intermediary pathways related to ASCVD. These include body composition, cardiorespiratory fitness, muscle strength and functionality and the intestinal microbiome, which are increasingly recognized as major determinants of cardiovascular health. Evidence points to partially overlapping mechanisms, including effects on inflammatory and nutrient sensing pathways, endocrine signalling, autonomic function and autophagy. Of particular relevance is the potential of low-risk lifestyle factors to impact on plaque vulnerability through altered adipose tissue and skeletal muscle phenotype and secretome. Collectively, low-risk lifestyle factors cause a set of phenotypic adaptations shifting tissue cross-talk from a proinflammatory milieu conducive for high-risk atherosclerosis to an anti-atherogenic milieu. The ketone body ß-hydroxybutyrate, through inhibition of the NLRP-3 inflammasome, is likely to be an intermediary for many of these observed benefits. Adhering to low-risk lifestyle factors adds to the prognostic value of optimal risk factor management, and benefit occurs even when the impact on conventional risk markers is discouragingly minimal or not present. The aims of this review are (a) to discuss novel lifestyle risk factors and their underlying biochemical principles and (b) to provide new perspectives on potentially more feasible recommendations to improve long-term adherence to low-risk lifestyle factors.},
}

@article {pmid31407437,
year = {2019},
author = {Daubert, DM and Weinstein, BF},
title = {Biofilm as a risk factor in implant treatment.},
journal = {Periodontology 2000},
volume = {81},
number = {1},
pages = {29-40},
doi = {10.1111/prd.12280},
pmid = {31407437},
issn = {1600-0757},
abstract = {This article summarizes the microbiological findings at dental implants, drawing distinctions between the peri-implant microbiome and the periodontal microbiome, and summarizes what is known regarding biofilm as a risk factor for specific stages of implant treatment. Targeted microbial analysis is reviewed as well as the latest results from open-ended sequencing of the peri-implant flora. At this time there remains a lack of consensus for a specific microbial profile that is associated with peri-implantitis, suggesting that there may be other factors which influence the microbiome such as titanium surface dissolution. Therapeutic interventions to address the biofilm are presented at the preoperative, perioperative, and postoperative stages. Evidence supports that perioperative chlorhexidine reduces biofilm-related implant complications and failure. Regular maintenance for dental implants is also shown to reduce peri-implant mucositis and implant failure. Maintenance procedures should aim to disrupt the biofilm without damaging the titanium dioxide surface layer in an effort to prevent further oxidation. Evidence supports the use of glycine powder air polishing as a valuable adjunct to conventional therapies for use at implant maintenance visits. For the treatment of peri-implantitis, nonsurgical therapy has not been shown to be effective, and while surgical intervention is not always predictable, it has been shown to be superior to nonsurgical treatment for decontamination of the implant surface that is not covered by bone.},
}

@article {pmid31407325,
year = {2019},
author = {Cardenas-de la Garza, JA and Haidari, W and Feldman, SR},
title = {Microbiome, probiotics and dermatology.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjd.18350},
pmid = {31407325},
issn = {1365-2133},
}

@article {pmid31407304,
year = {2019},
author = {Hu, A and Lu, Y and Hernández García, M and Dumont, MG},
title = {Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {163-174},
doi = {10.1007/978-1-4939-9721-3_13},
pmid = {31407304},
issn = {1940-6029},
abstract = {Metatranscriptomics is a powerful tool for capturing gene expression patterns in microbial communities and investigating their responses to environmental conditions. Stable isotope probing (SIP) is a method to target specific functional groups of microorganisms in environmental samples. The combination of RNA-SIP with metatranscriptomic analysis enhances the detection and identification of mRNA from target microorganisms. In this chapter we provide a protocol for RNA-SIP, mRNA enrichment, and mRNA preparation for high-throughput sequencing using an example of targeting methanotrophs in rice field soil.},
}

@article {pmid31407294,
year = {2019},
author = {Ghori, NU and Moreira-Grez, B and Vuong, P and Waite, I and Morald, T and Wise, M and Whiteley, AS},
title = {RNA Stable Isotope Probing (RNA-SIP).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {31-44},
doi = {10.1007/978-1-4939-9721-3_3},
pmid = {31407294},
issn = {1940-6029},
abstract = {Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation of heavier mass isotopes into the RNA after cellular utilization of labeled substrates pulsed into the community. Labeled RNAs are subsequently separated from unlabeled RNAs by density gradient centrifugation followed by identification of the RNAs by sequencing. Therefore, RNA stable isotope probing is a culture-independent technique that provides simultaneous information about microbiome community, composition and function. This chapter presents the detailed protocol for performing an RNA-SIP experiment, including the formation, ultracentrifugation, and fractional analyses of stable isotope-labeled RNAs extracted from environmental samples.},
}

@article {pmid31407091,
year = {2019},
author = {Knapp, GC and Sharma, A and Olopade, B and Alatise, OI and Olasehinde, O and Arije, OO and Castle, PE and Kingham, TP},
title = {An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria.},
journal = {World journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00268-019-05100-0},
pmid = {31407091},
issn = {1432-2323},
support = {P30 CA008748/CA/NCI NIH HHS/United States ; },
abstract = {INTRODUCTION: The fecal immunochemical test (FIT) for hemoglobin is recommended for colorectal cancer (CRC) screening in resource-limited environments. However, there are several unique variables that may alter FIT performance in this setting, including endemic intestinal parasites and high ambient temperature. This prospective study evaluated the performance of FIT in asymptomatic, average-risk individuals of screening age in rural Nigeria.

METHODS: Three hundred and twenty-four community volunteers completed a questionnaire and provided stool specimens for parasitology and microbiome analysis. Specimens were frozen and stored at -80 °C. Of 324 subjects, 139 met criteria for average-risk CRC screening and had a stool sample for analysis. These were thawed and tested with a qualitative FIT. Specimens positive for occult blood were retested every two days to evaluate the impact of time and temperature on test performance.

RESULTS: Of 139 individuals, 69 (49.6%) were positive for intestinal parasites and 10 (7.2%) were positive for occult blood. The most common pathogen was Cryptosporidium (40.6%). Among patients with intestinal parasites, 10.1% (7/69) had a positive FIT. Only 4.3% (3/70) of patients without parasites had a positive FIT (p = 0.208). On bivariate analysis, sociodemographic variables were not associated with a positive FIT result. Thirty percent (3/10) of the FIT-positive specimens became FIT-negative with routine storage.

CONCLUSION: Although a positive FIT result was more common in those with parasitic infection, the relationship was not significant in this small cohort. The impact of high ambient temperature on test positivity may necessitate shorter processing time guidelines for equatorial countries. Additional prospective studies are needed to validate FIT performance in Nigeria.},
}

@article {pmid31407021,
year = {2019},
author = {Bockoven, AA and Bondy, EC and Flores, MJ and Kelly, SE and Ravenscraft, AM and Hunter, MS},
title = {What Goes Up Might Come Down: the Spectacular Spread of an Endosymbiont Is Followed by Its Decline a Decade Later.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01417-4},
pmid = {31407021},
issn = {1432-184X},
support = {DEB-1020460//Division of Environmental Biology/ ; IOS-1256905//Division of Integrative Organismal Systems/ ; },
abstract = {Facultative, intracellular bacterial symbionts of arthropods may dramatically affect host biology and reproduction. The length of these symbiont-host associations may be thousands to millions of years, and while symbiont loss is predicted, there have been very few observations of a decline of symbiont infection rates. In a population of the sweet potato whitefly species (Bemisia tabaci MEAM1) in Arizona, USA, we documented the frequency decline of a strain of Rickettsia in the Rickettsia bellii clade from near-fixation in 2011 to 36% of whiteflies infected in 2017. In previous studies, Rickettsia had been shown to increase from 1 to 97% from 2000 to 2006 and remained at high frequency for at least five years. At that time, Rickettsia infection was associated with both fitness benefits and female bias. In the current study, we established matrilines of whiteflies from the field (2016, Rickettsia infection frequency = 58%) and studied (a) Rickettsia vertical transmission, (b) fitness and sex ratios associated with Rickettsia infection, (c) symbiont titer, and (d) bacterial communities within whiteflies. The vertical transmission rate was high, approximately 98%. Rickettsia infection in the matrilines was not associated with fitness benefits or sex ratio bias and appeared to be slightly costly, as more Rickettsia-infected individuals produced non-hatching eggs. Overall, the titer of Rickettsia in the matrilines was lower in 2016 than in the whiteflies collected in 2011, but the titer distribution appeared bimodal, with high- and low-titer lines, and constancy of the average titer within lines over three generations. We found neither association between Rickettsia titer and fitness benefits or sex ratio bias nor evidence that Rickettsia was replaced by another secondary symbiont. The change in the interaction between symbiont and host in 2016 whiteflies may explain the drop in symbiont frequency we observed.},
}

@article {pmid31406492,
year = {2018},
author = {Brown, RE and Short, SP and Williams, CS},
title = {Colorectal Cancer and Metabolism.},
journal = {Current colorectal cancer reports},
volume = {14},
number = {6},
pages = {226-241},
doi = {10.1007/s11888-018-0420-y},
pmid = {31406492},
issn = {1556-3790},
abstract = {Purpose of Review: Metabolic reprogramming is essential for the rapid proliferation of cancer cells and is thus recognized as a hallmark of cancer. In this review, we will discuss the etiologies and effects of metabolic reprogramming in colorectal cancer.

Recent Findings: Changes in cellular metabolism may precede the acquisition of driver mutations ultimately leading to colonocyte transformation. Oncogenic mutations and loss of tumor suppressor genes further reprogram CRC cells to upregulate glycolysis, glutaminolysis, one-carbon metabolism, and fatty acid synthesis. These metabolic changes are not uniform throughout tumors, as subpopulations of tumor cells may rely on different pathways to adapt to nutrient availability in the local tumor microenvironment. Finally, metabolic cross-communication between stromal cells, immune cells, and the gut microbiota enable CRC growth, invasion, and metastasis.

Summary: Altered cellular metabolism occurs in CRC at multiple levels, including in the cells that make up the bulk of CRC tumors, cancer stem cells, the tumor microenvironment, and host-microbiome interactions. This knowledge may inform the development of improved screening and therapeutics for CRC.},
}

@article {pmid31406349,
year = {2019},
author = {Doan, T and Hinterwirth, A and Worden, L and Arzika, AM and Maliki, R and Abdou, A and Kane, S and Zhong, L and Cummings, SL and Sakar, S and Chen, C and Cook, C and Lebas, E and Chow, ED and Nachamkin, I and Porco, TC and Keenan, JD and Lietman, TM},
title = {Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-019-0533-0},
pmid = {31406349},
issn = {1546-170X},
abstract = {The MORDOR I trial1, conducted in Niger, Malawi and Tanzania, demonstrated that mass azithromycin distribution to preschool children reduced childhood mortality1. However, the large but simple trial design precluded determination of the mechanisms involved. Here we examined the gut microbiome of preschool children from 30 Nigerien communities randomized to either biannual azithromycin or placebo. Gut microbiome γ-diversity was not significantly altered (P = 0.08), but the relative abundances of two Campylobacter species, along with another 33 gut bacteria, were significantly reduced in children treated with azithromycin at the 24-month follow-up. Metagenomic analysis revealed functional differences in gut bacteria between treatment groups. Resistome analysis showed an increase in macrolide resistance gene expression in gut microbiota in communities treated with azithromycin (P = 0.004). These results suggest that prolonged mass azithromycin distribution to reduce childhood mortality reduces certain gut bacteria, including known pathogens, while selecting for antibiotic resistance.},
}

@article {pmid31406314,
year = {2019},
author = {},
title = {Vast pool of new proteins is found, thanks to the human microbiome.},
journal = {Nature},
volume = {572},
number = {7769},
pages = {287},
doi = {10.1038/d41586-019-02404-y},
pmid = {31406314},
issn = {1476-4687},
}

@article {pmid31406307,
year = {2019},
author = {Segata, N},
title = {No bacteria found in healthy placentas.},
journal = {Nature},
volume = {572},
number = {7769},
pages = {317-318},
doi = {10.1038/d41586-019-02262-8},
pmid = {31406307},
issn = {1476-4687},
}

@article {pmid31406230,
year = {2019},
author = {He, X and Parenti, M and Grip, T and Lönnerdal, B and Timby, N and Domellöf, M and Hernell, O and Slupsky, CM},
title = {Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11589},
doi = {10.1038/s41598-019-47953-4},
pmid = {31406230},
issn = {2045-2322},
abstract = {Human milk delivers an array of bioactive components that safeguard infant growth and development and maintain healthy gut microbiota. Milk fat globule membrane (MFGM) is a biologically functional fraction of milk increasingly linked to beneficial outcomes in infants through protection from pathogens, modulation of the immune system and improved neurodevelopment. In the present study, we characterized the fecal microbiome and metabolome of infants fed a bovine MFGM supplemented experimental formula (EF) and compared to infants fed standard formula (SF) and a breast-fed reference group. The impact of MFGM on the fecal microbiome was moderate; however, the fecal metabolome of EF-fed infants showed a significant reduction of several metabolites including lactate, succinate, amino acids and their derivatives from that of infants fed SF. Introduction of weaning food with either human milk or infant formula reduces the distinct characteristics of breast-fed- or formula-fed- like infant fecal microbiome and metabolome profiles. Our findings support the hypothesis that higher levels of protein in infant formula and the lack of human milk oligosaccharides promote a shift toward amino acid fermentation in the gut. MFGM may play a role in shaping gut microbial activity and function.},
}

@article {pmid31406033,
year = {2019},
author = {Kobayashi, A and Tsuchida, S and Ueda, A and Yamada, T and Murata, K and Nakamura, H and Ushida, K},
title = {Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.19-0014},
pmid = {31406033},
issn = {1347-7439},
abstract = {The transgenerational maintenance of symbiotic microbes that benefit host nutrition and health is evolutionarily advantageous. In some vertebrate lineages, coprophagy is used as a strategy for effectively transmitting microbes across generations. However, this strategy has still not been studied in birds. Accordingly, the aim of the present study was to evaluate the role of maternal cecal feces consumption by Japanese rock ptarmigan (Lagopus muta japonica) chicks as a strategy for acquiring essential gut microbes. Both the duration of coprophagy behavior by the chicks and the development process of the chick cecal microbiome (n=20 one- to three-week-old chicks, from three broods) were investigated. In all three broods, coprophagy behavior was only observed from 3 to 18 days of age. Furthermore, there was no significant difference in the number of bacterial operational taxonomic units (OTUs) in 1-week-old chicks (n=651) and adults (n=609), and most of the main OTUs observed in the adults were already present in the 1-week-old chicks. These results indicate that, in this precocial bird species, coprophagy may contribute to the early establishment of cecal bacteria that are essential for food digestion and, thus, chick survival. In fact, Japanese rock ptarmigan chicks consume the same food as their hens from the time of hatching. This behavior may have applications to ex-situ conservation.},
}

@article {pmid31405831,
year = {2019},
author = {van Hecke, O and Fuller, A and Bankhead, C and Jenkins-Jones, S and Francis, N and Moore, M and Butler, C and Wang, K},
title = {Antibiotic exposure and 'response failure' for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care.},
journal = {The British journal of general practice : the journal of the Royal College of General Practitioners},
volume = {},
number = {},
pages = {},
doi = {10.3399/bjgp19X705089},
pmid = {31405831},
issn = {1478-5242},
abstract = {BACKGROUND: Childhood antibiotic exposure has important clinically relevant implications. These include disruption to the microbiome, antibiotic resistance, and clinical workload manifesting as treatment 'failure'.

