@article {pmid30415449,
year = {2018},
author = {Wang, F and Men, X and Zhang, G and Liang, K and Xin, Y and Wang, J and Li, A and Zhang, H and Liu, H and Wu, L},
title = {Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos.},
journal = {AMB Express},
volume = {8},
number = {1},
pages = {182},
doi = {10.1186/s13568-018-0713-1},
pmid = {30415449},
issn = {2191-0855},
support = {2017CP01//Yunnan Academy of Tobacco Sciences Project/ ; ZDYF2017155//Hainan's Key Project of Research and Development Plan/ ; 2017252//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; },
abstract = {Selection of optimal primer pairs in 16S rRNA gene sequencing is a pivotal issue in microorganism diversity analysis. However, limited effort has been put into investigation of specific primer sets for analysis of the bacterial diversity of aging flue-cured tobaccos (AFTs), as well as prediction of the function of the bacterial community. In this study, the performance of four primer pairs in determining bacterial community structure based on 16S rRNA gene sequences in AFTs was assessed, and the functions of genes were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Results revealed that the primer set 799F-1193R covering the amplification region V5V6V7 gave a more accurate picture of the bacterial community structure of AFTs, with lower co-amplification levels of chloroplast and mitochondrial genes, and more genera covered than when using the other primers. In addition, functional gene prediction suggested that the microbiome of AFTs was involved in kinds of interested pathways. A high abundance of functional genes involved in nitrogen metabolism was detected in AFTs, reflecting a high level of bacteria involved in degrading harmful nitrogen compounds and generating nitrogenous nutrients for others. Additionally, the functional genes involved in biosynthesis of valuable metabolites and degradation of toxic compounds provided information that the AFTs possess a huge library of microorganisms and genes that could be applied to further studies. All of these findings provide a significance reference for researchers working on the bacterial diversity assessment of tobacco-related samples.},
}

@article {pmid30415359,
year = {2018},
author = {Malfertheiner, P and Venerito, M and Schulz, C},
title = {Helicobacter pylori Infection: New Facts in Clinical Management.},
journal = {Current treatment options in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11938-018-0209-8},
pmid = {30415359},
issn = {1092-8472},
abstract = {PURPOSE: The global prevalence of Helicobacter pylori remains high in spite of its significant downwards trajectory in many regions. The clinical management of H. pylori infection merits guidance to meet ongoing challenges on whom and how to test, prevent, and cure related diseases.

RECENT FINDINGS: Several international guidelines and consensus reports have updated the management strategies for cure of the H. pylori infection. The definition of H. pylori gastritis as an infectious disease independent of whether or not presenting with clinical manifestations and symptoms has broadened the use of the test and treat strategy. Patients on selected long-term medications, such as aspirin, other anti-platelet agents, NSAIDs, and PPIs should be considered for H. pylori test and treat. Important progress is made with initiatives in primary and secondary gastric cancer prevention. Uncertainties persist in the interpretation of the role of H. pylori in association with extragastric diseases. Selection of therapies needs to address individual antibiotic resistance and regional surveillance of resistance for the adoption of an effective treatment algorithm.

CONCLUSION: Clinical aspects of H. pylori infection have evolved over time and the therapeutic management requires continuous adaptation. A vaccine is still a non-fulfilled promise. The future will tell us more about the role of H. pylori in interactions with the gut microbiome.},
}

@article {pmid30415167,
year = {2018},
author = {Singh, JP and Ojinnaka, EU and Krumins, JA and Goodey, NM},
title = {Abiotic factors determine functional outcomes of microbial inoculation of soils from a metal contaminated brownfield.},
journal = {Ecotoxicology and environmental safety},
volume = {168},
number = {},
pages = {450-456},
doi = {10.1016/j.ecoenv.2018.10.114},
pmid = {30415167},
issn = {1090-2414},
abstract = {Whole community microbial inoculation can improve soil function in contaminated environments. Here we conducted a case study to investigate whether biotic factors (inoculum) or abiotic factors (soil base) have more impact on the extracellular enzymatic activities in a whole community microbial inoculation. To this end, we cross-inoculated microbial communities between two heavy metal-contaminated soils, with high and low extracellular enzyme activities, respectively. We measured extracellular phosphatase activity, a proxy for soil function, after self- and cross-inoculation of microbial communities into sterilized soils, and all activities were normalized to non-inoculated controls. We found that inoculation increased phosphatase activity in the soils. For soils treated with different inocula, we found significant differences in the microbial community compositions but no significant differences in the extracellular phosphatase activities normalized to their respective sterilized, non-inoculated controls (4.7 ± 1.8 and 3.3 ± 0.5 for soils inoculated with microbial communities from 146 to 43, respectively). On the other hand, normalized phosphatase activities between the two soil bases were significantly different (4.1 ± 0.12 and 1.9 ± 0.12 for soil bases 146 and 43, respectively) regardless of the source of the inoculum that did not vary between soil bases. The results indicate that the abiotic properties of the soils were a significant predictor for phosphatase activity but not for the end-point composition of the microbial community. The findings suggest that targeted microbial inocula from metal contaminated soils can increase phosphatase activity, and likely soil functioning in general, but the degree to which this happens depends on the abiotic environment, in this case, metal contamination.},
}

@article {pmid30415160,
year = {2018},
author = {Davison, JM and Wischmeyer, PE},
title = {Probiotic and synbiotic therapy in the critically ill: State of the art.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {59},
number = {},
pages = {29-36},
doi = {10.1016/j.nut.2018.07.017},
pmid = {30415160},
issn = {1873-1244},
abstract = {Recent medical history has largely viewed our bacterial symbionts as pathogens to be eradicated rather than as essential partners in optimal health. However, one of the most exciting scientific advances in recent years has been the realization that commensal microorganisms (our microbiome) play vital roles in human physiology in nutrition, vitamin synthesis, drug metabolism, protection against infection, and recovery from illness. Recent data show that loss of "health-promoting" microbes and overgrowth of pathogenic bacteria (dysbiosis) in patients in the intensive care unit (ICU) appears to contribute to nosocomial infections, sepsis, and poor outcomes. Dysbiosis results from many factors, including ubiquitous antibiotic use and altered nutrition delivery in illness. Despite modern antibiotic therapy, infections and mortality from often multidrug-resistant organisms are increasing. This raises the question of whether restoration of a healthy microbiome via probiotics or synbiotics (probiotic and prebiotic combinations) to intervene on ubiquitous ICU dysbiosis would be an optimal intervention in critical illness to prevent infection and to improve recovery. This review will discuss recent innovative experimental data illuminating mechanistic pathways by which probiotics and synbiotics may provide clinical benefit. Furthermore, a review of recent clinical data demonstrating that probiotics and synbiotics can reduce complications in ICU and other populations will be undertaken. Overall, growing data for probiotic and symbiotic therapy reveal a need for definitive clinical trials of these therapies, as recently performed in healthy neonates. Future studies should target administration of probiotics and synbiotics with known mechanistic benefits to improve patient outcomes. Optimally, future probiotic and symbiotic studies will be conducted using microbiome signatures to characterize actual ICU dysbiosis and determine, and perhaps even personalize, ideal probiotic and symbiotic therapies.},
}

@article {pmid30414595,
year = {2018},
author = {Valdes, AM and Menni, C},
title = {Inflammatory markers and mediators in heart disease.},
journal = {Aging},
volume = {},
number = {},
pages = {},
doi = {10.18632/aging.101640},
pmid = {30414595},
issn = {1945-4589},
}

@article {pmid30414380,
year = {2018},
author = {Cześnikiewicz-Guzik, M and Nosalski, R and Mikolajczyk, TP and Vidler, F and Dohnal, T and Dembowska, E and Graham, D and Harrison, DG and Guzik, TJ},
title = {Th1 type immune responses to Porphyromonas gingivalis antigens exacerbate Angiotensin II dependent hypertension and vascular dysfunction.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.14536},
pmid = {30414380},
issn = {1476-5381},
abstract = {BACKGROUND AND PURPOSE: Emerging evidence indicates that hypertension is mediated by immune mechanisms. We hypothesized that exposure to Porphyromonas gingivalis antigens, commonly encountered in periodontal disease, can enhance immune activation in hypertension and exacerbate blood pressure elevation, vascular inflammation and vascular dysfunction.

EXPERIMENTAL APPROACH: Th1 immune response were elicited through immunizations using Porphyromonas gingivalis lysate antigens (10ug) conjugated with aluminium oxide (50ug) and IL-12 (1ug). The hypertension and vascular endothelial dysfunction evoked by sub-pressor doses of Angiotensin II (0.25mg/kg/day) were studied and vascular inflammation was quantified by flow cytometry and real time polymerase chain reaction.

KEY RESULTS: Systemic T cell activation, characteristic for hypertension, was exacerbated by P. gingivalis antigen stimulations. This translated into increased aortic vascular inflammation with enhanced leukocytes, in particular, T cell and macrophage infiltration. Expression of the Th1 cytokines, Interferon-γ and Tumour Necrosis Factor-α and the transcription factor TBX21 was increased in aortas of P. gingivalis/Interleukin-12/aluminium oxide immunized mice, while IL-4 and TGF-β were unchanged. These immune changes in mice with induced T helper type 1 immune responses were associated with enhanced blood pressure elevation and endothelial dysfunction compared to control mice in response to two weeks infusion of a sub-pressor dose of Angiotensin II.

CONCLUSION AND IMPLICATIONS: These studies support the concept that Th1 immune responses induced by bacterial antigens such as P. gingivalis can increase sensitivity to sub-pressor pro-hypertensive insults such as low dose Angiotensin II, therefore providing a mechanistic link between chronic infection such as periodontitis and hypertension.},
}

@article {pmid30414225,
year = {2018},
author = {Mullaney, TG and Lam, D and Kluger, R and D'Souza, B},
title = {Randomized controlled trial of probiotic use for post-colonoscopy symptoms.},
journal = {ANZ journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1111/ans.14883},
pmid = {30414225},
issn = {1445-2197},
abstract = {BACKGROUND: Symptoms of bloating, discomfort and altered bowel function persist post-colonoscopy in up to 20% of patients. A previous randomized controlled trial of probiotics for post-colonoscopy symptoms has demonstrated a reduction in duration of pain with the use of probiotics. This was performed with air insufflation and the question was asked whether the effect would persist with the use of carbon dioxide to insufflate the colon.

METHODS: Eligible patients were recruited and randomized to receive either probiotic or placebo capsules post colonoscopy. A questionnaire was completed documenting the presence of pre-procedural and post-procedural symptoms for the following 2 weeks. The results were entered into a database and processed by an independent statistician. The primary outcome was mean pain score and incidence of bloating over the first 7 days and at 14 days post procedure. The secondary outcome was the time to return of normal bowel function.

RESULTS: Two hundred and forty participants were recruited and randomized (120 probiotic and 120 placebo). Data were available for 75 patients in the probiotic and 75 in the placebo group. There was no significant difference between groups in post-procedural discomfort, bloating nor time to return of normal bowel function. Subgroup analysis of the patients with preexisting symptoms showed a reduction in incidence of bloating with the use of probiotics.

CONCLUSION: There may be a role for the use of probiotics in the subgroup of patients with preexisting symptoms; however, routine use of probiotics to ameliorate post-procedural symptoms of carbon dioxide insufflation colonoscopy cannot be advocated.},
}

@article {pmid30414158,
year = {2019},
author = {Bosch, TCG},
title = {Hydra as Model to Determine the Role of FOXO in Longevity.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1890},
number = {},
pages = {231-238},
doi = {10.1007/978-1-4939-8900-3_19},
pmid = {30414158},
issn = {1940-6029},
abstract = {In non-senescent Hydra, continuously high activity of transcription factor FOXO contributes to continuous stem cell proliferation. Here, we describe how genetic manipulation of Hydra polyps using embryo-microinjection allows uncovering the role of FOXO in coordinating both stem cell proliferation and antimicrobial peptide0073 , effector molecules of the innate immune system, and regulators of the microbiome.},
}

@article {pmid30413754,
year = {2018},
author = {Tuncil, YE and Thakkar, RD and Marcia, ADR and Hamaker, BR and Lindemann, SR},
title = {Divergent short-chain fatty acid production and succession of colonic microbiota arise in fermentation of variously-sized wheat bran fractions.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16655},
doi = {10.1038/s41598-018-34912-8},
pmid = {30413754},
issn = {2045-2322},
abstract = {Though the physical structuring of insoluble dietary fiber sources may strongly impact their processing by microbiota in the colon, relatively little mechanistic information exists to explain how these aspects affect microbial fiber fermentation. Here, we hypothesized that wheat bran fractions varying in size would be fermented differently by gut microbiota, which would lead to size-dependent differences in metabolic fate (as short-chain fatty acids; SCFAs) and community structure. To test this hypothesis, we performed an in vitro fermentation assay in which wheat bran particles from a single source were separated by sieving into five size fractions and inoculated with fecal microbiota from three healthy donors. SCFA production, measured by gas chromatography, uncovered size fraction-dependent relationships between total SCFAs produced as well as the molar ratios of acetate, propionate, and butyrate. 16S rRNA sequencing revealed that these size-dependent metabolic outcomes were accompanied by the development of divergent microbial community structures. We further linked these distinct results to subtle, size-dependent differences in chemical composition. These results suggest that physical context can drive differences in microbiota composition and function, that fiber-microbiota interaction studies should consider size as a variable, and that manipulating the size of insoluble fiber-containing particles might be used to control gut microbiome composition and metabolic output.},
}

@article {pmid30413478,
year = {2018},
author = {Poudel, R and Jumpponen, A and Kennelly, MM and Rivard, CL and Gomez-Montano, L and Garrett, KA},
title = {Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01765-18},
pmid = {30413478},
issn = {1098-5336},
abstract = {Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and theory to predict microbial assemblages are still limited. Here we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, selfgrafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. OTU-based bacterial diversity was greater in Maxifort compared to nongraft controls, whereas bacterial diversity in the controls (selfgraft and nongraft) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the selfgraft was similar to the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a PERMANOVA analysis, there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and the rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.IMPORTANCE Understanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and the rhizosphere. Comparing the bacterial communities in control treatments (nongraft and selfgraft plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatments, which may represent candidate taxa useful for biocontrol and in biofertilizers.},
}

@article {pmid30412889,
year = {2018},
author = {Nathani, NM and Mootapally, C and Dave, BP},
title = {Antibiotic resistance genes allied to the pelagic sediment microbiome in the Gulf of Khambhat and Arabian Sea.},
journal = {The Science of the total environment},
volume = {653},
number = {},
pages = {446-454},
doi = {10.1016/j.scitotenv.2018.10.409},
pmid = {30412889},
issn = {1879-1026},
abstract = {Antibiotics have been widely spread in the environments, imposing profound stress on the resistome of the residing microbes. Marine microbiomes are well established large reservoirs of novel antibiotics and corresponding resistance genes. The Gulf of Khambhat is known for its extreme tides and complex sedimentation process. We performed high throughput sequencing and applied bioinformatics techniques on pelagic sediment microbiome across four coordinates of the Gulf of Khambhat to assess the marine resistome, its corresponding bacterial community and compared with the open Arabian Sea sample. We identified a total of 2354 unique types of resistance genes, with most abundant and diverse gene profile in the area that had anthropogenic activities being carried out on-shore. The genes with >1% abundance in all samples included carA, macB, sav1866, tlrC, srmB, taeA, tetA, oleC and bcrA which belonged to the macrolides, glycopeptides and peptide drug classes. ARG enriched phyla distribution was quite varying between all the sites, with Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes among the dominant phyla. Based on the outcomes, we also propose potential biomarker candidates Desulfovibrio, Thermotaga and Pelobacter for antibiotic monitoring in the two of the Gulf samples probable contamination prone environments, and genera Nitrosocccus, Marinobacter and Streptomyces in the rest of the three studied samples. Outcomes support the concept that ARGs naturally originate in environments and human activities contribute to the dissemination of antibiotic resistance.},
}

@article {pmid30412640,
year = {2018},
author = {Lin, C and Culver, J and Weston, B and Underhill, E and Gorky, J and Dhurjati, P},
title = {GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0207072},
doi = {10.1371/journal.pone.0207072},
pmid = {30412640},
issn = {1932-6203},
abstract = {Knowledge of the spatial and temporal dynamics of the gut microbiome is essential to understanding the state of human health, as over a hundred diseases have been correlated with changes in microbial populations. Unfortunately, due to the complexity of the microbiome and the limitations of in vivo and in vitro experiments, studying spatial and temporal dynamics of gut bacteria in a biological setting is extremely challenging. Thus, in silico experiments present an excellent alternative for studying such systems. In consideration of these issues, we have developed a user-friendly agent-based model, GutLogo, that captures the spatial and temporal development of four representative bacterial genera populations in the ileum. We demonstrate the utility of this model by simulating population responses to perturbations in flow rate, nutrition, and probiotics. While our model predicts distinct changes in population levels due to these perturbations, most of the simulations suggest that the gut populations will return to their original steady states once the disturbance is removed. We hope that, in the future, the GutLogo model is utilized and customized by interested parties, as GutLogo can serve as a basic modeling framework for simulating a variety of physiological scenarios and can be extended to capture additional complexities of interest.},
}

@article {pmid30412600,
year = {2018},
author = {Shah, MS and DeSantis, T and Yamal, JM and Weir, T and Ryan, EP and Cope, JL and Hollister, EB},
title = {Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0207002},
doi = {10.1371/journal.pone.0207002},
pmid = {30412600},
issn = {1932-6203},
abstract = {Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa. The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity remains unclear. In this study, we systematically analyzed previously published 16S rRNA sequence data from CRC patients with matched tumor:tumor-adjacent biopsies (n = 294 pairs, n = 588 biospecimens) and matched tumor biopsy:fecal pairs (n = 42 pairs, n = 84 biospecimens). Procrustes analyses, random effects regression, random forest (RF) modeling, and inferred functional pathway analyses were conducted to assess community similarity and microbial diversity across heterogeneous patient groups and studies. Our results corroborate previously reported association of increased Fusobacterium with tumor biopsies. Parvimonas and Streptococcus abundances were also elevated while Faecalibacterium and Ruminococcaceae abundances decreased in tumors relative to tumor-adjacent biopsies and stool samples from the same case. With the exception of these limited taxa, the majority of findings from individual studies were not confirmed by other 16S rRNA gene-based datasets. RF models comparing tumor and tumor-adjacent specimens yielded an area under curve (AUC) of 64.3%, and models of tumor biopsies versus fecal specimens exhibited an AUC of 82.5%. Although some taxa were shared between fecal and tumor samples, their relative abundances varied substantially. Inferred functional analysis identified potential differences in branched amino acid and lipid metabolism. Microbial markers that reliably occur in tumor tissue can have implications for microbiome based and microbiome targeting therapeutics for CRC.},
}

