@article {pmid30654045,
year = {2019},
author = {Toivonen, L and Camargo, CA and Gern, JE and Bochkov, YA and Mansbach, JM and Piedra, PA and Hasegawa, K},
title = {Association between rhinovirus species and nasopharyngeal microbiota in infants with severe bronchiolitis.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.12.1004},
pmid = {30654045},
issn = {1097-6825},
abstract = {Among 774 infants with severe bronchiolitis, rhinovirus species related to distinct nasopharyngeal microbiota. Infants with rhinovirus-A were more likely to have Haemophilus-dominant microbiota profile, while those with rhinovirus-C were more likely to have Moraxella-dominant profile.},
}
@article {pmid30653931,
year = {2019},
author = {Vuong, HE and Hsiao, EY},
title = {Gut Microbes Join the Social Network.},
journal = {Neuron},
volume = {101},
number = {2},
pages = {196-198},
doi = {10.1016/j.neuron.2018.12.035},
pmid = {30653931},
issn = {1097-4199},
abstract = {The gut microbiome is increasingly implicated in the regulation of social behavior across model organisms. In this issue of Neuron, Sgritta et al. (2018) examine the role of the gut microbiome in social reward circuits and sociability in three mouse models of autism spectrum disorder.},
}
@article {pmid30653021,
year = {2019},
author = {Niederberger, C},
title = {Re: Testicular Microbiome in Azoospermic Men-First Evidence of the Impact of an Altered Microenvironment.},
journal = {The Journal of urology},
volume = {},
number = {},
pages = {},
doi = {10.1097/01.JU.0000553265.88701.d4},
pmid = {30653021},
issn = {1527-3792},
}
@article {pmid30652494,
year = {2019},
author = {Kalantar, KL and Moazed, F and Christenson, SC and Wilson, J and Deiss, T and Belzer, A and Vessel, K and Caldera, S and Jauregui, A and Bolourchi, S and DeRisi, JL and Calfee, CS and Langelier, C},
title = {A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota.},
journal = {American journal of physiology. Lung cellular and molecular physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajplung.00476.2018},
pmid = {30652494},
issn = {1522-1504},
abstract = {Accurate and informative microbiologic testing is essential for guiding diagnosis and management of pneumonia in critically ill patients. Sampling of tracheal aspirate (TA) is less invasive compared to mini-bronchoalveolar lavage (mBAL) and is now recommended as a frontline diagnostic approach in mechanically ventilated patients, despite the historical belief that TA was suboptimal due to contamination from oral microbes. Advancements in metagenomic next generation sequencing (mNGS) now permit assessment of airway microbiota without a need for culture, and as such provide an opportunity to examine differences between mBAL and TA at a resolution previously unachievable. Here, we engaged shotgun mNGS to quantitatively assess the airway microbiome in matched mBAL and TA specimens from a prospective cohort of critically ill adults. We observed moderate differences betweensampletypes across all subjects, however we found significant compositional similarity in subjects with bacterial pneumonia, whose microbial communities were characterized by a dominant pathogen. In addition, we found that both mBAL and TA were similar in terms of microbialrelative abundance, abundance of oropharyngeal taxa, and microbial diversity. Our findings suggest that TA sampling provides a similar assessment of airway microbiota as more invasive testing by mBAL, and that this similarity is most significant in the setting of bacterial pneumonia.},
}
@article {pmid30652422,
year = {2019},
author = {Pearson, T and Caporaso, JG and Yellowhair, M and Bokulich, NA and Padi, M and Roe, DJ and Wertheim, BC and Linhart, M and Martinez, JA and Bilagody, C and Hornstra, H and Alberts, DS and Lance, P and Thompson, PA},
title = {Effects of ursodeoxycholic acid on the gut microbiome and colorectal adenoma development.},
journal = {Cancer medicine},
volume = {},
number = {},
pages = {},
doi = {10.1002/cam4.1965},
pmid = {30652422},
issn = {2045-7634},
support = {NIH/NCI U54CA143924//Native American Cancer Prevention/ ; U54CA143925//Native American Cancer Prevention/ ; 1565100//NSF/ ; R01 CA151708//NSF/ ; P30 CA023074/BC/NCI NIH HHS/United States ; },
abstract = {It has been previously reported that ursodeoxycholic acid (UDCA), a therapeutic bile acid, reduced risk for advanced colorectal adenoma in men but not women. Interactions between the gut microbiome and fecal bile acid composition as a factor in colorectal cancer neoplasia have been postulated but evidence is limited to small cohorts and animal studies. Using banked stool samples collected as part of a phase III randomized clinical trial of UDCA for the prevention of colorectal adenomatous polyps, we compared change in the microbiome composition after a 3-year intervention in a subset of participants randomized to oral UDCA at 8-10 mg/kg of body weight per day (n = 198) or placebo (n = 203). Study participants randomized to UDCA experienced compositional changes in their microbiome that were statistically more similar to other individuals in the UDCA arm than to those in the placebo arm. This reflected a UDCA-associated shift in microbial community composition (P < 0.001), independent of sex, with no evidence of a UDCA effect on microbial richness (P > 0.05). These UDCA-associated shifts in microbial community distance metrics from baseline to end-of-study were not associated with risk of any or advanced adenoma (all P > 0.05) in men or women. Separate analyses of microbial networks revealed an overrepresentation of Faecalibacterium prausnitzii in the post-UDCA arm and an inverse relationship between F prausnitzii and Ruminococcus gnavus. In men who received UDCA, the overrepresentation of F prausnitzii and underrepresentation of R gnavus were more prominent in those with no adenoma recurrence at follow-up compared to men with recurrence. This relationship was not observed in women. Daily UDCA use modestly influences the relative abundance of microbial species in stool and affects the microbial network composition with suggestive evidence for sex-specific effects of UDCA on stool microbial community composition as a modifier of colorectal adenoma risk.},
}
@article {pmid30652367,
year = {2019},
author = {Romero, S and Nastasa, A and Chapman, A and Kwong, WK and Foster, LJ},
title = {The Honey Bee Gut Microbiota: Strategies for Study and Characterization.},
journal = {Insect molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/imb.12567},
pmid = {30652367},
issn = {1365-2583},
abstract = {Gut microbiota research is an emerging field that improves our understanding of the ecological and functional dynamics of gut environments. The honey bee gut microbiota is a highly rewarding community to study, as honey bees are critical pollinators of many crops for human consumption and produce valuable commodities such as honey and wax. Most significantly, unique characteristics of the Apis mellifera gut habitat make it a valuable model system. This review discusses methods and pipelines used in the study of the gut microbiota of A. mellifera and closely related species for four main purposes: identifying microbiota taxonomy, characterizing microbiota genomes (microbiome), characterizing microbiota-microbiota interactions, and identifying functions of the microbial community in the gut. The purpose of this contribution is to increase understanding of honey bee gut microbiota, to facilitate bee microbiota and microbiome research in general, and to aid design of future experiments in this growing field. This article is protected by copyright. All rights reserved.},
}
@article {pmid30652107,
year = {2018},
author = {Soderborg, TK and Friedman, JE},
title = {Imbalance in gut microbes from babies born to obese mothers increases gut permeability and myeloid cell adaptations that provoke obesity and NAFLD.},
journal = {Microbial cell (Graz, Austria)},
volume = {6},
number = {1},
pages = {102-104},
doi = {10.15698/mic2019.01.666},
pmid = {30652107},
issn = {2311-2638},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disease affecting nearly 40% of obese youth and up to 10% of the general pediatric population. A key aspect of NAFLD pathogenesis is proinflammatory hepatic macrophage activation and hepatic recruitment of circulating monocytes, which originate from the bone marrow. In neonates, the activation and polarization of myeloid immune cells are normally shaped in part by systemic factors derived from intestinal microbiota during the first 1000 days of life. Perturbations of the gut microbiome, and in turn the metabolites and bacterial products released systemically, can affect the functional phenotype of these immune cells. Evidence in germ-free mice has shown that fecal microbial transfer from obese mice or obese human donors promotes obesity and inflammation in the recipients, suggesting a direct role for the gut microbiome in promoting obesity and possibly NAFLD. Indeed, patients suffering from NAFLD show evidence for dysbiosis, increased gut permeability, and changes in bile acids that drive the progression of hepatic inflammation toward non-alcoholic steatohepatitis (NASH), the more severe form of the disease. Compared with infants born to normal-weight mothers, we previously showed that the gut microbiome from neonates born to obese mothers is compositionally distinct. However, whether this alteration in early gut microbiota in infants born to obese mothers can cause inflammatory processes that initiate development of NAFLD or obesity is unknown. How these alterations contribute to long-term immune cell mediated liver inflammation and progression of NAFLD needs to be determined. Our recently published work (Soderborg et al., Nat Commun 9:4462) demonstrates a causative role of early life microbiome dysbiosis in infants born to mothers with obesity in novel pathways that promote developmental programming of NAFLD.},
}
@article {pmid30652093,
year = {2018},
author = {Shigematsu, Y and Inamura, K},
title = {Gut microbiome: a key player in cancer immunotherapy.},
journal = {Hepatobiliary surgery and nutrition},
volume = {7},
number = {6},
pages = {479-480},
doi = {10.21037/hbsn.2018.10.02},
pmid = {30652093},
issn = {2304-3881},
}
@article {pmid30651985,
year = {2019},
author = {Guevarra, RB and Lee, JH and Lee, SH and Seok, MJ and Kim, DW and Kang, BN and Johnson, TJ and Isaacson, RE and Kim, HB},
title = {Piglet gut microbial shifts early in life: causes and effects.},
journal = {Journal of animal science and biotechnology},
volume = {10},
number = {},
pages = {1},
doi = {10.1186/s40104-018-0308-3},
pmid = {30651985},
issn = {1674-9782},
abstract = {The gut microbiome has long been known to play fundamentally important roles in the animal health and the well-being of its host. As such, the establishment and maintenance of a beneficial gut microbiota early in life is crucial in pigs, since early gut colonizers are pivotal in the establishment of permanent microbial community structures affecting the health and growth performance of pigs later in life. Emphasizing this importance of early gut colonizers, it is critical to understand the factors impacting the establishment of the piglet gut microbiome at weaning. Factors include, among others, diet, in-feed antibiotics, probiotics and prebiotic administration. The impact of these factors on establishment of the gut microbiome of piglets at weaning includes effects on piglet gut microbial diversity, structure, and succession. In this review, we thoroughly reviewed the most recent findings on the piglet gut microbiome shifts as influenced by weaning, and how these microbiome changes brought about by various factors that have been shown to affect the development of microbiota in piglets. This review will provide a general overview of recent studies that can help to facilitate the design of new strategies to modulate the gut microbiome in order to enhance gastrointestinal health, growth performance and well-being of piglets.},
}
@article {pmid30651726,
year = {2018},
author = {Bencard, A and Whiteley, LE},
title = {Mind the Gut-displaying microbiome research through artistic collaboration.},
journal = {Microbial ecology in health and disease},
volume = {29},
number = {2},
pages = {1555433},
doi = {10.1080/16512235.2018.1555433},
pmid = {30651726},
issn = {0891-060X},
abstract = {This paper presents the Mind the Gut exhibition, opened in 2017 at the Medical Museion, the University of Copenhagen's museum for the culture and history of medicine. It is an experimental exhibition combining science, art, and history in an examination of the relationship between mind and gut, including the trillions of microbes that inhabits them. Mind the Gut was the result of a 2-year-long research and curatorial process, which began in 2015 when Museion was awarded the Bikuben Foundation Vision Award. The exhibition brings together the long history of attempts to understand and intervene in the relationship between mind and gut, between emotions and digestion with cutting-edge biomedical research, and includes the perspectives of science, medicine, and personal experience, via a combination of artworks, historical objects from the Medical Museion collections, items from laboratories, and individual stories. The exhibition is organized around different ways the body has been handled in order to intervene in interactions between mind, gut, and bacteria, including imaging, electrifying, feeding, drugging, and opening surgically. This paper outlines some of the thoughts on science communication that motivated the exhibition, discussing why the displays emphasize the exploratory over the explanatory. Also discussed are several artistic collaborations that formed part of the displays. Ultimately, Mind the Gut is created to be a public space that encourages reflection and curiosity, by showing how biomedicine fits into social, cultural, historical, and directly personal contexts. The exhibition does not aim to provide answers about what food the visitors should eat or what the truth of how gut and brain interactions might be. Rather, it emphasizes process over result, hopefully encouraging the visitors to ask their own questions of the relationship between mind and gut, between body and microbes.},
}
@article {pmid30651683,
year = {2018},
author = {Shah, S},
title = {Salivaomics: The current scenario.},
journal = {Journal of oral and maxillofacial pathology : JOMFP},
volume = {22},
number = {3},
pages = {375-381},
doi = {10.4103/jomfp.JOMFP_171_18},
pmid = {30651683},
issn = {0973-029X},