AIM: To examine the relationship between the number of antibiotic courses prescribed to preschool children for acute respiratory tract infections (RTI), in the preceding year, and subsequent RTIs that failed to respond to antibiotic treatment ('response failures').

DESIGN AND SETTING: A cohort study using UK primary care data from the Clinical Practice Research Datalink, 2009 to 2016.

METHOD: Children aged 12 to 60 months (1 to 5 years) who were prescribed an antibiotic for an acute RTI (upper and lower RTI or otitis media) were included. One random index antibiotic course for RTI per child was selected. Exposure was the number of antibiotic prescriptions for acute RTI up to 12 months before the index antibiotic prescription. The outcome was 'response failure' up to 14 days after index antibiotic prescription, defined as: subsequent antibiotic prescription; referral; hospital admission; death; or emergency department attendance within 3 days. The authors used logistic regression models to estimate the odds between antibiotic exposure and response failure.

RESULTS: Out of 114 329 children who were prescribed an antibiotic course for acute RTI, children who received ≥2 antibiotic courses for acute RTIs in the preceding year had greater odds of response failure; one antibiotic course: adjusted odds ratio (OR) 1.03 (95% confidence interval [CI] = 0.88 to 1.21), P = 0.67, n = 230 children; ≥2 antibiotic courses: adjusted OR 1.32 (CI = 1.04 to 1.66), P = 0.02, n = 97.

CONCLUSION: Childhood antibiotic exposure for acute RTI may be a good predictor for subsequent response failure (but not necessarily because of antibiotic treatment failure). Further research is needed to improve understanding of the mechanisms underlying response failure.},
}

@article {pmid31405168,
year = {2019},
author = {Raghuvanshi, R and Grayson, AG and Schena, I and Amanze, O and Suwintono, K and Quinn, RA},
title = {Microbial Transformations of Organically Fermented Foods.},
journal = {Metabolites},
volume = {9},
number = {8},
pages = {},
doi = {10.3390/metabo9080165},
pmid = {31405168},
issn = {2218-1989},
abstract = {Fermenting food is an ancient form of preservation ingrained many in human societies around the world. Westernized diets have moved away from such practices, but even in these cultures, fermented foods are seeing a resurgent interested due to their believed health benefits. Here, we analyze the microbiome and metabolome of organically fermented vegetables, using a salt brine, which is a common 'at-home' method of food fermentation. We found that the natural microbial fermentation had a strong effect on the food metabolites, where all four foods (beet, carrot, peppers and radishes) changed through time, with a peak in molecular diversity after 2-3 days and a decrease in diversity during the final stages of the 4-day process. The microbiome of all foods showed a stark transition from one that resembled a soil community to one dominated by Enterobacteriaceae, such as Erwinia spp., within a single day of fermentation and increasing amounts of Lactobacillales through the fermentation process. With particular attention to plant natural products, we observed significant transformations of polyphenols, triterpenoids and anthocyanins, but the degree of this metabolism depended on the food type. Beets, radishes and peppers saw an increase in the abundance of these compounds as the fermentation proceeded, but carrots saw a decrease through time. This study showed that organically fermenting vegetables markedly changed their chemistry and microbiology but resulted in high abundance of Enterobacteriaceae which are not normally considered as probiotics. The release of beneficial plant specialized metabolites was observed, but this depended on the fermented vegetable.},
}

@article {pmid31405111,
year = {2019},
author = {Derovs, A and Laivacuma, S and Krumina, A},
title = {Targeting Microbiota: What Do We Know about It at Present?.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {55},
number = {8},
pages = {},
doi = {10.3390/medicina55080459},
pmid = {31405111},
issn = {1648-9144},
abstract = {The human microbiota is a variety of different microorganisms. The composition of microbiota varies from host to host, and it changes during the lifetime. It is known that microbiome may be changed because of a diet, bacteriophages and different processes for example, such as inflammation. Like all other areas of medicine, there is a continuous growth in the area of microbiology. Different microbes can reside in all sites of a human body, even in locations that were previously considered as sterile; for example, liver, pancreas, brain and adipose tissue. Presently one of the etiological factors for liver disease is considered to be pro-inflammatory changes in a host's organism. There are lot of supporting data about intestinal dysbiosis and increased intestinal permeability and its effect on development of liver disease pointing to the gut-liver axis. The gut-liver axis affects pathogenesis of many liver diseases, such as chronic hepatitis B, chronic hepatitis C, alcoholic liver disease, non-alcoholic liver disease, non-alcoholic steatohepatitis, liver cirrhosis and hepatocellular carcinoma. Gut microbiota has been implicated in the regulation of brain health, emphasizing the gut-brain axis. Also, experiments with mice showed that microorganisms have significant effects on the blood-brain barrier integrity. Microbiota can modulate a variety of mechanisms through the gut-liver axis and gut-brain axis. Normal intestinal flora impacts the health of a host in many positive ways, but there is now significant evidence that intestinal microbiota, especially altered, have the ability to impact the pathologies of many diseases through different inflammatory mechanisms. At this point, many of the pathophysiological reactions in case of microbial disbyosis are still unclear.},
}

@article {pmid31405081,
year = {2019},
author = {Tarantola, A and Horwood, PF and Goarant, C and Bertrand, S and Merilles, OEA and Pedron, T and Klement-Frutos, E and Sansonetti, P and Quintana-Murci, L and Richard, V},
title = {Counting Oceanians of Non-European, Non-Asian Descent (ONENA) in the South Pacific to Make Them Count in Global Health.},
journal = {Tropical medicine and infectious disease},
volume = {4},
number = {3},
pages = {},
doi = {10.3390/tropicalmed4030114},
pmid = {31405081},
issn = {2414-6366},
abstract = {Several diseases and vulnerabilities associated with genetic or microbial factors are more frequent among populations of Oceanian, Non-European, Non-Asian descent (ONENA). ONENA are specific and have long been isolated geographically. To our knowledge, there are no published official, quantitative, aggregated data on the populations impacted by these excess vulnerabilities in Oceania. We searched official census reports for updated estimates of the total population for each of the Pacific Island Countries and Territories (including Australia) and the US State of Hawaii, privileging local official statistical or censual sources. We multiplied the most recent total population estimate by the cumulative percentage of the ONENA population as determined in official reports. Including Australia and the US State of Hawaii, Oceania counts 27 countries and territories, populated in 2016 by approximately 41 M inhabitants (17 M not counting Australia) among which approximately 12.5 M (11.6 M not counting Australia) consider themselves of entire or partial ONENA ancestry. Specific genetic and microbiome traits of ONENA may be unique and need further investigation to adjust risk estimates, risk prevention, diagnostic and therapeutic strategies, to the benefit of populations in the Pacific and beyond.},
}

@article {pmid31404532,
year = {2019},
author = {Bajaj, JS and Sharma, A and Dudeja, PK},
title = {Targeting Gut Microbiome Interactions in Service-related Gastrointestinal and Liver Diseases of Veterans: Meeting Summary.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.07.060},
pmid = {31404532},
issn = {1528-0012},
}

@article {pmid31404300,
year = {2019},
author = {Luo, L and Guo, C and Wang, L and Zhang, J and Deng, L and Luo, K and Huang, H and Liu, Y and Mei, X and Zhu, S and Yang, M},
title = {Negative Plant-Soil Feedback Driven by Re-assemblage of the Rhizosphere Microbiome With the Growth of Panax notoginseng.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1597},
doi = {10.3389/fmicb.2019.01597},
pmid = {31404300},
issn = {1664-302X},
abstract = {There is a concerted understanding of the accumulation of soil pathogens as the major driving factor of negative plant-soil feedback (NPSF). However, our knowledge of the connection between plant growth, pathogen build-up and soil microbiome assemblage is limited. In this study, significant negative feedback between the soil and sanqi (Panax notoginseng) was found, which were caused by the build-up of the soil-borne pathogens Fusarium oxysporum, F. solani, and Monographella cucumerina. Soil microbiome analysis revealed that the rhizospheric fungal and bacterial communities were changed with the growth of sanqi. Deep analysis of the phylum and genus levels corroborated that rhizospheric fungal Ascomycota, including the soil-borne pathogens F. oxysporum, F. solani, and especially M. cucumerina, were significantly enriched with the growth of sanqi. However, the bacteria Firmicutes and Acidobacteria, including the genera Pseudomonas, Bacillus, Acinetobacter and Burkholderia, were significantly suppressed with the growth of sanqi. Using microbial isolation and in vitro dual culture tests, we found that most isolates derived from the suppressed bacterial genera showed strong antagonistic ability against the growth of sanqi soil-borne pathogens. Interestingly, inoculation of these suppressed isolates in consecutively cultivated soil could significantly alleviate NPSF. In summary, sanqi growth can suppress antagonistic bacteria through re-assemblage of the rhizosphere microbiome and cause the accumulation of soil-borne pathogens, eventually building negative feedback loops between the soil and plants.},
}

@article {pmid31404278,
year = {2019},
author = {Yurgel, SN and Nearing, JT and Douglas, GM and Langille, MGI},
title = {Metagenomic Functional Shifts to Plant Induced Environmental Changes.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1682},
doi = {10.3389/fmicb.2019.01682},
pmid = {31404278},
issn = {1664-302X},
abstract = {The Vaccinium angustifolium (wild blueberry) agricultural system involves transformation of the environment surrounding the plant to intensify plant propagation and to improve fruit yield, and therefore is an advantageous model to study the interaction between soil microorganisms and plant-host interactions. We studied this system to address the question of a trade-off between microbial adaptation to a plant-influenced environment and its general metabolic capabilities. We found that many basic metabolic functions were similarly represented in bulk soil and rhizosphere microbiomes overall. However, we identified a niche-specific difference in functions potentially beneficial for microbial survival in the rhizosphere but that might also reduce the ability of microbes to withstand stresses in bulk soils. These functions could provide the microbiome with additional capabilities to respond to environmental fluctuations in the rhizosphere triggered by changes in the composition of root exudates. Based on our analysis we hypothesize that the rhizosphere-specific pathways involved in xenobiotics biodegradation could provide the microbiome with functional flexibility to respond to plant stress status.},
}

@article {pmid31404250,
year = {2019},
author = {Abdelfattah, A and Sanzani, SM and Wisniewski, M and Berg, G and Cacciola, SO and Schena, L},
title = {Revealing Cues for Fungal Interplay in the Plant-Air Interface in Vineyards.},
journal = {Frontiers in plant science},
volume = {10},
number = {},
pages = {922},
doi = {10.3389/fpls.2019.00922},
pmid = {31404250},
issn = {1664-462X},
abstract = {Plant-associated microorganisms play a crucial role in plant health and productivity. Belowground microbial diversity is widely reported as a major factor in determining the composition of the plant microbiome. In contrast, much less is known about the role of the atmosphere in relation to the plant microbiome. The current study examined the hypothesis that the atmospheric microbiome influences the composition of fungal communities of the aboveground organs (flowers, fruit, and leaves) of table grape and vice versa. The atmosphere surrounding grape plantings exhibited a significantly higher level of fungal diversity relative to the nearby plant organs and shared a higher number of phylotypes (5,536 OTUs, 40.3%) with the plant than between organs of the same plant. Using a Bayesian source tracking approach, plant organs were determined to be the major source of the atmospheric fungal community (92%). In contrast, airborne microbiota had only a minor contribution to the grape microbiome, representing the source of 15, 4, and 35% of the fungal communities of leaves, flowers, and fruits, respectively. Moreover, data indicate that plant organs and the surrounding atmosphere shared a fraction of each other's fungal communities, and this shared pool of fungal taxa serves as a two-way reservoir of microorganisms. Microbial association analysis highlighted more positive than negative interactions between fungal phylotypes. Positive interactions were more common within the same environment, while negative interactions appeared to occur more frequently between different environments, i.e., atmosphere, leaf, flower, and fruit. The current study revealed the interplay between the fungal communities of the grape phyllosphere with the surrounding air. Plants were identified as a major source of recruitment for the atmospheric microbiome, while the surrounding atmosphere contributed only a small fraction of the plant fungal community. The results of the study suggested that the plant-air interface modulates the plant recruitment of atmospheric fungi, taking a step forward in understanding the plant holobiont assembly and how the atmosphere surrounding plants plays a role in this process. The impact of plants on the atmospheric microbiota has several biological and epidemiological implications for plants and humans.},
}

@article {pmid31403473,
year = {2019},
author = {Robinson, JI and Weir, WH and Crowley, JR and Hink, T and Reske, KA and Kwon, JH and Burnham, CD and Dubberke, ER and Mucha, PJ and Henderson, JP},
title = {Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections.},
journal = {The Journal of clinical investigation},
volume = {130},
number = {},
pages = {},
doi = {10.1172/JCI126905},
pmid = {31403473},
issn = {1558-8238},
abstract = {Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization.},
}

@article {pmid31403049,
year = {2019},
author = {Tibbs, TN and Lopez, LR and Arthur, JC},
title = {The influence of the microbiota on immune development, chronic inflammation, and cancer in the context of aging.},
journal = {Microbial cell (Graz, Austria)},
volume = {6},
number = {8},
pages = {324-334},
doi = {10.15698/mic2019.08.685},
pmid = {31403049},
issn = {2311-2638},
abstract = {From birth, the microbiota plays an essential role in human development by educating host immune responses. Proper maturation of the immune system perturbs chronic inflammation and the pathogenesis of disease by preventing inappropriate immune responses. While many have detailed the roles of specific microbial groups in immune development and human disease, it remains to be elucidated how the microbiota influences the immune system during aging. Furthermore, it is not yet understood how age-related changes to the microbiota and immune system influence the development of age-related diseases. In this review, we outline the role of the microbiota in immune system development as well as functional changes that occur to immune cell populations during immunosenescence. In addition, we highlight how commensal microbes influence the pathogenesis of cancer, a prominent disease of aging. The information provided herein suggests that age-related changes to the microbiota and immune system should be considered in disease treatment and prevention strategies.},
}

@article {pmid31403004,
year = {2019},
author = {Kauser, I and Ciesielski, M and Poretsky, RS},
title = {Ultraviolet disinfection impacts the microbial community composition and function of treated wastewater effluent and the receiving urban river.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7455},
doi = {10.7717/peerj.7455},
pmid = {31403004},
issn = {2167-8359},
abstract = {Background: In the United States, an estimated 14,748 wastewater treatment plants (WWTPs) provide wastewater collection, treatment, and disposal service to more than 230 million people. The quality of treated wastewater is often assessed by the presence or absence of fecal indicator bacteria. UV disinfection of wastewater is a common final treatment step used by many wastewater treatment plants in order to reduce fecal coliform bacteria and other pathogens; however, its potential impacts on the total effluent bacterial community are seemingly varied. This is especially important given that urban WWTPs typically return treated effluent to coastal and riverine environments and thus are a major source of microorganisms, genes, and chemical compounds to these systems. Following rainfall, stormflow conditions can result in substantial increases to effluent flow into combined systems.