@article {pmid30412201,
year = {2018},
author = {Taroncher-Oldenburg, G and Jones, S and Blaser, M and Bonneau, R and Christey, P and Clemente, JC and Elinav, E and Ghedin, E and Huttenhower, C and Kelly, D and Kyle, D and Littman, D and Maiti, A and Maue, A and Olle, B and Segal, L and van Hylckama Vlieg, JET and Wang, J},
title = {Translating microbiome futures.},
journal = {Nature biotechnology},
volume = {36},
number = {11},
pages = {1037-1042},
doi = {10.1038/nbt.4287},
pmid = {30412201},
issn = {1546-1696},
}

@article {pmid30412196,
year = {2018},
author = {Kwak, MJ and Kong, HG and Choi, K and Kwon, SK and Song, JY and Lee, J and Lee, PA and Choi, SY and Seo, M and Lee, HJ and Jung, EJ and Park, H and Roy, N and Kim, H and Lee, MM and Rubin, EM and Lee, SW and Kim, JF},
title = {Author Correction: Rhizosphere microbiome structure alters to enable wilt resistance in tomato.},
journal = {Nature biotechnology},
volume = {36},
number = {11},
pages = {1117},
doi = {10.1038/nbt1118-1117},
pmid = {30412196},
issn = {1546-1696},
}

@article {pmid30411820,
year = {2018},
author = {Sapountzis, P and Nash, DR and Schiøtt, M and Boomsma, JJ},
title = {The evolution of abdominal microbiomes in fungus-growing ants.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.14931},
pmid = {30411820},
issn = {1365-294X},
abstract = {The attine ants are a monophyletic lineage that switched to fungus-farming ca. 55-60 MYA. They have become a model for the study of complex symbioses after additional fungal and bacterial symbionts were discovered, but their abdominal endosymbiotic bacteria remain largely unknown. Here we present a comparative microbiome analysis of endosymbiotic bacteria spanning the entire phylogenetic tree. We show that, across 17 representative sympatric species from eight genera sampled in Panama, abdominal microbiomes are dominated by Mollicutes, α- and γ-Proteobacteria, and Actinobacteria. Bacterial abundances increase from basal to crown branches in the phylogeny reflecting a shift towards putative specialized and abundant abdominal microbiota after the ants domesticated gongylidia-bearing cultivars, but before the origin of industrial-scale farming based on leaf-cutting herbivory. This transition coincided with the ancestral single colonization event of Central/North America ca. 20 MYA, documented in a recent phylogenomic study showing that the entire crown-group of the higher attine ants, including the leaf-cutting ants, evolved there and not in South America. Several bacterial species are located in gut tissues or abdominal organs of the evolutionarily derived, but not the basal attine ants. The composition of abdominal microbiomes appears to be affected by the presence/absence of defensive antibiotic-producing actinobacterial biofilms on the worker ants' cuticle, but the significance of this association remains unclear. The patterns of diversity, abundance, and sensitivity of the abdominal microbiomes that we obtained explore novel territory in the comparative analysis of attine fungus-farming symbioses and raise new questions for further in-depth research. This article is protected by copyright. All rights reserved.},
}

@article {pmid30411189,
year = {2018},
author = {Dror, H and Novak, L and Evans, JS and López-Legentil, S and Shenkar, N},
title = {Core and Dynamic Microbial Communities of Two Invasive Ascidians: Can Host-Symbiont Dynamics Plasticity Affect Invasion Capacity?.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1276-z},
pmid = {30411189},
issn = {1432-184X},
support = {2014025//United States - Israel Binational Science Foundation/ ; 2014025//United States - Israel Binational Science Foundation/ ; },
abstract = {Ascidians (Chordata, Ascidiacea) are considered to be prominent marine invaders, able to tolerate highly polluted environments and fluctuations in salinity and temperature. Here, we examined the seasonal and spatial dynamics of the microbial communities in the inner-tunic of two invasive ascidians, Styela plicata (Lesueur 1823) and Herdmania momus (Savigny 1816), in order to investigate the changes that occur in the microbiome of non-indigenous ascidians in different environments. Microbial communities were characterized using next-generation sequencing of partial (V4) 16S rRNA gene sequences. A clear differentiation between the ascidian-associated microbiome and bacterioplankton was observed, and two distinct sets of operational taxonomic units (OTUs), one core and the other dynamic, were recovered from both species. The relative abundance of the dynamic OTUs in H. momus was higher than in S. plicata, for which core OTU structure was maintained independently of location. Ten and seventeen core OTUs were identified in S. plicata and H. momus, respectively, including taxa with reported capabilities of carbon fixing, ammonia oxidization, denitrification, and heavy-metal processing. The ascidian-sourced dynamic OTUs clustered in response to site and season but significantly differed from the bacterioplankton community structure. These findings suggest that the associations between invasive ascidians and their symbionts may enhance host functionality while maintaining host adaptability to changing environmental conditions.},
}

@article {pmid30411009,
year = {2018},
author = {Van den Abbeele, P and Kamil, A and Fleige, L and Chung, Y and De Chavez, P and Marzorati, M},
title = {Different Oat Ingredients Stimulate Specific Microbial Metabolites in the Gut Microbiome of Three Human Individuals in Vitro.},
journal = {ACS omega},
volume = {3},
number = {10},
pages = {12446-12456},
doi = {10.1021/acsomega.8b01360},
pmid = {30411009},
issn = {2470-1343},
abstract = {We used a standardized in vitro simulation of the intestinal environment of three human donors to investigate the effect of six oat ingredients, which were produced by the application of different processing techniques, on the gut microbial community. Fructooligosaccharide was used as the positive control. Consistent changes in pH and gas production, on average -0.4 pH units and +32 kPa, indicated the high fermentability of the oat ingredients, and the resulting increased production of metabolites that are considered as beneficial for human health. These metabolites included acetate and lactate, but mostly propionate (+13.6 mM on average). All oat ingredients resulted in increased bifidobacteria levels with an average increase of 0.73 log. Moreover, a decreased production of proteolytic markers was observed, including branched short-chain fatty acids and ammonium. The results were donor-specific and product-specific. The results suggested an association between the total amounts of dietary fiber and the prebiotic potentials of different ingredients. Furthermore, as mechanical processing of oat products has previously been linked to increased extractability of dietary fibers, the obtained results suggest that different processing techniques might have impacted the potential functional properties of the final ingredients.},
}

@article {pmid30410727,
year = {2018},
author = {Morris, JJ},
title = {What is the hologenome concept of evolution?.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {},
doi = {10.12688/f1000research.14385.1},
pmid = {30410727},
issn = {2046-1402},
abstract = {All multicellular organisms are colonized by microbes, but a gestalt study of the composition of microbiome communities and their influence on the ecology and evolution of their macroscopic hosts has only recently become possible. One approach to thinking about the topic is to view the host-microbiome ecosystem as a "holobiont". Because natural selection acts on an organism's realized phenotype, and the phenotype of a holobiont is the result of the integrated activities of both the host and all of its microbiome inhabitants, it is reasonable to think that evolution can act at the level of the holobiont and cause changes in the "hologenome", or the collective genomic content of all the individual bionts within the holobiont. This relatively simple assertion has nevertheless been controversial within the microbiome community. Here, I provide a review of recent work on the hologenome concept of evolution. I attempt to provide a clear definition of the concept and its implications and to clarify common points of disagreement.},
}

@article {pmid30410609,
year = {2018},
author = {Wu, J and Xu, S and Xiang, C and Cao, Q and Li, Q and Huang, J and Shi, L and Zhang, J and Zhan, Z},
title = {Tongue Coating Microbiota Community and Risk Effect on Gastric Cancer.},
journal = {Journal of Cancer},
volume = {9},
number = {21},
pages = {4039-4048},
doi = {10.7150/jca.25280},
pmid = {30410609},
issn = {1837-9664},
abstract = {Background: Although oral hygiene and health have long been reported to be associated with increased risk of gastric cancer (GC), the direct relationship of oral microbes with the risk of GC have not been evaluated fully. We aimed to test whether tongue coating microbiome was associated with GC risk. Methods: Pyrosequencing of 16S rRNA gene of tongue coating microbiome was used in 57 newly diagnosed gastric adenocarcinomas and 80 healthy controls. Benjamini-Hochberg (BH) was applied for multiple comparison correction. Co-abundance group (CAGs) analysis was adopted. Results: We found that higher relative abundance of Firmicutes, and lower of Bacteroidetes were associated with increased risk of GC. In genus level, Streptococcus trended with a higher risk of GC, the four other genera (Neisseria, Prevotella, Prevotella7, and Porphyromonas) were found to have a decreased risk of GC. Different from overall GC and non-cardia cancer, Alloprevotella and Veillonella trended with the higher risk of cardia cancer. Finally, we analyzed the microbiota by determining CAGs and six clusters were identified. Except the Cluster 2 (mainly Streptococcus and Abiotrophia), the other clusters had an inverse association with GC. Of them, the Cluster 6 (mainly Prevotella and Prevotella7 etc) had a relatively good classification power with 0.76 of AUC. Conclusion: Microbiome in tongue coating may have potential guiding value for early detection and prevention of GC.},
}

@article {pmid30410285,
year = {2018},
author = {Alexander, W},
title = {2018 European Association for the Study of Diabetes.},
journal = {P & T : a peer-reviewed journal for formulary management},
volume = {43},
number = {11},
pages = {689-693},
pmid = {30410285},
issn = {1052-1372},
abstract = {We review sessions on the association of diuretic use and amputations, albiglutide and cardiovascular outcomes with diabetes and cardiovascular disease, how lorcaserin affects diabetes in overweight patients, how testosterone therapy improves diabetes in hypogonadal men, the pros and cons of gastric bypass surgery, how low-calorie sweeteners affect the gut microbiome, and more.},
}

@article {pmid30410105,
year = {2018},
author = {Tang, WHW and Li, DY and Hazen, SL},
title = {Dietary metabolism, the gut microbiome, and heart failure.},
journal = {Nature reviews. Cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41569-018-0108-7},
pmid = {30410105},
issn = {1759-5010},
abstract = {Advances in our understanding of how the gut microbiota contributes to human health and diseases have expanded our insight into how microbial composition and function affect the human host. Heart failure is associated with splanchnic circulation congestion, leading to bowel wall oedema and impaired intestinal barrier function. This situation is thought to heighten the overall inflammatory state via increased bacterial translocation and the presence of bacterial products in the systemic blood circulation. Several metabolites produced by gut microorganisms from dietary metabolism have been linked to pathologies such as atherosclerosis, hypertension, heart failure, chronic kidney disease, obesity, and type 2 diabetes mellitus. These findings suggest that the gut microbiome functions like an endocrine organ by generating bioactive metabolites that can directly or indirectly affect host physiology. In this Review, we discuss several newly discovered gut microbial metabolic pathways, including the production of trimethylamine and trimethylamine N-oxide, short-chain fatty acids, and secondary bile acids, that seem to participate in the development and progression of cardiovascular diseases, including heart failure. We also discuss the gut microbiome as a novel therapeutic target for the treatment of cardiovascular disease, and potential strategies for targeting intestinal microbial processes.},
}

@article {pmid30409838,
year = {2018},
author = {Tian, Y and Cai, J and Gui, W and Nichols, RG and Koo, I and Zhang, J and Anitha, M and Patterson, AD},
title = {Berberine Directly Impacts the Gut Microbiota to Promote Intestinal Farnesoid X Receptor Activation.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {},
number = {},
pages = {},
doi = {10.1124/dmd.118.083691},
pmid = {30409838},
issn = {1521-009X},
abstract = {Intestinal bacteria play an important role in bile acid metabolism and in the regulation of multiple host metabolic pathways (e.g., lipid and glucose homeostasis) through modulation of intestinal farnesoid X receptor (FXR) activity. Here, we examined the effect of berberine (BBR), a natural plant alkaloid, on intestinal bacteria using in vitro and in vivo models. In vivo, the metabolomic response and changes in mouse intestinal bacterial communities treated with BBR (100 mg/kg) for 5 days were assessed using NMR- and mass spectrometry-based metabolomics coupled with multivariate data analysis. Short-term BBR exposure altered intestinal bacteria by reducing the Clostridium cluster XIVa and IV and their bile salt hydrolase (BSH) activity, which resulted in the accumulation of taurocholic acid (TCA). The accumulation of TCA was associated with activation of intestinal FXR, which can mediate bile acid, lipid, and glucose metabolism. In vitro, isolated mouse cecal bacteria were incubated with three doses of BBR (0.1, 1, and 10 mg/ml) for 4 h in an anaerobic chamber. NMR-based metabolomics combined with flow cytometry was used to evaluate the direct physiologic and metabolic impact of BBR on the bacteria. In vitro, BBR exposure not only altered bacterial physiology, but also changed the bacterial community composition and function, especially reducing BSH expressing bacteria like Clostridium spp. These data suggest that BBR directly impacts bacteria to alter bile acid metabolism and activate FXR signaling. These data provide new insights into the link between intestinal bacteria, nuclear receptor signaling, and xenobiotics.},
}

@article {pmid30409598,
year = {2019},
author = {Wang, H and Shou, Y and Zhu, X and Xu, Y and Shi, L and Xiang, S and Feng, X and Han, J},
title = {Stability of vitamin B12 with the protection of whey proteins and their effects on the gut microbiome.},
journal = {Food chemistry},
volume = {276},
number = {},
pages = {298-306},
doi = {10.1016/j.foodchem.2018.10.033},
pmid = {30409598},
issn = {1873-7072},
abstract = {Cobalamin degrades in the presence of light and heat, which causes spectral changes and loss of coenzyme activity. In the presence of beta-lactoglobulin or alpha-lactalbumin, the thermal- and photostabilities of adenosylcobalamin (ADCBL) and cyanocobalamin (CNCBL) are increased by 10-30%. Similarly, the stabilities of ADCBL and CNCBL are increased in the presence of whey proteins by 19.7% and 2.2%, respectively, when tested in gastric juice for 2 h. Due to the limited absorption of cobalamin during digestion, excess cobalamin can enter the colon and modulate the gut microbiome. In a colonic model in vitro, supplementation with cobalamin and whey enhanced the proportions of Firmicutes and Bacteroidetes spp. and reduced those of Proteobacteria spp., which includes pathogens such as Escherichia and Shigella spp., and Pseudomonas spp. Thus, while complex formation could improve the stability and bioavailability of cobalamin, these complexes might also mediate gut microecology to influence human nutrition and health.},
}

@article {pmid30409559,
year = {2018},
author = {Shinde, R and McGaha, TL},
title = {The Aryl Hydrocarbon Receptor: Connecting Immunity to the Microenvironment.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2018.10.010},
pmid = {30409559},
issn = {1471-4981},
abstract = {The aryl hydrocarbon receptor (AhR) is a cytoplasmic receptor and transcription factor activated through cognate ligand binding. It is an important factor in immunity and tissue homeostasis, and structurally diverse compounds from the environment, diet, microbiome, and host metabolism can induce AhR activity. Emerging evidence suggests that AhR is a key sensor allowing immune cells to adapt to environmental conditions and changes in AhR activity have been associated with autoimmune disorders and cancer. Furthermore, AhR agonists or antagonists can impact immune disease outcomes identifying AhR as a potentially actionable target for immunotherapy. In this review, we describe known ligands stimulating AhR activity, downstream proinflammatory and suppressive mechanisms potentiated by AhR, and how this understanding is being applied to immunopathology to help control disease outcomes.},
}

@article {pmid30409169,
year = {2018},
author = {Ma, C and Sun, Z and Zeng, B and Huang, S and Zhao, J and Zhang, Y and Su, X and Xu, J and Wei, H and Zhang, H},
title = {Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {200},
doi = {10.1186/s40168-018-0578-1},
pmid = {30409169},
issn = {2049-2618},
support = {ID0E61AE8001//National Natural Science Foundation of China/ ; ID0EO2AE8002//Postdoctoral Science Foundation of Jiangsu Province/ ; },
abstract = {BACKGROUND: Mastitis, which affects nearly all lactating mammals including human, is generally thought to be caused by local infection of the mammary glands. For treatment, antibiotics are commonly prescribed, which however are of concern in both treatment efficacy and neonate safety. Here, using bovine mastitis which is the most costly disease in the dairy industry as a model, we showed that intestinal microbiota alone can lead to mastitis.

RESULTS: Fecal microbiota transplantation (FMT) from mastitis, but not healthy cows, to germ-free (GF) mice resulted in mastitis symptoms in mammary gland and inflammations in serum, spleen, and colon. Probiotic intake in parallel with FMT from diseased cows led to relieved mastitis symptoms in mice, by shifting the murine intestinal microbiota to a state that is functionally distinct from either healthy or diseased microbiota yet structurally similar to the latter. Despite conservation in mastitis symptoms, diseased cows and mice shared few mastitis-associated bacterial organismal or functional markers, suggesting striking divergence in mastitis-associated intestinal microbiota among lactating mammals. Moreover, an "amplification effect" of disease-health distinction in both microbiota structure and function was apparent during the cow-to-mouse FMT.

CONCLUSIONS: Hence, dysbiosis of intestinal microbiota may be one cause of mastitis, and probiotics that restore intestinal microbiota function are an effective and safe strategy to treat mastitis.},
}

@article {pmid30409123,
year = {2018},
author = {Rounge, TB and Meisal, R and Nordby, JI and Ambur, OH and de Lange, T and Hoff, G},
title = {Evaluating gut microbiota profiles from archived fecal samples.},
journal = {BMC gastroenterology},
volume = {18},
number = {1},
pages = {171},
doi = {10.1186/s12876-018-0896-6},
pmid = {30409123},
issn = {1471-230X},
support = {-//Cancer Registry of Norway Funds/ ; },
abstract = {BACKGROUND: Associations between colorectal cancer and microbiota have been identified. Archived fecal samples might be valuable sample sources for investigating causality in carcinogenesis and biomarkers discovery due to the potential of performing longitudinal studies. However, the quality, quantity and stability of the gut microbiota in these fecal samples must be assessed prior to such studies. We evaluated i) cross-contamination during analysis for fecal blood and ii) evaporation in stored perforated fecal immunochemical tests (iFOBT) samples, iii) temperature stability as well as iv) comparison of the gut microbiota diversity and composition in archived, iFOBT and fresh fecal samples in order to assess feasibility of large scale microbiota studies.