abstract = {For generations, blood has been the medium of choice for diagnosing most diseases and conditions. The reason for this is mainly the limitations of technology. The concept of oral diagnostics is preferred to more invasive methods. In recent years, it has become evident that the salivary constituents become detectably altered in response to certain disease states. Even so, what is most impressive is that salivary biomarkers not only arise in correlation with oral disorders but also those of distal tissues and organs. This suggests that oral fluids may represent a substantial reservoir of molecular and microbial information capable of communicating the onset or presence of disease throughout the body. An initiative of the National Institute of Dental and Craniofacial Research created a roadmap to achieve these goals whereby, with the use of oral fluids as the diagnostic medium, it would become possible to scrutinize the health and/or disease status of patients. The real promise of salivary analysis use is the ability of the patient or clinician to directly and continuously assess disease status, progression and therapeutic efficacy. The sensitive analysis may even allow presymptomatic diagnosis. There are five major diagnostic alphabets available in saliva namely, proteins, messenger RNAs, micro-RNAs (mi-RNAs), metabolic compounds and microbes which offer substantial advantages for salivary diagnostics because, the state of the disease may be associated with detectable changes in one, but not all, dimensions. Recently, the Salivaomics Knowledge Base (SKB) has been established by aligning the salivary biomarker discovery. The SKB constitutes data repository, management system and web resource fabricated to support human salivary proteomics, transcriptomics, miRNA, metabolomics and microbiome research.},
}
@article {pmid30651577,
year = {2019},
author = {Goethel, A and Turpin, W and Rouquier, S and Zanello, G and Robertson, SJ and Streutker, CJ and Philpott, DJ and Croitoru, K},
title = {Nod2 influences microbial resilience and susceptibility to colitis following antibiotic exposure.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41385-018-0128-y},
pmid = {30651577},
issn = {1935-3456},
abstract = {Inflammatory bowel disease (IBD) etiology involves genetic susceptibility, environmental triggers, and the gut microbiome. Antibiotic exposure is associated with IBD, both in early life and adulthood. Here, we investigated whether Nod2-deficiency influenced response of the gut microbiota to antibiotics and subsequent colitis susceptibility. Wild-type and Nod2-/- littermate mice were treated with amoxicillin as adults or neonates, and fecal samples were collected for 16S rRNA sequencing. Five weeks after antibiotic exposure, dextran sulfate sodium (DSS) colitis was induced. Antibiotic treatment altered the microbiota of adult WT and Nod2-/- mice, but recovery was delayed in Nod2-/- mice. Neonatal antibiotic treatment significantly changed the microbiota at weaning in WT and Nod2-/- littermates; however, Nod2-/- mice maintained reduced microbial diversity 14 days after cessation of antibiotics. Although treatment of adult mice did not influence susceptibility to colitis, neonatally treated Nod2-/- mice developed a more severe colitis. Moreover, the colitis phenotype was transferable through fecal transplantation into germ-free Nod2-/- recipients, and was associated with changes in intestinal T cells and the cytokine milieu following inflammation. These data demonstrate that neonatal antibiotic exposure has long-lasting influence on the microbiota and mucosal immunity, and may explain how NOD2 contributes to the risk of intestinal inflammation.},
}
@article {pmid30651402,
year = {2019},
author = {Mu, A and Kwong, JC and Isles, NS and Gonçalves da Silva, A and Schultz, MB and Ballard, SA and Lane, CR and Carter, GP and Williamson, DA and Seemann, T and Stinear, TP and Howden, BP},
title = {Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing.},
journal = {mSphere},
volume = {4},
number = {1},
pages = {},
doi = {10.1128/mSphere.00529-18},
pmid = {30651402},
issn = {2379-5042},
abstract = {Culture-independent methods that target genome fragments have shown promise in identifying certain pathogens, but the holy grail of comprehensive pathogen genome detection from microbiologically complex samples for subsequent forensic analyses remains a challenge. In the context of an investigation of a nosocomial outbreak, we used shotgun metagenomic sequencing of a human fecal sample and a neural network algorithm based on tetranucleotide frequency profiling to reconstruct microbial genomes and tested the same approach using rectal swabs from a second patient. The approach rapidly and readily detected the genome of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae in the patient fecal specimen and in the rectal swab sample, achieving a level of strain resolution that was sufficient for confident transmission inference during a highly clonal outbreak. The analysis also detected previously unrecognized colonization of the patient by vancomycin-resistant Enterococcus faecium, another multidrug-resistant bacterium.IMPORTANCE The study results reported here perfectly demonstrate the power and promise of clinical metagenomics to recover genome sequences of important drug-resistant bacteria and to rapidly provide rich data that inform outbreak investigations and treatment decisions, independently of the need to culture the organisms.},
}
@article {pmid30651010,
year = {2019},
author = {Metz, TD and McKinney, J and Allshouse, AA and Doucette Knierim, S and Carey, JC and Heyborne, KD},
title = {Exposure to group B streptococcal antibiotic prophylaxis and early childhood body mass index in a vaginal birth cohort.},
journal = {The journal of maternal-fetal &amp; neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians},
volume = {},
number = {},
pages = {1-171},
doi = {10.1080/14767058.2019.1571575},
pmid = {30651010},
issn = {1476-4954},
abstract = {OBJECTIVE: Perinatal antibiotic exposure may be associated with changes in both early infancy gut microbiota and later childhood obesity. Our objective was to evaluate if group B Streptococcus (GBS) antibiotic prophylaxis is associated with higher body mass index (BMI) in early childhood.<br><br>METHODS: Retrospective cohort study of mother/child dyads in a single hospital system over a 6-year period. All women with term, singleton, vertex, vaginal deliveries who received no antibiotics or received antibiotics only for GBS prophylaxis and whose children had BMIs available at 2-5 years of age were included. Children were divided into three groups for comparison: children born to GBS positive mothers that received antibiotics solely for GBS prophylaxis, children born to GBS negative women that received no antibiotics (healthy controls), and children born to GBS positive mothers who received no antibiotics. The primary outcome was the earliest available child BMI Z-score at 2-5 years of age. Multivariable linear regression was used to estimate differences in child BMI Z-scores between groups, adjusted for maternal BMI, age, race, parity, tobacco use, and child birthweight.<br><br>RESULTS: Of 4825 women, 786 (16.3%) were GBS positive and received prophylactic antibiotics, 3916 (81.2%) were GBS negative and received no antibiotics, and 123 (2.5%) were GBS positive but received no antibiotics. Childhood BMI Z-scores were similar between children exposed to intrapartum GBS prophylaxis and healthy controls who were unexposed in both unadjusted (mean (SE), 0.04 (0.04) versus -0.3 (0.02), p = 0.11) and adjusted (0.01 (0.05) versus -0.04 (0.03), p = 0.3) models.<br><br>CONCLUSIONS: Exposure to intrapartum antibiotic prophylaxis for GBS was not associated with higher early childhood BMI Z-scores compared to healthy controls.},
}
@article {pmid30650376,
year = {2019},
author = {Pronovost, GN and Hsiao, EY},
title = {Perinatal Interactions between the Microbiome, Immunity, and Neurodevelopment.},
journal = {Immunity},
volume = {50},
number = {1},
pages = {18-36},
doi = {10.1016/j.immuni.2018.11.016},
pmid = {30650376},
issn = {1097-4180},
abstract = {The microbiome modulates host immune function across the gastrointestinal tract, peripheral lymphoid organs, and central nervous system. In this review, we highlight emerging evidence that microbial effects on select immune phenotypes arise developmentally, where the maternal and neonatal microbiome influence immune cell ontogeny in the offspring during gestation and early postnatal life. We further discuss roles for the perinatal microbiome and early-life immunity in regulating normal neurodevelopmental processes. In addition, we examine evidence that abnormalities in microbiota-neuroimmune interactions during early life are associated with altered risk of neurological disorders in humans. Finally, we conclude by evaluating the potential implications of microbiota-immune interventions for neurological conditions. Continued progress toward dissecting mechanistic interactions between the perinatal microbiota, immune system, and nervous system might uncover fundamental insights into how developmental interactions across physiological systems inform later-life health and disease.},
}
@article {pmid30650116,
year = {2019},
author = {Akami, M and Andongma, AA and Zhengzhong, C and Nan, J and Khaeso, K and Jurkevitch, E and Niu, CY and Yuval, B},
title = {Intestinal bacteria modulate the foraging behavior of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae).},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210109},
doi = {10.1371/journal.pone.0210109},
pmid = {30650116},
issn = {1932-6203},
abstract = {The gut microbiome of insects directly or indirectly affects the metabolism, immune status, sensory perception and feeding behavior of its host. Here, we examine the hypothesis that in the oriental fruit fly (Bactrocera dorsalis, Diptera: Tephritidae), the presence or absence of gut symbionts affects foraging behavior and nutrient ingestion. We offered protein-starved flies, symbiotic or aposymbiotic, a choice between diets containing all amino acids or only the non-essential ones. The different diets were presented in a foraging arena as drops that varied in their size and density, creating an imbalanced foraging environment. Suppressing the microbiome resulted in significant changes of the foraging behavior of both male and female flies. Aposymbiotic flies responded faster to the diets offered in experimental arenas, spent more time feeding, ingested more drops of food, and were constrained to feed on time-consuming patches (containing small drops of food), when these offered the full complement of amino acids. We discuss these results in the context of previous studies on the effect of the gut microbiome on host behavior, and suggest that these be extended to the life history dimension.},
}
@article {pmid30649912,
year = {2019},
author = {Liu, H and Wang, Y and Sun, D and Jiang, H and Yang, F},
title = {Insight into the correlation between biochar amendment and shift in bacterial community four years after a single incorporation in soybean/maize-planted soils in north-eastern China.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2018-0366},
pmid = {30649912},
issn = {1480-3275},
abstract = {To date, there have been comparatively few reports addressing the correlation between biochar treatments, crop species and microbiome shifts. In this study, the shifts in soil bacterial community were investigated four years after a single incorporation of biochar in soybean- and maize-planted soils. Clear changes in bacterial community composition and structure were detected in the soybean-planted soil amended with low-titer biochar (7.89 t/ha), whereas such changes in the maize-planted soil were not observed at the same biochar amendment rate, suggesting a more sensitive influence on bacterial community in the soybean-planted soil than that in the maize-planted soil. The bacterial abundance in the maize-planted soil was reduced significantly with the increasing biochar addition (15.78 t/ha and 47.34 t/ha), which was probably due to the substances inhibition originated from biochar. Both the bacterial community and biomarkers in soil under biochar amendment varied with planted crops, which mean different responses of bacterial community to biochar amendment. All these results suggested that biochar might influence bacterial community in maize- and soybean-growing soils under different mechanisms. Our findings should be valuable for in-depth understanding the potential mechanism of soil microbiome changes following biochar incorporation and for biochar application in agriculture.},
}
@article {pmid30649714,
year = {2019},
author = {Baranowski, T and Motil, KJ and Moreno, JP},
title = {Multi-etiological Perspective on Child Obesity Prevention.},
journal = {Current nutrition reports},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13668-019-0256-3},
pmid = {30649714},
issn = {2161-3311},
support = {58-3092-5-001//Agricultural Research Service/ ; },
abstract = {PURPOSE OF REVIEW: The simple energy balance model of obesity is inconsistent with the available findings on obesity etiology, prevention, and treatment. Yet, the most commonly stated causes of pediatric obesity are predicated on this model. A more comprehensive biological model is needed upon which to base behavioral interventions aimed at obesity prevention. In this light, alternative etiologies are little investigated and thereby poorly understood.<br><br>RECENT FINDINGS: Three candidate alternate etiologies are briefly presented: infectobesity, the gut microbiome, and circadian rhythms. Behavioral child obesity preventive investigators need to collaborate with biological colleagues to more intensively analyze the behavioral aspects of these etiologies and to generate innovative procedures for preventing a multi-etiological problem, e.g., group risk analysis, triaging for likely causes of obesity.},
}
@article {pmid30649314,
year = {2019},
author = {Kostanjšek, R and Prodan, Y and Stres, B and Trontelj, P},
title = {Composition of the cutaneous bacterial community of a cave amphibian, Proteus anguinus.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz007},
pmid = {30649314},
issn = {1574-6941},
abstract = {The European cave salamander Proteus anguinus is a charismatic amphibian endemic to the concealed and inaccessible subterranean waters of the Dinaric Karst. Despite its exceptional conservation importance not much is known about its ecology and interactions with the groundwater microbiome. The cutaneous microbiota of amphibians is an important driver of metabolic capabilities and immunity, and thus a key factor of their wellbeing and survival. We used high-throughput 16S rRNA gene sequencing based on seven variable regions to examine the bacteriome of the skin of five distinct evolutionary lineages of P. anguinus and in their groundwater environment. The skin bacteriomes turned out to be strongly filtered subsamples of the environmental microbial community. The resident microbiota of the analyzed individuals was dominated by five bacterial taxa. Despite an indicated functional redundancy, the cutaneous bacteriome of P. anguinus presumably provides protection against invading microbes by occupying the niche, and thus could serve as indicator of health status. Besides conservation implications for P. anguinus, our results provide a baseline for future studies on other endangered neotenic salamanders.},