Methods: Here, we conducted a lab-scale UV disinfection on WWTP effluent using UV dosage of 100 mJ/cm2 and monitored the active microbiome in UV-treated effluent and untreated effluent over the course of 48 h post-exposure using 16S rRNA sequencing. In addition, we simulated stormflow conditions with effluent UV-treated and untreated effluent additions to river water and compared the microbial communities to those in baseflow river water. We also tracked the functional profiles of genes involved in tetracycline resistance (tetW) and nitrification (amoA) in these microcosms using RT-qPCR.

Results: We showed that while some organisms, such as members of the Bacteroidetes, are inhibited by UV disinfection and overall diversity of the microbial community decreases following treatment, many organisms not only survive, but remain active. These include common WWTP-derived organisms such as Comamonadaceae and Pseudomonas. When combined with river water to mimic stormflow conditions, these organisms can persist in the environment and potentially enhance microbial functions such as nitrification and antibiotic resistance.},
}

@article {pmid31402678,
year = {2019},
author = {Martin, J},
title = {Reproducibility: the search for microbiome standards.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {},
doi = {10.2144/btn-2019-0096},
pmid = {31402678},
issn = {1940-9818},
abstract = {The reproducibility crisis is resulting in a lot of discussion in various scientific fields. This feature explores the latest technologies, methods and projects relevant to the biological laboratory and aiming to solve this problem.},
}

@article {pmid31402478,
year = {2019},
author = {Veit-Rubin, N and De Tayrac, R and Cartwright, R and Franklin-Revill, L and Warembourg, S and Dunyach-Remy, C and Lavigne, JP and Khullar, V},
title = {Abnormal vaginal microbiome associated with vaginal mesh complications.},
journal = {Neurourology and urodynamics},
volume = {},
number = {},
pages = {},
doi = {10.1002/nau.24129},
pmid = {31402478},
issn = {1520-6777},
abstract = {AIMS: To identify differences in the vaginal microbiomes of women after transvaginal mesh (TVM) surgery for pelvic organ prolapse with and without mesh-associated complications.

METHODS: Patients with complications were eligible as cases, patients without as controls. DNA was isolated and the V1-2 region of the 16S ribosomal RNA gene was amplified and sequenced. Overall richness was quantified using Chao1. Overall diversity was expressed as Shannon diversity and screened for group differences using analysis of variance. Multivariate differences among groups were evaluated with functions from R.

RESULTS: We recruited 14 patients after mesh exposure, 5 after contraction, and 21 as controls. The average number of operational taxonomic unit was 74.79 (SD ± 63.91) for controls, 57.13 (SD ± 58.74) after exposures, and 92.42 (SD ± 50.01) after contractions. Total 89.6% of bacteria in controls, 86.4% in previous exposures, and 81.3% in contractions were classified as either Firmicutes, Proteobacteria, or Actinobacteria (P < .001). Veillonella spp. was more abundant in patients after contraction (P = .045). The individual microbiomes varied, and we did not detect any significant differences in richness but a trend towards higher diversity with complications.

CONCLUSIONS: The presence of Veillonella spp. could be associated with mesh contraction. Our study did not identify vaginal microbiotic dysbiosis as a factor associated with exposure. Larger cohort studies would be needed to distinguish the vaginal microbiome of women predisposed to mesh-related complications for targeted phenotyping of patients who could benefit from TVM surgery.},
}

@article {pmid31402327,
year = {2019},
author = {Pietzke, M and Meiser, J and Vazquez, A},
title = {Formate metabolism in health and disease.},
journal = {Molecular metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmet.2019.05.012},
pmid = {31402327},
issn = {2212-8778},
abstract = {BACKGROUND: Formate is a one-carbon molecule at the crossroad between cellular and whole body metabolism, between host and microbiome metabolism, and between nutrition and toxicology. This centrality confers formate with a key role in human physiology and disease that is currently unappreciated.

SCOPE OF REVIEW: Here we review the scientific literature on formate metabolism, highlighting cellular pathways, whole body metabolism, and interactions with the diet and the gut microbiome. We will discuss the relevance of formate metabolism in the context of embryonic development, cancer, obesity, immunometabolism, and neurodegeneration.

MAJOR CONCLUSIONS: We will conclude with an outlook of some open questions bringing formate metabolism into the spotlight.},
}

@article {pmid31402227,
year = {2019},
author = {Abreu, DPB and Peixoto, MP and Luz, HR and Zeringóta, V and Santolin, ÍDAC and Famadas, KM and Faccini, JLH and McIntosh, D},
title = {Two for the price of one: Co-infection with Rickettsia bellii and spotted fever group Rickettsia in Amblyomma (Acari: Ixodidae) ticks recovered from wild birds in Brazil.},
journal = {Ticks and tick-borne diseases},
volume = {},
number = {},
pages = {101266},
doi = {10.1016/j.ttbdis.2019.101266},
pmid = {31402227},
issn = {1877-9603},
abstract = {The bacterium Rickettsia bellii has been detected in 25 species of ticks in the American continents, but its pathogenic potential is considered as undetermined. A possible role for this species in the phenomenon of transovarial exclusion of pathogenic members of the spotted fever group (SFG) of Rickettsia has been suggested and co-infections with pathogenic species have been reported infrequently in both North and South America. Traditional methods for the molecular detection of rickettsial agents in ticks focus largely on the identification of sequences found in SFG Rickettsia, an approach that may overlook the presence of co-infections with R. bellii. Two novel, species-specific polymerase chain reaction (PCR) assays, targeting the genes encoding the surface cell antigen (Sca), autotransporter proteins sca9 and sca14, were developed and validated for the detection of R. bellii using 150 Amblyomma ticks collected from wild birds in Brazil. Co-infection of R. bellii infected ticks was evaluated using a novel PCR assay targeting the ompA sequence characteristic of SFG Rickettsia. Preliminary species-level identification was achieved by restriction fragment length polymorphism (RFLP) analysis and subsequently confirmed by sequencing of amplicons. Nine out of seventy-three Amblyomma longirostre and one of two Amblyomma calcaratum ticks were shown to be co-infected with R. bellii and Rickettsia amblyommatis, while two out of sixty-seven Amblyomma sp. haplotype Nazaré ticks were recorded as co-infected with R. bellii and the Rickettsia parkeri-like bacterium, strain ApPR. Interestingly, our data represent the first records of R. bellii in association with A. calcaratum and Amblyomma sp. haplotype Nazaré. The novel PCR-RFLP systems reported herein, provide an alternative, rapid and cost-efficient (relative to strategies based on sequencing or real-time PCR), approach to evaluate rickettsial co-infection of ticks, a potentially significant phenomenon that has most likely been underestimated to date.},
}

@article {pmid31401751,
year = {2019},
author = {Chen, J and Yu, B and Chen, D and Zheng, P and Luo, Y and Huang, Z and Luo, J and Mao, X and Yu, J and He, J},
title = {Changes of porcine gut microbiota in response to dietary chlorogenic acid supplementation.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10025-8},
pmid = {31401751},
issn = {1432-0614},
support = {2016TD0028//the Youth Innovation teams of animal Feed Biotechnology of Sichuan Province/ ; 2018NZDZX0005//the key Research and Development program of Sichuan Province/ ; },
abstract = {Chlorogenic acids (CGA), the most abundant natural polyphenol present in human diet and plants, have attracted considerable research interest because of their broad bioactivities including the antimicrobial activity. However, little is known about their influences on intestinal bacterial communities. Here, we described a response in intestinal microbiome to CGA using a porcine model. Twenty-four weaned pigs were allotted to two groups and fed with a basal diet or a basal diet containing 1000 mg/kg CGA. Results showed that CGA significantly increased the length of the small intestine (P < 0.05) and enhanced the activity of diamine oxidase (DAO) and the concentration of MHC-II in the jejunal and ileal mucosa (P < 0.05). Moreover, the acetate concentration in ileum and cecum digesta, and the propionate and butyrate concentrations in the cecum digesta, were significantly elevated by CGA (P < 0.05). Interestingly, CGA significantly increased the total 16S rRNA gene copies and bacterial alpha diversity in the cecum (P < 0.05). The relative abundance of bacteria from phyla Firmicutes and Bacteroidetes was increased in the cecum digesta (P < 0.05), whereas the abundance of bacteria from phylum Protebacteria was decreased by CGA (P < 0.05). Importantly, pigs on CGA-containing diet had higher abundance of Lactobacillus spp., Prevotella spp., Anaerovibrio spp., and Alloprevotella spp. in the cecum (P < 0.05). Not only did our study suggest a synergic response of intestinal barrier function and microbiota to the CGA, but the result will also contribute to understanding of the mechanisms behind the CGA-modulated gut health.},
}

@article {pmid31401351,
year = {2019},
author = {Acker, KP and Wong Fok Lung, T and West, E and Craft, J and Narechania, A and Smith, H and O'Brien, K and Moustafa, AM and Lauren, C and Planet, PJ and Prince, A},
title = {Strains of Staphylococcus aureus that Colonize and Infect Skin Harbor Mutations in Metabolic Genes.},
journal = {iScience},
volume = {19},
number = {},
pages = {281-290},
doi = {10.1016/j.isci.2019.07.037},
pmid = {31401351},
issn = {2589-0042},
abstract = {Staphylococcus aureus is the most common cause of skin and soft tissue infections, yet the bacterial genetic changes associated with adaptation to human skin are not well characterized. S. aureus strains isolated from patients with chronic skin colonization and intermittent infection were used to determine the staphylococcal genotypes or phenotypes associated with adaptation to human skin. We demonstrate that polymorphisms in metabolic genes, particularly those involved in the tricarboxylic acid cycle, the fumarate-succinate axis, and the generation of terminal electron transporters, are unexpectedly common. These skin-adapted strains activated glycolysis and hypoxia-inducible factor-1α, interleukin (IL)-1β, and IL-18 release from keratinocytes and promoted dermatopathology equivalent to a methicillin-resistant Staphylococcus aureus USA300 control in a murine model of infection. However, in contrast to USA300, a skin-adapted isolate failed to generate protection from a secondary infectious challenge. Within the context of human skin, there appears to be selection for S. aureus metabolic adaptive changes that promote glycolysis and maintain pathogenicity.},
}

@article {pmid31400786,
year = {2019},
author = {Li, JW and Fang, B and Pang, GF and Zhang, M and Ren, FZ},
title = {Age- and diet-specific effects of chronic exposure to chlorpyrifos on hormones, inflammation and gut microbiota in rats.},
journal = {Pesticide biochemistry and physiology},
volume = {159},
number = {},
pages = {68-79},
doi = {10.1016/j.pestbp.2019.05.018},
pmid = {31400786},
issn = {1095-9939},
abstract = {Chlorpyrifos is a pesticide frequently detected in food and has been reported to disturb endocrine and gut health, which was regulated by gut microbiota and enteroendocrine cells. In this study, newly weaned (3 week) and adult (8 week) male rats fed a normal- or high- fat diet were chronically exposed to 0.3 mg chlorpyrifos/kg bodyweight/day. The effects of chlorpyrifos exposure on serum hormone levels, proinflammatory cytokines and gut microbiota were evaluated. Chronic exposure to chlorpyrifos significantly decreased the concentrations of luteinizing hormone, follicule stimulating hormone and testosterone, which was found only in the normal-fat diet. The counteracted effect of high-fat diet was also found in gut hormones and proinflammatory cytokines. Significantly higher concentrations of glucagon-like peptide-1, pancreatic polypeptide, peptide tyrosine tyrosine (PYY), ghrelin, gastric inhibitory poly-peptide, IL-6, monocyte chemoattractant protein-1, and TNF-α were found in rats exposed to chlorpyrifos beginning at newly weaned, whereas only the PYY, ghrelin and IL-6 concentrations increased significantly in rats exposed in adulthood. Furthermore, a decrease in epinephrine induced by chlorpyrifos exposure was found in rats exposed to chlorpyrifos beginning at newly weaned, regardless of their diet. Chlorpyrifos-induced disturbances in the microbiome community structure were more apparent in rats fed a high-fat diet and exposed beginning at newly weaned. The affected bacteria included short-chain fatty acid-producing bacteria (Romboutsia, Turicibacter, Clostridium sensu stricto 1, norank_f_Coriobacteriaceae, Faecalibaculum, Parasutterella and norank_f__Erysipelotrichaceae), testosterone-related genus (Turicibacter, Brevibacterium), pathogenic bacteria (Streptococcus), and inflammation-related bacteria (unclassified_f__Ruminococcaceae, Ruminococcaceae_UCG-009, Parasutterella, Oscillibacter), which regulated the endocrine system via the hypothalamic-pituitary-adrenal axis, as well as the immune response and gut barrier. Early exposure accelerated the endocrine-disturbing effect and immune responses of chlorpyrifos, although these effects can be eased or recovered by a high-fat diet. This study helped clarify the relationship between disrupted endocrine function and gut microbiota dysbiosis induced by food contaminants such as pesticides.},
}