METHODS: The microbiota profiles were obtained by sequencing the V3-V4 region of 16S rDNA gene.

RESULTS: The iFOBT does not introduce any cross-sample contamination detectable by qPCR. Neither could we detect evaporation during freeze-thaw cycle of perforated iFOBT samples. Our results confirm room temperature stability of the gut microbiome. Diverse microbial profiles were achieved in 100% of fresh, 81% of long-term archived and 96% of iFOBT samples. Microbial diversity and composition were comparable between fresh and iFOBT samples, however, diversity differed significantly between long-term archived, fresh and iFOBT samples.

CONCLUSION: Our data showed that it is feasible to exploit archived fecal sample sets originally collected for testing of fecal blood. The advantages of using these sample sets for microbial biomarker discovery and longitudinal observational studies are the availability of high-quality diagnostic and follow-up data. However, care must be taken when microbiota are profiled in long-term archived fecal samples.},
}

@article {pmid30409105,
year = {2018},
author = {Heeney, DD and Zhai, Z and Bendiks, Z and Barouei, J and Martinic, A and Slupsky, C and Marco, ML},
title = {Lactobacillus plantarum bacteriocin is associated with intestinal and systemic improvements in diet-induced obese mice and maintains epithelial barrier integrity in vitro.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/19490976.2018.1534513},
pmid = {30409105},
issn = {1949-0984},
abstract = {We investigated the Lactobacillus plantarum bacteriocin plantaricin EF (PlnEF) system for its contributions to L. plantarum mediated benefits in a mouse model of diet-induced obesity. C57BL/6J mice on a high-fat diet (HFD) were administered a rifampicin resistant mutant of L. plantarum NCMIB8826 (NICMB8826-R) or an isogenic ΔplnEFI mutant strain, LM0419, every 48 h for nine weeks. Mice fed wild-type L. plantarum, but not LM0419, reduced their consumption of the HFD starting three weeks into the study and exhibited an overall 10% reduction in weight gain. The responses were independent of glucose homeostasis, as both NCMIB8826-R and LM0419 fed mice had improved oral glucose tolerance compared to sham controls. Although bacteriocins have antibacterial properties, the ileal, cecal, and fecal microbiota and cecocolic metabolomes were unchanged between mice fed either wild-type L. plantarum or the ΔplnEFI mutant. Instead, only mice fed NCMIB8826-R showed an increased production of ZO-1 in ileal tissues. To verify a potential role for the plantaricin EF system in supporting intestinal epithelial function, synthesized PlnEF peptides were applied to Caco-2 cell monolayers challenged with TNF-α and IFN-γ. The combination of PlnE and PlnF were required to prevent sustained cytokine-induced losses to Caco-2 cell para- and transcellular permeability and elevated IL-8 levels. In conclusion, this study shows that probiotic L. plantarum ameliorates the effects of obesogenic diets through a mechanism that involves the plantaricin EF system and likely includes L. plantarum - induced fortification of the intestinal epithelium.},
}

@article {pmid30409024,
year = {2018},
author = {Maki, KA and Diallo, AF and Lockwood, MB and Franks, AT and Green, SJ and Joseph, PV},
title = {Considerations When Designing a Microbiome Study: Implications for Nursing Science.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {1099800418811639},
doi = {10.1177/1099800418811639},
pmid = {30409024},
issn = {1552-4175},
abstract = {Nurse scientists play an important role in studying complex relationships among human genetics, environmental factors, and the microbiome, all of which can contribute to human health and disease. Therefore, it is essential that they have the tools necessary to execute a successful microbiome research study. The purpose of this article is to highlight important methodological factors for nurse scientists to consider when designing a microbiome study. In addition to considering factors that influence host-associated microbiomes (i.e., microorganisms associated with organisms such as humans, mice, and rats), this manuscript highlights study designs and methods for microbiome analysis. Exemplars are presented from nurse scientists who have incorporated microbiome methods into their program of research. This review is intended to be a resource to guide nursing-focused microbiome research and highlights how study of the microbiome can be incorporated to answer research questions.},
}

@article {pmid30404281,
year = {2016},
author = {Kang, TH and Kim, HJ},
title = {Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems.},
journal = {Micromachines},
volume = {7},
number = {7},
pages = {},
doi = {10.3390/mi7070107},
pmid = {30404281},
issn = {2072-666X},
abstract = {The human intestine is a dynamic organ where the complex host-microbe interactions that orchestrate intestinal homeostasis occur. Major contributing factors associated with intestinal health and diseases include metabolically-active gut microbiota, intestinal epithelium, immune components, and rhythmical bowel movement known as peristalsis. Human intestinal disease models have been developed; however, a considerable number of existing models often fail to reproducibly predict human intestinal pathophysiology in response to biological and chemical perturbations or clinical interventions. Intestinal organoid models have provided promising cytodifferentiation and regeneration, but the lack of luminal flow and physical bowel movements seriously hamper mimicking complex host-microbe crosstalk. Here, we discuss recent advances of human intestinal microphysiological systems, such as the biomimetic human "Gut-on-a-Chip" that can employ key intestinal components, such as villus epithelium, gut microbiota, and immune components under peristalsis-like motions and flow, to reconstitute the transmural 3D lumen-capillary tissue interface. By encompassing cutting-edge tools in microfluidics, tissue engineering, and clinical microbiology, gut-on-a-chip has been leveraged not only to recapitulate organ-level intestinal functions, but also emulate the pathophysiology of intestinal disorders, such as chronic inflammation. Finally, we provide potential perspectives of the next generation microphysiological systems as a personalized platform to validate the efficacy, safety, metabolism, and therapeutic responses of new drug compounds in the preclinical stage.},
}

@article {pmid30408565,
year = {2018},
author = {DeFilipp, Z and Hohmann, E and Jenq, RR and Chen, YB},
title = {Fecal microbiota transplantation: restoring the injured microbiome after allogeneic hematopoietic cell transplantation.},
journal = {Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbmt.2018.10.022},
pmid = {30408565},
issn = {1523-6536},
abstract = {Disruption of the intestinal microbiome early after allogeneic hematopoietic cell transplantation (allo-HCT) has been linked to adverse outcomes in transplant recipients. To date, it remains unknown as to whether microbiome-directed interventions will be able to impact important clinical endpoints. Fecal microbiota transplantation (FMT) is a compelling intervention to restore healthy diversity to the intestinal microenvironment after allo-HCT, but currently has no established role in transplant recipients. In this review, we examine the utilization of FMT as treatment for Clostridium difficile infections and acute graft-versus-host disease, as well as a restorative intervention early after allo-HCT. Ongoing and planned studies will help determine the ultimate role of FMT in recipients of allo-HCT.},
}

@article {pmid30408471,
year = {2018},
author = {Wah, DTO and Ossenkopp, KP and Bishnoi, I and Kavaliers, M},
title = {Predator odor exposure in early adolescence influences the effects of the bacterial product, propionic acid, on anxiety, sensorimotor gating, and acoustic startle response in male rats in later adolescence and adulthood.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.physbeh.2018.11.003},
pmid = {30408471},
issn = {1873-507X},
abstract = {It is becoming evident than the adolescent period is a sensitive period in stress response programming. Stressors during this time may alter signaling from the gut microbiome, which has been shown to increase the risk for psychiatric disorders. It was hypothesized that adolescent stressors may potentiate the symptoms of anxiety and sensory abnormalities induced by a gut bacterial product, the short-chain fatty acid, propionic acid (PPA). The present study investigated the effects of repeated predator odor exposure during early adolescence on male rats administered PPA in late adolescence and adulthood on a behavioral test battery. Male adolescent Long-Evans rats were repeatedly exposed to a worn or unworn cat collar stimulus in early adolescence on postnatal days (P) 28, P30, P32, and P34. They were administered either PPA (500 mg/kg i.p.), or its vehicle in late adolescence on P40 and P43, and were subsequently tested on the light-dark anxiety task and acoustic startle task, respectively. In adulthood, the rats were again injected with PPA or its vehicle on P74 and P77, and subsequently tested on the light-dark apparatus and acoustic startle task, respectively. The repeated predator odor exposure was aversive and produced long-term anxiogenic effects as measured by the light-dark apparatus. PPA decreased activity and percent prepulse inhibition of the acoustic startle response, with its effects on vertical activity, a putative measure of escape behavior, being potentiated by prior predator stress. PPA's effects in adulthood were diminished in comparison to adolescence. These results suggest the importance of evaluating the effects of early adolescent stress on subsequent environmental insults on the development of behavioral abnormalities.},
}

@article {pmid30408195,
year = {2018},
author = {Kodama, WA and Xu, Z and Metcalf, JL and Song, SJ and Harrison, N and Knight, R and Carter, DO and Happy, CB},
title = {Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue.},
journal = {Journal of forensic sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/1556-4029.13949},
pmid = {30408195},
issn = {1556-4029},
support = {2014-R2-CX-K011//National Institute of Justice/ ; //Office of Justice Programs/ ; //US Department of Justice/ ; },
abstract = {Microbes can be used effectively as trace evidence, at least in research settings. However, it is unknown whether skin microbiomes change prior to autopsy and, if so, whether these changes interfere with linking objects to decedents. The current study included microbiomes from 16 scenes of death in the City and County of Honolulu and tested whether objects at the scenes can be linked to individual decedents. Postmortem skin microbiomes were stable during repeated sampling up to 60 h postmortem and were similar to microbiomes of an antemortem population. Objects could be traced to decedents approximately 75% of the time, with smoking pipes and medical devices being especially accurate (100% match), house and car keys being poor (0%), and other objects like phones intermediate (~80%). These results show that microbes from objects at death scenes can be matched to individual decedents, opening up a new method of establishing associations and identifications.},
}

@article {pmid30408037,
year = {2018},
author = {Wu, HX and Chen, X and Chen, H and Lu, Q and Yang, Z and Ren, W and Liu, J and Shao, S and Wang, C and King-Jones, K and Chen, MS},
title = {Variation and diversification of the microbiome of Schlechtendalia chinensis on two alternate host plants.},
journal = {PloS one},
volume = {13},
number = {11},
pages = {e0200049},
doi = {10.1371/journal.pone.0200049},
pmid = {30408037},
issn = {1932-6203},
abstract = {Schlechtendalia chinensis, a gall-inducing aphid, has two host plants in its life cycle. Its wintering host is a moss (typically Plagiomnium maximoviczii) and its main host is Rhus chinensis (Sumac), on which it forms galls during the summer. This study investigated bacteria associated with S. chinensis living on the two different host plants by sequencing 16S rRNAs. A total of 183 Operational Taxonomic Units (OTUs) from 50 genera were identified from aphids living on moss, whereas 182 OTUs from 49 genera were found from aphids living in Sumac galls. The most abundant bacterial genus among identified OTUs from aphids feeding on both hosts was Buchnera. Despite similar numbers of OTUs, the composition of bacterial taxa showed significant differences between aphids living on moss and those living on R. chinensis. Specifically, there were 12 OTUs from 5 genera (family) unique to aphids living on moss, and 11 OTUs from 4 genera (family) unique to aphids feeding in galls on R. chinensis. Principal Coordinate Analysis (PCoA) also revealed that bacteria from moss-residing aphids clustered differently from aphids collected from galls. Our results provide a foundation for future analyses on the roles of symbiotic bacteria in plant-aphid interactions in general, and how gall-specific symbionts differ in this respect.},
}

@article {pmid30407581,
year = {2018},
author = {Dempsey, JL and Wang, D and Siginir, G and Fei, Q and Raftery, D and Gu, H and Cui, JY},
title = {Pharmacological Activation of PXR and CAR Down-regulates Distinct Bile Acid-metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfy271},
pmid = {30407581},
issn = {1096-0929},
abstract = {The gut microbiome regulates important host metabolic pathways including xenobiotic metabolism and intermediary metabolism, such as the conversion of primary bile acids (BAs) into secondary BAs. The nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are well-known regulators for xenobiotic biotransformation in liver. However, little is known regarding the potential effects of PXR and CAR on the composition and function of the gut microbiome. To test our hypothesis that activation of PXR and CAR regulates gut microbiota and secondary BA synthesis, nine-week-old male conventional (CV) and germ-free (GF) mice were orally gavaged with corn oil, PXR agonist PCN (75 mg/kg), or CAR agonist TCPOBOP (3 mg/kg) once daily for four days. PCN and TCPOBOP decreased two taxa in the Bifidobacterium genus, which corresponded with decreased gene abundance of the BA-deconjugating enzyme bile salt hydrolase. In liver and small intestinal content (SIC) of GF mice, there was a TCPOBOP-mediated increase in total, primary, and conjugated BAs corresponding with increased Cyp7a1 mRNA. Bifidobacterium, Dorea, Peptociccaceae, Anaeroplasma, and Ruminococcus positively correlated with T-UDCA in LIC, but negatively correlated with T-CDCA in serum. In conclusion, PXR and CAR activation down-regulates BA-metabolizing bacteria in the intestine and modulates BA homeostasis in a gut microbiota-dependent manner.},
}

@article {pmid30407218,
year = {2018},
author = {Zhang, X and Guo, R and Kambara, H and Ma, F and Luo, HR},
title = {The role of CXCR2 in acute inflammatory responses and its antagonists as anti-inflammatory therapeutics.},
journal = {Current opinion in hematology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOH.0000000000000476},
pmid = {30407218},
issn = {1531-7048},
abstract = {PURPOSE OF REVIEW: CXCR2 is key stimulant of immune cell migration and recruitment, especially of neutrophils. Alleviating excessive neutrophil accumulation and infiltration could prevent prolonged tissue damage in inflammatory disorders. This review focuses on recent advances in our understanding of the role of CXCR2 in regulating neutrophil migration and the use of CXCR2 antagonists for therapeutic benefit in inflammatory disorders.

RECENT FINDINGS: Recent studies have provided new insights into how CXCR2 signaling regulates hematopoietic cell mobilization and function in both health and disease. We also summarize several CXCR2 regulatory mechanisms during infection and inflammation such as via Wip1, T-bet, P-selectin glycoprotein ligand-1, granulocyte-colony-stimulating factor, and microbiome. Moreover, we provide an update of studies investigating CXCR2 blockade in the laboratory and in clinical trials.

SUMMARY: Neutrophil homeostasis, migration, and recruitment must be precisely regulated. The CXCR2 signaling pathway is a potential target for modifying neutrophil dynamics in inflammatory disorders. We discuss the recent clinical use of CXCR2 antagonists for controlling inflammation.},
}

@article {pmid30406866,
year = {2018},
author = {Whidbey, C and Wright, AT},
title = {Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities.},
journal = {Current topics in microbiology and immunology},
volume = {},
number = {},
pages = {},
doi = {10.1007/82_2018_128},
pmid = {30406866},
issn = {0070-217X},
abstract = {Microorganisms living in community are critical to life on Earth, playing numerous and profound roles in the environment and human and animal health. Though their essentiality to life is clear, the mechanistic underpinnings of community structure, interactions, and functions are largely unexplored and in need of function-dependent technologies to unravel the mysteries. Activity-based protein profiling offers unprecedented molecular-level characterization of functions within microbial communities and provides an avenue to determine how external exposures result in functional alterations to microbiomes. Herein, we illuminate the current state and prospective contributions of ABPP as it relates to microbial communities. We provide details on the design, development, and validation of probes, challenges associated with probing in complex microbial communities, provide some specific examples of the biological applications of ABPP in microbes and microbial communities, and highlight potential areas for development. The future of ABPP holds real promise for understanding and considerable impact in microbiome studies associated with personalized medicine, precision agriculture, veterinary health, environmental studies, and beyond.},
}

@article {pmid30406643,
year = {2018},
author = {Gao, B and Chi, L and Tu, P and Gao, N and Lu, K},
title = {The carbamate aldicarb altered the gut microbiome, metabolome and lipidome of C57BL/6J mice.},
journal = {Chemical research in toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.chemrestox.8b00179},
pmid = {30406643},
issn = {1520-5010},
abstract = {The gut microbiome is highly involved in numerous aspects of host physiology, from energy harvest to stress response, and can confer many benefits to the host. The gut microbiome development could be affected by genetic and environmental factors, including the pesticides. The carbamate insecticide aldicarb has been extensively used in agriculture, which raises serious public health concern. However, the impact of aldicarb on the gut microbiome, host metabolome and lipidome has not been well studied yet. Herein, we use multi-omics approaches, including16S rRNA sequencing, shotgun metagenomics sequencing, metabolomics and lipidomics, to elucidate aldicarb-induced toxicity in the gut microbiome and the host metabolic homeostasis. We demonstrated that aldicarb perturbed the gut microbiome development trajectory, enhanced gut bacterial pathogenicity, altered complex lipid profile, induced oxidative stress, protein degradation and DNA damage. The brain metabolism was also disturbed by the aldicarb exposure. These findings may provide a novel understanding of the toxicity of carbamate insecticides.},
}

@article {pmid30406186,
year = {2018},
author = {Li, Y and Dugyala, SR and Ptacek, TS and Gilmore, JH and Frohlich, F},
title = {Maternal Immune Activation Alters Adult Behavior, Gut Microbiome and Juvenile Brain Oscillations in Ferrets.},
journal = {eNeuro},
volume = {5},
number = {5},
pages = {},
doi = {10.1523/ENEURO.0313-18.2018},
pmid = {30406186},
issn = {2373-2822},
abstract = {Maternal immune activation (MIA) has been identified as a causal factor in psychiatric disorders by epidemiological studies in humans and mechanistic studies in rodent models. Addressing this gap in species between mice and human will accelerate the understanding of the role of MIA in the etiology of psychiatric disorders. Here, we provide the first study of MIA in the ferret (Mustela putorius furo), an animal model with a rich history of developmental investigations due to the similarities in developmental programs and cortical organization with primates. We found that after MIA by injection of PolyIC in the pregnant mother animal, the adult offspring exhibited reduced social behavior, less eye contact with humans, decreased recognition memory, a sex-specific increase in amphetamine-induced hyperlocomotion, and altered gut microbiome. We also studied the neurophysiological properties of the MIA ferrets in development by in-vivo recordings of the local field potential (LFP) from visual cortex in five- to six-week-old animals, and found that the spontaneous and sensory-evoked LFP had decreased power, especially in the gamma frequency band. Overall, our results provide the first evidence for the detrimental effect of MIA in ferrets and support the use of the ferret as an intermediate model species for the study of disorders with neurodevelopmental origin.},
}