}
@article {pmid30649204,
year = {2019},
author = {Saha, S and Johnson, J and Pal, S and Weinstock, G and Rajasekaran, S},
title = {MSC: a metagenomic sequence classification algorithm.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/bty1071},
pmid = {30649204},
issn = {1367-4811},
abstract = {Motivation: Metagenomics is the study of genetic materials directly sampled from natural habitats. It has the potential to reveal previously hidden diversity of microscopic life largely due to the existence of highly parallel and low-cost next-generation sequencing (NGS) technology. Conventional approaches align metagenomic reads onto known reference genomes to identify microbes in the sample. Since such a collection of reference genomes is very large, the approach often needs high-end computing machines with large memory which is not often available to researchers. Alternative approaches follow an alignment-free methodology where the presence of a microbe is predicted using the information about the unique k-mers present in the microbe genomes. However, such approaches suffer from high false positives due to trading off the value of k with the computational resources. In this article we propose a highly efficient metagenomic sequence classification algorithm (MSC) that is a hybrid of both approaches. Instead of aligning reads to the full genomes, MSC aligns reads onto a set of carefully chosen, shorter and highly discriminating model sequences built from the unique k-mers of each of the target sequences.<br><br>Results: Microbiome researchers are generally interested in two objectives of a taxonomic classifier: 1) to detect prevalence, i.e., the taxa present in a sample, and 2) to estimate their relative abundances. MSC is primarily designed to detect prevalence and experimental results show that MSC is indeed a more effective and efficient algorithm compared to the other state-of-the-art algorithms in terms of accuracy, memory, and runtime. Moreover, MSC outputs an approximate estimate of the abundances.<br><br>Availability: The implementations are freely available for non-commercial purposes. They can be downloaded from https://drive.google.com/open?id=1XirkAamkQ3ltWvI1W1igYQFusp9DHtVl.},
}
@article {pmid30649168,
year = {2019},
author = {Griffith, JC and Morgan, XC},
title = {Invited Commentary: Improving accessibility of the Human Microbiome Project data through integration with R/Bioconductor.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwz007},
pmid = {30649168},
issn = {1476-6256},
abstract = {Alterations in the composition of the microbiota have been implicated in many diseases. The Human Microbiome Project (HMP) provides a comprehensive reference dataset of the &quot;normal&quot; human microbiome of 242 healthy adults at five major body sites. The HMP used both 16S ribosomal RNA gene sequencing and whole-genome metagenomic sequencing to profile the subjects' microbial communities. However, accessing and analyzing the HMP dataset still presents technical and bioinformatic challenges, as researchers must import the microbiome data, integrate phylogenetic trees, and access and merge public and restricted metadata. In this issue, the HMP16SData R/Bioconductor package developed by Schiffer and colleagues (Am J Epidemiol. XXX; XX (XX): XX-XXX) greatly simplifies access to the HMP data by combining 16S taxonomic abundance data, public patient metadata, and phylogenetic trees as a single data object. The authors also provide an interface for users with approved dbGaP projects to easily retrieve and merge the controlled-access HMP metadata. This package has a broad range of appeal to researchers across disciplines and with various levels of expertise in using R and/or other statistical tools. This will translate to improved data accessibility for public health research, with data from healthy individuals serving as a reference for disease-associated studies.},
}
@article {pmid30649166,
year = {2019},
author = {Schiffer, L and Azhar, R and Shepherd, L and Ramos, M and Geistlinger, L and Huttenhower, C and Dowd, JB and Segata, N and Waldron, L},
title = {HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor.},
journal = {American journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/aje/kwz006},
pmid = {30649166},
issn = {1476-6256},
abstract = {Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 239 healthy American adults, to produce the first comprehensive reference for the composition and variation of the &quot;healthy&quot; human microbiome. Publicly-available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.},
}
@article {pmid30649054,
year = {2019},
author = {Maurice, JB and Garvey, L and Tsochatzis, EA and Wiltshire, M and Cooke, G and Guppy, N and McDonald, J and Marchesi, J and Nelson, M and Kelleher, P and Goldin, R and Thursz, M and Lemoine, M},
title = {Monocyte-Macrophage activation is associated with NAFLD and liver fibrosis in HIV mono-infection independently of the gut microbiome and bacterial translocation.},
journal = {AIDS (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAD.0000000000002133},
pmid = {30649054},
issn = {1473-5571},
abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is common among people living with HIV. There is limited data available on the pathophysiology of NAFLD and the development of fibrosis in this population.<br><br>OBJECTIVES: to investigate the association of bacterial translocation, adipose tissue dysfunction, monocyte activation and gut dysbiosis in patients with HIV mono-infection and NAFLD.<br><br>METHODS: Cases with biopsy-proven NAFLD and HIV mono-infection were age and sex-matched to HIV+ and HIV- controls. Markers of bacterial translocation (lipopolysaccharide-binding protein (LBP), bacterial DNA and lipopolysaccharide (LPS)), adipose tissue dysfunction (leptin, adiponectin) and monocyte activation (sCD14 and sCD163) were measured by ELISA. Hepatic patterns of macrophage activation were explored with immunohistochemistry. 16 s rRNA sequencing was performed with stool.<br><br>RESULTS: Thirty-three cases were included (≥F2 fibrosis n = 16), matched to HIV+ (n = 29) and HIV- (n = 17) controls. Cases with NAFLD were more obese (BMI 31.0 ± 4.4 kg/m vs 24.1 ± 2.8 kg/m p < 0.001) and had significantly increased levels of sCD14, sCD163 and higher leptin to adiponectin ratio versus HIV+ controls. Cases with ≥F2 verses < F2 fibrosis had increased sCD14 (1.4 ± 0.4 vs 1.1 ± 0.3 μg/ml, p = 0.023) and sCD163 (1.0 ± 0.3 vs 0.8 ± 0.3 μg/ml, p = 0.060) which correlated with waist circumference (sCD14 p = 0.022, sCD163 p = 0.011). Immunohistochemistry showed increased hepatic portal macrophage clusters in patients with fibrosis. No markers of bacterial translocation or changes to the microbiome were associated with NAFLD or fibrosis.<br><br>CONCLUSION: NAFLD fibrosis stage in HIV mono-infected patients is associated with monocyte activation in the context of obesity, which may be independent of bacterial translocation and gut microbiome.},
}
@article {pmid30649052,
year = {2019},
author = {Cook, RR and Fulcher, JA and Tobin, NH and Li, F and Lee, D and Javanbakht, M and Brookmeyer, R and Shoptaw, S and Bolan, R and Aldrovandi, GM and Gorbach, PM},
title = {Effects of HIV viremia on the gastrointestinal microbiome of young men who have sex with men.},
journal = {AIDS (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1097/QAD.0000000000002132},
pmid = {30649052},
issn = {1473-5571},
abstract = {OBJECTIVE: We employed a high-dimensional covariate adjustment method in microbiome analysis to better control for behavioral and clinical confounders, and in doing so examine the effects of HIV on the rectal microbiome.<br><br>DESIGN: Three hundred eighty-three men who have sex with men were grouped into four HIV viremia categories: HIV negative (n = 200), HIV+ undetectable (HIV RNA < 20 copies/mL; n = 66), HIV+ suppressed (RNA 20-200 copies/mL; n = 72) and HIV+ viremic (RNA > 200 copies/mL; n = 45).<br><br>METHODS: We performed 16S rRNA gene sequencing on rectal swab samples and used inverse probability of treatment-weighted marginal structural models to examine differences in microbial composition by HIV viremia category.<br><br>RESULTS: HIV viremia explained a significant amount of variability in microbial composition in both unadjusted and covariate-adjusted analyses (R = .011, p = .02). Alterations in bacterial taxa were more apparent with increasing viremia. Relative to the HIV negative group, HIV+ undetectable participants showed depletions in Brachyspira, Campylobacter, and Parasutterella while suppressed participants demonstrated depletions in Barnesiella, Brachyspira and Helicobacter. The microbial signature of viremic men was most distinct, showing enrichment in inflammatory genera Peptoniphilus, Porphyromonas, and Prevotella and depletion of Bacteroides, Brachyspira, and Faecalibacterium, among others.<br><br>CONCLUSIONS: Our study shows that, after accounting for the influence of multiple confounding factors, HIV is associated with dysbiosis in the gastrointestinal microbiome in a dose-dependent manner. This analytic approach may allow for better identification of true microbial associations by limiting the effects of confounding, and thus improve comparability across future studies.},
}
@article {pmid30648974,
year = {2019},
author = {Deng, F and Li, Y and Zhao, J},
title = {The gut microbiome of healthy long-living people.},
journal = {Aging},
volume = {},
number = {},
pages = {},
doi = {10.18632/aging.101771},
pmid = {30648974},
issn = {1945-4589},
}
@article {pmid30648419,
year = {2019},
author = {BenIsrael, M and Wanner, P and Aravena, R and Parker, BL and Haack, EA and Tsao, DT and Dunfield, KE},
title = {Toluene biodegradation in the vadose zone of a poplar phytoremediation system identified using metagenomics and toluene-specific stable carbon isotope analysis.},
journal = {International journal of phytoremediation},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/15226514.2018.1523873},
pmid = {30648419},
issn = {1549-7879},
abstract = {Biodegradation is an important mechanism of action of phytoremediation systems, but performance evaluation is challenging. We applied metagenomic molecular approaches and compound-specific stable carbon isotope analysis to assess biodegradation of toluene in the vadose zone at an urban pilot field system where hybrid poplars were planted to remediate legacy impacts to an underlying shallow fractured bedrock aquifer. Carbon isotope ratios were compared spatio-temporally between toluene dissolved in groundwater and in the vapor phase. Enrichment of 13C from toluene in the vapor phase compared to groundwater provided evidence for biodegradation in the vadose zone. Total bacterial abundance (16S rRNA) and abundance and expression of degradation genes were determined in rhizosphere soil (DNA and RNA) and roots (DNA) using quantitative PCR. Relative abundances of degraders in the rhizosphere were on average higher at greater depths, except for enrichment of PHE-encoding communities that more strongly followed patterns of toluene concentrations detected. Quantification of RMO and PHE gene transcripts supported observations of active aerobic toluene degradation. Finally, spatially-variable numbers of toluene degraders were detected in poplar roots. We present multiple lines of evidence for biodegradation in the vadose zone at this site, contributing to our understanding of mechanisms of action of the phytoremediation system.},
}
@article {pmid30648012,
year = {2019},
author = {Wu, SH and Huang, BH and Gao, J and Wang, S and Liao, PC},
title = {The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6147},
doi = {10.7717/peerj.6147},
pmid = {30648012},
issn = {2167-8359},
abstract = {Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.},
}
@article {pmid30647970,
year = {2018},
author = {Zam, W},
title = {Gut Microbiota as a Prospective Therapeutic Target for Curcumin: A Review of Mutual Influence.},
journal = {Journal of nutrition and metabolism},
volume = {2018},
number = {},
pages = {1367984},
doi = {10.1155/2018/1367984},
pmid = {30647970},
issn = {2090-0724},
abstract = {Background: Turmeric is a spice that has recently received much interest and has been widely used in Ayurvedic medicine. Turmeric products are diarylheptanoids and have been characterized as safe. They are termed as curcuminoids that consists essentially of three major compounds: curcumin, demethoxycurcumin, and bisdemethoxycurcumin. Curcumin is a lipophilic polyphenol that has poor systemic bioavailability and suffers from biotransformation by human intestinal microflora to yield different metabolites that are easily conjugated to glucuronides and sulfate O-conjugated derivatives. Recently, an increasing number of studies have indicated that dysbiosis is linked with many metabolic diseases, though gut microbiota could be a novel potential therapeutic target.<br><br>Scope and Approach: Thus, it is suspected that curcumin and its derivatives exert direct regulative effects on the gut microbiota which could explain the paradox between curcumin's poor systemic bioavailability and its widely reported pharmacological activities.<br><br>Key Findings and Conclusions: This article summarizes a range of studies that highlight the interaction between curcumin and gut microbiota and considers opportunities for microbiome-targeting therapies using turmeric extract.},
}
@article {pmid30647905,
year = {2018},
author = {Bullerdiek, J and Rommel, B},
title = {Factors targeting MED12 to drive tumorigenesis?.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {359},
doi = {10.12688/f1000research.14227.1},
pmid = {30647905},
issn = {2046-1402},