@article {pmid31400403,
year = {2019},
author = {Shamoon, M and Martin, NM and L O'Brien, C},
title = {Recent Advances in Gut Microbiota Mediated Therapeutic Targets in Inflammatory Bowel Diseases: Emerging Modalities for Future Pharmacological Implications.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {104344},
doi = {10.1016/j.phrs.2019.104344},
pmid = {31400403},
issn = {1096-1186},
abstract = {The inflammatory bowel diseases (IBDs) are chronic inflammatory conditions, which are increasing in prevalence worldwide. The IBDs are thought to result from an aberrant immune response to gut microbes in genetically susceptible individuals. Dysbiosis of the gut microbiome, both functional and compositional, promotes patient susceptibility to colonization by pathobionts. Manipulating gut microbial communities and gut microbiota-immune system interactions to restore gut homeostasis or reduce inflammation are appealing therapeutic models. We discuss the therapeutic potential of precision microbiota editing, natural and engineered probiotics, the use of gut microbiota-derived metabolites in colitogenic phenotypes, and intestinal stem cells, in maintaining gut microbiota balance, restoring the mucosal barrier, and having positive immunomodulatory effects in experimental IBD. This review highlights that we are only just beginning to understand the complexity of the microbiota and how it can be manipulated for health benefits, including treatment and prevention of the clinical IBDs in future.},
}

@article {pmid31400370,
year = {2019},
author = {Engevik, M and Versalovic, J},
title = {Taking a Closer Look at the Biogeography of the Human Gastrointestinal Microbiome.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.08.006},
pmid = {31400370},
issn = {1528-0012},
}

@article {pmid31399743,
year = {2019},
author = {Bascuñán, KA and Araya, M and Roncoroni, L and Doneda, L and Elli, L},
title = {Dietary Gluten as a Conditioning Factor of the Gut Microbiota in Celiac Disease.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/advances/nmz080},
pmid = {31399743},
issn = {2156-5376},
abstract = {The gut microbiota plays a relevant role in determining an individual's health status, and the diet is a major factor in modulating the composition and function of gut microbiota. Gluten constitutes an essential dietary component in Western societies and is the environmental trigger of celiac disease. The presence/absence of gluten in the diet can change the diversity and proportions of the microbial communities constituting the gut microbiota. There is an intimate relation between gluten metabolism and celiac disease pathophysiology and gut microbiota; their interrelation defines intestinal health and homeostasis. Environmental factors modify the intestinal microbiota and, in turn, its changes modulate the mucosal and immune responses. Current evidence from studies of young and adult patients with celiac disease increasingly supports that dysbiosis (i.e., compositional and functional alterations of the gut microbiome) is present in celiac disease, but to what extent this is a cause or consequence of the disease and whether the different intestinal diseases (celiac disease, ulcerative colitis, Crohn disease) have specific change patterns is not yet clear. The use of bacterial-origin enzymes that help completion of gluten digestion is of interest because of the potential application as coadjuvant in the current treatment of celiac disease. In this narrative review, we address the current knowledge on the complex interaction between gluten digestion and metabolism, celiac disease, and the intestinal microbiota.},
}

@article {pmid31399723,
year = {2019},
author = {Bolyen, E and Rideout, JR and Dillon, MR and Bokulich, NA and Abnet, CC and Al-Ghalith, GA and Alexander, H and Alm, EJ and Arumugam, M and Asnicar, F and Bai, Y and Bisanz, JE and Bittinger, K and Brejnrod, A and Brislawn, CJ and Brown, CT and Callahan, BJ and Caraballo-Rodríguez, AM and Chase, J and Cope, EK and Da Silva, R and Diener, C and Dorrestein, PC and Douglas, GM and Durall, DM and Duvallet, C and Edwardson, CF and Ernst, M and Estaki, M and Fouquier, J and Gauglitz, JM and Gibbons, SM and Gibson, DL and Gonzalez, A and Gorlick, K and Guo, J and Hillmann, B and Holmes, S and Holste, H and Huttenhower, C and Huttley, GA and Janssen, S and Jarmusch, AK and Jiang, L and Kaehler, BD and Kang, KB and Keefe, CR and Keim, P and Kelley, ST and Knights, D and Koester, I and Kosciolek, T and Kreps, J and Langille, MGI and Lee, J and Ley, R and Liu, YX and Loftfield, E and Lozupone, C and Maher, M and Marotz, C and Martin, BD and McDonald, D and McIver, LJ and Melnik, AV and Metcalf, JL and Morgan, SC and Morton, JT and Naimey, AT and Navas-Molina, JA and Nothias, LF and Orchanian, SB and Pearson, T and Peoples, SL and Petras, D and Preuss, ML and Pruesse, E and Rasmussen, LB and Rivers, A and Robeson, MS and Rosenthal, P and Segata, N and Shaffer, M and Shiffer, A and Sinha, R and Song, SJ and Spear, JR and Swafford, AD and Thompson, LR and Torres, PJ and Trinh, P and Tripathi, A and Turnbaugh, PJ and Ul-Hasan, S and van der Hooft, JJJ and Vargas, F and Vázquez-Baeza, Y and Vogtmann, E and von Hippel, M and Walters, W and Wan, Y and Wang, M and Warren, J and Weber, KC and Williamson, CHD and Willis, AD and Xu, ZZ and Zaneveld, JR and Zhang, Y and Zhu, Q and Knight, R and Caporaso, JG},
title = {Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41587-019-0252-6},
pmid = {31399723},
issn = {1546-1696},
abstract = {An amendment to this paper has been published and can be accessed via a link at the top of the paper.},
}

@article {pmid31399563,
year = {2019},
author = {Russell, JT and Roesch, LFW and Ördberg, M and Ilonen, J and Atkinson, MA and Schatz, DA and Triplett, EW and Ludvigsson, J},
title = {Genetic risk for autoimmunity is associated with distinct changes in the human gut microbiome.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {3621},
doi = {10.1038/s41467-019-11460-x},
pmid = {31399563},
issn = {2041-1723},
support = {-INO-2018-637-A-N//JDRF/United States ; },
abstract = {Susceptibility to many human autoimmune diseases is under strong genetic control by class II human leukocyte antigen (HLA) allele combinations. These genes remain by far the greatest risk factors in the development of type 1 diabetes and celiac disease. Despite this, little is known about HLA influences on the composition of the human gut microbiome, a potential source of environmental influence on disease. Here, using a general population cohort from the All Babies in Southeast Sweden study, we report that genetic risk for developing type 1 diabetes autoimmunity is associated with distinct changes in the gut microbiome. Both the core microbiome and beta diversity differ with HLA risk group and genotype. In addition, protective HLA haplotypes are associated with bacterial genera Intestinibacter and Romboutsia. Thus, general population cohorts are valuable in identifying potential environmental triggers or protective factors for autoimmune diseases that may otherwise be masked by strong genetic control.},
}

@article {pmid31399369,
year = {2019},
author = {Thingholm, LB and Rühlemann, MC and Koch, M and Fuqua, B and Laucke, G and Boehm, R and Bang, C and Franzosa, EA and Hübenthal, M and Rahnavard, A and Frost, F and Lloyd-Price, J and Schirmer, M and Lusis, AJ and Vulpe, CD and Lerch, MM and Homuth, G and Kacprowski, T and Schmidt, CO and Nöthlings, U and Karlsen, TH and Lieb, W and Laudes, M and Franke, A and Huttenhower, C},
title = {Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2019.07.004},
pmid = {31399369},
issn = {1934-6069},
abstract = {Obesity and type 2 diabetes (T2D) are metabolic disorders that are linked to microbiome alterations. However, their co-occurrence poses challenges in disentangling microbial features unique to each condition. We analyzed gut microbiomes of lean non-diabetic (n = 633), obese non-diabetic (n = 494), and obese individuals with T2D (n = 153) from German population and metabolic disease cohorts. Microbial taxonomic and functional profiles were analyzed along with medical histories, serum metabolomics, biometrics, and dietary data. Obesity was associated with alterations in microbiome composition, individual taxa, and functions with notable changes in Akkermansia, Faecalibacterium, Oscillibacter, and Alistipes, as well as in serum metabolites that correlated with gut microbial patterns. However, microbiome associations were modest for T2D, with nominal increases in Escherichia/Shigella. Medications, including antihypertensives and antidiabetics, along with dietary supplements including iron, were significantly associated with microbiome variation. These results differentiate microbial components of these interrelated metabolic diseases and identify dietary and medication exposures to consider in future studies.},
}

@article {pmid31399081,
year = {2019},
author = {Jiang, P and Green, SJ and Chlipala, GE and Turek, FW and Vitaterna, MH},
title = {Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {113},
doi = {10.1186/s40168-019-0724-4},
pmid = {31399081},
issn = {2049-2618},
support = {NNX15AL05G/NASA/NASA/United States ; },
abstract = {BACKGROUND: Space environment imposes a range of challenges to mammalian physiology and the gut microbiota, and interactions between the two are thought to be important in mammalian health in space. While previous findings have demonstrated a change in the gut microbial community structure during spaceflight, specific environmental factors that alter the gut microbiome and the functional relevance of the microbiome changes during spaceflight remain elusive.

METHODS: We profiled the microbiome using 16S rRNA gene amplicon sequencing in fecal samples collected from mice after a 37-day spaceflight onboard the International Space Station. We developed an analytical tool, named STARMAPs (Similarity Test for Accordant and Reproducible Microbiome Abundance Patterns), to compare microbiome changes reported here to other relevant datasets. We also integrated the gut microbiome data with the publically available transcriptomic data in the liver of the same animals for a systems-level analysis.

RESULTS: We report an elevated microbiome alpha diversity and an altered microbial community structure that were associated with spaceflight environment. Using STARMAPs, we found the observed microbiome changes shared similarity with data reported in mice flown in a previous space shuttle mission, suggesting reproducibility of the effects of spaceflight on the gut microbiome. However, such changes were not comparable with those induced by space-type radiation in Earth-based studies. We found spaceflight led to significantly altered taxon abundance in one order, one family, five genera, and six species of microbes. This was accompanied by a change in the inferred microbial gene abundance that suggests an altered capacity in energy metabolism. Finally, we identified host genes whose expression in the liver were concordantly altered with the inferred gut microbial gene content, particularly highlighting a relationship between host genes involved in protein metabolism and microbial genes involved in putrescine degradation.

CONCLUSIONS: These observations shed light on the specific environmental factors that contributed to a robust effect on the gut microbiome during spaceflight with important implications for mammalian metabolism. Our findings represent a key step toward a better understanding the role of the gut microbiome in mammalian health during spaceflight and provide a basis for future efforts to develop microbiota-based countermeasures that mitigate risks to crew health during long-term human space expeditions.},
}

@article {pmid31398959,
year = {2019},
author = {Brosseau, C and Selle, A and Palmer, DJ and Prescott, SL and Barbarot, S and Bodinier, M},
title = {Prebiotics: Mechanisms and Preventive Effects in Allergy.},
journal = {Nutrients},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/nu11081841},
pmid = {31398959},
issn = {2072-6643},
abstract = {Allergic diseases now affect over 30% of individuals in many communities, particularly young children, underscoring the need for effective prevention strategies in early life. These allergic conditions have been linked to environmental and lifestyle changes driving the dysfunction of three interdependent biological systems: microbiota, epithelial barrier and immune system. While this is multifactorial, dietary changes are of particular interest in the altered establishment and maturation of the microbiome, including the associated profile of metabolites that modulate immune development and barrier function. Prebiotics are non-digestible food ingredients that beneficially influence the health of the host by 1) acting as a fermentable substrate for some specific commensal host bacteria leading to the release of short-chain fatty acids in the gut intestinal tract influencing many molecular and cellular processes; 2) acting directly on several compartments and specifically on different patterns of cells (epithelial and immune cells). Nutrients with prebiotic properties are therefore of central interest in allergy prevention for their potential to promote a more tolerogenic environment through these multiple pathways. Both observational studies and experimental models lend further credence to this hypothesis. In this review, we describe both the mechanisms and the therapeutic evidence from preclinical and clinical studies exploring the role of prebiotics in allergy prevention.},
}

@article {pmid31398880,
year = {2019},
author = {Robinson, H and Barrett, H and Gomez-Arango, L and McIntyre, HD and Callaway, L and Dekker Nitert, M},
title = {Ketonuria Is Associated with Changes to the Abundance of Roseburia in the Gut Microbiota of Overweight and Obese Women at 16 Weeks Gestation: A Cross-Sectional Observational Study.},
journal = {Nutrients},
volume = {11},
number = {8},
pages = {},
doi = {10.3390/nu11081836},
pmid = {31398880},
issn = {2072-6643},
support = {1028575//National Health and Medical Research Council/ ; },
abstract = {The gut microbiome in pregnancy has been associated with various maternal metabolic and hormonal markers involved in glucose metabolism. Maternal ketones are of particular interest due to the rise in popularity of low-carbohydrate diets. We assessed for differences in the composition of the gut microbiota in pregnant women with and without ketonuria at 16 weeks gestation. Fecal samples were obtained from 11 women with fasting ketonuria and 11 matched controls. The samples were analyzed to assess for differences in gut microbiota composition by 16S rRNA sequencing. Supervised hierarchical clustering analysis showed significantly different beta-diversity between women with and without ketonuria, but no difference in the alpha-diversity. Group comparisons and network analysis showed that ketonuria was associated with an increased abundance of the butyrate-producing genus Roseburia. The bacteria that contributed the most to the differences in the composition of the gut microbiota included Roseburia, Methanobrevibacter, Uncl. RF39, and Dialister in women with ketonuria and Eggerthella, Phascolarctobacterium, Butyricimonas, and Uncl. Coriobacteriaceae in women without ketonuria. This study found that the genus Roseburia is more abundant in the gut microbiota of pregnant women with ketonuria. Roseburia is a butyrate producing bacterium and may increase serum ketone levels.},
}