@article {pmid30406117,
year = {2018},
author = {Shang, Y and Kumar, S and Oakley, B and Kim, WK},
title = {Chicken Gut Microbiota: Importance and Detection Technology.},
journal = {Frontiers in veterinary science},
volume = {5},
number = {},
pages = {254},
doi = {10.3389/fvets.2018.00254},
pmid = {30406117},
issn = {2297-1769},
abstract = {Sustainable poultry meat and egg production is important to provide safe and quality protein sources in human nutrition worldwide. The gastrointestinal (GI) tract of chickens harbor a diverse and complex microbiota that plays a vital role in digestion and absorption of nutrients, immune system development and pathogen exclusion. However, the integrity, functionality, and health of the chicken gut depends on many factors including the environment, feed, and the GI microbiota. The symbiotic interactions between host and microbe is fundamental to poultry health and production. The diversity of the chicken GI microbiota is largely influenced by the age of the birds, location in the digestive tract and diet. Until recently, research on the poultry GI microbiota relied on conventional microbiological techniques that can only culture a small proportion of the complex community comprising the GI microbiota. 16S rRNA based next generation sequencing is a powerful tool to investigate the biological and ecological roles of the GI microbiota in chicken. Although several challenges remain in understanding the chicken GI microbiome, optimizing the taxonomic composition and biochemical functions of the GI microbiome is an attainable goal in the post-genomic era. This article reviews the current knowledge on the chicken GI function and factors that influence the diversity of gut microbiota. Further, this review compares past and current approaches that are used in chicken GI microbiota research. A better understanding of the chicken gut function and microbiology will provide us new opportunities for the improvement of poultry health and production.},
}

@article {pmid30406045,
year = {2018},
author = {Tsaousis, AD and Hamblin, KA and Elliott, CR and Young, L and Rosell-Hidalgo, A and Gourlay, CW and Moore, AL and van der Giezen, M},
title = {The Human Gut Colonizer Blastocystis Respires Using Complex II and Alternative Oxidase to Buffer Transient Oxygen Fluctuations in the Gut.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {371},
doi = {10.3389/fcimb.2018.00371},
pmid = {30406045},
issn = {2235-2988},
abstract = {Blastocystis is the most common eukaryotic microbe in the human gut. It is linked to irritable bowel syndrome (IBS), but its role in disease has been contested considering its widespread nature. This organism is well-adapted to its anoxic niche and lacks typical eukaryotic features, such as a cytochrome-driven mitochondrial electron transport. Although generally considered a strict or obligate anaerobe, its genome encodes an alternative oxidase. Alternative oxidases are energetically wasteful enzymes as they are non-protonmotive and energy is liberated in heat, but they are considered to be involved in oxidative stress protective mechanisms. Our results demonstrate that the Blastocystis cells themselves respire oxygen via this alternative oxidase thereby casting doubt on its strict anaerobic nature. Inhibition experiments using alternative oxidase and Complex II specific inhibitors clearly demonstrate their role in cellular respiration. We postulate that the alternative oxidase in Blastocystis is used to buffer transient oxygen fluctuations in the gut and that it likely is a common colonizer of the human gut and not causally involved in IBS. Additionally the alternative oxidase could act as a protective mechanism in a dysbiotic gut and thereby explain the absence of Blastocystis in established IBS environments.},
}

@article {pmid30405968,
year = {2018},
author = {Cicala, F and Cisterna-Céliz, JA and Moore, JD and Rocha-Olivares, A},
title = {Structure, dynamics and predicted functional role of the gut microbiota of the blue (Haliotis fulgens) and yellow (H. corrugata) abalone from Baja California Sur, Mexico.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5830},
doi = {10.7717/peerj.5830},
pmid = {30405968},
issn = {2167-8359},
abstract = {The GI microbiota of abalone contains a highly complex bacterial assemblage playing an essential role in the overall health of these gastropods. The gut bacterial communities of abalone species characterized so far reveal considerable interspecific variability, likely resulting from bacterial interactions and constrained by the ecology of their abalone host species; however, they remain poorly investigated. Additionally, the extent to which structural changes in the microbiota entail functional shifts in metabolic pathways of bacterial communities remains unexplored. In order to address these questions, we characterized the gut microbiota of the northeast Pacific blue (Haliotis fulgens or HF) and yellow (Haliotis corrugata or HC) abalone by 16S rRNA gene pyrosequencing to shed light on: (i) their gut microbiota structure; (ii) how bacteria may interact among them; and (iii) predicted shifts in bacterial metabolic functions associated with the observed structural changes. Our findings revealed that Mycoplasma dominated the GI microbiome in both species. However, the structure of the bacterial communities differed significantly in spite of considerable intraspecific variation. This resulted from changes in predominant species composition in each GI microbiota, suggesting host-specific adaptation of bacterial lineages to these sympatric abalone. We hypothesize that the presence of exclusive OTUs in each microbiota may relate to host-specific differences in competitive pressure. Significant differences in bacterial diversity were found between species for the explored metabolic pathways despite their functional overlap. A more diverse array of bacteria contributed to each function in HC, whereas a single or much fewer OTUs were generally observed in HF. The structural and functional analyses allowed us to describe a significant taxonomic split and functional overlap between the microbiota of HF and HC abalone.},
}

@article {pmid30405931,
year = {2018},
author = {Singer, G and Kashofer, K and Castellani, C and Till, H},
title = {Hirschsprung's Associated Enterocolitis (HAEC) Personalized Treatment with Probiotics Based on Gene Sequencing Analysis of the Fecal Microbiome.},
journal = {Case reports in pediatrics},
volume = {2018},
number = {},
pages = {3292309},
doi = {10.1155/2018/3292309},
pmid = {30405931},
issn = {2090-6803},
abstract = {Approximately 40% of children with Hirschsprung's disease (HD) suffer from Hirschsprung's associated enterocolitis (HAEC) despite correct surgery. Disturbances of the intestinal microbiome may play a role. Treatment with probiotics based on individual analyses of the fecal microbiome has not been published for HD patients with recurrent HAEC yet. A boy with trisomy 21 received transanal pull-through at the age of 6 months for rectosigmoid HD. With four years, he suffered from recurrent episodes of HAEC. The fecal microbiome was measured during three healthy and three HAEC episodes by next-generation sequencing. The patient was started on daily probiotics for 3 months; the fecal microbiome was measured weekly. The fecal microbiome differed significantly between healthy and HAEC episodes. HAEC episodes were associated with significant decreases of Actinobacteria and significant increases of Bacteroidetes and Proteobacteria. Probiotic treatment led to a significant increase of alpha diversity and a significant increase of Bifidobacterium and Streptococcus as well as decreases of Rikenellaceae, Pseudobutyrivibrio, Blautia, and Lachnospiraceae. A longitudinal observation of the microbiome has never been performed following correction of Hirschsprung's disease. Probiotic treatment significantly changed the fecal microbiome; the alterations were not limited to strains contained in the administered probiotics.},
}

@article {pmid30405664,
year = {2018},
author = {Syranidou, E and Thijs, S and Avramidou, M and Weyens, N and Venieri, D and Pintelon, I and Vangronsveld, J and Kalogerakis, N},
title = {Responses of the Endophytic Bacterial Communities of Juncus acutus to Pollution With Metals, Emerging Organic Pollutants and to Bioaugmentation With Indigenous Strains.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1526},
doi = {10.3389/fpls.2018.01526},
pmid = {30405664},
issn = {1664-462X},
abstract = {Plants and their associated bacteria play a crucial role in constructed wetlands. In this study, the impact of different levels of pollution and bioaugmentation with indigenous strains individually or in consortia was investigated on the composition of the endophytic microbial communities of Juncus acutus. Five treatments were examined and compared in where the wetland plant was exposed to increasing levels of metal pollution (Zn, Ni, Cd) and emerging pollutants (BPA, SMX, CIP), enriched with different combinations of single or mixed endophytic strains. High levels of mixed pollution had a negative effect on alpha diversity indices of the root communities; moreover, the diversity indices were negatively correlated with the increasing metal concentrations. It was demonstrated that the root communities were separated depending on the level of mixed pollution, while the family Sphingomonadaceae exhibited the higher relative abundance within the root endophytic communities from high and low polluted treatments. This study highlights the effects of pollution and inoculation on phytoremediation efficiency based on a better understanding of the plant microbiome community composition.},
}

@article {pmid30405651,
year = {2018},
author = {Dita, M and Barquero, M and Heck, D and Mizubuti, ESG and Staver, CP},
title = {Fusarium Wilt of Banana: Current Knowledge on Epidemiology and Research Needs Toward Sustainable Disease Management.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1468},
doi = {10.3389/fpls.2018.01468},
pmid = {30405651},
issn = {1664-462X},
abstract = {Banana production is seriously threatened by Fusarium wilt (FW), a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense (Foc). In the mid-twentieth century FW, also known as "Panama disease", wiped out the Gros Michel banana industry in Central America. The devastation caused by Foc race 1 was mitigated by a shift to resistant Cavendish cultivars, which are currently the source of 99% of banana exports. However, a new strain of Foc, the tropical race 4 (TR4), attacks Cavendish clones and a diverse range of other banana varieties. Foc TR4 has been restricted to East and parts of Southeast Asia for more than 20 years, but since 2010 the disease has spread westward into five additional countries in Southeast and South Asia (Vietnam, Laos, Myanmar, India, and Pakistan) and at the transcontinental level into the Middle East (Oman, Jordan, Lebanon, and Israel) and Africa (Mozambique). The spread of Foc TR4 is of great concern due to the limited knowledge about key aspects of disease epidemiology and the lack of effective management models, including resistant varieties and soil management approaches. In this review we summarize the current knowledge on the epidemiology of FW of banana, highlighting knowledge gaps in pathogen survival and dispersal, factors driving disease intensity, soil and plant microbiome and the dynamics of the disease. Comparisons with FW in other crops were also made to indicate possible differences and commonalities. Our current understanding of the role of main biotic and abiotic factors on disease intensity is reviewed, highlighting research needs and futures directions. Finally, a set of practices and their impact on disease intensity are discussed and proposed as an integrative management approach that could eventually be used by a range of users, including plant protection organizations, researchers, extension workers and growers.},
}

@article {pmid30405595,
year = {2018},
author = {Lai, KP and Ng, AH and Wan, HT and Wong, AY and Leung, CC and Li, R and Wong, CK},
title = {Dietary Exposure to the Environmental Chemical, PFOS on the Diversity of Gut Microbiota, Associated With the Development of Metabolic Syndrome.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2552},
doi = {10.3389/fmicb.2018.02552},
pmid = {30405595},
issn = {1664-302X},
abstract = {The gut microbiome is a dynamic ecosystem formed by thousands of diverse bacterial species. This bacterial diversity is acquired early in life and shaped over time by a combination of multiple factors, including dietary exposure to distinct nutrients and xenobiotics. Alterations of the gut microbiota composition and associated metabolic activities in the gut are linked to various immune and metabolic diseases. The microbiota could potentially interact with xenobiotics in the gut environment as a result of their board enzymatic capacities and thereby affect the bioavailability and toxicity of the xenobiotics in enterohepatic circulation. Consequently, microbiome-xenobiotic interactions might affect host health. Here, we aimed to investigate the effects of dietary perfluorooctane sulfonic acid (PFOS) exposure on gut microbiota in adult mice and examine the induced changes in animal metabolic functions. In mice exposed to dietary PFOS for 7 weeks, body PFOS and lipid contents were measured, and to elucidate the effects of PFOS exposure, the metabolic functions of the animals were assessed using oral glucose-tolerance test and intraperitoneal insulin-tolerance and pyruvate-tolerance tests; moreover, on Day 50, cecal bacterial DNA was isolated and subject to 16S rDNA sequencing. Our results demonstrated that PFOS exposure caused metabolic disturbances in the animals, particularly in lipid and glucose metabolism, but did not substantially affect the diversity of gut bacterial species. However, marked modulations were detected in the abundance of metabolism-associated bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, and Cyanobacteria, including, at different taxonomic levels, Turicibacteraceae, Turicibacterales, Turicibacter, Dehalobacteriaceae, Dehalobacterium, Allobaculum, Bacteroides acidifaciens, Alphaproteobacteria, and 4Cod-2/YS2. The results of PICRUSt analysis further indicated that PFOS exposure perturbed gut metabolism, inducing notable changes in the metabolism of amino acids (arginine, proline, lysine), methane, and a short-chain fatty acid (butanoate), all of which are metabolites widely recognized to be associated with inflammation and metabolic functions. Collectively, our study findings provide key information regarding the biological relevance of microbiome-xenobiotic interactions associated with the ecology of gut microbiota and animal energy metabolism.},
}

@article {pmid30405589,
year = {2018},
author = {Jarvis, KG and Daquigan, N and White, JR and Morin, PM and Howard, LM and Manetas, JE and Ottesen, A and Ramachandran, P and Grim, CJ},
title = {Microbiomes Associated With Foods From Plant and Animal Sources.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2540},
doi = {10.3389/fmicb.2018.02540},
pmid = {30405589},
issn = {1664-302X},
abstract = {Food microbiome composition impacts food safety and quality. The resident microbiota of many food products is influenced throughout the farm to fork continuum by farming practices, environmental factors, and food manufacturing and processing procedures. Currently, most food microbiology studies rely on culture-dependent methods to identify bacteria. However, advances in high-throughput DNA sequencing technologies have enabled the use of targeted 16S rRNA gene sequencing to profile complex microbial communities including non-culturable members. In this study we used 16S rRNA gene sequencing to assess the microbiome profiles of plant and animal derived foods collected at two points in the manufacturing process; post-harvest/pre-retail (cilantro) and retail (cilantro, masala spice mixes, cucumbers, mung bean sprouts, and smoked salmon). Our findings revealed microbiome profiles, unique to each food, that were influenced by the moisture content (dry spices, fresh produce), packaging methods, such as modified atmospheric packaging (mung bean sprouts and smoked salmon), and manufacturing stage (cilantro prior to retail and at retail). The masala spice mixes and cucumbers were comprised mainly of Proteobacteria, Firmicutes, and Actinobacteria. Cilantro microbiome profiles consisted mainly of Proteobacteria, followed by Bacteroidetes, and low levels of Firmicutes and Actinobacteria. The two brands of mung bean sprouts and the three smoked salmon samples differed from one another in their microbiome composition, each predominated by either by Firmicutes or Proteobacteria. These data demonstrate diverse and highly variable resident microbial communities across food products, which is informative in the context of food safety, and spoilage where indigenous bacteria could hamper pathogen detection, and limit shelf life.},
}

@article {pmid30405577,
year = {2018},
author = {Bertelli, C and Courtois, S and Rosikiewicz, M and Piriou, P and Aeby, S and Robert, S and Loret, JF and Greub, G},
title = {Reduced Chlorine in Drinking Water Distribution Systems Impacts Bacterial Biodiversity in Biofilms.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2520},
doi = {10.3389/fmicb.2018.02520},
pmid = {30405577},
issn = {1664-302X},
abstract = {In drinking water distribution systems (DWDS), a disinfectant residual is usually applied to limit bacterial regrowth. However, delivering water with no or reduced chlorine residual could potentially decrease the selection for antimicrobial resistant microorganisms, favor bacterial regrowth and result in changes in bacterial populations. To evaluate the feasibility of water reduction in local DWDS while ensuring water safety, water quality was measured over 2 months in two different networks, each of them harboring sub-areas with normal and reduced chlorine. Water quality remained good in chlorine reduced samples, with limited development of total flora and absence of coliforms. Furthermore, 16S rRNA amplicon-based metagenomics was used to investigate the diversity and the composition of microbial communities in the sub-networks. Taxonomic classification of sequence reads showed a reduced bacterial diversity in sampling points with higher chlorine residuals. Chlorine disinfection created more homogeneous bacterial population, dominated by Pseudomonas, a genus that contains some major opportunistic pathogens such as P. aeruginosa. In the absence of chlorine, a larger and unknown biodiversity was unveiled, also highlighted by a decreased rate of taxonomic classification to the genus and species level. Overall, this experiment in a functional DWDS will facilitate the move toward potable water delivery systems without residual disinfectants and will improve water taste for consumers.},
}

@article {pmid30405571,
year = {2018},
author = {Biagi, E and Aceti, A and Quercia, S and Beghetti, I and Rampelli, S and Turroni, S and Soverini, M and Zambrini, AV and Faldella, G and Candela, M and Corvaglia, L and Brigidi, P},
title = {Microbial Community Dynamics in Mother's Milk and Infant's Mouth and Gut in Moderately Preterm Infants.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2512},
doi = {10.3389/fmicb.2018.02512},
pmid = {30405571},
issn = {1664-302X},
abstract = {Mother's own milk represents the optimal source for preterm infant nutrition, as it promotes immune defenses and gastrointestinal function, protects against necrotizing enterocolitis, improves long-term clinical outcome and is hypothesized to drive gut microbiota assembly. Preterm infants at birth usually do not receive their mother's milk directly from the breast, because active suckling and coordination between suckling, swallowing and breathing do not develop until 32-34 weeks gestational age, but actual breastfeeding is usually possible as they grow older. Here, we enrolled moderately preterm infants (gestational age 32-34 weeks) to longitudinally characterize mothers' milk and infants' gut and oral microbiomes, up to more than 200 days after birth, through 16S rRNA sequencing. This peculiar population offers the chance to disentangle the differential contribution of human milk feeding per se vs. actual breastfeeding in the development of infant microbiomes, that have both been acknowledged as crucial contributors to short and long-term infant health status. In this cohort, the milk microbiome composition seemed to change following the infant's latching to the mother's breast, shifting toward a more diverse microbial community dominated by typical oral microbes, i.e., Streptococcus and Rothia. Even if all infants in the present study were fed human milk, features typical of healthy, full term, exclusively breastfed infants, i.e., high percentages of Bifidobacterium and low abundances of Pseudomonas in fecal and oral samples, respectively, were detected in samples taken after actual breastfeeding started. These findings underline the importance of encouraging not only human milk feeding, but also an early start of actual breastfeeding in preterm infants, since the infant's latching to the mother's breast might constitute an independent factor helping the health-promoting assembly of the infant gut microbiome.},
}