abstract = {Mediator Subcomplex 12 (MED12) is part of the transcriptional preinitiation machinery. Mutations of its gene predominantly occur in two types of highly frequent benign tumors, uterine leiomyomas and fibroadenomas of the breast, where they apparently act as driver mutations. Nevertheless, their presence is not restricted to benign tumors having been found at considerable frequencies in uterine leiomyosarcomas, malignant phyllodes tumors, and chronic lymphocytic leukemia also. Most of the mutations are located within exon 2 of the gene but in rare cases the intron 1/exon 2 boundary or exon 1 are affected. As to their type, predominantly single nucleotide exchanges with a hotspot in one codon are found, but small deletions clustering around that hotspot also are not uncommon. According to their presumed classification as gain-of-function mutations, these latter deletions are leaving the open reading frame intact. As to the types of mutations, so far no apparent differences between the tumor entities affected have emerged. Interestingly, this pattern with small deletions clustered around the hotspot of single nucleotide exchanges resembles that seen as a result of targeted gene editing. In contrast to other driver mutations the percentage of MED12-mutation positive tumors of independent clonal origin increases with the number of tumors per patient suggesting unknown etiological factors supporting site specific mutagenesis. These factors may act by inducing simultaneous site-specific double strand breaks the erroneous repair of which may lead to corresponding mutations. As inducers of DNA damage and its repair such as foreign nucleic acids of the microbiome displaying sequence homology to the putative target site might play a role. Interestingly, a 16 base pair homology of the hotspot to a putative terminator base-paired hairpin sequence of a Staphylococcus aureus tRNA gene cluster has been noted which might form R-loop like structures with its target sequence thus inducing said changes.},
}
@article {pmid30647128,
year = {2019},
author = {Alimov, I and Menon, S and Cochran, N and Maher, R and Wang, Q and Alford, J and Concannon, JB and Yang, Z and Harrington, E and Llamas, L and Lindeman, A and Hoffman, G and Schuhmann, T and Russ, C and Reece-Hoyes, J and Canham, SM and Cai, X},
title = {Bile acid analogues are activators of Pyrin inflammasome.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1074/jbc.RA118.005103},
pmid = {30647128},
issn = {1083-351X},
abstract = {Bile acids are critical metabolites in the gastrointestinal tract which contribute to maintaining intestinal immune homeostasis through crosstalk with the gut microbiota. The conversion of bile acids by the gut microbiome is now recognized as a factor affecting both host metabolism and immune responses, but its physiological roles remain unclear. We conducted a screen for microbiome metabolites that would function as inflammasome activators and herein report the identification of 12-oxo-lithocholic acid, (BAA485), a potential microbiome-derived bile acid metabolite. We demonstrate the more potent analog 11-oxo-12S-hydroxy lithocholic acid methyl ester (BAA473) can induce secretion of interleukin-18 (IL18) through activation of the inflammasome in both myeloid and intestinal epithelial cells. Using a genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) screen with compound induced pyroptosis in THP-1 cells, we identified inflammasome activation by BAA473 is Pyrin-dependent (MEFV). To our knowledge, the bile acid analogues BAA485 and BAA473 are the first small molecule activators of the Pyrin inflammasome. We surmise that Pyrin inflammasome activation through microbiota-modified bile acid metabolites such as BAA473 and BAA485 plays a role in gut microbiota regulated intestinal immune response. The discovery of these two bioactive compounds may help further unveil the importance of Pyrin in gut homeostasis and autoimmune diseases.},
}
@article {pmid30646834,
year = {2019},
author = {Vallianou, NG and Tzortzatou-Stathopoulou, F},
title = {Microbiota and cancer: an update.},
journal = {Journal of chemotherapy (Florence, Italy)},
volume = {},
number = {},
pages = {1-5},
doi = {10.1080/1120009X.2018.1541046},
pmid = {30646834},
issn = {1973-9478},
abstract = {The number of microbes in the human intestine is approximately 1 × 1014, while the number of eukaryotic cells in the human body is around 1 × 1013. As a result of co-evolution of the host mucosal immune system and the microbiota, both have developed multiple mechanisms to maintain homeostasis. Nevertheless, when these mechanisms are disturbed by pathogenic bacteria, which invade this fragile environment, the immune system responds to the microbiota and may support tumour growth in the intestine. Data advocate that the microbiota and its interactions with the host could also be implicated in carcinogenesis in other organs. It is nowadays suggested that developing methods to selectively manipulate components of the microbiota and ultimately target tumorigenesis represents a complex but exciting challenge. In this review, the main pathogenetic mechanisms of the interplay between the microbiome and the innate system, which may be implicated in tumorigenesis are discussed. Also, the importance of the gut microbiota regarding efficacy and toxicity of current chemotherapeutic agents, as well as the direct antitumor properties of the microbiota, will be reviewed.},
}
@article {pmid30646486,
year = {2019},
author = {Chen, S and Ou, Y and Zhao, L and Li, Y and Qiao, Z and Hao, Y and Ren, F},
title = {Differential Effects of Lactobacillus casei Strain Shirota on Patients With Constipation Regarding Stool Consistency in China.},
journal = {Journal of neurogastroenterology and motility},
volume = {25},
number = {1},
pages = {148-158},
doi = {10.5056/jnm17085},
pmid = {30646486},
issn = {2093-0879},
abstract = {Background/Aims: Probiotics are expected to confer benefits on patients with constipation, but how probiotics act on constipated patients with variable stool consistencies remains unclear. We investigated the effect of Lactobacillus casei strain Shirota (LcS) on constipation-related symptoms, especially stool consistency, of constipated patients.<br><br>Methods: Constipated patients meeting the Rome III criteria were divided into 3 groups according to the Bristol Stool Form Scale (BSFS): hard (hard stool [HS], BSFS ＜ 3), normal (normal stool [NS], ≤ 3 BSFS ≤ 4), and soft (soft stool [SS], 4 ＜ BSFS ≤ 5) stools. Subjects in each group consumed a probiotic beverage containing 10¹⁰ colony-forming units of LcS daily for 28 days.<br><br>Results: LcS intervention significantly alleviated constipation-related symptoms and increased defecation frequency in all subjects. Four weeks of LcS supplementation softened the hard stools in HS, hardened the soft stools in SS, and did not alter the ideal stool consistency in NS. The short-chain fatty acid (SCFA) concentrations were highest in SS, followed by NS and HS. LcS intervention increased the stool SCFA levels in HS but reduced or did not alter the levels in NS and SS. LcS intervention increased the Pseudobutyrivibrio and Roseburia abundances in HS and decreased the Pseudobutyrivibrio abundance in SS.<br><br>Conclusions: LcS supplementation improved the constipation-related symptoms in constipated subjects. Differences in baseline stool consistency could result in different anti-constipation effects of LcS intervention. LcS balanced the stool consistency-softened the HS and hardened the SS. These effects could be associated with modulation of the gut microbiota and SCFA production.},
}
@article {pmid30646475,
year = {2019},
author = {Kowalski, K and Mulak, A},
title = {Brain-Gut-Microbiota Axis in Alzheimer's Disease.},
journal = {Journal of neurogastroenterology and motility},
volume = {25},
number = {1},
pages = {48-60},
doi = {10.5056/jnm18087},
pmid = {30646475},
issn = {2093-0879},
abstract = {Disturbances along the brain-gut-microbiota axis may significantly contribute to the pathogenesis of neurodegenerative disorders. Alzheimer's disease (AD) is the most frequent cause of dementia characterized by a progressive decline in cognitive function associated with the formation of amyloid beta (Aβ) plaques and neurofibrillary tangles. Alterations in the gut microbiota composition induce increased permeability of the gut barrier and immune activation leading to systemic inflammation, which in turn may impair the blood-brain barrier and promote neuroinflammation, neural injury, and ultimately neurodegeneration. Recently, Aβ has also been recognized as an antimicrobial peptide participating in the innate immune response. However, in the dysregulated state, Aβ may reveal harmful properties. Importantly, bacterial amyloids through molecular mimicry may elicit cross-seeding of misfolding and induce microglial priming. The Aβ seeding and propagation may occur at different levels of the brain-gut-microbiota axis. The potential mechanisms of amyloid spreading include neuron-to-neuron or distal neuron spreading, direct blood-brain barrier crossing or via other cells as astrocytes, fibroblasts, microglia, and immune system cells. A growing body of experimental and clinical data confirms a key role of gut dysbiosis and gut microbiota-host interactions in neurodegeneration. The convergence of gut-derived inflammatory response together with aging and poor diet in the elderly contribute to the pathogenesis of AD. Modification of the gut microbiota composition by food-based therapy or by probiotic supplementation may create new preventive and therapeutic options in AD.},
}
@article {pmid30646427,
year = {2019},
author = {Zhong, Y and Yang, Y and Liu, P and Xu, R and Rensing, C and Fu, X and Liao, H},
title = {Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities.},
journal = {Plant, cell &amp; environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.13519},
pmid = {30646427},
issn = {1365-3040},
abstract = {Rhizosphere bacterial communities are vital for plants, yet the composition of rhizobacterial communities and the complex interactions between roots and microbiota, or between microbiota, are largely unknown. In this study, we investigated the structure and composition of rhizobacterial communities in two soybean cultivars and their recombinant inbred lines (RILs) contrasting in nodulation through 16S rRNA amplicon sequencing in two years of field trials. Our results demonstrate that soybean plants are able to select microbes from bulk soils at the taxonomic and functional level. Soybean genotype significantly influenced the structure of rhizobacterial communities, and resulted in dramatically different co-occurrence networks of rhizobacterial communities between different genotypes of soybean plants. Furthermore, the introduction of exogenous rhizobia through inoculation altered soybean rhizobacterial communities in genotype dependent manner. Rhizobium inoculation not only stimulated the proliferation of potential beneficial microbes, but also increased connections in rhizobacterial networks and changed the hub microbes, all of which led to the association of distinctive bacterial communities. Taken together, we demonstrated that the assembly of soybean rhizobacterial communities was determined by both genotype and the introduction of exogenous rhizobia. These findings bolster the feasibility of root microbiome engineering through inoculation of specific microbial constituents.},
}
@article {pmid30645678,
year = {2019},
author = {Quigley, EMM},
title = {The Spectrum of Small Intestinal Bacterial Overgrowth (SIBO).},
journal = {Current gastroenterology reports},
volume = {21},
number = {1},
pages = {3},
doi = {10.1007/s11894-019-0671-z},
pmid = {30645678},
issn = {1534-312X},
abstract = {PURPOSE OF REVIEW: To critically review recent (past 3 years) literature on the definition, diagnosis, and management of small intestinal bacterial overgrowth (SIBO).<br><br>RECENT FINDINGS: While various series continue to illustrate the occurrence of SIBO in disease states where well-known risk factors for its occurrence are present (hypochlorhydria, disorders of intestinal structure or motor function, pancreatic insufficiency, and chronic liver disease, for example), the current challenge is in defining the limits of SIBO. Is SIBO truly common among those with &quot;functional&quot; gastrointestinal symptoms where there is no evidence of maldigestion or malabsorption; the original hallmarks of SIBO? Our attempts to address this question continue to be hampered by the limitations of our diagnostic tool kit. There is hope-the application of modern molecular techniques to the study of the small intestinal microbiome, together with some innovative sampling techniques, such as real-time intestinal gas sampling, may soon allow us to truly define the spectrum of SIBO. SIBO, once removed from its original confines as a cause of malabsorption syndrome, has proven to be an elusive and moving target. Only the most rigorous studies employing validated methodologies will finally corral this mysterious entity.},
}
@article {pmid30644970,
year = {2019},
author = {Kelly, CR and Ananthakrishnan, AN},
title = {Manipulating the Microbiome With Fecal Transplantation to Treat Ulcerative Colitis.},
journal = {JAMA},
volume = {321},
number = {2},
pages = {151-152},
doi = {10.1001/jama.2018.20397},
pmid = {30644970},
issn = {1538-3598},
}
@article {pmid30644566,
year = {2019},
author = {McClanahan, D and Yeh, A and Firek, B and Zettle, S and Rogers, M and Cheek, R and Nguyen, MVL and Gayer, CP and Wendell, SG and Mullett, SJ and Morowitz, MJ},
title = {Pilot Study of the Effect of Plant-Based Enteral Nutrition on the Gut Microbiota in Chronically Ill Tube-Fed Children.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.1504},
pmid = {30644566},
issn = {1941-2444},
abstract = {BACKGROUND: Dietary intake sharply impacts the structure and function of the gut microbiota, which is important for childhood health. However, little is known about the microbiota of children who cannot eat by mouth. Standard enteral formulas for supplemental nutrition are low in fiber and high in processed sugars and are commonly associated with gastrointestinal side effects. In this pilot study, we examined the effects of plant-based enteral nutrition (PBEN) upon the gut bacteria of chronically ill children.<br><br>METHODS: Ten children (median age 3.5 years, age range 2-8 years) dependent upon conventional enteral formula were transitioned to PBEN for 2 months. Microbial diversity within fecal samples collected before and after PBEN was assessed by 16S ribosomal RNA gene sequence analysis and was compared with rectal swabs from healthy children. Fecal short-chain fatty acids and bile acids were measured in parallel.<br><br>RESULTS: Relative to control samples, fecal samples from study subjects were depleted of commensals (eg, Faecalibacterium) and enriched with pathogens (eg, Enterococcus). Postintervention samples from study subjects were more similar to healthy controls. Most subjects experienced PBEN-induced alterations in the gut microbiota, but these changes varied significantly across individuals. Clinical diaries indicated that PBEN was well tolerated, with improvement in symptoms noted in several subjects.<br><br>CONCLUSION: Results from this pilot study suggest that PBEN is well tolerated and could improve the health of the microbiota in chronically ill children. This trial provides a rationale for systematic evaluation of PBEN in clinical trials of children who require supplemental nutrition.},
}
@article {pmid30644442,
year = {2019},
author = {Haron, MH and Tyler, HL and Chandra, S and Moraes, RM and Jackson, CR and Pugh, ND and Pasco, DS},