@article {pmid31398630,
year = {2019},
author = {Mortelé, O and Iturrospe, E and Breynaert, A and Verdickt, E and Xavier, BB and Lammens, C and Malhotra-Kumar, S and Jorens, PG and Pieters, L and van Nuijs, ALN and Hermans, N},
title = {Optimization of an in vitro gut microbiome biotransformation platform with chlorogenic acid as model compound: From fecal sample to biotransformation product identification.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {175},
number = {},
pages = {112768},
doi = {10.1016/j.jpba.2019.07.016},
pmid = {31398630},
issn = {1873-264X},
abstract = {Recent data clearly show that the gut microbiota plays a significant role in the biotransformation of many endogenous molecules and xenobiotics, leading to a potential influence of this microbiotic metabolism on activation, inactivation and possible toxicity of these compounds. To study the colonic biotransformation of xenobiotics by the gut microbiome, in vitro models are often used as they allow dynamic and multiple sampling overtime. However, the pre-analytical phase should be carefully optimized to enable biotransformation product identification representative for the in vivo situation. During this study, chlorogenic acid was used as a model compound to optimize a ready-to-use gut microbiome biotransformation platform using an in vitro gastrointestinal dialysis-model with colon phase together with an instrumental platform using liquid chromatography coupled to high resolution mass spectrometry (LC-QTOF-MS). Identification of the biotransformation products of chlorogenic acid was performed using complementary suspect and non-targeted data analysis approaches (MZmine + R and MPP workflow). Concerning the pre-analytical phase, (i) the influence of different incubation media (Wilkins-Chalgren Anaerobic Broth (WCB) and (versus) phosphate buffer) and different incubation times (prior to implementation in the colonic stage of the dialysis model) on fecal bacterial composition and concentration were investigated and (ii) four different sample preparation methods (centrifugation, extraction, sonication and freeze-drying) were evaluated targeting colonic biotransformation of chlorogenic acid. WCB as incubation medium showed to introduce substantial variation in the bacterial composition of the fecal samples, while the sterile phosphate buffer guaranteed a closer resemblance to the in vivo composition. Furthermore, incubation during 24 h in sterile phosphate buffer as medium showed no significant increase or decrease in anaerobic bacterial concentration, concluding that incubation prior to the colonic stage is not needed. Concerning sample preparation, centrifugation, sonication and extraction gave similar results, while freeze-drying appeared to be inferior. The extraction method was selected as an optimal sample preparation method given the quick execution together with a good instrumental sensitivity. This study optimized a ready-to-use platform to investigate colonic biotransformation of xenobiotics by using chlorogenic acid as a model compound. This platform can be used in the future to study differences in colonic biotransformation of xenobiotics using fecal samples of different patient groups.},
}

@article {pmid31398337,
year = {2019},
author = {Riquelme, E and Zhang, Y and Zhang, L and Montiel, M and Zoltan, M and Dong, W and Quesada, P and Sahin, I and Chandra, V and San Lucas, A and Scheet, P and Xu, H and Hanash, SM and Feng, L and Burks, JK and Do, KA and Peterson, CB and Nejman, D and Tzeng, CD and Kim, MP and Sears, CL and Ajami, N and Petrosino, J and Wood, LD and Maitra, A and Straussman, R and Katz, M and White, JR and Jenq, R and Wargo, J and McAllister, F},
title = {Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes.},
journal = {Cell},
volume = {178},
number = {4},
pages = {795-806.e12},
doi = {10.1016/j.cell.2019.07.008},
pmid = {31398337},
issn = {1097-4172},
abstract = {Most patients diagnosed with resected pancreatic adenocarcinoma (PDAC) survive less than 5 years, but a minor subset survives longer. Here, we dissect the role of the tumor microbiota and the immune system in influencing long-term survival. Using 16S rRNA gene sequencing, we analyzed the tumor microbiome composition in PDAC patients with short-term survival (STS) and long-term survival (LTS). We found higher alpha-diversity in the tumor microbiome of LTS patients and identified an intra-tumoral microbiome signature (Pseudoxanthomonas-Streptomyces-Saccharopolyspora-Bacillus clausii) highly predictive of long-term survivorship in both discovery and validation cohorts. Through human-into-mice fecal microbiota transplantation (FMT) experiments from STS, LTS, or control donors, we were able to differentially modulate the tumor microbiome and affect tumor growth as well as tumor immune infiltration. Our study demonstrates that PDAC microbiome composition, which cross-talks to the gut microbiome, influences the host immune response and natural history of the disease.},
}

@article {pmid31397072,
year = {2019},
author = {Jones, BP and Saso, S and L'Heveder, A and Bracewell-Milnes, T and Thum, MY and Diaz-Garcia, C and MacIntyre, DA and Quiroga, I and Ghaem-Maghami, S and Testa, G and Johannesson, L and Bennett, PR and Yazbek, J and Smith, JR},
title = {The vaginal microbiome in uterine transplantation.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.15881},
pmid = {31397072},
issn = {1471-0528},
abstract = {Women with congenital absolute uterine factor infertility (AUFI) often need vaginal restoration to optimise sexual function. Given their lack of procreative ability, little consideration has previously been given to the resultant vaginal microbiome (VM). Uterine transplantation (UTx) now offers the opportunity to restore these women's reproductive potential. The structure of the VM is associated with clinical and reproductive implications that are intricately intertwined with the process of UTx. Consideration of how vaginal restoration methods impact VM is now warranted and assessment of the VM in future UTx procedures is essential to understand the interrelation of the VM and clinical and reproductive outcomes. TWEETABLE ABSTRACT: The vaginal microbiome has numerous implications for clinical and reproductive outcomes in the context of uterine transplantation.},
}

@article {pmid31397054,
year = {2019},
author = {Payne, D and Dunham, EC and Mohr, E and Miller, I and Arnold, A and Erickson, R and Fones, EM and Lindsay, MR and Colman, DR and Boyd, ES},
title = {Geologic legacy spanning >90 years explains unique Yellowstone hot spring geochemistry and biodiversity.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14775},
pmid = {31397054},
issn = {1462-2920},
abstract = {Little is known about how the geological history of an environment shapes its physical and chemical properties and how these, in turn, influence the assembly of communities. Evening Primrose (EP), a moderately acidic hot spring (pH 5.6, 77.4°C) in Yellowstone National Park (YNP), has undergone dramatic physicochemical change linked to seismic activity. Here, we show that this legacy of geologic change led to the development of an unusual sulfur-rich, anoxic chemical environment that supports a unique archaeal-dominated and anaerobic microbial community. Metagenomic sequencing and informatics analyses reveal that >96% of this community is supported by dissimilatory reduction or disproportionation of inorganic sulfur compounds, including a novel, deeply diverging sulfate reducing thaumarchaeote. When compared to other YNP metagenomes, the inferred functions of EP populations were like those from sulfur-rich acidic springs, suggesting that sulfur may overprint the predominant influence of pH on the composition of hydrothermal communities. Together, these observations indicate that the dynamic geological history of EP underpins its unique geochemistry and biodiversity, emphasizing the need to consider the legacy of geologic change when describing processes that shape the assembly of communities. Originality-Significance Statement All environments are geologically dynamic over varying timescales. However, how the legacy of geologic change influences the physical and chemical properties of an environment and how these, in turn, influence the assembly of microbiomes is understudied. Here, we examine the recent geologic history of a well-studied hydrothermal system in Yellowstone National Park and show that its legacy of geologic change led to the development of an unusual sulfur-rich, anoxic chemical environment that supports a unique archaeal-dominated microbiome. The energy metabolism of >96% of the community is supported by anaerobic dissimilation of inorganic sulfur, including that of a novel sulfate reducing thaumarchaote. The results provide new insight into thermophilic sulfur cycling and underscore the need to consider the legacy of geologic and environmental change when describing processes that shape the assembly of communities. This article is protected by copyright. All rights reserved.},
}

@article {pmid31396795,
year = {2019},
author = {Athanasiou, S and Pitsouni, E and Douskos, A and Salvatore, S and Loutradis, D and Grigoriadis, T},
title = {Intravaginal energy-based devices and sexual health of female cancer survivors: a systematic review and meta-analysis.},
journal = {Lasers in medical science},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10103-019-02855-9},
pmid = {31396795},
issn = {1435-604X},
abstract = {A systematic review and meta-analysis was undertaken to assess the efficacy and safety of intravaginal energy-based therapies (laser and radiofrequency) on sexual health of cancer survivors (CS) (breast cancer (BCS) and/or gynecological cancer (GCS)). PubMed, Scopus, Web of Science, and Cochrane Library were searched until 21/02/2019. Quality of reporting, methodology, and body of evidence were assessed using STROBE, MINORS, and GRADE. Primary outcomes were dyspareunia, dryness, and sexual health (FSFI, FSDS-R). Secondary outcomes were burning, itching, dysuria, incontinence, Vaginal Health Index Score (VHIS), microbiome-cytokine evaluation, and adverse events. Main analyses, subgroup analyses, and sensitivity analyses were performed. Eight observational studies (n = 274) were eligible for inclusion. None of the studies evaluated radiofrequency. BCS and BCS-GCS were included in 87% and 13% of studies, respectively. All primary outcomes improved significantly with the exception of FSDS-R (dyspareunia (5 studies (n = 233), standardized mean difference (StdMD) (- 1.17), 95%CI [- 1.59, - 0.75]; p < 0.001; I2 = 55%), vaginal dryness (4 studies (n = 183), StdMD (- 1.98), 95%CI [- 3.31, - 0.65]; p = 0.003; I2 = 91%), FSFI (2 studies, n = 28, MD (12.79), 95%CI [7.69, 17.89]; p < 0.001; I2 = 0%). Itching, dysuria, and VHIS increased significantly, while burning was not improved. Serious adverse events were not observed by any of the studies. Intravaginal laser therapies appear to have a positive effect on dyspareunia, vaginal dryness, and FSFI of CS. However, the quality of evidence is "very low," with no data on intravaginal radiofrequency therapy. Further research with high-quality RCTs and long-term follow-up is needed to evaluate the value of energy-based devices as a therapeutic option for CS with sexual problems.},
}

@article {pmid31396571,
year = {2019},
author = {Gupta, S and Mortensen, MS and Schjørring, S and Trivedi, U and Vestergaard, G and Stokholm, J and Bisgaard, H and Krogfelt, KA and Sørensen, SJ},
title = {Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing.},
journal = {Communications biology},
volume = {2},
number = {},
pages = {291},
doi = {10.1038/s42003-019-0540-1},
pmid = {31396571},
issn = {2399-3642},
abstract = {Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare the diagnostic efficiency of the two methods using a large number of samples (n = 1,748 fecal and n = 1,790 hypopharyngeal), among healthy children at different time points. Here we show that bacteria identified by NGS represented 75.70% of the unique bacterial species cultured in each sample, while TCM only identified 23.86% of the bacterial species found by amplicon sequencing. We discuss the pros and cons of both methods and provide perspective on how NGS can be implemented effectively in clinical settings.},
}

@article {pmid31396400,
year = {2019},
author = {Zarei, I and Oppel, RC and Borresen, EC and Brown, RJ and Ryan, EP},
title = {Modulation of plasma and urine metabolome in colorectal cancer survivors consuming rice bran.},
journal = {Integrative food, nutrition and metabolism},
volume = {6},
number = {3},
pages = {},
doi = {10.15761/IFNM.1000252},
pmid = {31396400},
issn = {2056-8339},
abstract = {Rice bran has bioactive phytochemicals with cancer protective actions that involve metabolism by the host and the gut microbiome. Globally, colorectal cancer (CRC) is the third leading cause of cancer-related death and the increased incidence is largely attributed to poor dietary patterns, including low daily fiber intake. A dietary intervention trial was performed to investigate the impact of rice bran consumption on the plasma and urine metabolome of CRC survivors. Nineteen CRC survivors participated in a randomized-controlled trial that included consumption of heat-stabilized rice bran (30 g/day) or a control diet without rice bran for 4 weeks. A fasting plasma and first void of the morning urine sample were analyzed by non-targeted metabolomics using ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). After 4 weeks of either rice bran or control diets, 12 plasma and 16 urine metabolites were significantly different between the groups (p≤0.05). Rice bran intake increased relative abundance of plasma mannose (1.373-fold) and beta-citrylglutamate (BCG) (1.593-fold), as well as increased urine N-formylphenylalanine (2.191-fold) and dehydroisoandrosterone sulfate (DHEA-S) (4.488-fold). Diet affected metabolites, such as benzoate, mannose, eicosapentaenoate (20:5n3) (EPA), and N-formylphenylalanine have been previously reported for cancer protection and were identified from the rice bran food metabolome. Nutritional metabolome changes following increased consumption of whole grains such as rice bran warrants continued investigation for colon cancer control and prevention attributes as dietary biomarkers for positive effects are needed to reduce high risk for colorectal cancer recurrence.},
}

@article {pmid31396200,
year = {2019},
author = {Sakai-Kawada, FE and Ip, CG and Hagiwara, KA and Awaya, JD},
title = {Biosynthesis and Bioactivity of Prodiginine Analogs in Marine Bacteria, Pseudoalteromonas: A Mini Review.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1715},
doi = {10.3389/fmicb.2019.01715},
pmid = {31396200},
issn = {1664-302X},
abstract = {The Prodiginine family consists of primarily red-pigmented tripyrrole secondary metabolites that were first characterized in the Gram-negative bacterial species Serratia marcescens and demonstrates a wide array of biological activities and applications. Derivatives of prodiginine have since been characterized in the marine γ-proteobacterium, Pseudoalteromonas. Although biosynthetic gene clusters involved in prodiginine synthesis display homology among genera, there is an evident structural difference in the resulting metabolites. This review will summarize prodiginine biosynthesis, bioactivity, and gene regulation in Pseudoalteromonas in comparison to the previously characterized species of Serratia, discuss the ecological contributions of Pseudoalteromonas in the marine microbiome and their eukaryotic hosts, and consider the importance of modern functional genomics and classic DNA manipulation to understand the overall prodiginine biosynthesis pathway.},
}