@article {pmid30405455,
year = {2018},
author = {Horne, R and Foster, JA},
title = {Metabolic and Microbiota Measures as Peripheral Biomarkers in Major Depressive Disorder.},
journal = {Frontiers in psychiatry},
volume = {9},
number = {},
pages = {513},
doi = {10.3389/fpsyt.2018.00513},
pmid = {30405455},
issn = {1664-0640},
abstract = {Advances in understanding the role of the microbiome in physical and mental health are at the forefront of medical research and hold potential to have a direct impact on precision medicine approaches. In the past 7 years, we have studied the role of microbiota-brain communication on behavior in mouse models using germ-free mice, mice exposed to antibiotics, and healthy specific pathogen free mice. Through our work and that of others, we have seen an amazing increase in our knowledge of how bacteria signal to the brain and the implications this has for psychiatry. Gut microbiota composition and function are influenced both by genetics, age, sex, diet, life experiences, and many other factors of psychiatric and bodily disorders and thus may act as potential biomarkers of the gut-brain axis that could be used in psychiatry and co-morbid conditions. There is a particular need in major depressive disorder and other mental illness to identify biomarkers that can stratify patients into more homogeneous groups to provide better treatment and for development of new therapeutic approaches. Peripheral outcome measures of host-microbe bidirectional communication have significant translational value as biomarkers. Enabling stratification of clinical populations, based on individual biological differences, to predict treatment response to pharmacological and non-pharmacological interventions. Here we consider the links between co-morbid metabolic syndrome and depression, focusing on biomarkers including leptin and ghrelin in combination with assessing gut microbiota composition, as a potential tool to help identify individual differences in depressed population.},
}

@article {pmid30405366,
year = {2018},
author = {Russo, EB},
title = {Cannabis Therapeutics and the Future of Neurology.},
journal = {Frontiers in integrative neuroscience},
volume = {12},
number = {},
pages = {51},
doi = {10.3389/fnint.2018.00051},
pmid = {30405366},
issn = {1662-5145},
abstract = {Neurological therapeutics have been hampered by its inability to advance beyond symptomatic treatment of neurodegenerative disorders into the realm of actual palliation, arrest or reversal of the attendant pathological processes. While cannabis-based medicines have demonstrated safety, efficacy and consistency sufficient for regulatory approval in spasticity in multiple sclerosis (MS), and in Dravet and Lennox-Gastaut Syndromes (LGS), many therapeutic challenges remain. This review will examine the intriguing promise that recent discoveries regarding cannabis-based medicines offer to neurological therapeutics by incorporating the neutral phytocannabinoids tetrahydrocannabinol (THC), cannabidiol (CBD), their acidic precursors, tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA), and cannabis terpenoids in the putative treatment of five syndromes, currently labeled recalcitrant to therapeutic success, and wherein improved pharmacological intervention is required: intractable epilepsy, brain tumors, Parkinson disease (PD), Alzheimer disease (AD) and traumatic brain injury (TBI)/chronic traumatic encephalopathy (CTE). Current basic science and clinical investigations support the safety and efficacy of such interventions in treatment of these currently intractable conditions, that in some cases share pathological processes, and the plausibility of interventions that harness endocannabinoid mechanisms, whether mediated via direct activity on CB1 and CB2 (tetrahydrocannabinol, THC, caryophyllene), peroxisome proliferator-activated receptor-gamma (PPARγ; THCA), 5-HT1A (CBD, CBDA) or even nutritional approaches utilizing prebiotics and probiotics. The inherent polypharmaceutical properties of cannabis botanicals offer distinct advantages over the current single-target pharmaceutical model and portend to revolutionize neurological treatment into a new reality of effective interventional and even preventative treatment.},
}

@article {pmid30405234,
year = {2018},
author = {Eisenstein, M},
title = {Ulcerative colitis: towards remission.},
journal = {Nature},
volume = {563},
number = {7730},
pages = {S33},
doi = {10.1038/d41586-018-07276-2},
pmid = {30405234},
issn = {1476-4687},
}

@article {pmid30405233,
year = {2018},
author = {Eisenstein, M},
title = {Gut reaction.},
journal = {Nature},
volume = {563},
number = {7730},
pages = {S34-S35},
doi = {10.1038/d41586-018-07277-1},
pmid = {30405233},
issn = {1476-4687},
}

@article {pmid30405201,
year = {2018},
author = {Wankhade, UD and Zhong, Y and Kang, P and Alfaro, M and Chintapalli, SV and Piccolo, BD and Mercer, KE and Andres, A and Thakali, KM and Shankar, K},
title = {Maternal High-Fat Diet Programs Offspring Liver Steatosis in a Sexually Dimorphic Manner in Association with Changes in Gut Microbial Ecology in Mice.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16502},
doi = {10.1038/s41598-018-34453-0},
pmid = {30405201},
issn = {2045-2322},
support = {6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; 6251-51000-010-05S//USDA | Agricultural Research Service (ARS)/ ; },
abstract = {The contributions of maternal diet and obesity in shaping offspring microbiome remain unclear. Here we employed a mouse model of maternal diet-induced obesity via high-fat diet feeding (HFD, 45% fat calories) for 12 wk prior to conception on offspring gut microbial ecology. Male and female offspring were provided access to control or HFD from weaning until 17 wk of age. Maternal HFD-associated programming was sexually dimorphic, with male offspring from HFD dams showing hyper-responsive weight gain to postnatal HFD. Likewise, microbiome analysis of offspring cecal contents showed differences in α-diversity, β-diversity and higher Firmicutes in male compared to female mice. Weight gain in offspring was significantly associated with abundance of Lachnospiraceae and Clostridiaceae families and Adlercreutzia, Coprococcus and Lactococcus genera. Sex differences in metagenomic pathways relating to lipid metabolism, bile acid biosynthesis and immune response were also observed. HFD-fed male offspring from HFD dams also showed worse hepatic pathology, increased pro-inflammatory cytokines, altered expression of bile acid regulators (Cyp7a1, Cyp8b1 and Cyp39a1) and serum bile acid concentrations. These findings suggest that maternal HFD alters gut microbiota composition and weight gain of offspring in a sexually dimorphic manner, coincident with fatty liver and a pro-inflammatory state in male offspring.},
}

@article {pmid30405146,
year = {2018},
author = {Lloyd, MM and Pespeni, MH},
title = {Microbiome shifts with onset and progression of Sea Star Wasting Disease revealed through time course sampling.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {16476},
doi = {10.1038/s41598-018-34697-w},
pmid = {30405146},
issn = {2045-2322},
support = {IOS-1555058//National Science Foundation (NSF)/ ; IOS-1555058//National Science Foundation (NSF)/ ; },
abstract = {The recent outbreak of Sea Star Wasting Disease (SSWD) is one of the largest marine epizootics in history, but the host-associated microbial community changes specific to disease progression have not been characterized. Here, we sampled the microbiomes of ochre sea stars, Pisaster ochraceus, through time as animals stayed healthy or became sick and died with SSWD. We found community-wide differences in the microbiomes of sick and healthy sea stars, changes in microbial community composition through disease progression, and a decrease in species richness of the microbiome in late stages of SSWD. Known beneficial taxa (Pseudoalteromonas spp.) decreased in abundance at symptom onset and through disease progression, while known pathogenic (Tenacibaculum spp.) and putatively opportunistic bacteria (Polaribacter spp. and Phaeobacter spp.) increased in abundance in early and late disease stages. Functional profiling revealed microbes more abundant in healthy animals performed functions that inhibit growth of other microbes, including pathogen detection, biosynthesis of secondary metabolites, and degradation of xenobiotics. Changes in microbial composition with disease onset and progression suggest that a microbial imbalance of the host could lead to SSWD or be a consequence of infection by another pathogen. This work highlights the importance of the microbiome in SSWD and also suggests that a healthy microbiome may help confer resistance to SSWD.},
}

@article {pmid30405010,
year = {2018},
author = {Rodríguez-Rabassa, M and López, P and Rodríguez-Santiago, RE and Cases, A and Felici, M and Sánchez, R and Yamamura, Y and Rivera-Amill, V},
title = {Cigarette Smoking Modulation of Saliva Microbial Composition and Cytokine Levels.},
journal = {International journal of environmental research and public health},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/ijerph15112479},
pmid = {30405010},
issn = {1660-4601},
support = {NIMHD-G12-MD007579//National Institutes of Health/ ; 5 NU58DP005055-05-00//Centers for Disease Control and Prevention/ ; },
abstract = {Tobacco use has been implicated as an immunomodulator in the oral cavity and contributes to the development of oral cancer. In the present study, we investigated the effects of cigarette smoking on bacterial diversity and host responses compared to healthy nonsmoking controls. Saliva samples were collected from eighteen smokers and sixteen nonsmoking individuals by passive drool. The 16S rRNA gene was used to characterize the salivary microbiome by using the Illumina MiSeq platform. Cytokine and chemokine expression analyses were performed to evaluate the host response. Significant differences in cytokine and chemokine expression levels of MDC, IL-10, IL-5, IL-2, IL-4, IL-7, adrenocorticotropic hormone (ACTH), insulin, and leptin were observed between smokers and nonsmokers. Taxonomic analyses revealed differences between the two groups, and some bacterial genera associated with the smokers group had correlations with hormones and cytokines identified as statistically different between smokers and nonsmokers. These factors have been associated with inflammation and carcinogenesis in the oral cavity. The data obtained may aid in the identification of the interactions between the salivary microbiome, host inflammatory responses, and metabolism in smokers.},
}

@article {pmid30404810,
year = {2018},
author = {Harvey, E and Rose, K and Eden, JS and Lo, N and Abeyasuriya, T and Shi, M and Doggett, SL and Holmes, EC},
title = {Extensive Diversity of RNA Viruses in Australian Ticks.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01358-18},
pmid = {30404810},
issn = {1098-5514},
abstract = {Understanding the microbiome of ticks in Australia is of considerable interest given the ongoing debate over whether Lyme disease, and its causative agent the bacterium Borrelia burgdorferi sensu lato, are present in Australia. The diversity of bacteria infecting Australian ticks has been studied using both culture and metagenomics based techniques. However, little is known about the virome of Australian ticks, including whether this includes viruses with the potential to infect mammals. We used a meta-transcriptomics approach to reveal the diversity and evolution of viruses from Australian ticks collected from two locations on the central-east coast of Australia, including metropolitan Sydney. From this we identified 19 novel RNA viruses belonging to 12 families, as well as one previously described RNA virus. The majority of these viruses were related to arthropod-associated viruses suggesting that they do not utilize mammalian hosts. However, two novel viruses discovered in ticks feeding on bandicoot marsupials clustered closely within the mammalian-associated hepacivirus and pestivirus groups (family Flaviviridae). Another bandicoot tick yielded a novel coltivirus (family Reoviridae) - a group of largely tick-associated viruses containing the known human pathogen Colorado tick fever virus and its relative Eyach virus. Importantly, our transcriptomic data provided no evidence for the presence of B. burgdorferi s.l. in any tick sample, providing further evidence against the presence of Lyme Disease in Australia. In sum, this study reveals that Australian ticks harbor a diverse virome, including some viruses that merit additional screening in the context of emerging infectious disease.IMPORTANCE Each year a growing number of individuals along the east coast of Australia experience debilitating disease following tick bites. As there is no evidence for the presence of the causative agent of Lyme disease, Borrelia Burgdorferi sensu lato, in Australian ticks, the etiological basis of this disease syndrome remains controversial. To characterize the viruses associated with Australian ticks, particularly those that might be associated with mammalian infection, we performed unbiased RNA sequencing on 146 ticks collected across two locations along the coast of New South Wales, Australia. This revealed 19 novel RNA viruses from a diverse set of families. Notably, three of these viruses clustered with known mammalian viruses, including a novel coltivirus that was related to the human pathogen Colorado tick fever virus.},
}

@article {pmid30404570,
year = {2018},
author = {Alam, A and Neish, A},
title = {Role of gut microbiota in intestinal wound healing and barrier function.},
journal = {Tissue barriers},
volume = {},
number = {},
pages = {1-22},
doi = {10.1080/21688370.2018.1539595},
pmid = {30404570},
issn = {2168-8370},
abstract = {The mammalian intestine harbors a highly complex and abundant ensemble of bacteria that flourish in a nutrient-rich environment while profoundly influencing many aspects of host biology. The intestine coevolved with its resident microbes in a manner where the mucosa developed a barrier function to segregate the resident microbes from the rest of the body, and yet paradoxically, allowing integration of microbial signals for the host benefit. In this review, we provided a comprehensive overview of why the gut microbiota is key to the efficient development and maintenance of the intestinal barrier. We also highlighted how a destabilized equilibrium between gut microbiota and the host may eventuate in a wide range of intestinal diseases characterized by the disrupted intestinal barrier. Finally, the review delineated how microenvironmental changes in the injured mucosa result in an enrichment of a pro-regenerating consortium of bacteria, which augments mucosal wound repair and restoration of barrier functions.},
}

@article {pmid30404568,
year = {2018},
author = {Bajorek, S and Parker, L and Li, N and Winglee, K and Weaver, M and Johnson, J and Sioda, M and Gauthier, J and Lemas, DJ and Jobin, C and Lorca, G and Neu, J and Fodor, AA},
title = {Initial microbial community of the neonatal stomach immediately after birth.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/19490976.2018.1520578},
pmid = {30404568},
issn = {1949-0984},
abstract = {The purpose of this prospective cross-sectional cohort pilot study is to explore the initial microbial community of gastric aspirate fluid as collected immediately after birth and its relationships with mode of delivery and preterm birth. Twenty-nine gastric aspirate samples collected immediately after birth from infants born between 24-40 weeks gestation were analyzed for microbial composition. Total microbial content was low in many samples, with a substantial number sharing taxonomic composition with negative controls. qPCR targeting the 16S rRNA gene showed that infants delivered vaginally had a higher microbial load than infants delivered by C-section. Some pre-term samples showed high relative abundance of genus Ureaplasma, consistent with previous literature that has implicated infections with this taxon as a potential cause of pre-term birth. Vaginally born term infant samples, by contrast, had significantly higher levels of genus Lactobacillus with Lactobacillus crispatus the most dominant species. Microbial evaluation showed that vaginally born term infant gastric aspirate samples had higher levels of lactobacilli than pre-terms. Samples from many infants had low microbial load near the edge of the detection limit.},
}

@article {pmid30403635,
year = {2018},
author = {Zheng, H and Wang, H and Dewhurst, R and Roehe, R},
title = {Improving the Inference of Co-occurrence Networks in the Bovine Rumen Microbiome.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1109/TCBB.2018.2879342},
pmid = {30403635},
issn = {1557-9964},
abstract = {The importance of the composition and signature of rumen microbial communities has gained increasing attention. One of the key techniques was to infer co-abundance networks through correlation analysis based on relative abundances. In this study, we proposed the use of a framework including a compendium of two correlation measures and three dissimilarity metrics to mitigate the compositional effect in the inference of significant associations in the bovine rumen microbiome. We tested the framework on rumen microbiome data including both 16S rRNA and KEGG genes associated with methane production in cattle. Based on the identification of significant positive and negative associations supported by multiple metrics, two co-occurrence networks, e.g. co-presence and mutual-exclusion networks, were constructed. Significant modules associated with methane emissions were identified. In comparison to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations. To bridge together different co-presence and mutual-exclusion relations, a multiplex network model has been proposed for integrative analysis of co-occurrence networks which has great potential to support the prediction of animal phytotypes and to provide additional insights into biological mechanisms of the microbiome associated with the traits.},
}

@article {pmid30402924,
year = {2018},
author = {Ketchesin, KD and Becker-Krail, D and McClung, CA},
title = {Mood-Related Central and Peripheral Clocks.},
journal = {The European journal of neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1111/ejn.14253},
pmid = {30402924},
issn = {1460-9568},
abstract = {Mood disorders, including major depression, bipolar disorder, and seasonal affective disorder, are debilitating disorders that affect a significant portion of the global population. Individuals suffering from mood disorders often show significant disturbances in circadian rhythms and sleep. Moreover, environmental disruptions to circadian rhythms can precipitate or exacerbate mood symptoms in vulnerable individuals. Circadian clocks exist throughout the central nervous system and periphery, where they regulate a wide variety of physiological processes implicated in mood regulation. These processes include monoaminergic and glutamatergic transmission, HPA axis function, metabolism, and immune function. While there seems to be a clear link between circadian rhythm disruption and mood regulation, the mechanisms that underlie this association remain unclear. This review will touch on the interactions between the circadian system and each of these processes and discuss their potential role in the development of mood disorders. While clinical studies are presented, much of the review will focus on studies in animal models, which are attempting to elucidate the molecular cellular mechanisms in which circadian genes regulate mood. This article is protected by copyright. All rights reserved.},
}

@article {pmid30402873,
year = {2018},
author = {Ceresola, ER and Ferrarese, R and Preti, A and Canducci, F},
title = {Targeting patients' microbiota with probiotics and natural fibers in adults and children with constipation.},
journal = {European review for medical and pharmacological sciences},
volume = {22},
number = {20},
pages = {7045-7057},
pmid = {30402873},
issn = {2284-0729},
abstract = {OBJECTIVE: Functional constipation (FC) is a common condition in which the gut microbiota composition plays a fundamental role. The increasing knowledge on the role of gut microbes in the regulation of gut motility and stool consistency has allowed reconsidering, with a new scientific-based approach, the possibility to target the composition of intestinal bacterial populations for FC treatment. In this review, we evaluate recent attempts that used prebiotics, natural fibers or probiotics to treat FC, with a deep microbiome-based focus.

MATERIALS AND METHODS: This is a literature review of articles published in Medline, Web of Science, and the Cochrane Library. Studies on FC in adults and children were identified using the following terms: constipation AND probiotics OR prebiotics OR synbiotics PR fibers OR microbiome OR microbiota. Selected animal studies were also considered if showing mechanistic observations.