title = {Plant microbiome-dependent immune enhancing action of Echinacea purpurea is enhanced by soil organic matter content.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {136},
doi = {10.1038/s41598-018-36907-x},
pmid = {30644442},
issn = {2045-2322},
support = {R01AT007042//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT007042//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 58-6060-6-015//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {We previously demonstrated that extracts from Echinacea purpurea material varied substantially in their ability to activate macrophages in vitro and that this variation was due to differences in their content of bacterial components. The purpose of the current study was to identify soil conditions (organic matter, nitrogen, and moisture content) that alter the macrophage activation potential of E. purpurea and determine whether these changes in activity correspond to shifts in the plant-associated microbiome. Increased levels of soil organic matter significantly enhanced macrophage activation exhibited by the root extracts of E. purpurea (p < 0.0001). A change in soil organic matter content from 5.6% to 67.4% led to a 4.2-fold increase in the macrophage activation potential of extracts from E. purpurea. Bacterial communities also differed significantly between root materials cultivated in soils with different levels of organic matter (p < 0.001). These results indicate that the level of soil organic matter is an agricultural factor that can alter the bacterial microbiome, and thereby the activity, of E. purpurea roots. Since ingestion of bacterial preparation (e.g., probiotics) is reported to impact human health, it is likely that the medicinal value of Echinacea is influenced by cultivation conditions that alter its associated bacterial community.},
}
@article {pmid30644049,
year = {2019},
author = {Gong, B and Huang, H and Peng, C and Wang, J and Ma, J and Liu, X and Ouyang, S and Huang, SL and Wu, H},
title = {The microbiomic and environmental analysis of sediments in the Indo-Pacific humpback dolphin (Sousa chinensis) habitat in the Northern Beibu Gulf, China.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11356-018-3976-9},
pmid = {30644049},
issn = {1614-7499},
support = {31560727//National Natural Science Foundation of China/ ; 31570875//National Natural Science Foundation of China/ ; 41776174//National Natural Science Foundation of China/ ; 2014GXNSFBA118135//Guangxi Natural Science Foundation/ ; 2017TS03//Foundation of Guangxi Key Laboratory of Marine Disaster in the Beibu Gulf, Qinzhou University/ ; 2016ZYB07//Foundation of the Key Laboratory of Coastal Science and Engineering, Beibu Gulf, Guangxi/ ; },
abstract = {The northern Beibu Gulf is one of the major habitats for the Indo-Pacific humpback dolphin (Sousa chinensis) in China. In this habitat, the core distribution zone of humpback dolphins was confined to the Sanniang Bay (SNB) and Dafengjiang River Estuary (DRE) areas. In our present research, the sediments of 14 sampling sites across the SNB and DRE waters were collected and further conducted for microbiomic and environmental analysis to explore the ecosystem characteristics of major humpback dolphin habitats in Northern Beibu Gulf. The environmental condition includes ammonia nitrogen (NH4+-N), nitrate nitrogen (NO3--N), dissolved reactive phosphorus (DRP), sulfur content in the form of sulfuric acid (SO42--S), Fe, and heavy metals (including Cu, Zn, Cd, Pb, and As). The composition of the bacterial community was characterized by 16S ribosomal DNA analysis of the V3-V4 regions using the Illumina-based sequencing platform. The environmental characteristic of the nutrient elements and heavy metals indicated that SNB suffered more anthropogenic impact than DRE. The comparably higher concentration of NH4+-N, NO3--N, DRP, Pb, and Cd in the SNB region was detected. The comparably higher nutrients in the SNB may have resulted in higher biomass and lower dissolved oxygen (DO) profile, which was further proved by Landsat thermal image data. The microbiome analysis showed that the DRE region was oligotrophic and SNB reflected an anaerobic environment in the sediments. Environmental factors rather than the spatial distance determined the similarity of bacterial community among different sites. Ecological associations between environmental, oceanographic, and bacterial characteristics were illustrated, which exhibited strong mutual associations. Our findings presented a feasibility that integrates empirical and remote sensing data to distinguish ecological features and evaluate ecosystem healthiness for the humpback dolphin habitats.},
}
@article {pmid30643883,
year = {2019},
author = {Franco Filho, LC and Barata, RR and Cardoso, JF and Massafra, JMV and Lemos, PDS and Casseb, LMN and Cruz, ACR and Nunes, MRT},
title = {Metagenomic Analysis of Samples from Three Bat Species Collected in the Amazon Rain Forest.},
journal = {Microbiology resource announcements},
volume = {8},
number = {2},
pages = {},
doi = {10.1128/MRA.01422-18},
pmid = {30643883},
issn = {2576-098X},
abstract = {We report here the sequencing of five microbiome samples collected from different bat species in the Amazon rain forest. All contigs matching virus sequences were assigned to members of the Retroviridae family, while the bacterial contigs matched several bacterial species mostly belonging to the Proteobacteria phylum.},
}
@article {pmid30643852,
year = {2019},
author = {Alves da Silva, AV and de Castro Oliveira, SB and Di Rienzi, SC and Brown-Steinke, K and Dehan, LM and Rood, JK and Carreira, VS and Le, H and Maier, EA and Betz, KJ and Aihara, E and Ley, RE and Preidis, GA and Shen, L and Moore, SR},
title = {Murine Methyl Donor Deficiency Impairs Early Growth in Association with Dysmorphic Small Intestinal Crypts and Reduced Gut Microbial Community Diversity.},
journal = {Current developments in nutrition},
volume = {3},
number = {1},
pages = {nzy070},
doi = {10.1093/cdn/nzy070},
pmid = {30643852},
issn = {2475-2991},
abstract = {Background: Folate and choline are essential methyl donor nutrients throughout the life span; however, the adverse effects of combined deficiency on early growth, intestinal epithelial morphology, and the gut microbiome remain only partially understood.<br><br>Objectives: We investigated the effects of dietary folate and choline deficiency on early growth, small intestinal (SI) epithelial architecture, and the gut microbiota of mice. To explore potential mechanisms for adverse effects on gut epithelial morphology, we also evaluated gene expression and DNA methylation in mouse intestinal epithelial organoids (enteroids) maintained in methyl donor-deficient (MDD) conditions.<br><br>Methods: Pregnant dams were administered 1 of 4 diets: 1) control diet (CD-), 2) an isocaloric MDD- diet, or 3) CD+ and 4) MDD+ formulations containing 1% succinylsulfathiazole to inhibit folate-producing gut bacteria. We weaned pups to their dams' diet at 3 wk of age and monitored body weight and tail length pre- and postweaning. We measured serum folate, SI crypt morphology, and microbiota composition at 7 wk of age.<br><br>Results: Both MDD+ and MDD- diets impaired early ponderal and linear growth, lowered serum folate concentrations, and produced patchy areas of increased crypt depth throughout the SI. Succinylsulfathiazole increased crypt depth independently of diet. MDD or succinylsulfathiazole, alone or in combination, altered the gut microbiome, with decreased Bacteroidales and Clostridiales, increased Lactobacillales and Erysipelotrichaceae taxa, and decreased α-diversity indexes. Enteroids maintained in MDD media displayed dysmorphic crypt domains, altered expression of stem cell and secretory differentiation genes, and decreased DNA methylation of the glycosylation genes Beta-1,4-N-Acetyl-Galactosaminyltransferase-1 (B4galnt1) and Phosphoethanolamine/Phosphocholine-Phosphatase (Phospho1).<br><br>Conclusion: MDD impairs ponderal and linear growth in mice in association with dysmorphic SI crypts and reduced gut microbial diversity. In vitro methyl donor deficiency similarly induced dysmorphic crypts in mouse enteroids in conjunction with altered gene expression and DNA methylation.},
}
@article {pmid30643689,
year = {2019},
author = {Kirchoff, NS and Udell, MAR and Sharpton, TJ},
title = {The gut microbiome correlates with conspecific aggression in a small population of rescued dogs (Canis familiaris).},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e6103},
doi = {10.7717/peerj.6103},
pmid = {30643689},
issn = {2167-8359},
abstract = {Aggression is a serious behavioral disorder in domestic dogs that endangers both dogs and humans. The underlying causes of canine aggression are poorly resolved and require illumination to ensure effective therapy. Recent research links the compositional diversity of the gut microbiome to behavioral and psychological regulation in other mammals, such as mice and humans. Given these observations, we hypothesized that the composition of the canine gut microbiome could associate with aggression. We analyzed fecal microbiome samples collected from a small population of pit bull type dogs seized from a dogfighting organization. This population included 21 dogs that displayed conspecific aggressive behaviors and 10 that did not. Beta-diversity analyses support an association between gut microbiome structure and dog aggression. Additionally, we used a phylogenetic approach to resolve specific clades of gut bacteria that stratify aggressive and non-aggressive dogs, including clades within Lactobacillus, Dorea, Blautia, Turicibacter, and Bacteroides. Several of these taxa have been implicated in modulating mammalian behavior as well as gastrointestinal disease states. Although sample size limits this study, our findings indicate that gut microorganisms are linked to dog aggression and point to an aggression-associated physiological state that interacts with the gut microbiome. These results also indicate that the gut microbiome may be useful for diagnosing aggressive behaviors prior to their manifestation and potentially discerning cryptic etiologies of aggression.},
}
@article {pmid30643680,
year = {2019},
author = {Duguma, D and Hall, MW and Smartt, CT and Debboun, M and Neufeld, JD},
title = {Microbiota variations in Culex nigripalpus disease vector mosquito of West Nile virus and Saint Louis Encephalitis from different geographic origins.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6168},
doi = {10.7717/peerj.6168},
pmid = {30643680},
issn = {2167-8359},
abstract = {Although mosquito microbiota are known to influence reproduction, nutrition, disease transmission, and pesticide resistance, the relationship between host-associated microbial community composition and geographical location is poorly understood. To begin addressing this knowledge gap, we characterized microbiota associated with adult females of Culex nigripalpus mosquito vectors of Saint Louis Encephalitis and West Nile viruses sampled from three locations in Florida (Vero Beach, Palmetto Inland, and Palmetto Coast). High-throughput sequencing of PCR-amplified 16S rRNA genes demonstrated significant differences among microbial communities of mosquitoes sampled from the three locations. Mosquitoes from Vero Beach (east coast Florida) were dominated by uncultivated Asaia sp. (Alphaproteobacteria), whereas microbiota associated with mosquitoes collected from two mosquito populations at Palmetto (west coast Florida) sites were dominated by uncultured Spironema culicis (Spirochaetes), Salinisphaera hydrothermalis (Gammaproteobacteria), Spiroplasma (Mollicutes), uncultured Enterobacteriaceae, Candidatus Megaira (Alphaproteobacteria; Rickettsiae), and Zymobacter (Gammaproteobacteria). The variation in taxonomic profiles of Cx. nigripalpus gut microbial communities, especially with respect to dominating taxa, is a potentially critical factor in understanding disease transmission and mosquito susceptibility to insecticides among different mosquito populations.},
}
@article {pmid30643213,
year = {2019},
author = {Ronda, C and Chen, SP and Cabral, V and Yaung, SJ and Wang, HH},
title = {Metagenomic engineering of the mammalian gut microbiome in situ.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-018-0301-y},
pmid = {30643213},
issn = {1548-7105},
abstract = {Engineering of microbial communities in open environments remains challenging. Here we describe a platform used to identify and modify genetically tractable mammalian microbiota by engineering community-wide horizontal gene transfer events in situ. With this approach, we demonstrate that diverse taxa in the mouse gut microbiome can be modified directly with a desired genetic payload. In situ microbiome engineering in living animals allows novel capabilities to be introduced into established communities in their native milieu.},
}
@article {pmid30642603,
year = {2019},
author = {Chermprapai, S and Ederveen, THA and Broere, F and Broens, EM and Schlotter, YM and van Schalkwijk, S and Boekhorst, J and van Hijum, SAFT and Rutten, VPMG},
title = {The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study.},
journal = {Veterinary microbiology},
volume = {229},
number = {},
pages = {90-99},
doi = {10.1016/j.vetmic.2018.12.022},
pmid = {30642603},
issn = {1873-2542},
abstract = {Canine atopic dermatitis is a genetically predisposed inflammatory and pruritic allergic skin disease that is often complicated by (secondary) bacterial and fungal (yeast) infections. High-throughput DNA sequencing was used to characterize the composition of the microbiome (bacteria and fungi) inhabiting specific sites of skin in healthy dogs and dogs with atopic dermatitis (AD) before and after topical antimicrobial treatment. Skin microbiome samples were collected from six healthy control dogs and three dogs spontaneously affected by AD by swabbing at (non-) predilection sites before, during and after treatment. Bacteria and fungi were profiled by Illumina sequencing of the 16S ribosomal RNA gene of bacteria (16S) and the internally transcribed spacer of the ribosomal gene cassette in fungi (ITS). The total cohort of dogs showed a high diversity of microbes on skin with a strong individual variability of both 16S and ITS profiles. The genera of Staphylococcus and Porphyromonas were dominantly present both on atopic and healthy skin and across all skin sites studied. In addition, bacterial and fungal alpha diversity were similar at the different skin sites. The topical antimicrobial treatment increased the diversity of bacterial and fungal compositions in course of time on both AD and healthy skin.},
}
@article {pmid30642560,
year = {2019},
author = {de Nonneville, A},
title = {[Gut microbiome influences efficacy of immunotherapy].},
journal = {Bulletin du cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bulcan.2018.12.004},