@article {pmid31396198,
year = {2019},
author = {Malmuthuge, N and Griebel, PJ},
title = {A Novel Animal Model for Regional Microbial Dysbiosis of the Pioneer Microbial Community.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1706},
doi = {10.3389/fmicb.2019.01706},
pmid = {31396198},
issn = {1664-302X},
abstract = {Pioneer microbiota colonizing the newborn gastrointestinal tract has long-lasting effects on host health. Restoration of the gut microbial community, following dysbiosis during the neonatal period, may be one strategy to prevent undesirable health outcomes linked to an altered neonatal gut microbiome. Without appropriate animal models that recreate the prolonged human neonatal developmental period it is not possible to effectively analyze interventions designed to restore regional microbial populations. Our study used a lamb model in which intestinal segments were surgically isolated (blind-ended) in fetal lambs to create early microbial dysbiosis by delaying post-natal exposure to intestinal ingesta. Intestinal segments isolated in utero retained blood flow, innervation, and lymphatic drainage through the mesenteric attachment. Continuity of the fetal gastro-intestinal tract was re-established by side-to-side anastomosis of intestine proximal and distal to each isolated intestinal segment. Microbial restoration was then implemented in neonatal lambs by reconnecting a portion of the in utero isolated intestinal segments to adjacent intestinal tract 1 and 7 days after birth. Bacterial communities colonizing the adjacent intestine, in utero isolated intestinal segments, and reconnected intestinal segments were profiled using 16S amplicon sequencing on days 1, 7, and 56 of age. The in utero isolated intestinal segments were colonized 1 day after birth but the density of active bacteria was reduced and community composition altered when compared to adjacent intestine. Proteobacteria dominated the adjacent small intestine at early time points (day 1 and day 7) with a shift to primarily Firmicutes on day 56, consistent with establishment of an anaerobic bacterial community. In contrast, Proteobacteria persisted as the predominant community for 56 days in the in utero isolated intestinal segments. There was, however, almost full restoration of the microbial community composition in the in utero isolated intestinal segments following reconnection to the adjacent intestine. The density of beneficial bacteria, especially Bifidobacterium, remained significantly lower in the reconnected intestinal segments at 56 days when compared to adjacent intestine. Post-natal persistence of a stable pioneer community (Proteobacteria) in the in utero isolated intestinal segments provides a model system to study the temporal effects of regional microbial dysbiosis throughout a prolonged neonatal period.},
}

@article {pmid31396197,
year = {2019},
author = {Damjanovic, K and van Oppen, MJH and Menéndez, P and Blackall, LL},
title = {Experimental Inoculation of Coral Recruits With Marine Bacteria Indicates Scope for Microbiome Manipulation in Acropora tenuis and Platygyra daedalea.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1702},
doi = {10.3389/fmicb.2019.01702},
pmid = {31396197},
issn = {1664-302X},
abstract = {Coral-associated microorganisms are essential for maintaining the health of the coral holobiont by participating in nutrient cycling and protecting the coral host from pathogens. Under stressful conditions, disruption of the coral prokaryotic microbiome is linked to increased susceptibility to diseases and mortality. Inoculation of corals with beneficial microbes could confer enhanced stress tolerance to the host and may be a powerful tool to help corals thrive under challenging environmental conditions. Here, we explored the feasibility of coral early life stage microbiome manipulation by repeatedly inoculating coral recruits with a bacterial cocktail generated in the laboratory. Co-culturing the two species Acropora tenuis and Platygyra daedalea allowed us to simultaneously investigate the effect of host factors on the coral microbiome. Inoculation cocktails were regularly prepared from freshly grown pure bacterial cultures, which were hence assumed viable, and characterized via the optical density measurement of each individual strain put in suspension. Coral early recruits were inoculated seven times over 3 weeks and sampled once 36 h following the last inoculation event. At this time point, the cumulative inoculations with the bacterial cocktails had a strong effect on the bacterial community composition in recruits of both coral species. While the location of bacterial cells within the coral hosts was not assessed, metabarcoding using the 16S rRNA gene revealed that two and six of the seven bacterial strains administered through the cocktails were significantly enriched in inoculated recruits of A. tenuis and P. daedalea, respectively, compared to control recruits. Despite being reared in the same environment, A. tenuis and P. daedalea established significantly different bacterial communities, both in terms of taxonomic composition and diversity measurements. These findings indicate that coral host factors as well as the environmental bacterial pool play a role in shaping coral-associated bacterial community composition. Host factors may include microbe transmission mode (horizontal versus maternal) and host specificity. While the long-term stability of taxa included in the bacterial inocula as members of the host-associated microbiome remains to be evaluated, our results provide support for the feasibility of coral microbiome manipulation, at least in a laboratory setting.},
}

@article {pmid31396183,
year = {2019},
author = {Tian, W and Wang, H and Xiang, X and Wang, R and Xu, Y},
title = {Structural Variations of Bacterial Community Driven by Sphagnum Microhabitat Differentiation in a Subalpine Peatland.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1661},
doi = {10.3389/fmicb.2019.01661},
pmid = {31396183},
issn = {1664-302X},
abstract = {Sphagnum microbiomes play an important role in the northern peatland ecosystems. However, information about above and belowground microbiomes related to Sphagnum at subtropical area remains largely limited. In this study, microbial communities from Sphagnum palustre peat, S. palustre green part, and S. palustre brown part at the Dajiuhu Peatland, in central China were investigated via 16S rRNA gene amplicon sequencing. Results indicated that Alphaproteobacteria was the dominant class in all samples, and the classes Acidobacteria and Gammaproteobacteria were abundant in S. palustre peat and S. palustre brown part samples, respectively. In contrast, the class Cyanobacteria dominated in S. palustre green part samples. Microhabitat differentiation mainly contributes to structural differences of bacterial microbiome. In the S. palustre peat, microbial communities were significantly shaped by water table and total nitrogen content. Our study is a systematical investigation on above and belowground bacterial microbiome in a subalpine Sphagnum peatland and the results offer new knowledge about the distribution of bacterial microbiome associated with different microhabitats in subtropical area.},
}

@article {pmid31396172,
year = {2019},
author = {Wassermann, B and Müller, H and Berg, G},
title = {An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples?.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1629},
doi = {10.3389/fmicb.2019.01629},
pmid = {31396172},
issn = {1664-302X},
abstract = {Apples are among the most consumed fruits world-wide. They represent a source of direct human exposure to bacterial communities, which is less studied. We analyzed the apple microbiome to detect differences between tissues and the impact of organic and conventional management by a combined approach of 16S rRNA gene amplicon analysis and qPCR, and visualization using fluorescence in situ hybridization and confocal laser scanning microscopy (FISH-CLSM). Each apple fruit harbors different tissues (stem, peel, fruit pulp, seeds, and calyx), which were colonized by distinct bacterial communities. Interestingly, fruit pulp and seeds were bacterial hot spots, while the peel was less colonized. In all, approximately 108 16S rRNA bacterial gene copy numbers were determined in each g apple. Abundances were not influenced by the management practice but we found a strong reduction in bacterial diversity and evenness in conventionally managed apples. In addition, despite the similar structure in general dominated by Proteobacteria (80%), Bacteroidetes (9%), Actinobacteria (5%), and Firmicutes (3%), significant shifts of almost 40% of bacterial genera and orders were monitored. Among them, especially bacterial signatures known for health-affecting potential were found to be enhanced in conventionally managed apples. Our results suggest that we consume about 100 million bacterial cells with one apple. Although this amount was the same, the bacterial composition was significantly different in conventionally and organically produced apples.},
}

@article {pmid31396165,
year = {2019},
author = {Wei, L and Wu, Q and Zhang, J and Guo, W and Gu, Q and Wu, H and Wang, J and Lei, T and Chen, M and Wu, M and Li, A},
title = {Composition and Dynamics of Bacterial Communities in a Full-Scale Mineral Water Treatment Plant.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {1542},
doi = {10.3389/fmicb.2019.01542},
pmid = {31396165},
issn = {1664-302X},
abstract = {The aim of this study was to gain insight into the bacterial composition and dynamics in a mineral water treatment system (MWTS). The bacterial community of a full-scale mineral water treatment plant in the Maofeng Mountain, South China, was studied using high-throughput sequencing combined with cultivation-based techniques in both the dry and wet season. Overall, adenosine tri-phosphate (ATP) concentration (6.47 × 10-11 - 3.32 × 10-8 M) and heterotrophic plate counts (HPC) (3 - 1.29 × 103 CFU/mL) of water samples in the wet season were lower than those (ATP concentration 5.10 × 10-11 - 6.96 × 10-8 M, HPC 2 - 1.97 × 103 CFU/mL) in the dry season throughout the whole MWTS. The microbial activity and biomass of water samples obviously changed along with treatment process. All 300 isolates obtained using cultivation-based techniques were distributed in 5 phyla, 7 classes, and 19 genera. Proteobacteria accounted for 55.7% (167) of the total isolates, among which predominant genus was Pseudomonas (19.3%). Illumina sequencing analysis of 16s rRNA genes revealed 15 bacterial phyla (relative abundance >0.1%) as being identified in all water samples. Among these, Proteobacteria constituted the dominant bacteria microbiota in all water samples. A large shift in the proportion of Bacteroidetes, Actinobacteria, and Firmicutes was obtained during the treatment process, with the proportion of Bacteroidetes, Actinobacteria decreasing sharply, whereas that of Firmicutes increased and predominated in the final water product. The core microbiome, which was still present in whole MWTS comprised several genera including Pseudomonas, Acinetobacter, Clostridium, and Mycobacterium, that contain species that are opportunistic pathogens, suggesting a potential threat for mineral water microbiology safety. This study is the first to investigate the bacterial community of a full-scale mineral water treatment plant in China. The results provided data regarding the bacteria composition and dynamics in an MWTS, which will contribute to the beneficial manipulation of the mineral water microbiome.},
}

@article {pmid31396097,
year = {2019},
author = {Wu, R and Zhao, D and An, R and Wang, Z and Li, Y and Shi, B and Ni, Q},
title = {Linggui Zhugan Formula Improves Glucose and Lipid Levels and Alters Gut Microbiota in High-Fat Diet-Induced Diabetic Mice.},
journal = {Frontiers in physiology},
volume = {10},
number = {},
pages = {918},
doi = {10.3389/fphys.2019.00918},
pmid = {31396097},
issn = {1664-042X},
abstract = {Background: The gut microbiota plays important roles in the occurrence and development of obesity and diabetes through participating in nutrient absorption and metabolism. Microecological regulation is likely to be key to understanding the effects of Chinese medicine. The Linggui Zhugan (LGZG) formula is a well-known Chinese medicine for controlling obesity in the clinic. However, its pharmacological effects and mechanism of action in diabetes require further exploration. Objective: To evaluate the effects of LGZG on body weight, glycemic control, lipid levels, and gut microbiota in high-fat diet-induced diabetic mice. Methods: High-fat diet-induced diabetic mice were subjected to an 8-week protocol of LGZG administration. We then evaluated the pharmacological effects of LGZG and its influence on gut microbes in fecal samples using the 16S rRNA-based microbiome profiling technique. Results: LGZG administration significantly reduced body weight and body fat mass in diabetic mice. Compared with the high-fat diet control group, LGZG favorably influenced blood glucose control, decreased blood glucose levels, and increased glucose tolerance, accompanied by an improvement in lipid metabolism. Furthermore, the global community composition and relative abundance of many taxa differed between mice fed chow or a high-fat diet. As expected, LGZG supplementation altered the general community structure of gut microbiota, the Firmicutes/Bacteroidetes ratio, and the relative abundance of certain bacteria, such as Bacteroides, Lactobacillus, Oscillospira, and Helicobacter. Conclusion: LGZG effectively controlled obesity and relieved insulin resistance, which may be closely related to its impact on gut microbiota.},
}

@article {pmid31395904,
year = {2019},
author = {El-Sayed, ASA and Mohamed, NZ and Safan, S and Yassin, MA and Shaban, L and Shindia, AA and Shad Ali, G and Sitohy, MZ},
title = {Restoring the Taxol biosynthetic machinery of Aspergillus terreus by Podocarpus gracilior Pilger microbiome, with retrieving the ribosome biogenesis proteins of WD40 superfamily.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {11534},
doi = {10.1038/s41598-019-47816-y},
pmid = {31395904},
issn = {2045-2322},
abstract = {Attenuating the Taxol yield of Aspergillus terreus with the subculturing and storage were the technical challenges that prevent this fungus to be a novel platform for industrial Taxol production. Thus, the objective of this study was to unravel the metabolic machineries of A. terreus associated with attenuation of Taxol productivity, and their restoring potency upon cocultivation with the Podocarpus gracilior microbiome. The Taxol yield of A. terreus was drastically reduced with the fungal subculturing. At the 10th subculture, the yield of Taxol was reduced by four folds (78.2 µg/l) comparing to the original culture (268 µg/l), as authenticated from silencing of molecular expression of the Taxol-rate limiting enzymes (GGPPS, TDS, DBAT and BAPT) by qPCR analyses. The visual fading of A. terreus conidial pigmentation with the subculturing, revealing the biosynthetic correlation of melanin and Taxol. The level of intracellular acetyl-CoA influx was reduced sequentially with the fungal subculturing, rationalizing the decreasing on Taxol and melanin yields. Fascinatingly, the Taxol biosynthetic machinery and cellular acetyl-CoA of A. terreus have been completely restored upon addition of 3% surface sterilized leaves of P. gracilior, suggesting the implantation of plant microbiome on re-triggering the molecular machinery of Taxol biosynthesis, their transcriptional factors, and/or increasing the influx of Acetyl-CoA. The expression of the proteins of 74.4, 68.2, 37.1 kDa were exponentially suppressed with A. terreus subculturing, and strongly restored upon addition of P. gracilior leaves, ensuring their profoundly correlation with the molecular expression of Taxol biosynthetic genes. From the proteomic analysis, the restored proteins 74.4 kDa of A. terreus upon addition of P. gracilior leaves were annotated as ribosome biogenesis proteins YTM and microtubule-assembly proteins that belong to WD40 superfamily. Thus, further ongoing studies for molecular cloning and expression of these genes with strong promotors in A. terreus, have been initiated, to construct a novel platform of metabolically stable A. terreus for sustainable Taxol production. Attenuating the Taxol yield of A. terreus with the multiple-culturing and storage might be due to the reduction on main influx of acetyl-CoA, or downregulation of ribosome biogenesis proteins that belong to WD40 protein superfamily.},
}