RESULTS: FC is associated with alteration in microbiome composition. Motility and fecal consistency are affected with different efficacy by the type of fiber, prebiotic or probiotic strain used in patients.

CONCLUSIONS: Selected bacterial strains, mainly belonging to the Bifidobacterium genus, and some poorly or non-fermented natural fibers, such as Psyllium, may significantly improve FC and may represent the basis for an effective supplementation.},
}

@article {pmid30402680,
year = {2018},
author = {Shah, A and Morrison, M and Holtmann, G},
title = {A novel treatment for patients with constipation: Dawn of a new age for translational microbiome research?.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12664-018-0912-3},
pmid = {30402680},
issn = {0975-0711},
}

@article {pmid30402335,
year = {2018},
author = {Hwang, JS and Im, CR and Im, SH},
title = {Erratum: Immune Disorders and Its Correlation with Gut Microbiome.},
journal = {Immune network},
volume = {18},
number = {5},
pages = {e40},
doi = {10.4110/in.2018.18.e40},
pmid = {30402335},
issn = {1598-2629},
abstract = {[This corrects the article on p. 129 in vol. 12, PMID: 23091436.].},
}

@article {pmid30402068,
year = {2018},
author = {Al Rubaiee, Z and Al-Murayati, H and Møller, AP},
title = {Recapture probability, flight morphology, and microorganisms.},
journal = {Current zoology},
volume = {64},
number = {3},
pages = {277-283},
doi = {10.1093/cz/zox030},
pmid = {30402068},
issn = {1674-5507},
abstract = {Microorganisms on and within organisms are ubiquitous and interactions with their hosts range from mutualistic over commensal, to pathogenic. We hypothesized that microorganisms might affect the ability of barn swallows Hirundo rustica to escape from potential predators, with positive associations between the abundance of microorganisms and escape ability implying mutualistic effects, while negative associations would imply antagonistic effects. We quantified escape behavior as the ability to avoid capture in a mist net and hence as a small number of recaptures. Because recapture probability may also depend on timing of reproduction and reproductive success, we also tested whether the association between recapture and microorganisms was mediated by an association between recapture and life history. We found intermediate to strong positive relationships between recapture probability and abundance of Bacillus megaterium, but not abundance of other bacteria or fungi. The abundance of B. megaterium was associated with an advance in laying date and an increase in reproductive success. However, these effects were independent of the number of recaptures. This interpretation is supported by the fact that there was no direct correlation between laying date and reproductive success on one hand and the number of recaptures on the other. These findings have implications not only for predator-prey interactions, but also for capture-mark-recapture analyses of vital rates such as survival and dispersal.},
}

@article {pmid30401869,
year = {2018},
author = {Rackaityte, E and Lynch, SV},
title = {Rules of engagement in the gut microbiome.},
journal = {Nature medicine},
volume = {24},
number = {11},
pages = {1642-1644},
doi = {10.1038/s41591-018-0242-0},
pmid = {30401869},
issn = {1546-170X},
}

@article {pmid30401779,
year = {2018},
author = {Bratburd, JR and Keller, C and Vivas, E and Gemperline, E and Li, L and Rey, FE and Currie, CR},
title = {Gut Microbial and Metabolic Responses to Salmonella enterica Serovar Typhimurium and Candida albicans.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.02032-18},
pmid = {30401779},
issn = {2150-7511},
abstract = {The gut microbiota confers resistance to pathogens of the intestinal ecosystem, yet the dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. Here, we use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice "humanized" with a synthetic human microbiome, or infected humanized mice. In Salmonella-infected mice, by 3 days into infection, microbiome community structure and function changed substantially, with a rise in Enterobacteriaceae strains and a reduction in biosynthetic gene cluster potential. In contrast, Candida-infected mice had few microbiome changes. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.IMPORTANCE The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year (E. Scallan, R. M. Hoekstra, F. J. Angulo, R. V. Tauxe, et al., Emerg Infect Dis 17:7-15, 2011, https://doi.org/10.3201/eid1701.P11101), and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States (Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013, 2013). Using a gnotobiotic mouse model, we investigate potential changes in gut microbial community structure and function during infection using metagenomics and metabolomics. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection, potentially in response to host oxidative stress.},
}

@article {pmid30401772,
year = {2018},
author = {Blau, K and Bettermann, A and Jechalke, S and Fornefeld, E and Vanrobaeys, Y and Stalder, T and Top, EM and Smalla, K},
title = {The Transferable Resistome of Produce.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.01300-18},
pmid = {30401772},
issn = {2150-7511},
abstract = {Produce is increasingly recognized as a reservoir of human pathogens and transferable antibiotic resistance genes. This study aimed to explore methods to characterize the transferable resistome of bacteria associated with produce. Mixed salad, arugula, and cilantro purchased from supermarkets in Germany were analyzed by means of cultivation- and DNA-based methods. Before and after a nonselective enrichment step, tetracycline (TET)-resistant Escherichia coli were isolated and plasmids conferring TET resistance were captured by exogenous plasmid isolation. TET-resistant E. coli isolates, transconjugants, and total community DNA (TC-DNA) from the microbial fraction detached from leaves or after enrichment were analyzed for the presence of resistance genes, class 1 integrons, and various plasmids by real-time PCR and PCR-Southern blot hybridization. Real-time PCR primers were developed for IncI and IncF plasmids. TET-resistant E. coli isolated from arugula and cilantro carried IncF, IncI1, IncN, IncHI1, IncU, and IncX1 plasmids. Three isolates from cilantro were positive for IncN plasmids and blaCTX-M-1 From mixed salad and cilantro, IncF, IncI1, and IncP-1β plasmids were captured exogenously. Importantly, whereas direct detection of IncI and IncF plasmids in TC-DNA failed, these plasmids became detectable in DNA extracted from enrichment cultures. This confirms that cultivation-independent DNA-based methods are not always sufficiently sensitive to detect the transferable resistome in the rare microbiome. In summary, this study showed that an impressive diversity of self-transmissible multiple resistance plasmids was detected in bacteria associated with produce that is consumed raw, and exogenous capturing into E. coli suggests that they could transfer to gut bacteria as well.IMPORTANCE Produce is one of the most popular food commodities. Unfortunately, leafy greens can be a reservoir of transferable antibiotic resistance genes. We found that IncF and IncI plasmids were the most prevalent plasmid types in E. coli isolates from produce. This study highlights the importance of the rare microbiome associated with produce as a source of antibiotic resistance genes that might escape cultivation-independent detection, yet may be transferred to human pathogens or commensals.},
}

@article {pmid30401457,
year = {2018},
author = {Santos-Cortez, RLP and Chiong, CM and Frank, DN and Ryan, AF and Giese, APJ and Bootpetch Roberts, T and Daly, KA and Steritz, MJ and Szeremeta, W and Pedro, M and Pine, H and Yarza, TKL and Scholes, MA and Llanes, EGDV and Yousaf, S and Friedman, N and Tantoco, MLC and Wine, TM and Labra, PJ and Benoit, J and Ruiz, AG and de la Cruz, RAR and Greenlee, C and Yousaf, A and Cardwell, J and Nonato, RMA and Ray, D and Ong, KMC and So, E and Robertson, CE and Dinwiddie, J and Lagrana-Villagracia, SM and , and Gubbels, SP and Shaikh, RS and Cass, SP and Einarsdottir, E and Lee, NR and Schwartz, DA and Gloria-Cruz, TLI and Bamshad, MJ and Yang, IV and Kere, J and Abes, GT and Prager, JD and Riazuddin, S and Chan, AL and Yoon, PJ and Nickerson, DA and Cutiongco-de la Paz, EM and Streubel, SO and Reyes-Quintos, MRT and Jenkins, HA and Mattila, P and Chan, KH and Mohlke, KL and Leal, SM and Hafrén, L and Chonmaitree, T and Sale, MM and Ahmed, ZM},
title = {FUT2 Variants Confer Susceptibility to Familial Otitis Media.},
journal = {American journal of human genetics},
volume = {103},
number = {5},
pages = {679-690},
doi = {10.1016/j.ajhg.2018.09.010},
pmid = {30401457},
issn = {1537-6605},
abstract = {Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154∗) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202∗) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2 × 10-5) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154∗) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10-7) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants-namely p.Ala104Val, p.Arg138Cys, p.Trp154∗, and p.Arg202∗-reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.},
}

@article {pmid30401435,
year = {2018},
author = {Koh, A and Molinaro, A and Ståhlman, M and Khan, MT and Schmidt, C and Mannerås-Holm, L and Wu, H and Carreras, A and Jeong, H and Olofsson, LE and Bergh, PO and Gerdes, V and Hartstra, A and de Brauw, M and Perkins, R and Nieuwdorp, M and Bergström, G and Bäckhed, F},
title = {Microbially Produced Imidazole Propionate Impairs Insulin Signaling through mTORC1.},
journal = {Cell},
volume = {175},
number = {4},
pages = {947-961.e17},
doi = {10.1016/j.cell.2018.09.055},
pmid = {30401435},
issn = {1097-4172},
abstract = {Interactions between the gut microbiota, diet, and the host potentially contribute to the development of metabolic diseases. Here, we identify imidazole propionate as a microbially produced histidine-derived metabolite that is present at higher concentrations in subjects with versus without type 2 diabetes. We show that imidazole propionate is produced from histidine in a gut simulator at higher concentrations when using fecal microbiota from subjects with versus without type 2 diabetes and that it impairs glucose tolerance when administered to mice. We further show that imidazole propionate impairs insulin signaling at the level of insulin receptor substrate through the activation of p38γ MAPK, which promotes p62 phosphorylation and, subsequently, activation of mechanistic target of rapamycin complex 1 (mTORC1). We also demonstrate increased activation of p62 and mTORC1 in liver from subjects with type 2 diabetes. Our findings indicate that the microbial metabolite imidazole propionate may contribute to the pathogenesis of type 2 diabetes.},
}

@article {pmid30400268,
year = {2018},
author = {Ojo-Okunola, A and Nicol, M and du Toit, E},
title = {Human Breast Milk Bacteriome in Health and Disease.},
journal = {Nutrients},
volume = {10},
number = {11},
pages = {},
doi = {10.3390/nu10111643},
pmid = {30400268},
issn = {2072-6643},
support = {U54HG009824//NIH Office of the Director/ ; 1U01AI110466-01A1//H3Africa U01 AWARD FROM THE NATIONAL INSTITUTES OF HEALTH OF THE USA/ ; OPP1017641; OPP1017579//Bill and Melinda Gates Foundation/ ; },
abstract = {It is well-known that, beyond nutritional components, human breast milk (HBM) contains a wide variety of non-nutritive bio-factors perfectly suited for the growing infant. In the pre-2000 era, HBM was considered sterile and devoid of micro-organisms. Though HBM was not included as part of the human microbiome project launched in 2007, great strides have been made in studying the bacterial diversity of HBM in both a healthy state and diseased state, and in understanding their role in infant health. HBM provides a vast array of beneficial micro-organisms that play a key role in colonizing the infant's mucosal system, including that of the gut. They also have a role in priming the infant's immune system and supporting its maturation. In this review, we provide an in-depth and updated insight into the immunomodulatory, metabolic, and anti-infective role of HBM bacteriome (bacterial community) and its effect on infant health. We also provide key information from the literature by exploring the possible origin of microbial communities in HBM, the bacterial diversity in this niche and the determinants influencing the HBM bacteriome. Lastly, we investigate the role of the HBM bacteriome in maternal infectious disease (human immunodeficiency virus (HIV) and mastitis)), and cancer. Key gaps in HBM bacterial research are also identified.},
}

@article {pmid30399554,
year = {2018},
author = {Liang, B and Ma, J and Cai, W and Li, Z and Liu, W and Qi, M and Zhao, Y and Ma, X and Deng, Y and Wang, A and Zhou, J},
title = {Response of chloramphenicol-reducing biocathode resistome to continuous electrical stimulation.},
journal = {Water research},
volume = {148},
number = {},
pages = {398-406},
doi = {10.1016/j.watres.2018.10.073},
pmid = {30399554},
issn = {1879-2448},
abstract = {Understanding the fate of overall antibiotic resistance genes (ARGs) during the biological treatment of antibiotic containing wastewater is a central issue for the water ecological safety assessment. Although the microbial electrode-respiration based biotransformation process could significantly detoxify some antibiotic contaminants, e.g. chloramphenicol (CAP), the response of CAP-reducing biocathode microbiome and resistome to continuous electrical stimulation, especially ARGs network interactions, are poorly understood. Here, using highthroughput functional gene array (GeoChip v4.6) and Illumina 16S rRNA gene MiSeq sequencing, the structure, composition, diversity and network interactions of CAP-reducing biocathode microbiome and resistome in response to continuous electrical stimulation were investigated. Our results indicate that the CAP bioelectroreduction process could significantly accelerate the elimination of antibacterial activity of CAP during CAP-containing wastewater treatment compared to the pure bioreduction process. Continuous electrical stimulation could obviously alter both the microbiome and resistome structures and consistently decrease the phylogenetic, functional and overall ARGs diversity and network complexity within the CAP-reducing biofilms. The relative abundances of overall ARGs and specific CAP resistance related major facilitator superfamily (MFS) transporter genes were significantly negatively correlated with the reduction efficiency of CAP to inactive antibacterial product AMCl (partially dechlorinated aromatic amine), which may reduce the ecological risk associated with the evolution of multidrug-resistant bacteria and ARGs during antibiotic-containing wastewater treatment process. This study offers new insights into the response of an antibiotic reducing biocathode resistome to continuous electrical stimulation and provides useful information on the assessment of overall ARGs risk for the bioelectrochemical treatment of antibiotic contaminants.},
}

@article {pmid30399404,
year = {2018},
author = {Hantsoo, L and Jašarević, E and Criniti, S and McGeehan, B and Tanes, C and Sammel, MD and Elovitz, MA and Compher, C and Wu, G and Epperson, CN},
title = {Childhood Adversity Impact on Gut Microbiota and Inflammatory Response to Stress During Pregnancy.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2018.11.005},
pmid = {30399404},
issn = {1090-2139},
abstract = {BACKGROUND: Adverse childhood experiences (ACEs), such as abuse or chronic stress, program an exaggerated adult inflammatory response to stress. Emerging rodent research suggests that the gut microbiome may be a key mediator in the association between early life stress and dysregulated glucocorticoid-immune response. However, ACE impact on inflammatory response to stress, or on the gut microbiome, have not been studied in human pregnancy, when inflammation increases risk of poor outcomes. The aim of this study was to assess the relationships among ACE, the gut microbiome, and cytokine response to stress in pregnant women.

METHODS: Physically and psychiatrically healthy adult pregnant women completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and gave a single stool sample between 20 and 26 weeks gestation. Stool DNA was isolated and 16S sequencing was performed. Three 24-hour food recalls were administered to assess dietary nutrient intake. A subset of women completed the Trier Social Stress Test (TSST) at 22-34 weeks gestation; plasma interleukin-6 (IL-6), interleukin-1β (IL-1β), high sensitivity C-reactive protein (hsCRP), tumor necrosis factor α (TNF-α), and cortisol were measured at four timepoints pre and post stressor, and area under the curve (AUC) was calculated.

RESULTS: Forty-eight women completed the ACE-Q and provided stool; 19 women completed the TSST. Women reporting 2 or more ACEs (high ACE) had greater differential abundance of gut Prevotella than low ACE participants (q=5.7x10^-13). Abundance of several gut taxa were significantly associated with cortisol, IL-6, TNF-α and CRP AUCs regardless of ACE status. IL-6 response to stress was buffered among high ACE women with high intake of docosahexaenoic acid (DHA) (p=0.03) and eicosapentaenoic acid (EPA) (p=0.05).