pmid = {30642560},
issn = {1769-6917},
}
@article {pmid30642394,
year = {2019},
author = {Hitschfeld, M and Tovar, E and Gupta, S and Bik, EM and Palmer, C and Hoaglin, MC and Almonacid, DE and Richman, J and Apte, ZS},
title = {The role of a sequencing-based clinical intestinal screening test in patients at high-risk for Clostridium difficile and other pathogens: a case report.},
journal = {Journal of medical case reports},
volume = {13},
number = {1},
pages = {9},
doi = {10.1186/s13256-018-1919-1},
pmid = {30642394},
issn = {1752-1947},
abstract = {BACKGROUND: Hospitalization and antibiotic treatment can put patients at high risk for Clostridium difficile infection, where a disturbance of the gut microbiome allows for Clostridium difficile proliferation and associated symptoms, including mild, moderate, or severe diarrhea. Clostridium difficile infection is challenging to treat, often recurrent, and leads to almost 30,000 annual deaths in the USA alone. Here we present a case where SmartGut™, an at-home, self-administered sequencing-based clinical intestinal screening test, was used to identify the presence of Clostridium difficile in a patient with worsening diarrhea. Identification of this pathogen and subsequent treatment led to a significant improvement in symptoms.<br><br>CASE PRESENTATION: The patient is a 29-year-old white woman with a history of severe irritable bowel syndrome with diarrhea, hemorrhoidectomy, and anal sphincterotomy complicated by a perianal fistula and perirectal abscesses that required extended courses of broad-spectrum antibiotics. In June 2016, she developed intermittent Clostridium difficile infections, which required continued antibiotic use. Months later she used an at-home, self-administered, intestinal microbial test, the first of which was negative for the presence of Clostridium difficile, but it detected the relative abundance of microbes associated with irritable bowel syndrome outside the healthy reference ranges. In the subsequent 2 months after the negative Clostridium difficile result, her gastrointestinal symptoms worsened dramatically. A second microbiome test resulted in a positive Clostridium difficile finding and continued abnormal microbial parameters, which led the treating physician to refer her to a gastroenterologist. Additional testing confirmed the presence of Clostridium difficile with a toxin-positive strain. She received treatment immediately and her gastrointestinal symptoms improved significantly over the next week.<br><br>CONCLUSIONS: This case report suggests that more frequent DNA testing for Clostridium difficile infections may be indicated in patients that are at high-risk for Clostridium difficile infection, especially for patients with irritable bowel syndrome, and those who undergo gastrointestinal surgery and/or an extended antibiotic treatment. This report also shows that such testing could be effectively performed using at-home, self-administered sequencing-based clinical intestinal microbial screening tests. Further research is needed to investigate whether the observations reported here extrapolate to a larger cohort of patients.},
}
@article {pmid30642389,
year = {2019},
author = {Li, F and Hitch, TCA and Chen, Y and Creevey, CJ and Guan, LL},
title = {Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {6},
doi = {10.1186/s40168-019-0618-5},
pmid = {30642389},
issn = {2049-2618},
support = {BB/E/W/10964A01 and BBS/OS/GC/000011B//BBSRC/ ; 2013R029R//Alberta Livestock and Meat Agency/ ; 2015P008R//Alberta Livestock and Meat Agency/ ; Discovery//Natural Sciences and Engineering Research Council of Canada/ ; Doctoral Scholarship//Alberta Innovates - Technology Futures/ ; Scholarship//GPLER/ ; },
abstract = {BACKGROUND: Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.<br><br>RESULTS: Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.<br><br>CONCLUSIONS: Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.},
}
@article {pmid30642327,
year = {2019},
author = {Hurley, E and Barrett, MPJ and Kinirons, M and Whelton, H and Ryan, CA and Stanton, C and Harris, HMB and O'Toole, PW},
title = {Comparison of the salivary and dentinal microbiome of children with severe-early childhood caries to the salivary microbiome of caries-free children.},
journal = {BMC oral health},
volume = {19},
number = {1},
pages = {13},
doi = {10.1186/s12903-018-0693-1},
pmid = {30642327},
issn = {1472-6831},
abstract = {BACKGROUND: The main objectives of this study were to describe and compare the microbiota of 1) deep dentinal lesions of deciduous teeth of children affected with severe early childhood caries (S-ECC) and 2) the unstimulated saliva of these children and 3) the unstimulated saliva of caries-free children, and to compare microbiota compositional differences and diversity of taxa in these sampled sites.<br><br>METHODS: Children with S-ECC and without S-ECC were recruited. The saliva of all children with and without S-ECC was sampled along with the deep dentinal microbiota from children affected by S-ECC. The salivary microbiota of children affected by S-ECC (n = 68) was compared to that of caries-free children (n = 70), by Illumina MiSeq sequencing of 16S rRNA amplicons. Finally, the caries microbiota of deep dentinal lesions of those children with S-ECC was investigated.<br><br>RESULTS: Using two beta diversity metrics (Bray Curtis dissimilarity and UniFrac distance), the caries microbiota was found to be distinct from that of either of the saliva groups (caries-free &amp; caries-active) when bacterial abundance was taken into account. However, when the comparison was made by measuring only presence and absence of bacterial taxa, all three microbiota types separated. While the alpha diversity of the caries microbiota was lowest, the diversity difference between the caries samples and saliva samples was statistically significant (p < 0.001). The major phyla of the caries active dentinal microbiota were Firmicutes (median abundance value 33.5%) and Bacteroidetes (23.2%), with Neisseria (10.3%) being the most abundant genus, followed by Prevotella (10%). The caries-active salivary microbiota was dominated by Proteobacteria (median abundance value 38.2%) and Bacteroidetes (27.8%) with the most abundant genus being Neisseria (16.3%), followed by Porphyromonas (9.5%). Caries microbiota samples were characterized by high relative abundance of Streptococcus mutans, Prevotella spp., Bifidobacterium and Scardovia spp.<br><br>CONCLUSIONS: Distinct differences between the caries microbiota and saliva microbiota were identified, with separation of both salivary groups (caries-active and caries-free) whereby rare taxa were highlighted. While the caries microbiota was less diverse than the salivary microbiota, the presence of these rare taxa could be the difference between health and disease in these children.},
}
@article {pmid30642207,
year = {2019},
author = {Emerson, D},
title = {The role of iron-oxidizing bacteria in biocorrosion: a review.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/08927014.2018.1526281},
pmid = {30642207},
issn = {1029-2454},
abstract = {Lithotrophic iron-oxidizing bacteria depend on reduced iron, Fe(II), as their primary energy source, making them natural candidates for growing in association with steel infrastructure and potentially contributing to microbially influenced corrosion (MIC). This review summarizes recent work on the role of iron-oxidizing bacteria (FeOB) in MIC. By virtue of producing complex 3-dimensional biofilms that result from the accumulation of iron-oxides, FeOB may aid in the colonization of steel surfaces by other microbes involved in MIC. Evidence points to a successional pattern occurring whereby FeOB are early colonizers of mild steel (MS), followed by sulfate-reducing bacteria and other microbes, although studies of aged corrosion products indicate that FeOB do establish a long-term presence. There is evidence that only specific clades of FeOB, with unique adaptations for growing on steel surfaces are part of the MIC community. These are discussed in the context of the larger MIC microbiome.},
}
@article {pmid30642052,
year = {2019},
author = {Niccolai, E and Boem, F and Russo, E and Amedei, A},
title = {The Gut⁻Brain Axis in the Neuropsychological Disease Model of Obesity: A Classical Movie Revised by the Emerging Director &quot;Microbiome&quot;.},
journal = {Nutrients},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/nu11010156},
pmid = {30642052},
issn = {2072-6643},
support = {Prot. n°2018.005//Fondazione Cassa di Risparmio Pistoia e Pescia/ ; Programma Attuativo Regionale Toscana funded by FAS - MICpROBIMM//Regione Toscana/ ; },
abstract = {The worldwide epidemic of obesity has become an important public health issue, with serious psychological and social consequences. Obesity is a multifactorial disorder in which various elements (genetic, host, and environment), play a definite role, even if none of them satisfactorily explains its etiology. A number of neurological comorbidities, such as anxiety and depression, charges the global obesity burden, and evidence suggests the hypothesis that the brain could be the seat of the initial malfunction leading to obesity. The gut microbiome plays an important role in energy homeostasis regulating energy harvesting, fat deposition, as well as feeding behavior and appetite. Dietary patterns, like the Western diet, are known to be a major cause of the obesity epidemic, probably promoting a dysbiotic drift in the gut microbiota. Moreover, the existence of a &quot;gut⁻brain axis&quot; suggests a role for microbiome on hosts' behavior according to different modalities, including interaction through the nervous system, and mutual crosstalk with the immune and the endocrine systems. In the perspective of obesity as a real neuropsychological disease and in light of the discussed considerations, this review focuses on the microbiome role as an emerging director in the development of obesity.},
}
@article {pmid30642013,
year = {2019},
author = {Gianchecchi, E and Fierabracci, A},
title = {Recent Advances on Microbiota Involvement in the Pathogenesis of Autoimmunity.},
journal = {International journal of molecular sciences},
volume = {20},
number = {2},
pages = {},
doi = {10.3390/ijms20020283},
pmid = {30642013},
issn = {1422-0067},
support = {Ricerca Corrente 201802P004265//Ministero della Salute/ ; },
abstract = {Autoimmune disorders derive from genetic, stochastic, and environmental factors that all together interact in genetically predisposed individuals. The impact of an imbalanced gut microbiome in the pathogenesis of autoimmunity has been suggested by an increasing amount of experimental evidence, both in animal models and humans. Several physiological mechanisms, including the establishment of immune homeostasis, are influenced by commensal microbiota in the gut. An altered microbiota composition produces effects in the gut immune system, including defective tolerance to food antigens, intestinal inflammation, and enhanced gut permeability. In particular, early findings reported differences in the intestinal microbiome of subjects affected by several autoimmune conditions, including prediabetes or overt disease compared to healthy individuals. The present review focuses on microbiota-host homeostasis, its alterations, factors that influence its composition, and putative involvement in the development of autoimmune disorders. In the light of the existing literature, future studies are necessary to clarify the role played by microbiota modifications in the processes that cause enhanced gut permeability and molecular mechanisms responsible for autoimmunity onset.},
}
@article {pmid30641975,
year = {2019},
author = {Bowyer, RCE and Jackson, MA and Le Roy, CI and Ni Lochlainn, M and Spector, TD and Dowd, JB and Steves, CJ},
title = {Socioeconomic Status and the Gut Microbiome: A TwinsUK Cohort Study.},
journal = {Microorganisms},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/microorganisms7010017},
pmid = {30641975},
issn = {2076-2607},
support = {WT081878MA//Wellcome Trust/United Kingdom ; R21 AI21784-01//National Institutes of Health/ ; },
abstract = {Socioeconomic inequalities in health and mortality are well established, but the biological mechanisms underlying these associations are less understood. In parallel, the gut microbiome is emerging as a potentially important determinant of human health, but little is known about its broader environmental and social determinants. We test the association between gut microbiota composition and individual- and area-level socioeconomic factors in a well-characterized twin cohort. In this study, 1672 healthy volunteers from twin registry TwinsUK had data available for at least one socioeconomic measure, existing fecal 16S rRNA microbiota data, and all considered co-variables. Associations with socioeconomic status (SES) were robust to adjustment for known health correlates of the microbiome; conversely, these health-microbiome associations partially attenuated with adjustment for SES. Twins discordant for IMD (Index of Multiple Deprivation) were shown to significantly differ by measures of compositional dissimilarity, with suggestion the greater the difference in twin pair IMD, the greater the dissimilarity of their microbiota. Future research should explore how SES might influence the composition of the gut microbiota and its potential role as a mediator of differences associated with SES.},
}
@article {pmid30641967,
year = {2019},
author = {Yoon, WJ and Kim, HN and Park, E and Ryu, S and Chang, Y and Shin, H and Kim, HL and Yi, SY},
title = {The Impact of Cholecystectomy on the Gut Microbiota: A Case-Control Study.},
journal = {Journal of clinical medicine},
volume = {8},
number = {1},
pages = {},
doi = {10.3390/jcm8010079},
pmid = {30641967},
issn = {2077-0383},
support = {NRF-2018R1D1A1B07-050067//National Research Foundation of Korea/ ; 2-2018-0257-001-1//Pharmbio Korea Co., Ltd./ ; },
abstract = {Cholecystectomy alters the bile flow into the intestine and the enterohepatic circulation of the bile acids; this may affect the gut microbiota. We assessed the gut microbiota composition of patients who had undergone cholecystectomy and compared with those who had not. From a cohort of 1463 adult participants who underwent comprehensive health screening examinations, 27 subjects who had undergone cholecystectomy (cholecystectomy group) and 81 age- and sex-matched subjects who had not (control group) were selected. Clinical parameters were collected and compared. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from fecal samples. We evaluated differences in the overall microbial composition and in the abundance of taxa. The two groups were comparable with respect to clinical characteristics and laboratory results. The actual number of taxa observed in a sample (observed features) was significantly lower in the cholecystectomy group than in the control group (p = 0.042). The beta diversity of Jaccard distance index was significantly different between the two groups (p = 0.027). Blautia obeum and Veillonella parvula were more abundant in the cholecystectomy group. The difference in the diversity of the gut microbiota between the cholecystectomy and control groups was subtle. However, B. obeum and V. parvula, which have azoreductase activity, were more abundant in the cholecystectomy group. The impact of such changes in the gut microbiota on health remains to be determined.},