@article {pmid31395434,
year = {2019},
author = {Hendricks, AJ and Mills, BW and Shi, VY},
title = {Skin bacterial transplant in atopic dermatitis: Knowns, unknowns and emerging trends.},
journal = {Journal of dermatological science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jdermsci.2019.07.001},
pmid = {31395434},
issn = {1873-569X},
abstract = {Dysbiosis is a key pathogenic factor in the cycle of skin barrier impairment and inflammation in atopic dermatitis (AD). Skin microbial composition in AD is characterized by increased presence of Staphylococcus aureus (S. aureus) and decrease in microbial diversity and commensal bacterial species. Attenuation of S. aureus-driven inflammation aids in breaking the itch-scratch cycle via modulation of the cutaneous immune response. Skin bacterial transplant (SBT), a form of bacteriotherapy, is an intriguing treatment modality for restoration of a healthy skin microbiome in AD patients. Studies on the effects of topically-applied bacterial products, probiotics and SBT have yielded promising results in animal models and human studies of AD. This review discusses the rationale and evidence for SBT in AD and outlines future investigative directions for the clinical application of microbiome restoration in dermatology.},
}

@article {pmid31395001,
year = {2019},
author = {Langohr, I},
title = {From Newly Described Diseases in Artic Foxes to the Connection Between Cancer and the Gut Microbiome: Award-Winning Presentations Await You at the 2019 ACVP and ASVCP Concurrent Annual Meeting.},
journal = {Veterinary pathology},
volume = {56},
number = {5},
pages = {654-655},
doi = {10.1177/0300985819860205},
pmid = {31395001},
issn = {1544-2217},
}

@article {pmid31394347,
year = {2019},
author = {Tang, M and Xu, C and Chen, K and Yan, Q and Mao, W and Liu, W and Ritz, B},
title = {Hexachlorocyclohexane exposure alters the microbiome of colostrum in Chinese breastfeeding mothers.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {254},
number = {Pt A},
pages = {112900},
doi = {10.1016/j.envpol.2019.07.068},
pmid = {31394347},
issn = {1873-6424},
abstract = {Breast milk, especially colostrum, is not just a source of nutrients and immune factors for the newborn, but also accumulates environmental persistent pollutants and its diverse microbes affect the early colonization of the newborn's gut. Little is known about associations between environmental pollutants and the microbial composition of human colostrum. We assessed the influence of hexachlorocyclohexane (HCH), a persistent organic pollutant (POP), in colostrums on the microbial composition of human colostrum samples. HCH concentrations in 89 colostrum samples collected from a population living on the easternmost island of China were measured via gas chromatography equipped with mass spectrometer (GC-MS), HCH exposure risks for infants via dietary intake of breast milk were assessed, and for 29 colostrum samples the microbiota were profiled using 16S rRNA gene pyrosequencing to assess the association with HCH exposure levels. Our study confirmed high colostrum exposure levels of total HCHs (12.19 ± 13.68 μg L-1) in this Chinese population. We predominantly identified Proteobacteria (67.6%) and Firmicutes (25.1%) in colostrum and microbial diversity at the genus level differed between samples with different HCH levels; e.g., Pseudomonas which contains several HCH degrading strains was found in significantly higher abundance in γ-HCH rich samples. Also, microbes that were statistically significantly associated with HCH levels were also highly correlated with each other (false discovery rate (FDR)＜0.01) and clustered in network analysis. Microbial diversity is associated with HCH levels in human colostrum and these associations might be attributable to their HCH degrading ability. These finding provide first insights into the role that environmental persistent pollutants may play in the microbial composition of human colostrum and the colonization of the infant gut.},
}

@article {pmid31394285,
year = {2019},
author = {Jess, T and Jensen, BW and Andersson, M and Villumsen, M and Allin, KH},
title = {Inflammatory Bowel Disease Increases Risk of Type 2 Diabetes in a Nationwide Cohort Study.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2019.07.052},
pmid = {31394285},
issn = {1542-7714},
abstract = {BACKGROUND & AIMS: The intestine regulates glucose homeostasis, but it is not clear whether chronic intestinal inflammation affects risk for type 2 diabetes. We investigated the long-term risk of type 2 diabetes in patients with inflammatory bowel diseases (IBD) in a nationwide cohort study in Denmark.

METHODS: In a nationwide population-based cohort of 6,028,844 persons in Denmark, we compared data from individuals with a diagnosis of IBD (Crohn's disease [CD] or ulcerative colitis UC]) with data from individuals without IBD, from 1977 through 2014. Persons with type 2 diabetes were identified in the National Patient Register. Risk is presented as standardized incidence ratios (SIR) with 95% CIs.

RESULTS: During 736,072 person-years of follow-up, 3436 patients with IBD developed type 2 diabetes vs 2224 expected (SIR, 1.54; 95% CI, 1.49-1.60). The risk was significantly increased in patients with UC (SIR, 1.54; 95% CI, 1.48-1.60), in patients with CD (SIR, 1.57; 95% CI, 1.47-1.67), in women (SIR, 1.51; 95% CI, 1.44-1.59), and in men (SIR, 1.57; 95% CI, 1.50-1.65). The risk was highest the first year after a diagnosis of IBD (SIR, 4.48; 95% CI, 4.16-4.83), but remained increased for 20 or more years following the diagnosis (SIR, 1.26; 95% CI, 1.16-1.38). The increased risk could not be accounted for by frequency of health care contacts or corticosteroid exposure. Patients who received a diagnosis of IBD from 2003 through 2014 (SIR, 1.79; 95% CI, 1.67-1.91) had a significantly higher risk of type 2 diabetes than patients who received a diagnosis of IBD from 1977 through 1988 (SIR, 1.47; 95% CI, 1.39-1.56) or 1989 through 2002 (SIR, 1.48; 95% CI, 1.41-1.56) (P<.001).

CONCLUSIONS: In a population-based cohort study, we found an increased risk of type 2 diabetes in patients with UC or CD, with highest risk estimates from 2003 through 2014, compared with earlier years. Studies are needed to determine the effects of IBD treatment on risk of type 2 diabetes.},
}

@article {pmid31394208,
year = {2019},
author = {Christian, LM},
title = {The Gut Microbiome and Mental Health: Taking Baby Steps.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2019.08.001},
pmid = {31394208},
issn = {1090-2139},
}

@article {pmid31394110,
year = {2019},
author = {Vinasco, K and Mitchell, HM and Kaakoush, NO and Castaño-Rodríguez, N},
title = {Microbial carcinogenesis: Lactic acid bacteria in gastric cancer.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbcan.2019.07.004},
pmid = {31394110},
issn = {1879-2561},
abstract = {While Helicobacter pylori is a fundamental risk factor, gastric cancer (GC) aetiology involves combined effects of microbial (both H. pylori and nonH. pylori), host and environmental factors. Significant differences exist between the gastric microbiome of those with gastritis, intestinal metaplasia and GC, suggesting that dysbiosis in the stomach is dynamic and correlates with progression to GC. Most notably, a consistent increase in abundance of lactic acid bacteria (LAB) has been observed in GC patients including Streptococcus, Lactobacillus, Bifidobacterium and Lactococcus. This review summarises how LAB can influence GC by a number of mechanisms that include supply of exogenous lactate -a fuel source for cancer cells that promotes inflammation, angiogenesis, metastasis, epithelial-mesenchymal transition and immune evasion-, production of reactive oxygen species and N-nitroso compounds, as well as anti-H. pylori properties that enable colonization by other nonH. pylori carcinogenic pathobionts.},
}

@article {pmid31393934,
year = {2019},
author = {Barone, M and Turroni, S and Rampelli, S and Soverini, M and D'Amico, F and Biagi, E and Brigidi, P and Troiani, E and Candela, M},
title = {Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context.},
journal = {PloS one},
volume = {14},
number = {8},
pages = {e0220619},
doi = {10.1371/journal.pone.0220619},
pmid = {31393934},
issn = {1932-6203},
abstract = {The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more "ancestral" configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods-albeit with the exclusion of grains and pulses-along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.},
}

@article {pmid31393583,
year = {2019},
author = {Qin, SM and Bai, WQ and Zhang, KY and Ding, XM and Bai, SP and Wang, JP and Peng, HW and Yang, YF and Chen, C and Zeng, QF},
title = {Different microbiomes are found in healthy breeder ducks and those with foot pad dermatitis.},
journal = {Poultry science},
volume = {},
number = {},
pages = {},
doi = {10.3382/ps/pez456},
pmid = {31393583},
issn = {1525-3171},
abstract = {Foot pad dermatitis (FPD) is a serious problem of the modern poultry industry, negatively affecting birds' welfare and health status, walking and feeding activity, growth performance, carcass quality, and economic performance of meat production. The gut microbiome in poultry with FPD has not been previously investigated. Therefore, we compared the cecal microbiomes of 8 breeding ducks with FPD to 8 control ducks (breeders with apparently healthy feet) by pyrosequencing the bacterial 16S ribosomal RNA gene. The results showed a significant β-diversity (P < 0.05) of cecal microbiota presented between healthy and FPD-affected breeder ducks. The plasma endotoxins, interleukin 1β (IL-1β), IL-17, IL-6, IL-10, and tumor necrosis factor-α concentration, and the abundance of class Clostridia in FPD-affected ducks was markedly higher (P < 0.05), however, the abundance of genus Prevotella, Lactobacillus, Lachnospiraceae UCG-008, and the Firmicutes to Bacteroidetes ratio in FPD-affected ducks was significantly lower (P < 0.05) when compared to healthy ducks. These findings suggest when duck breeders are affected with FPD, ducks show an increased inflammatory response and a difference of structure and composition of the cecal microbiome.},
}

@article {pmid31393334,
year = {2019},
author = {Kansal, S and Catto-Smith, AG and Boniface, K and Thomas, S and Cameron, DJ and Oliver, M and Alex, G and Kirkwood, CD and Wagner, J},
title = {Variation of Gut Mucosal Microbiome with ASCA Status in Pediatric Crohn's Disease.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPG.0000000000002461},
pmid = {31393334},
issn = {1536-4801},
abstract = {OBJECTIVES: Crohn's Disease (CD) is a chronic relapsing condition possibly caused by a dysbiotic microbiome. About 30-60% of CD patients have antibodies to Saccharomyces cerevisiae (ASCA), but any association with gut microbiota is unexplored. We hypothesized that ASCA positivity would predict a signature microbial status and clinical phenotype.

METHODS: Ileocolonic mucosal biopsies were obtained from children with CD (n = 135), and controls without inflammatory bowel disease (n = 45). Comparison was made between ASCA status, microbial diversity and clinical characteristics.

RESULTS: ASCA was highly specific but poorly sensitive for the diagnosis of CD. In patients with CD, ASCA positivity was associated with older age (≥10 years), ileocolonic disease and long-term risk of surgery. Microbial alpha and beta diversity were similar in CD patients with or without ASCA, but significantly less when compared to non-IBD controls. Microbial richness was similar across all three groups. Fourteen bacterial species were associated with ASCA positive CD patients and 14 species with ASCA negative patients (p < 0.05). After using a false discovery rate correction Ruminococcus torques and bacterium Yersinia enterolitica 61 remained significantly associated with CD ASCA positivity (p = 0.0178), while Enterobacter cloacae and Faecalibacterium prausnitzii were significantly associated with CD ASCA negativity (p = 0.0178 and 0.0342).

CONCLUSION: ASCA positive and ASCA negative CD patients have significant differences in gut microbiome composition, which could possibly be influencing the phenotype of the disease.},
}

@article {pmid31393213,
year = {2019},
author = {ElRakaiby, MT and Gamal-Eldin, S and Amin, MA and Aziz, RK},
title = {Hospital Microbiome Variations As Analyzed by High-Throughput Sequencing.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/omi.2019.0111},
pmid = {31393213},
issn = {1557-8100},
abstract = {Hospital-acquired infections remain a serious threat to human life and are becoming a top public health issue. As the latest advances in sequencing technologies have allowed the unbiased identification of bacterial communities, we aimed to implement emerging omics technologies to characterize a hospital's microbiome at the center of Cairo, Egypt. To this end, we screened surfaces and inanimate objects in the hospital, focusing on bed sheets and door knobs, with additional screening for resistant microbes and resistance genes. While bacterial load and community composition were not dramatically different between door knobs of hospital units with different hygiene levels, the bacterial communities on door knob samples were richer and more diverse than those detected on bed sheets. Bacteria detected on door knobs were a mix of those associated with dust/particulate matter/debris (e.g., Bacillus, Geobacillus, Aeribacillus) and skin-associated bacteria (e.g., Staphylococcus, Corynebacterium). The latter were among the core genera shared by all analyzed samples. Conversely, bacteria that were more abundant in bed sheets were not associated with a particular source (e.g., Pseudomonas and Nitrobacter). Resistance screening indicated an expansion of a mobile beta-lactamase-encoding gene (blaTEM), reflecting its current global spread. This study is a first step toward more comprehensive screening of hospital surfaces and correlating their microbiome with hospital outbreaks or chronic infections. We conclude that, as hospitals are unique built environments, these findings can inform future infection control strategies in hospitals and health care-related built environments, and attest to the importance of the emerging hospital microbiome research field.},
}

@article {pmid31393014,
year = {2019},
author = {Zengin, G and Ferrante, C and Orlando, G and Zheleva-Dimitrova, D and Gevrenova, R and Recinella, L and Chiavaroli, A and Leone, S and Brunetti, L and Aumeeruddy, MZ and Aktumsek, A and Mahomoodally, MF and Angelini, P and Covino, S and Venanzoni, R and Tirillini, B and Menghini, L},
title = {Chemical profiling and pharmaco-toxicological activity of Origanum sipyleum extracts: Exploring for novel sources for potential therapeutic agents.},
journal = {Journal of food biochemistry},
volume = {},
number = {},
pages = {e13003},
doi = {10.1111/jfbc.13003},
pmid = {31393014},
issn = {1745-4514},
support = {//Italian Ministry of University/ ; },
abstract = {The phytochemical, antiradical, and enzyme inhibition profile of three solvent extracts (ethyl acetate, methanol, water) of Origanum sipyleum were assessed. We also performed a pharmacological study in order to explore protective effects induced by extracts in inflamed colon. LC-MS analysis revealed that the extracts contained different classes of phenolics. The aqueous extract showed the highest antioxidant and acetylcholinesterase (AChE) inhibitory effects. Total phenol and flavonoid contents were highest in aqueous and ethyl acetate extract, respectively. All extracts were effective in reducing colon pro-oxidant and pro-inflammatory biomarkers. The extracts revealed also able to inhibit fungal and bacterial species involved in ulcerative colitis, including Candida albicans, Candida tropicalis, Staphylococcus aureus, and Staphylococcus thyphimurium. Finally, we also showed the antiproliferative effects exerted by the EA extracts on human colon cancer HCT116 cell line. Concluding, our results indicated that O. sipyleum extracts displayed promising therapeutic properties which warrants further validation. PRACTICAL APPLICATIONS: The present phytochemical and biological studies, including antioxidant, anti-inflammatory, and antimicrobic assessments, showed significant protective effects exerted by O. sipyleum extracts in an experimental model of ulcerative colitis. The results are intriguing and suggest potential applications O. sipyleum extracts as sources of natural agents for the management of clinical symptoms related to ulcerative colitis, characterized by increased burden of oxidative stress and microbiome dysbiosis.},
}