DISCUSSION: Our findings suggest that multiple childhood adversities are associated with changes in gut microbiota composition during pregnancy, and such changes may contribute to altered inflammatory and glucocorticoid response to stress. While preliminary, this is the first study to demonstrate an association between gut microbiota and acute glucocorticoid-immune response to stress in a clinical sample. Finally, exploratory analyses suggested that high ACE women with high dietary intake of ω-3 polyunsaturated fatty acids (PUFAs) had a dampened inflammatory response to acute stress, suggesting potentially protective effects of ω-3s in this high-risk population. Given the adverse effects of inflammation on pregnancy and the developing fetus, mechanisms by which childhood adversity influence the gut-brain axis and potential protective factors such as diet should be further explored.},
}

@article {pmid30399327,
year = {2018},
author = {O'Connor, H and MacSharry, J and Bueso, YF and Lindsay, S and Kavanagh, EL and Tangney, M and Clyne, M and Saldova, R and McCann, A},
title = {Resident bacteria in breast cancer tissue: pathogenic agents or harmless commensals?.},
journal = {Discovery medicine},
volume = {26},
number = {142},
pages = {93-102},
pmid = {30399327},
issn = {1944-7930},
abstract = {Breast cancer is the second most common cancer in women. Recent evidence identifies a unique microbiome in breast tissue; a site previously thought to be sterile. The identification that this microbiome varies considerably from healthy subjects to cancer patients has prompted investigations into the role of specific bacterial species in oncogenesis. Indeed, certain bacteria have been shown to aid cancer development in vitro by promoting genomic instability, invasion, and chemotherapy resistance. However, the in vivo role of the breast microbiome in cancer appears to be more complex, involving numerous interactions between its constituent species and host cells. As such, reduced abundances of species which exert a protective effect against oncogenesis have come into focus and there is an emerging consensus that states of microbial dysbiosis, in which the normal balance of bacterial species is altered, can contribute to the development of cancer. This review summarizes the findings to date from the available literature pertaining to the microbiome in breast cancer and outlines areas worthy of further investigation.},
}

@article {pmid30399141,
year = {2018},
author = {Aw, WC and Towarnicki, SG and Melvin, RG and Youngson, NA and Garvin, MR and Hu, Y and Nielsen, S and Thomas, T and Pickford, R and Bustamante, S and Vila-Sanjurjo, A and Smyth, GK and Ballard, JWO},
title = {Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness.},
journal = {PLoS genetics},
volume = {14},
number = {11},
pages = {e1007735},
doi = {10.1371/journal.pgen.1007735},
pmid = {30399141},
issn = {1553-7404},
abstract = {Diet may be modified seasonally or by biogeographic, demographic or cultural shifts. It can differentially influence mitochondrial bioenergetics, retrograde signalling to the nuclear genome, and anterograde signalling to mitochondria. All these interactions have the potential to alter the frequencies of mtDNA haplotypes (mitotypes) in nature and may impact human health. In a model laboratory system, we fed four diets varying in Protein: Carbohydrate (P:C) ratio (1:2, 1:4, 1:8 and 1:16 P:C) to four homoplasmic Drosophila melanogaster mitotypes (nuclear genome standardised) and assayed their frequency in population cages. When fed a high protein 1:2 P:C diet, the frequency of flies harbouring Alstonville mtDNA increased. In contrast, when fed the high carbohydrate 1:16 P:C food the incidence of flies harbouring Dahomey mtDNA increased. This result, driven by differences in larval development, was generalisable to the replacement of the laboratory diet with fruits having high and low P:C ratios, perturbation of the nuclear genome and changes to the microbiome. Structural modelling and cellular assays suggested a V161L mutation in the ND4 subunit of complex I of Dahomey mtDNA was mildly deleterious, reduced mitochondrial functions, increased oxidative stress and resulted in an increase in larval development time on the 1:2 P:C diet. The 1:16 P:C diet triggered a cascade of changes in both mitotypes. In Dahomey larvae, increased feeding fuelled increased β-oxidation and the partial bypass of the complex I mutation. Conversely, Alstonville larvae upregulated genes involved with oxidative phosphorylation, increased glycogen metabolism and they were more physically active. We hypothesise that the increased physical activity diverted energy from growth and cell division and thereby slowed development. These data further question the use of mtDNA as an assumed neutral marker in evolutionary and population genetic studies. Moreover, if humans respond similarly, we posit that individuals with specific mtDNA variations may differentially metabolise carbohydrates, which has implications for a variety of diseases including cardiovascular disease, obesity, and perhaps Parkinson's Disease.},
}

@article {pmid30398470,
year = {2018},
author = {Sirota, M and Thomas, CG and Liu, R and Zuhl, M and Banerjee, P and Wong, RJ and Quaintance, CC and Leite, R and Chubiz, J and Anderson, R and Chappell, J and Kim, M and Grobman, W and Zhang, G and Rokas, A and England, SK and Parry, S and Shaw, GM and Simpson, JL and Thomson, E and Butte, AJ and , },
title = {Enabling precision medicine in neonatology, an integrated repository for preterm birth research.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180219},
doi = {10.1038/sdata.2018.219},
pmid = {30398470},
issn = {2052-4463},
abstract = {Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of 'omics' data, which together with integrative computational approaches, can help refine the current knowledge about disease mechanisms, diagnostics, and therapeutics. Here we describe the March of Dimes' Database for Preterm Birth Research (http://www.immport.org/resources/mod), a unique resource that contains a variety of 'omics' datasets related to preterm birth. The database is open publicly, and as of January 2018, links 13 molecular studies with data across tens of thousands of patients from 6 measurement modalities. The data in the repository are highly diverse and include genomic, transcriptomic, immunological, and microbiome data. Relevant datasets are augmented with additional molecular characterizations of almost 25,000 biological samples from public databases. We believe our data-sharing efforts will lead to enhanced research collaborations and coordination accelerating the overall pace of discovery in preterm birth research.},
}

@article {pmid30398150,
year = {2018},
author = {Matos, RC and Leulier, F},
title = {Everyone wins.},
journal = {eLife},
volume = {7},
number = {},
pages = {},
doi = {10.7554/eLife.42676},
pmid = {30398150},
issn = {2050-084X},
abstract = {Aeromonas bacteria living in the gut of zebrafish produce a specific molecule to pacify the immune system of their host.},
}

@article {pmid30397546,
year = {2018},
author = {Md Zoqratt, MZH and Eng, WWH and Thai, BT and Austin, CM and Gan, HM},
title = {Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e5826},
doi = {10.7717/peerj.5826},
pmid = {30397546},
issn = {2167-8359},
abstract = {Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3-V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.},
}

@article {pmid30397444,
year = {2018},
author = {Ma, ZS},
title = {DAR (diversity-area relationship): Extending classic SAR (species-area relationship) for biodiversity and biogeography analyses.},
journal = {Ecology and evolution},
volume = {8},
number = {20},
pages = {10023-10038},
doi = {10.1002/ece3.4425},
pmid = {30397444},
issn = {2045-7758},
abstract = {I extend the classic SAR, which has achieved status of ecological law and plays a critical role in global biodiversity and biogeography analyses, to general DAR (diversity-area relationship). The extension was aimed to remedy a serious application limitation of the traditional SAR that only addressed one aspect of biodiversity scaling-species richness scaling over space, but ignoring species abundance information. The extension was further inspired by a recent consensus that Hill numbers offer the most appropriate measures for alpha-diversity and multiplicative beta-diversity. In particular, Hill numbers are essentially a series of Renyi's entropy values weighted differently along the rare-common-dominant spectrum of species abundance distribution and are in the units of effective number of species (or species equivalents such as OTUs). I therefore postulate that Hill numbers should follow the same or similar law of the traditional SAR. I test the postulation with the American gut microbiome project (AGP) dataset of 1,473 healthy North American individuals. I further propose three new concepts and develop their statistical estimation formulae based on the new DAR extension, including: (i) DAR profile-z-q relationship (DAR scaling parameter z at different diversity order q), (ii) PDO (pair-wise diversity overlap) profile-g-q relationship (PDO parameter g at order q, and (iii) MAD (maximal accrual diversity: Dmax) profile-Dmax-q. While the classic SAR is a special case of our new DAR profile, the PDO and MAD profiles offer novel tools for analyzing biodiversity (including alpha-diversity and beta-diversity) and biogeography over space.},
}

@article {pmid30397357,
year = {2018},
author = {Tirosh, O and Conlan, S and Deming, C and Lee-Lin, SQ and Huang, X and , and Su, HC and Freeman, AF and Segre, JA and Kong, HH},
title = {Expanded skin virome in DOCK8-deficient patients.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41591-018-0211-7},
pmid = {30397357},
issn = {1546-170X},
abstract = {Human microbiome studies have revealed the intricate interplay of host immunity and bacterial communities to achieve homeostatic balance. Healthy skin microbial communities are dominated by bacteria with low viral representation1-3, mainly bacteriophage. Specific eukaryotic viruses have been implicated in both common and rare skin diseases, but cataloging skin viral communities has been limited. Alterations in host immunity provide an opportunity to expand our understanding of microbial-host interactions. Primary immunodeficient patients manifest with various viral, bacterial, fungal, and parasitic infections, including skin infections4. Dedicator of cytokinesis 8 (DOCK8) deficiency is a rare primary human immunodeficiency characterized by recurrent cutaneous and systemic infections, as well as atopy and cancer susceptibility5. DOCK8, encoding a guanine nucleotide exchange factor highly expressed in lymphocytes, regulates actin cytoskeleton, which is critical for migration through collagen-dense tissues such as skin6. Analyzing deep metagenomic sequencing data from DOCK8-deficient skin samples demonstrated a notable increase in eukaryotic viral representation and diversity compared with healthy volunteers. De novo assembly approaches identified hundreds of novel human papillomavirus genomes, illuminating microbial dark matter. Expansion of the skin virome in DOCK8-deficient patients underscores the importance of immune surveillance in controlling eukaryotic viral colonization and infection.},
}

@article {pmid30397052,
year = {2018},
author = {Zhanel, G and Critchley, I and Lin, LY and Alvandi, N},
title = {Microbiological Profile of Sarecycline: A Novel Targeted Spectrum Tetracycline for the Treatment of Acne Vulgaris.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1128/AAC.01297-18},
pmid = {30397052},
issn = {1098-6596},
abstract = {Sarecycline is the first narrow spectrum tetracycline-class antibiotic being developed for acne treatment. In addition to exhibiting activity against important skin/soft tissue pathogens, sarecycline exhibits targeted antibacterial activity against clinical isolates of Cutibacterium acnes In the current study, sarecycline was 16 to 32-fold less active than broad spectrum tetracyclines-such as minocycline and doxycycline-against aerobic Gram-negative bacilli associated with normal human intestinal microbiome. Also, reduced activity against Escherichia coli was observed in vivo in a murine septicemia model with PD50 values at >40 mg/kg and 5.72 mg/kg for sarecycline and doxycycline, respectively. Sarecycline was also 4 to 8-fold less active against representative anaerobic bacteria that also comprise normal human intestinal microbiome. Additionally, sarecycline displayed a low propensity for resistance development in C. acnes strains, with spontaneous mutation frequencies of 10-10 at 4 to 8-times the MIC, similar to minocycline and vancomycin. When tested against Gram-positive pathogens with defined tetracycline resistance mechanisms, sarecycline was more active than tetracycline against the tet(K) and tet(M) strains, with MIC ranging from 0.125 to 1.0 ug/mL and 8 ug/mL, respectively, compared with 16 to 64 ug/mL and 64 ug/mL for tetracycline, respectively. However, sarecycline activity in the tet(K) and tet(M) strains were decreased compared to wildtype, which demonstrated MIC ranging from 0.06 to 0.25 ug/mL, though not as pronounced as tetracycline. These findings support sarecycline as a narrow spectrum tetracycline-class antibiotic that is an effective agent for the treatment of acne and further warrants investigation into the potential reduced effects on the gut microbiome.},
}

@article {pmid30396567,
year = {2018},
author = {Christianson, MS and Bellver, J},
title = {Innovations in assisted reproductive technologies: impact on contemporary donor egg practice and future advances.},
journal = {Fertility and sterility},
volume = {110},
number = {6},
pages = {994-1002},
doi = {10.1016/j.fertnstert.2018.09.020},
pmid = {30396567},
issn = {1556-5653},
abstract = {Innovations in assisted reproductive technologies (ART) have driven progress in the donor egg field since the birth of the first baby derived from a donor egg in 1983. Over time, donor oocytes have become an increasingly used option for patients unable to conceive with autologous oocytes. In donor egg, the unique separation of the oocyte source and recipient uterus has created a model that has propelled advances in ART. Progressive ART innovations that have optimized the oocyte donor and resulting embryo include the following: evaluation of ovarian reserve, controlled ovarian hyperstimulation regimens that reduce the risk of ovarian hyperstimulation syndrome, blastocyst culture, oocyte cryopreservation, and preimplantation genetic testing. For donor egg recipients, methods to optimize the endometrium to maximize implantation include endometrial receptivity testing, immunologic donor-recipient matching, and increased understanding of the uterine microbiome.},
}

@article {pmid30396371,
year = {2018},
author = {Meisel, JS and Nasko, DJ and Brubach, B and Cepeda-Espinoza, V and Chopyk, J and Corrada-Bravo, H and Fedarko, M and Ghurye, J and Javkar, K and Olson, ND and Shah, N and Allard, SM and Bazinet, AL and Bergman, NH and Brown, A and Caporaso, JG and Conlan, S and DiRuggiero, J and Forry, SP and Hasan, NA and Kralj, J and Luethy, PM and Milton, DK and Ondov, BD and Preheim, S and Ratnayake, S and Rogers, SM and Rosovitz, MJ and Sakowski, EG and Schliebs, NO and Sommer, DD and Ternus, KL and Uritskiy, G and Zhang, SX and Pop, M and Treangen, TJ},
title = {Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD, January 10, 2018.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {197},
doi = {10.1186/s40168-018-0582-5},
pmid = {30396371},
issn = {2049-2618},
support = {R01-AI-100947//National Institutes of Health/ ; U54CA143924//National Institutes of Health/ ; U54CA143925//National Institutes of Health/ ; IIS-1513615//National Science Foundation (US)/ ; 1565100//National Science Foundation (US)/ ; DEB1556574//National Science Foundation (US)/ ; W911NF-17-2-0089//Intelligence Advanced Research Projects Activity (US)/ ; R01 GM114267//National Institutes of Health (US)/ ; HSHQDC-15-C-00064//Science and Technology Directorate/ ; },
abstract = {The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.},
}

@article {pmid30396369,
year = {2018},
author = {Armstrong, AJS and Shaffer, M and Nusbacher, NM and Griesmer, C and Fiorillo, S and Schneider, JM and Preston Neff, C and Li, SX and Fontenot, AP and Campbell, T and Palmer, BE and Lozupone, CA},
title = {An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {198},
doi = {10.1186/s40168-018-0580-7},
pmid = {30396369},
issn = {2049-2618},
support = {R01 DK108366//National Institute of Diabetes and Digestive and Kidney Diseases/ ; R01 DK104047//National Institute of Diabetes and Digestive and Kidney Diseases/ ; U01 HL098996//National Heart, Lung, and Blood Institute/ ; U01 HL121816//National Heart, Lung, and Blood Institute/ ; T32 AI052066//National Institute of Allergy and Infectious Diseases/ ; 2 T15 LM009451-06//U.S. National Library of Medicine/ ; },
abstract = {BACKGROUND: Gut microbiome characteristics associated with HIV infection are of intense research interest but a deep understanding has been challenged by confounding factors across studied populations. Notably, a Prevotella-rich microbiome described in HIV-infected populations is now understood to be common in men who have sex with men (MSM) regardless of HIV status, but driving factors and potential health implications are unknown.

RESULTS: Here, we further define the MSM-associated gut microbiome and describe compositional differences between the fecal microbiomes of Prevotella-rich MSM and non-MSM that may underlie observed pro-inflammatory properties. Furthermore, we show relatively subtle gut microbiome changes in HIV infection in MSM and women that include an increase in potential pathogens that is ameliorated with antiretroviral therapy (ART). Lastly, using a longitudinal cohort, we describe microbiome changes that happen after ART initiation.

CONCLUSIONS: This study provides an in-depth characterization of microbiome differences that occur in a US population infected with HIV and demonstrates the degree to which these differences may be driven by lifestyle factors, ART, and HIV infection itself. Understanding microbiome compositions that occur with sexual behaviors that are high risk for acquiring HIV and untreated and ART-treated HIV infection will guide the investigation of immune and metabolic functional implications to ultimately target the microbiome therapeutically.},
}

@article {pmid30396009,
year = {2018},
author = {Woerner, AE and Novroski, NMM and Wendt, FR and Ambers, A and Wiley, R and Schmedes, SE and Budowle, B},
title = {Forensic human identification with targeted microbiome markers using nearest neighbor classification.},
journal = {Forensic science international. Genetics},
volume = {38},
number = {},
pages = {130-139},
doi = {10.1016/j.fsigen.2018.10.003},
pmid = {30396009},
issn = {1878-0326},
abstract = {From the perspective of forensics genetics, the human microbiome is a rich, relatively untapped resource for human identity testing. Since it varies within and among people, and perhaps temporally, the potential forensic applications of the use of the microbiome can exceed that of human identification. However, the same inherent variability in microbial distributions may pose a substantial barrier to forming predictions on an individual as the source of the microbial sample unless stable signatures of the microbiome are identified and targeted. One of the more commonly adopted strategies for microbial human identification relies on quantifying which taxa are present and their respective abundance levels. It remains an open question if such microbial signatures are more individualizing than estimates of the degree of genetic relatedness between microbial samples. This study attempts to address this question by contrasting two prediction strategies. The first approach uses phylogenetic distance to predict the host individual; thus it operates under the premise that microbes within individuals are more closely related than microbes between/among individuals. The second approach uses population genetic measures of diversity at clade-specific markers, serving as a fine-grained assessment of microbial composition and quantification. Both assessments were performed using targeted sequencing of 286 markers from 22 microbial taxa sampled in 51 individuals across three body sites measured in triplicate. Nearest neighbor and reverse nearest neighbor classifiers were constructed based on the pooled data and yielded 71% and 78% accuracy, respectively, when diversity was considered, and performed significantly worse when a phylogenetic distance was used (54% and 63% accuracy, respectively). However, empirical estimates of classification accuracy were 100% when conditioned on a maximum nearest neighbor distance when diversity was used, while identification based on a phylogenetic distance failed to reach saturation. These findings suggest that microbial strain composition is more individualizing than that of a phylogeny, perhaps indicating that microbial composition may be more individualizing than recent common ancestry. One inference that may be drawn from these findings is that host-environment interactions may maintain the targeted microbial profile and that this maintenance may not necessarily be repopulated by intra-individual microbial strains.},
}

@article {pmid30396006,
year = {2018},
author = {Velikonja, A and Lipoglavšek, L and Zorec, M and Orel, R and Avguštin, G},
title = {Alterations in gut microbiota composition and metabolic parameters after dietary intervention with barley beta glucans in patients with high risk for metabolic syndrome development.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anaerobe.2018.11.002},
pmid = {30396006},
issn = {1095-8274},
abstract = {Metabolic syndrome is a complex disease that is exponentially increasing in the western world, and diet is one of the possible ways to improve the metabolic status of patients. Barley beta glucans are dietary fibres that show promise for improvement cholesterol levels and postprandial glucose response, but they have been rarely investigated in human trials with concurrent focus on gut microbiota. A double-blind, placebo-controlled, randomised clinical trial was conducted with 43 volunteers with high risk for metabolic syndrome development or with diagnosed metabolic syndrome. During a four-week intervention study, participants consumed experimental bread containing 6 g of barley beta glucans or equal bread but without beta glucans. After dietary intervention, total plasma cholesterol decreased in the test group (-0.26 ± 0.54, p = 0.019), but not in the control group. Short chain fatty acids (SCFA) composition in faeces significantly changed with increase of propionic acid in test group (43.2%, p = 0.045) and with decrease of acetic acid in control group (41.8%, p = 0.011). The microbiome analysis based on Illumina paired end sequencing of 16S rRNA genes showed a decrease in microbial diversity and richness in the test group. The pre-intervention gut microbiota composition showed higher abundance of health associated Bifidobacterium spp. and Akkermansia municiphila within cholesterol-responsive group, showing that diet-induced metabolic response is possibly dependent on individual gut microbiota composition.},
}

@article {pmid30394894,
year = {2018},
author = {Dent, E and Hoogendijk, EO and Wright, ORL},
title = {New insights into the anorexia of ageing: from prevention to treatment.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000000525},
pmid = {30394894},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: Undernutrition in older adults is associated with frailty, functional decline, and mortality. The 'anorexia of ageing' is the age-related appetite and weight loss underpinning such undernutrition. This review examines the latest evidence for its prevention and treatment.