}
@article {pmid30641869,
year = {2019},
author = {Torcia, MG},
title = {Interplay among Vaginal Microbiome, Immune Response and Sexually Transmitted Viral Infections.},
journal = {International journal of molecular sciences},
volume = {20},
number = {2},
pages = {},
doi = {10.3390/ijms20020266},
pmid = {30641869},
issn = {1422-0067},
support = {62042012//Regione Toscana/ ; -//Istituto Toscano Tumori/ ; -//Ente Cassa di Risparmio di Firenze/ ; },
abstract = {The vaginal ecosystem is important for women's health and for a successful reproductive life, and an optimal host-microbial interaction is required for the maintenance of eubiosis. The vaginal microbiota is dominated by Lactobacillus species in the majority of women. Loss of Lactobacillus dominance promotes the colonization by anaerobic bacterial species with an increase in microbial diversity. Vaginal dysbiosis is a very frequent condition which affects the immune homeostasis, inducing a rupture in the epithelial barrier and favoring infection by sexually transmitted pathogens. In this review, we describe the known interactions among immune cells and microbial commensals which govern health or disease status. Particular attention is given to microbiota compositions which, through interplay with immune cells, facilitate the establishment of viral infections, such as Human Immunodeficiency Virus (HIV), Human Papilloma Virus (HPV), Herpes Simplex Virus 2 (HSV2).},
}
@article {pmid30640865,
year = {2018},
author = {Schnapp, Z and Hartman, C and Livnat, G and Shteinberg, M and Elenberg, Y},
title = {Decreased Fecal Calprotectin Levels in Cystic Fibrosis Patients After Antibiotic Treatment for Respiratory Exacerbation.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPG.0000000000002197},
pmid = {30640865},
issn = {1536-4801},
abstract = {OBJECTIVES: In all patients with cystic fibrosis (CF), gastrointestinal (GI) tract cystic fibrosis transmembrane conductance regulator (CFTR) dysfunction occurs early in life. .The identical pathophysiological triad of obstruction, infection and inflammation causes disease of the airways and in the intestinal tract (CF enteropathy). Mucus accumulation within GI tract is a niche for abnormal microbial colonization, leading to dysbiosis. Fecal calprotectin (FC) is a neutrophil cytosolic protein released during apoptosis and necrosis and reflects inflammatory status. Systemic antibiotic treatment for pulmonary exacerbations has been shown to improve systemic inflammatory markers as well as serum and sputum calprotectin. Antibiotic treatment aimed at pulmonary complaints may improve GI tract inflammatory status. We hypothesized that high levels of fecal calprotectin present during pulmonary exacerbation are due, in part, to multi-organ dysbiosis and thus should diminish with systemic antibiotic treatment.<br><br>METHODS: This prospective pilot study enrolled 14 patients with CF, with no current GI symptoms. FC levels and lung function were measured at the beginning and end of systemic antibiotic treatment.<br><br>RESULTS: Compared to pre-antibiotic treatment baseline values, end of treatment FC levels declined significantly after antibiotic treatment, P = 0.004 and similarly, there was significant improvement in FEV1.0, P = 0.002.<br><br>CONCLUSIONS: High levels of FC during respiratory exacerbation may reflect a systemic exacerbation rather than solely pulmonary. Antibiotic treatment lowered the FC levels possibly by its impact on the intestinal microbiome.},
}
@article {pmid30640740,
year = {2019},
author = {Polsinelli, VB and Marteau, L and Shah, SJ},
title = {The role of splanchnic congestion and the intestinal microenvironment in the pathogenesis of advanced heart failure.},
journal = {Current opinion in supportive and palliative care},
volume = {},
number = {},
pages = {},
doi = {10.1097/SPC.0000000000000414},
pmid = {30640740},
issn = {1751-4266},
abstract = {PURPOSE OF REVIEW: Right-sided heart failure, which is often present in the setting of advanced heart failure, is associated with cardiac cachexia, the cardiorenal syndrome, and adverse outcomes. Improved understanding of venous congestion of the splanchnic circulation, which may play a key role in the pathogenesis of right-sided heart failure, could lead to novel therapeutics to ameliorate heart failure. Here we provide an overview of right-sided heart failure, splanchnic hemodynamics, fluid homeostasis, and the intestinal microenvironment. We review recent literature to describe pathophysiologic mechanisms and possible therapeutics.<br><br>RECENT FINDINGS: Several possible mechanisms centered around upregulation of sodium-hydrogen exchanger-3 (NHE3) may form a causal link between right ventricular dysfunction, splanchnic congestion, and worsening heart failure. These include an anaerobic environment in enterocytes, resulting in reduced intracellular pH; increased sodium absorption by the gut via NHE3; decreased pH at the intestinal brush border thus altering the gut microbiome profile; increased bacterial synthesis of trimethylamine N-oxide; and decreased bacterial synthesis of short-chain fatty acids causing abnormal intestinal barrier function.<br><br>SUMMARY: Splanchnic congestion in the setting of right-sided heart failure may serve an important role in the pathogenesis of advanced heart failure, and further exploration of these mechanisms may lead to new therapeutic advances.},
}
@article {pmid30640680,
year = {2019},
author = {Chao, XP and Sun, TT and Wang, S and Fan, QB and Shi, HH and Zhu, L and Lang, JH},
title = {Correlation between the diversity of vaginal microbiota and the risk of high-risk human papillomavirus infection.},
journal = {International journal of gynecological cancer : official journal of the International Gynecological Cancer Society},
volume = {29},
number = {1},
pages = {28-34},
doi = {10.1136/ijgc-2018-000032},
pmid = {30640680},
issn = {1525-1438},
abstract = {OBJECTIVES: Since other genital infections enhance HIV susceptibility by inducing inflammation and evidence suggests that the vaginal microbiome plays a functional role in the persistence or regression of high-risk human papillomavirus (HPV) infections, we investigated the relationship between the composition of the vaginal microbiota and the risk of high-risk HPV infection.<br><br>METHODS: The study included 151 healthy women (65 HPV-positive and 86 HPV-negative) aged 20-65 at enrollment. Total genome DNA from samples was extracted using the hexadecyltrimethylammonium bromide (CTAB) CTAB method. The vaginal microbiota composition was determined by sequencing barcoded 16S rDNA gene fragments (V4) on Illumina HiSeq2500.<br><br>RESULTS: Of the 30 most abundant bacteria at the genus level, we found only six bacteria with a statistical difference between HPV-positive and HPV-negative women: Bacteroides, Acinetobacter, Faecalibacterium, Streptococcus, Finegoldia, and Moryella. Lactobacillus was the predominant genus and was detected in all women, but there was no significant difference between the two groups for L. iners, L. jensenii, and L. gasseri. Furthermore, we found 26 types of bacteria with a statistical difference at the species level between the two groups. Anaerobic bacteria such as Bacteroides plebeius, Acinetobacter lwoffii, and Prevotella buccae were found significantly more frequently in HPV-positive women, which is the most important finding of our study.<br><br>CONCLUSION: Our findings suggest a possible role for the composition of the vaginal microbiota as a modifier of high-risk HPV infection, and specific microbiota species may serve as sensors for changes in the cervical microenvironment associated with high-risk HPV infection. The exact molecular mechanism of the vaginal microbiota in the course of high-risk HPV infection and cervical neoplasia should be further explored. Future research should include intervention in the composition of the vaginal microbiota to reverse the course of high-risk HPV infection and the natural history of cervical neoplasia.},
}
@article {pmid30640553,
year = {2019},
author = {Ozkan, J and Willcox, MD},
title = {The Ocular Microbiome: Molecular Characterization of a Unique and Low Microbial Environment.},
journal = {Current eye research},
volume = {},
number = {},
pages = {},
doi = {10.1080/02713683.2019.1570526},
pmid = {30640553},
issn = {1460-2202},
abstract = {The ocular surface is continually exposed to bacteria from the environment and traditional culture-based microbiological studies have isolated a low diversity of microorganisms from this region. The use of culture-independent methods to define the ocular microbiome, primarily involving 16S ribosomal RNA gene sequencing, has shown that the microbial communities present on the ocular surface have a greater diversity than previously reported and appear to have an immune modulating function. These molecular techniques have been used to investigate the effect of contact lens wear and disease on the microbiota of the ocular surface and eyelids and these studies have consistently identified bacteria not previously identified in normal eyes. Recent studies also suggest a role of the ocular and non-ocular microbiome in retinal disease including age-related macular degeneration, glaucoma, uveitis and diabetic retinopathy. However, issues remain regarding the impact of contamination in these culture-independent sequencing techniques, particularly when investigating low microbial biomass samples from the eye. Ocular microbiome studies need to recognise the potential for contamination to impact findings and carefully control each stage of the experimental procedure and to utilise statistical methods to identify contamination signals.},
}
@article {pmid30639436,
year = {2019},
author = {Leung, DYM},
title = {The Microbiome and Allergic Diseases: A struggle between good and bad microbes.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2019.01.003},
pmid = {30639436},
issn = {1534-4436},
}
@article {pmid30639376,
year = {2019},
author = {Ferreira Felizardo, RJ and Mizuno Watanabe, IK and Dardi, P and Venturini Rossoni, L and Olsen Saraiva Câmara, N},
title = {The interplay among gut microbiota, hypertension and kidney diseases: the role of short-chain fatty acids.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.phrs.2019.01.019},
pmid = {30639376},
issn = {1096-1186},
abstract = {The bacteria community living in the gut maintains a symbiotic relationship with the host and its unbalance has been associated with progression of a wide range of intestinal and extra intestinal conditions. Hypertension and chronic kidney disease (CKD) are closely associated diseases with high incidence rates all over the world. Increasing data have supported the involvement of gut microbiome in the blood pressure regulation and the impairment of CKD prognosis. In hypertension, the reduced number of short-chain fatty acids (SCFAs) producing bacteria is associated with modifications in gut environment, involving reduction of the hypoxic gut profile and worsening of the microbial balance, leading to a loss of epithelial barrier integrity, development of gut inflammation and the reduction of SCFAs plasma levels. Those modifications compromise the blood pressure regulation and, as a consequence, favor the end organ damage, also affecting the kidneys. In CKD, impaired renal function leads to accumulation of high levels of uremic toxins that reach the intestine and cause alterations in bacteria composition and fecal metabolite profile, inducing a positive feedback that allows translocation of endotoxins into the bloodstream, which enhances local kidney inflammation and exacerbate kidney injury, compromising even more CKD prognosis. In line with these data, the use of prebiotics, probiotics and fecal microbiota transplantation are becoming efficient therapies to improve the gut dysbiosis aiming hypertension and CKD treatment. This review describes how changes in gut microbiota composition can affect the development of hypertension and the progression of kidney diseases, highlighting the importance of the gut microbial composition uncovering to improve human health maintenance and, especially, for the development of new alternative therapies.},
}
@article {pmid30639346,
year = {2019},
author = {Davidson, WF and Leung, DYM and Beck, LA and Berin, CM and Boguniewicz, M and Busse, WW and Chatila, TA and Geha, RS and Gern, JE and Guttman-Yassky, E and Irvine, AD and Kim, BS and Kong, HH and Lack, G and Nadeau, KC and Schwaninger, J and Simpson, A and Simpson, EL and Spergel, JM and Togias, A and Wahn, U and Wood, RA and Woodfolk, JA and Ziegler, SF and Plaut, M},
title = {Report from the National Institute of Allergy and Infectious Diseases Workshop on &quot;Atopic Dermatitis and the Atopic March: Mechanisms and Interventions&quot;.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2019.01.003},
pmid = {30639346},
issn = {1097-6825},
abstract = {Atopic dermatitis (AD) affects up to 20% of children world-wide and is an increasing public health problem particularly in developed countries. Although AD in infants and young children can resolve, there is a well-recognized, increased risk of sequential progression from AD to other atopic diseases including food allergy, allergic rhinitis, allergic asthma and allergic rhinoconjunctivitis; a process referred to as the &quot;atopic march&quot;. The mechanisms underlying the development of AD and subsequent progression to other atopic comorbidities, particularly food allergy, are incompletely understood and the subject of intense investigation. Other major research objectives are the development of effective strategies to prevent AD and food allergy as well as therapeutic interventions to inhibit the atopic march. In 2017, the Division of Allergy, Immunology and Transplantation of the National Institute of Allergy and Infectious Diseases sponsored a workshop to discuss current understanding and important advances in these research areas and to identify gaps in knowledge and future research directions. International and national experts in the field were joined by representatives from several National Institutes of Health institutes. Summaries of workshop presentations, key conclusions and recommendations are presented herein.},
}
@article {pmid30638679,
year = {2018},