@article {pmid31392094,
year = {2019},
author = {Ai, D and Pan, H and Li, X and Wu, M and Xia, LC},
title = {Association network analysis identifies enzymatic components of gut microbiota that significantly differ between colorectal cancer patients and healthy controls.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e7315},
doi = {10.7717/peerj.7315},
pmid = {31392094},
issn = {2167-8359},
abstract = {The human gut microbiota plays a major role in maintaining human health and was recently recognized as a promising target for disease prevention and treatment. Many diseases are traceable to microbiota dysbiosis, implicating altered gut microbial ecosystems, or, in many cases, disrupted microbial enzymes carrying out essential physio-biochemical reactions. Thus, the changes of essential microbial enzyme levels may predict human disorders. With the rapid development of high-throughput sequencing technologies, metagenomics analysis has emerged as an important method to explore the microbial communities in the human body, as well as their functionalities. In this study, we analyzed 156 gut metagenomics samples from patients with colorectal cancer (CRC) and adenoma, as well as that from healthy controls. We estimated the abundance of microbial enzymes using the HMP Unified Metabolic Analysis Network method and identified the differentially abundant enzymes between CRCs and controls. We constructed enzymatic association networks using the extended local similarity analysis algorithm. We identified CRC-associated enzymic changes by analyzing the topological features of the enzymatic association networks, including the clustering coefficient, the betweenness centrality, and the closeness centrality of network nodes. The network topology of enzymatic association network exhibited a difference between the healthy and the CRC environments. The ABC (ATP binding cassette) transporter and small subunit ribosomal protein S19 enzymes, had the highest clustering coefficient in the healthy enzymatic networks. In contrast, the Adenosylhomocysteinase enzyme had the highest clustering coefficient in the CRC enzymatic networks. These enzymic and metabolic differences may serve as risk predictors for CRCs and are worthy of further research.},
}

@article {pmid31391428,
year = {2019},
author = {Towhid, ST},
title = {Effect of High-salt Consumption on Rodent Gut Microbiome: A Meta-Analysis.},
journal = {Mymensingh medical journal : MMJ},
volume = {28},
number = {3},
pages = {567-573},
pmid = {31391428},
issn = {2408-8757},
abstract = {The global climate change brings about myriad of changes in the environment and ecosystem. The sea-level rise due to climate change results in salt-water intrusion into freshwater reservoirs of the coastal areas, increasing the salinity of the natural sources of potable water. People in the coastal areas consume saline water, exposing the intestinal tract to higher salt concentration on regular basis. This meta-analysis attempts to relate consumption of saline water to dysbiosis of rodent gut microbiome. Scientific reports were searched in PubMed/Medline, the Cochrane Library and Google Scholar. Original articles, abstracts and short communications were included depending on predetermined inclusion/exclusion criteria. A total of 8 original reports involving 124 rodents were included in this study. The pooled specificity and sensitivity of the reports were found to be 0.833 and 0.891 respectively by Meta Disc software v1.4. Pooled odds ratio and AUC were 20.056 and 0.896 respectively, implying a correlation between increased salt intake and gut microbiome dysbiosis (imbalance), measured from altered Firmicutes: Bacteroidetes ratio. Microbiome dysbiosis makes the intestine prone to enteric diseases. The outcomes of this meta-analysis indicates the dependence of mammalian gut microbiome on the amount of salt ingested, a condition aggravated by the global climate change and therefore necessitates similar studies on human populations living on coastal areas.},
}

@article {pmid31391094,
year = {2019},
author = {Kusstatscher, P and Zachow, C and Harms, K and Maier, J and Eigner, H and Berg, G and Cernava, T},
title = {Microbiome-driven identification of microbial indicators for postharvest diseases of sugar beets.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {112},
doi = {10.1186/s40168-019-0728-0},
pmid = {31391094},
issn = {2049-2618},
support = {282482//Austrian Research Promotion Agency FFG/ ; },
abstract = {BACKGROUND: Sugar loss due to storage rot has a substantial economic impact on the sugar industry. The gradual spread of saprophytic fungi such as Fusarium and Penicillium spp. during storage in beet clamps is an ongoing challenge for postharvest processing. Early detection of shifts in microbial communities in beet clamps is a promising approach for the initiation of targeted countermeasures during developing storage rot. In a combined approach, high-throughput sequencing of bacterial and fungal genetic markers was complemented with cultivation-dependent methods and provided detailed insights into microbial communities colonizing stored roots. These data were used to develop a multi-target qPCR technique for early detection of postharvest diseases.

RESULTS: The comparison of beet microbiomes from six clamps in Austria and Germany highlighted regional differences; nevertheless, universal indicators of the health status were identified. Apart from a significant decrease in microbial diversity in decaying sugar beets (p ≤ 0.01), a distinctive shift in the taxonomic composition of the overall microbiome was found. Fungal taxa such as Candida and Penicillium together with the gram-positive Lactobacillus were the main disease indicators in the microbiome of decaying sugar beets. In contrast, the genera Plectosphaerella and Vishniacozyma as well as a higher microbial diversity in general were found to reflect the microbiome of healthy beets. Based on these findings, a qPCR-based early detection technique was developed and confirmed a twofold decrease of health indicators and an up to 10,000-fold increase of disease indicators in beet clamps. This was further verified with analyses of the sugar content in storage samples.

CONCLUSION: By conducting a detailed assessment of temporal microbiome changes during the storage of sugar beets, distinct indicator species were identified that reflect progressing rot and losses in sugar content. The insights generated in this study provide a novel basis to improve current or develop next-generation postharvest management techniques by tracking disease indicators during storage.},
}

@article {pmid31390549,
year = {2019},
author = {Hitchings, R and Kelly, L},
title = {Drug Metabolism as a Community Effort.},
journal = {Cell metabolism},
volume = {30},
number = {2},
pages = {235-237},
doi = {10.1016/j.cmet.2019.07.005},
pmid = {31390549},
issn = {1932-7420},
abstract = {Levodopa (L-dopa) is the primary treatment for Parkinson's disease. The gut microbiome can metabolize levodopa, potentially leading to decreased efficacy and side effects, but responsible bacteria were unknown. Maini Rekdal et al. (2019) characterize enzymes in two gut bacteria that sequentially metabolize L-dopa and identify a novel inhibitor that may improve outcomes.},
}

@article {pmid31389891,
year = {2019},
author = {Tan, TL},
title = {CORR Insights®: Disruption of the Gut Microbiome Increases the Risk of Periprosthetic Joint Infection in Mice.},
journal = {Clinical orthopaedics and related research},
volume = {},
number = {},
pages = {},
doi = {10.1097/CORR.0000000000000891},
pmid = {31389891},
issn = {1528-1132},
}

@article {pmid31389815,
year = {2019},
author = {McMahan, ZH},
title = {Gastrointestinal involvement in systemic sclerosis: an update.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000000645},
pmid = {31389815},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: This review provides important updates in systemic sclerosis (SSc)-related gastrointestinal disease, specifically focusing on the most recent literature.

RECENT FINDINGS: In the past year, several studies were published that present interesting insights into SSc and gastrointestinal disease. Studies focusing on newly identified risk factors, novel approaches to diagnosis and assessment of disease activity, survival and quality of life demonstrate progress in our understanding of this challenging area. Additional data on specific SSc gastrointestinal-related topics, such as the link between gastrointestinal and pulmonary disease, nutrition, and the microbiome, are also now available.

SUMMARY: SSc gastrointestinal disease is heterogeneous in its clinical presentation, which presents a challenge in diagnosis and management. In the past year, several studies have evaluated risk factors and clinical features associated with specific gastrointestinal complications in SSc. Objective gastrointestinal testing may help to identify specific SSc gastrointestinal subgroups and provide diagnostic accuracy to guide targeted therapies. Survival in very early SSc is affected by the severity of gastrointestinal involvement. Other important gastrointestinal subsets, including patients with esophageal disease and interstitial lung disease, should carefully be considered when developing a management plan for this patient population.},
}

@article {pmid31389663,
year = {2019},
author = {Jayarathne, S and Stull, AJ and Park, OH and Kim, JH and Thompson, L and Moustaid-Moussa, N},
title = {Protective Effects of Anthocyanins in Obesity-Associated Inflammation and Changes in Gut Microbiome.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e1900149},
doi = {10.1002/mnfr.201900149},
pmid = {31389663},
issn = {1613-4133},
abstract = {Obesity is a complex disease and a major public health epidemic. Chronic, low-grade inflammation is a common underlying feature of obesity and associated metabolic diseases; adipose tissue is a major contributor to this systemic inflammation. Evidence shows that obesity-associated inflammation may originate from gut dysfunction, including changes in intestinal bacteria or microbiome profiles. Increasingly, food and plant bioactive compounds with antioxidant and anti-inflammatory properties have been proposed to ameliorate obesity-associated inflammation. Among these, we are interested in the health-promoting effects of anthocyanin-rich foods. Specifically, this review summarizes the reported benefits of anthocyanins in obesity-associated inflammation, and underlying molecular mechanisms, including the role of gut microbiome and cell signaling pathways regulated by anthocyanins both in vivo and in vitro. This article is protected by copyright. All rights reserved.},
}

@article {pmid31388730,
year = {2019},
author = {Haines, SR and Bope, A and Horack, JM and Meyer, ME and Dannemiller, KC},
title = {Quantitative evaluation of bioaerosols in different particle size fractions in dust collected on the International Space Station (ISS).},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10053-4},
pmid = {31388730},
issn = {1432-0614},
support = {Laboratory Start-up Funds//Ohio State University (US)/ ; },
abstract = {Exposure to bioaerosols can adversely influence human health through respiratory tract, eye, and skin irritation. Bioaerosol composition is unique on the International Space Station (ISS), where the size distribution of particles in the air differs from those on Earth. This is due to the lack of gravitational settling and sources of biological particles. However, we do not understand how microbes are influenced by particle size in this environment. We analyzed two types of samples from the ISS: (1) vacuum bag debris which had been sieved into five different size fractions and (2) passively collected particles on a tape substrate with a passive aerosol sampler. Using quantitative polymerase chain reaction (qPCR), the highest concentration of fungal spores was found in the 106-150 μm-sized sieved dust particles, while the highest concentration of bacterial cells was found in the 150-250 μm-sized sieved dust particles. Illumina MiSeq DNA sequencing revealed that particle size was associated with bacterial and fungal communities and statistically significant (p = 0.035, p = 0.036 respectively). Similar fungal and bacterial species were found within the passive aerosol sample and the sieved dust samples. The most abundant fungal species identified in the aerosol and sieved samples are commonly found in food and plant material. Abundant bacterial species were most associated with the oral microbiome and human upper respiratory tract. One limitation to this study was the suboptimal storage conditions of the sieved samples prior to analysis. Overall, our results indicate that microbial exposure in space may depend on particle size. This has implications for ventilation and filtration system design for future space vehicles and habitats.},
}

@article {pmid31388693,
year = {2019},
author = {Stoyancheva, G},
title = {Study of helveticin gene in Lactobacillus crispatus strains and evaluation of its use as a phylogenetic marker.},
journal = {Archives of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00203-019-01711-2},
pmid = {31388693},
issn = {1432-072X},
abstract = {Lactobacilli are a part of the human microbiome in healthy humans. Studies of their physiological and genetic characteristics are the basis for their use in probiotic preparations. This report is a brief description of the helveticin gene found in two Lactobacillus crispatus strains, which are a part of the human microbiome. Our analysis showed that the two variants of the gene are not solely characteristic of strains isolated from humans. In the phylogenetic analysis, we found that the studied sequence (this gene) showed a significant difference between the species of the genus Lactobacillus and could be used as a phylogenetic marker.},
}

@article {pmid31388591,
year = {2019},
author = {Agyirifo, DS and Wamalwa, M and Otwe, EP and Galyuon, I and Runo, S and Takrama, J and Ngeranwa, J},
title = {Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities.},
journal = {Heliyon},
volume = {5},
number = {7},
pages = {e02170},
doi = {10.1016/j.heliyon.2019.e02170},
pmid = {31388591},
issn = {2405-8440},
abstract = {Fermentation of Theobroma cacao L. beans is the most critical stage in the production of cocoa products such as chocolates and its derivatives. There is a limited understanding of the complex response of microbial diversity during cocoa bean fermentation. The aim of the present study was to investigate microbial communities in the cocoa bean fermentation heap using a culture-independent approach to elucidate microbial diversity, structure, functional annotation and mapping unto metabolic pathways. Genomic DNA was extracted and purified from a sample of cocoa beans fermentation heap and was followed by library preparations. Sequence data was generated on Illumina Hiseq 2000 paired-end technology (Macrogen Inc). Taxonomic analysis based on genes predicted from the metagenome identified a high percentage of Bacteria (90.0%), Yeast (9%), and bacteriophages (1%) from the cocoa microbiome. Lactobacillus (20%), Gluconacetobacter (9%), Acetobacter (7%) and Gluconobacter (6%) dominated this study. The mean species diversity, measured by Shannon alpha-diversity index, was estimated at 142.81. Assignment of metagenomic sequences to SEED database categories at 97% sequence similarity identified a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates and aromatic amino acids. Metabolism of aromatic compounds, amino acids and their derivatives and carbohydrates occupied 0.6%, 8% and 13% respectively. Overall, these results provide insights into the cocoa microbiome, identifying fermentation processes carried out broadly by complex microbial communities and metabolic pathways encoding aromatic compounds such as phenylacetaldehyde, butanediol, acetoin, and theobromine that are required for flavour and aroma production. The results obtained will help develop targeted inoculations to produce desired chocolate flavour or targeted metabolic pathways for the selection of microbes for good aroma and flavour compounds formation.},
}

@article {pmid31388177,
year = {2019},
author = {Stower, H},
title = {A microbiome aid for malnutrition.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-019-0553-9},
pmid = {31388177},
issn = {1546-170X},
}