RECENT FINDINGS: Existing nutritional therapies for the anorexia of ageing include supporting nutritional intake with fortified food or supplements, including omega-3 fatty acids, multivitamins, and vitamin D. The Mediterranean diet provides high fat intake and nutrient density in a moderate volume of colourful and flavoursome food and is strengthening in evidence for healthy ageing. Studies of the gut microbiome, which potentially regulates normal appetite by acting on the brain-gut communication axis, are pertinent. Utilization of the genetic profile of individuals to determine nutritional needs is an exciting advancement of the past decade and may become common practice.

SUMMARY: Prevention or early treatment of the anorexia of ageing in older adults is critical. Latest evidence suggests that once significant weight loss has occurred, aggressive nutritional support may not result in improved outcomes.},
}

@article {pmid30394861,
year = {2018},
author = {Siddharthan, R and Chapek, M and Warren, M and Martindale, R},
title = {Probiotics in Prevention of Surgical Site Infections.},
journal = {Surgical infections},
volume = {},
number = {},
pages = {},
doi = {10.1089/sur.2018.231},
pmid = {30394861},
issn = {1557-8674},
abstract = {Despite significant improvements in peri-operative care, surgical site infections (SSIs) remain an important contributor to morbidity, cost, and death. The human gastrointestinal tract is a complex microenvironment linking host cells and the indigenous microflora or "microbiome," creating a "super-organism" that engages in macro-nutrient and micro-nutrient extraction for the host while serving as a barrier to toxins and other detrimental bacterial end-products. Maintaining a healthy microbiome in the peri-operative period may enable control of multi-drug resistance (MDR) organisms, whereas use of antibiotics simply resets the dysbiotic relation by eliminating multiple strains of bacteria. Such loss of microbial diversity or abundance can slow wound healing. Use of pro-biotics to prevent infection has been evaluated in several studies, but their utility is not yet clear. There is a clear need for randomized trials to draw firm conclusions about their efficacy and to make clinical recommendations.},
}

@article {pmid30394587,
year = {2018},
author = {Bettoli, V and Manfredini, M and Massoli, L and Carillo, C and Barozzi, A and Amendolagine, G and Ruina, G and Musmeci, D and Libanore, M and Curtolo, A and Mantovani, L and Contini, C and Pellacani, G and Corazza, M},
title = {Rates of Antibiotic Resistance / Sensitivity in Bacterial Cultures of Hidradenitis Suppurativa Patients.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.15332},
pmid = {30394587},
issn = {1468-3083},
abstract = {BACKGROUND: Antibiotic (AB) treatment is one of the first steps in the management of Hidradenitis Suppurativa (HS). Bacteria, in HS patients, may play a double role, as triggering factors of inflammatory reactions and/or agents of infection.

OBJECTIVES: The aims of this study are: 1) to assess prevalence and AB resistance of bacterial growths in HS patients 2) assessment of the clinical relevance of obtained data in guiding the selection of the most effective AB therapy.

METHODS: Purulent material from 137 skin lesions of HS patients was collected with swabs. Bacterial flora and AB sensitivity were determined using microbiological cultures for aerobic and anaerobic bacteria.

RESULTS: A total of 114 samples resulted positive for bacteria. Sample were collected from the axillae, groin and perianal areas. A total of 163 single bacterial growths were observed; 55% were gram-positive and 44% were gram-negative. Among them, 18.4% were anaerobic. The most frequent bacterial families included enterobacteriacee (30.7%), staphylococcus (25.2%), and streptococcus (14.1%). The most frequent genus or species were proteus spp. (13.5%) and e.coli (9.8%). The prevalence of AB resistance observed was clindamycin 65.7%, rifampicin 69.3%, penicillin 70.0%, ciprofloxacin 74%, tetracycline 84.7% and erythromycin 89.0%. A limitation of the study is represented the short culture period adopted which may have impaired the isolation of anaerobes.

CONCLUSIONS: Bacterial growth in HS patients has shown a high level of resistance to ABs, including rifampicin, clindamycin and tetracyclines, cited as an empiric choice in HS therapeutic guidelines. A targeted and specific AB therapy, driven by microbiological evaluations with prolonged culture periods, seems more appropriate than empiric, generic, non-specific, therapeutic approaches. Current knowledge regarding HS bacterial AB resistance should be considered in the update of current therapeutic guidelines for HS. This article is protected by copyright. All rights reserved.},
}

@article {pmid30394174,
year = {2018},
author = {Dinan, TG and Cryan, JF},
title = {Schizophrenia and the Microbiome: Time to Focus on the Impact of Antipsychotic Treatment on the Gut Microbiota.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/15622975.2018.1540793},
pmid = {30394174},
issn = {1814-1412},
}

@article {pmid30393777,
year = {2018},
author = {Zhang, F and Zhao, S and Ren, C and Zhu, Y and Zhou, H and Lai, Y and Zhou, F and Jia, Y and Zheng, K and Huang, Z},
title = {CRISPRminer is a knowledge base for exploring CRISPR-Cas systems in microbe and phage interactions.},
journal = {Communications biology},
volume = {1},
number = {},
pages = {180},
doi = {10.1038/s42003-018-0184-6},
pmid = {30393777},
issn = {2399-3642},
abstract = {CRISPR-Cas systems not only play key roles in prokaryotic acquired immunity, but can also be adapted as powerful genome editing tools. Understanding the native role of CRISPR-Cas systems in providing adaptive immunity can lead to new CRISPR-based technologies. Here, we develop CRISPRminer, a knowledge base and web server to comprehensively collect and investigate the knowledge of CRISPR-Cas systems and generate instructive annotations, including CRISPR arrays and Cas protein annotation, CRISPR-Cas system classification, self-targeting events detection, microbe-phage interaction inference, and anti-CRISPR annotation. CRISPRminer is user-friendly and freely available at http://www.microbiome-bigdata.com/CRISPRminer.},
}

@article {pmid30393044,
year = {2018},
author = {De Santis, F and Del Vecchio, M and Castagnoli, L and De Braud, F and Franceschini, D and Fucà, G and Hiscott, J and Malmberg, KJ and McGranahan, N and Pietrantonio, F and Rivoltini, L and Sangaletti, S and Tagliabue, E and Tripodo, C and Vernieri, C and Zitvogel, L and Pupa, SM and Di Nicola, M},
title = {Innovative therapy, monoclonal antibodies, and beyond: Highlights from the eighth annual meeting.},
journal = {Cytokine & growth factor reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cytogfr.2018.10.005},
pmid = {30393044},
issn = {1879-0305},
abstract = {The eighth annual conference of "Innovative therapy, monoclonal antibodies, and beyond" was held in Milan on Jan. 26, 2018, and hosted by Fondazione IRCCS-Istituto Nazionale dei Tumori (Fondazione IRCCS INT). The conference was divided into two main scientific sessions, of i) pre-clinical assays and novel biotargets, and ii) clinical translation, as well as a third session of presentations from young investigators, which focused on recent achievements within Fondazione IRCCS INT on immunotherapy and targeted therapies. Presentations in the first session addressed the issue of cancer immunotherapy activity with respect to tumor heterogeneity, with key topics addressing: 1) tumor heterogeneity and targeted therapy, with the definition of the evolutionary Index as an indicator of tumor heterogeneity in both space and time; 2) the analysis of cancer evolution, with the introduction of the TRACERx Consortium-a multi-million pound UK research project focused on non-small cell lung cancer (NSCLC); 3) the use of anti-estrogen agents to boost immune recognition of breast cancer cells; and 4) the high degree of functional plasticity within the NK cell repertoire, including the expansion of adaptive NK cells following viral challenges. The second session addressed: 1) the effectiveness of radiotherapy to enhance the proportion of patients responsive to immune-checkpoint blockers (ICBs); 2) the use of MDSC scores in selecting melanoma patients with high probability to be responsive to ICBs; and 3) the relevance of the gut microbiome as a predictive factor, and the potential of its perturbation in increasing the immune response rate to ICBs. Overall, a picture emerged of tumor heterogeneity as the main limitation that impairs the effectiveness of anti-cancer therapies. Thus, the choice of a specific therapy based on reproducible and selective predictive biomarkers is an urgent unmet clinical need that should be addressed in order to increase the proportion of long-term responding patients and to improve the sustainability of novel drugs.},
}

@article {pmid30392721,
year = {2018},
author = {Cogdill, AP and Gaudreau, PO and Arora, R and Gopalakrishnan, V and Wargo, JA},
title = {The Impact of Intratumoral and Gastrointestinal Microbiota on Systemic Cancer Therapy.},
journal = {Trends in immunology},
volume = {39},
number = {11},
pages = {900-920},
doi = {10.1016/j.it.2018.09.007},
pmid = {30392721},
issn = {1471-4981},
abstract = {The human microbiome is a complex aggregate of microorganisms, and their genomes exert a number of influences crucial to the metabolic, immunologic, hormonal, and homeostatic function of the host. Recent work, both in preclinical mouse models and human studies, has shed light on the impact of gut and tumor microbiota on responses to systemic anticancer therapeutics. In light of this, strategies to target the microbiome to improve therapeutic responses are underway, including efforts to target gut and intratumoral microbes. Here, we discuss mechanisms by which microbiota may impact systemic and antitumor immunity, in addition to outstanding questions in the field. A deeper understanding of these is critical as we devise putative strategies to target the microbiome.},
}

@article {pmid30392534,
year = {2018},
author = {Yatera, K and Noguchi, S and Mukae, H},
title = {The microbiome in the lower respiratory tract.},
journal = {Respiratory investigation},
volume = {56},
number = {6},
pages = {432-439},
doi = {10.1016/j.resinv.2018.08.003},
pmid = {30392534},
issn = {2212-5353},
abstract = {With the advent of new technologies evaluating the microbiome in the sample such as next-generation sequencer (NGS), current increase of an interest in understanding of the lung microbiome and its roles in lung diseases are marked. Gathering the data of bacterial flora in the lung and their changes during disease courses is unraveling the pathogenesis and the mechanism of disease progression particularly in patients with bronchial asthma, chronic obstructive pulmonary disease and infectious lung diseases. To clarify the relationship between the lung microbiome and pulmonary diseases, new information may help us to create new treatment and prevention strategies of some pulmonary diseases by controlling the lung microbiome. Using bacterial 16S ribosomal RNA gene sequence, NGS can rapidly estimate large amount of bacterial sequences in the phylum and genus levels, and some of them in species levels in a very short period of time. In addition to new information of the microbiome using NGS in the respiratory tract, other techniques using basically Sanger method in combination with the clone library construction can also be useful to identify pathogenic bacterial species with their ratio in the respiratory samples such as bacterial pneumonia, lung abscess and nontuberculous mycobacteriosis. These modalities to identify and semi-quantify bacterial burden in the respiratory tract have revealed new bacterial information in each infectious lung disease. This review describes current understanding of the lung microbiome in several representative lung diseases.},
}

@article {pmid30392417,
year = {2018},
author = {Choy, ATF and Carnevale, I and Coppola, S and Meijer, LL and Kazemier, G and Zaura, E and Deng, D and Giovannetti, E},
title = {The microbiome of pancreatic cancer: from molecular diagnostics to new therapeutic approaches to overcome chemoresistance caused by metabolic inactivation of gemcitabine.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2018.1544495},
pmid = {30392417},
issn = {1744-8352},
abstract = {INTRODUCTION: Pancreatic cancer is a complex disease, with an extremely poor response to chemotherapy. Emerging evidence indicates that the tumor microenvironment (TME) might play an important role in mediating chemoresistance. Areas covered: The evaluated study by Geller and collaborators describes several bacterial species within pancreatic tumor tissues and TME and investigated their roles in gemcitabine chemoresistance. Intratumor bacteria express the enzyme cytidine deaminase (CDD), whose long form (CDDL) was shown to metabolize gemcitabine into its inactive metabolite. CDDL is mostly expressed by Gammaproteobacteria and this was among the most common species in pancreatic cancer tissues. Interestingly, mouse models of colorectal cancer injected with bacterial CDDL displayed a reduced response to gemcitabine, but this resistance was neutralized by the antibiotic ciprofloxacin. Expert Commentary: The increased knowledge on the microbiome in pancreatic tissues, as well as its role in chemoresistance, will provide innovative prognostic and therapeutic strategies.},
}

@article {pmid30392013,
year = {2018},
author = {Hendrikx, T and Schnabl, B},
title = {Antimicrobial proteins: intestinal guards to protect against liver disease.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00535-018-1521-8},
pmid = {30392013},
issn = {1435-5922},
abstract = {Alterations of gut microbes play a role in the pathogenesis and progression of many disorders including liver and gastrointestinal diseases. Both qualitative and quantitative changes in gut microbiota have been associated with liver disease. Intestinal dysbiosis can disrupt the integrity of the intestinal barrier leading to pathological bacterial translocation and the initiation of an inflammatory response in the liver. In order to sustain symbiosis and protect from pathological bacterial translocation, antimicrobial proteins (AMPs) such as a-defensins and C-type lectins are expressed in the gastrointestinal tract. In this review, we provide an overview of the role of AMPs in different chronic liver disease such as alcoholic steatohepatitis, non-alcoholic fatty liver disease, and cirrhosis. In addition, potential approaches to modulate the function of AMPs and prevent bacterial translocation are discussed.},
}

@article {pmid30391469,
year = {2018},
author = {Frost, F and Kacprowski, T and Rühlemann, M and Bülow, R and Kühn, JP and Franke, A and Heinsen, FA and Pietzner, M and Nauck, M and Völker, U and Völzke, H and Aghdassi, AA and Sendler, M and Mayerle, J and Weiss, FU and Homuth, G and Lerch, MM},
title = {Impaired Exocrine Pancreatic Function Associates With Changes in Intestinal Microbiota Composition and Diversity.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2018.10.047},
pmid = {30391469},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Changes in intestinal microbiome composition are associated with inflammatory, metabolic, and malignant disorders. We studied how exocrine pancreatic function affects intestinal microbiota.

METHODS: We performed 16S rRNA gene sequencing analysis of stool samples from 1795 volunteers from the population-based study of health in Pomerania who had no history of pancreatic disease. We also measured fecal pancreatic elastase by ELISA and performed quantitative imaging of secretin-stimulated pancreatic fluid secretion. Associations of exocrine pancreatic function with microbial diversity or individual genera were calculated by permutational analysis of variance or linear regression, respectively.

RESULTS: Differences in pancreatic elastase levels associated with significantly (P<.0001) greater changes in microbiota diversity than with participant age, body mass index, sex, smoking, alcohol consumption, or dietary factors. Significant changes in the abundance of thirty taxa, such as an increase in Prevotella (q<.0001) and a decrease of Bacteroides (q<.0001), indicated a shift from a type-1 to a type-2 enterotype. Changes in pancreatic fluid secretion alone were also associated with changes in microbial diversity (P=.0002), although to a lesser degree.

CONCLUSIONS: In an analysis of fecal samples from 1795 volunteers, pancreatic acinar cell, rather than duct cell, function is presently the single most significant host factor to be associated with changes in intestinal microbiota composition.},
}

@article {pmid30390805,
year = {2018},
author = {Wang, Q and Yang, F and Jia, H},
title = {Mining the Microbiome for Drug Targets.},
journal = {Methods in enzymology},
volume = {610},
number = {},
pages = {59-72},
doi = {10.1016/bs.mie.2018.09.014},
pmid = {30390805},
issn = {1557-7988},
abstract = {The human microbiome is our "other genome." Implicated in a growing list of complex diseases, for which genomic studies typically explain a portion of the disease susceptibility, the human gut microbiome has been at the spotlight for our understanding of human diseases. As the microbiome is intrinsically more variable than the human genome, it is important to take careful considerations at each step of a study. Here, we put forward our recommendations, which we envision would facilitate identification of true drug targets in the human microbiome in the colon as well as at other body sites.},
}

@article {pmid30390741,
year = {2018},
author = {Wu, BG and Segal, LN},
title = {The Lung Microbiome and Its Role in Pneumonia.},
journal = {Clinics in chest medicine},
volume = {39},
number = {4},
pages = {677-689},
doi = {10.1016/j.ccm.2018.07.003},
pmid = {30390741},
issn = {1557-8216},
abstract = {The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia.},
}

@article {pmid30390509,
year = {2018},
author = {Leng, L and Nobu, MK and Narihiro, T and Yang, P and Amy Tan, GY and Lee, PH},
title = {Shaping microbial consortia in coupling glycerol fermentation and carboxylate chain elongation for Co-production of 1,3-propanediol and caproate: Pathways and mechanisms.},
journal = {Water research},
volume = {148},
number = {},
pages = {281-291},
doi = {10.1016/j.watres.2018.10.063},
pmid = {30390509},
issn = {1879-2448},
abstract = {Glycerol is presently being generated in surplus with the rapid growth of the biodiesel industry and seeks ways to be upcycled, rather than to be treated with costs. Glycerol for the co-production of 1,3-propanediol (1,3-PDO) and caproate has a great prospect. Yet, its technical difficulty lies in the enhancement of caproate productivity, which requires the presence of ethanol as a co-substrate and necessitates the co-existence of functional microbes for glycerol fermentation and chain elongation. This study successfully achieved 6.38 mM C 1,3-PDO d-1 and 2.95 mM C caproate d-1 in a 2-L mixed-cultured semi-continuous fermenter with a glycerol-ethanol-acetate stoichiometric ratio of 4:3:1. Such conversions were mainly facilitated by a microbial community of Eubacterium limosum, Clostridium kluyveri and Massilibacterium senegalense. With such a synergistic microbiome, the co-production of 1,3-PDO and caproate was achieved from glycerol without ethanol addition. Based on metagenomics, E. limosum is capable of converting glycerol to 1,3-PDO, ethanol and H2, and also redirecting the electron potential of H2 into acetate via the Wood-Ljungdahl pathway, which is then used for chain elongation. C. kluyveri worked synergistically with E. limosum by consuming ethanol and acetate for caproate production. M. senegalense encodes for ethanol oxidation to acetate and butyrate, facilitating the generation of these intermediates for C. kluyveri elongation to caproate. During the transition between fermentation and elongation, an unexpected observation of poly-β-hydroxybutyrate (PHB) formation and reutilization by M. senegalense may be associated with butyrate formation for further caproate generation. The knowledge gleaned from the substrate constitute, microbial consortium and their synergetic metabolism demonstrates a resource upgrade potential for crude glycerol or glycerol-containing wastewater generated from the biodiesel industry.},
}