author = {Langan, D and Kim, EY and Moudgil, KD},
title = {Modulation of autoimmune arthritis by environmental 'hygiene' and commensal microbiota.},
journal = {Cellular immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cellimm.2018.12.005},
pmid = {30638679},
issn = {1090-2163},
abstract = {Observations in patients with autoimmune diseases and studies in animal models of autoimmunity have revealed that external environmental factors including exposure to microbes and the state of the host gut microbiota can influence susceptibility to autoimmunity and subsequent disease development. Mechanisms underlying these outcomes continue to be elucidated. These include deviation of the cytokine response and imbalance between pathogenic versus regulatory T cell subsets. Furthermore, specific commensal organisms are associated with enhanced severity of arthritis in susceptible individuals, while exposure to certain microbes or helminths can afford protection against this disease. In addition, the role of metabolites (e.g., short-chain fatty acids, tryptophan catabolites), produced either by the microbes themselves or from their action on dietary products, in modulation of arthritis is increasingly being realized. In this context, re-setting of the microbial dysbiosis in RA using prebiotics, probiotics, or fecal microbial transplant is emerging as a promising approach for the prevention and treatment of arthritis. It is hoped that advances in defining the interplay between gut microbiota, dietary products, and bioactive metabolites would help in the development of therapeutic regimen customized for the needs of individual patients in the near future.},
}
@article {pmid30638398,
year = {2019},
author = {Kara, SS and Volkan, B and Erten, I},
title = {Lactobacillus rhamnosus GG can protect malnourished children.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-8},
doi = {10.3920/BM2018.0071},
pmid = {30638398},
issn = {1876-2891},
abstract = {Malnutrition affects virtually all organ systems, and malnourished children are more prone to infections. These children have dysbiosis, but probiotics can restore the disrupted gut microbiome. We investigated the protective effects of Lactobacillus rhamnosus GG in malnourished children in terms of incidence of infection, and anthropometric and metabolic parameters. 50 intervention and 50 control patients, aged 6 months to 5 years, with body weight and height below -2 SD, were randomly and prospectively recruited. The controls received a calorie and protein-appropriate diet for 3 months, while the study group additionally received approximately 109 L. rhamnosus GG for 3 months. Infection episodes and nutritional status were compared between the groups. 38 intervention, 33 control patients completed the study and the two groups were similar at baseline. The study group had fewer upper respiratory tract infections and gastroenteritis episodes at each month and at the end of the study. Children in the study group experienced fewer total upper respiratory infections and urinary tract infections. Hospitalisation was more frequent in the control group during the third month and at the end of the study. Total infection numbers were higher in the control group at each month and at the end of the study (P<0.001 for each). Increments in body mass index (BMI) and BMI Z-scores were more pronounced in the study group (P=0.008 and P=0.02, respectively). Daily prophylactic use of L. rhamnosus GG at 109 bacteria in malnourished children prevents most infections and improves nutritional status when used together with appropriate diet.},
}
@article {pmid30637962,
year = {2019},
author = {Asante, J and Osei Sekyere, J},
title = {Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12735},
pmid = {30637962},
issn = {1758-2229},
abstract = {Our inability to cultivate most micro-organisms, specifically bacteria, in the laboratory has for many years restricted our view and understanding of the bacterial meta-resistome in all living and non-living environments. As a result, reservoirs, sources, and distribution of antibiotic resistance genes (ARGS) and antibiotic-producers, as well as the effects of human activity and antibiotics on the selection and dissemination of ARGs were not well comprehended. With the advances made in the fields of metagenomics and metatranscriptomics, many of the hitherto little-understood concepts are becoming clearer. Further, the discovery of antibiotics such as lugdinin and lactocillin from the human microbiota, buttressed the importance of these new fields. Metagenomics and metatranscriptomics are becoming important clinical diagnostic tools for screening and detecting pathogens and ARGs, assessing the effects of antibiotics, other xenobiotics, and human activity on the environment, characterizing the microbiome and the environmental resistome with lesser turnaround time and decreasing cost, as well as discovering antibiotic-producers. However, challenges with accurate binning, skewed ARGs databases, detection of less abundant and allelic variants of ARGs, and efficient mobilome characterization remain. Ongoing efforts in long-read, phased- and single-cell sequencing, strain-resolved binning, chromosomal-conformation capture, DNA-methylation binning, and deep-learning bioinformatic approaches offer promising prospects in reconstructing complete strain-level genomes and mobilomes from metagenomes. This article is protected by copyright. All rights reserved.},
}
@article {pmid30637938,
year = {2019},
author = {Gotoh, A and Ojima, MN and Katayama, T},
title = {Minority species influences microbiota formation: the role of Bifidobacterium with extracellular glycosidases in bifidus flora formation in breastfed infant guts.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.13366},
pmid = {30637938},
issn = {1751-7915},
support = {17J08530//JSPS Research Fellows/ ; 15H04481 and 17K19231//JSPS-KAKENHI/ ; //Institute for Fermentation/ ; },
abstract = {The human body houses a variety of microbial ecosystems, such as the microbiotas on the skin, in the oral cavity and in the digestive tract. The gut microbiota is one such ecosystem that contains trillions of bacteria, and it is well established that it can significantly influence host health and diseases. With the advancement in bioinformatics tools, numerous comparative studies based on 16S ribosomal RNA (rRNA) gene sequences, metabolomics, pathological and epidemical analyses have revealed the correlative relationship between the abundance of certain taxa and disease states or amount of certain causative bioactive compounds. However, the 16S rRNA-based taxonomic analyses using next-generation sequencing (NGS) technology essentially detect only the majority species. Although the entire gut microbiome consists of 1013 microbial cells, NGS read counts are given in multiples of 106 , making it difficult to determine the diversity of the entire microbiota. Some recent studies have reported instances where certain minority species play a critical role in creating locally stable conditions for other species by stabilizing the fundamental microbiota, despite their low abundance. These minority species act as 'keystone species', which is a species whose effect on the community is disproportionately large compared to its relative abundance. One of the attributes of keystone species within the gut microbiota is its extensive enzymatic capacity for substrates that are rare or difficult to degrade for other species, such as dietary fibres or host-derived complex glycans, like human milk oligosaccharides (HMOs). In this paper, we propose that more emphasis should be placed on minority taxa and their possible role as keystone species in gut microbiota studies by referring to our recent studies on HMO-mediated microbiota formation in the infant gut.},
}
@article {pmid30637341,
year = {2019},
author = {Blaustein, RA and McFarland, AG and Ben Maamar, S and Lopez, A and Castro-Wallace, S and Hartmann, EM},
title = {Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil.},
journal = {mSystems},
volume = {4},
number = {1},
pages = {},
doi = {10.1128/mSystems.00281-18},
pmid = {30637341},
issn = {2379-5077},
abstract = {Understanding underlying mechanisms involved in microbial persistence in the built environment (BE) is essential for strategically mitigating potential health risks. To test the hypothesis that BEs impose selective pressures resulting in characteristic adaptive responses, we performed a pangenomics meta-analysis leveraging 189 genomes (accessed from GenBank) of two epidemiologically important taxa, Bacillus cereus and Staphylococcus aureus, isolated from various origins: the International Space Station (ISS; a model BE), Earth-based BEs, soil, and humans. Our objectives were to (i) identify differences in the pangenomic composition of generalist and host-associated organisms, (ii) characterize genes and functions involved in BE-associated selection, and (iii) identify genomic signatures of ISS-derived strains of potential relevance for astronaut health. The pangenome of B. cereus was more expansive than that of S. aureus, which had a dominant core component. Genomic contents of both taxa significantly correlated with isolate origin, demonstrating an importance for biogeography and potential niche adaptations. ISS/BE-enriched functions were often involved in biosynthesis, catabolism, materials transport, metabolism, and stress response. Multiple origin-enriched functions also overlapped across taxa, suggesting conserved adaptive processes. We further characterized two mobile genetic elements with local neighborhood genes encoding biosynthesis and stress response functions that distinctively associated with B. cereus from the ISS. Although antibiotic resistance genes were present in ISS/BE isolates, they were also common in counterparts elsewhere. Overall, despite differences in microbial lifestyle, some functions appear common to remaining viable in the BE, and those functions are not typically associated with direct impacts on human health. IMPORTANCE The built environment contains a variety of microorganisms, some of which pose critical human health risks (e.g., hospital-acquired infection, antibiotic resistance dissemination). We uncovered a combination of complex biological functions that may play a role in bacterial survival under the presumed selective pressures in a model built environment-the International Space Station-by using an approach to compare pangenomes of bacterial strains from two clinically relevant species (B. cereus and S. aureus) isolated from both built environments and humans. Our findings suggest that the most crucial bacterial functions involved in this potential adaptive response are specific to bacterial lifestyle and do not appear to have direct impacts on human health.},
}
@article {pmid30637338,
year = {2018},
author = {Bai, Y and Tao, J and Zhou, J and Fan, Q and Liu, M and Hu, Y and Xu, Y and Zhang, L and Yuan, J and Li, W and Ze, X and Malard, P and Guo, Z and Yan, J and Li, M},
title = {Fucosylated Human Milk Oligosaccharides and N-Glycans in the Milk of Chinese Mothers Regulate the Gut Microbiome of Their Breast-Fed Infants during Different Lactation Stages.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00206-18},
pmid = {30637338},
issn = {2379-5077},
abstract = {The milk glycobiome has a significant impact on the gut microbiota of infants, which plays a pivotal role in health and development. Fucosylated human milk oligosaccharides (HMOs) and N-glycans on milk proteins are beneficial for the development of healthy gut microbiota, and the fucosylation levels of these glycans can be affected by the maternal fucosyltransferase 2 gene (FUT2). Here, we present results of longitudinal research on paired milk and stool samples from 56 Chinese mothers (CMs) and their breast-fed children. Changes of HMOs and fucosylated N-glycans in milk of CMs at different lactation stages were detected, which allowed characterization of the major differences in milk glycans and consequential effects on the gut microbiome of infants according to maternal FUT2 status. Significant differences in the abundance of total and fucosylated HMOs between secretor and nonsecretor CMs were noted, especially during early lactation. Despite a tendency toward decreasing milk protein concentrations, the fucosylation levels of milk N-glycans increased during late lactation. The changes in the levels of fucosylated HMOs and milk N-glycans were highly correlated with the growth of Bifidobacterium spp. and Lactobacillus spp. in the gut of infants during early and later lactation, respectively. Enriched expression of genes encoding glycoside hydrolases, glycosyl transferases, ATP-binding cassette (ABC) transporters, and permeases in infants fed by secretor CMs contributed to the promotion of these bacteria in infants. Our data highlight the important role of fucosylated milk glycans in shaping the gut microbiome of infants and provide a solid foundation for development of &quot;personalized&quot; nutrition for Chinese infants. IMPORTANCE Human milk glycans provide a broad range of carbon sources for gut microbes in infants. Levels of protein glycosylation in human milk vary during lactation and may also be affected by the stages of gestation and lactation and by the secretor status of the mother. This was the first study to evaluate systematically dynamic changes in human milk oligosaccharides and fucosylated N-glycans in the milk of Chinese mothers with different secretor statuses during 6 months of lactation. Given the unique single nucleotide polymorphism site (rs1047781, A385T) on the fucosyltransferase 2 gene among Chinese populations, our report provides a specific insight into the milk glycobiome of Chinese mothers, which may exert effects on the gut microbiota of infants that differ from findings from other study cohorts.},
}
@article {pmid30637337,
year = {2018},
author = {Bayer, K and Jahn, MT and Slaby, BM and Moitinho-Silva, L and Hentschel, U},
title = {Marine Sponges as Chloroflexi Hot Spots: Genomic Insights and High-Resolution Visualization of an Abundant and Diverse Symbiotic Clade.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00150-18},
pmid = {30637337},
issn = {2379-5077},
abstract = {Members of the widespread bacterial phylum Chloroflexi can dominate high-microbial-abundance (HMA) sponge microbiomes. In the Sponge Microbiome Project, Chloroflexi sequences amounted to 20 to 30% of the total microbiome of certain HMA sponge genera with the classes/clades SAR202, Caldilineae, and Anaerolineae being the most prominent. We performed metagenomic and single-cell genomic analyses to elucidate the functional gene repertoire of Chloroflexi symbionts of Aplysina aerophoba. Eighteen draft genomes were reconstructed and placed into phylogenetic context of which six were investigated in detail. Common genomic features of Chloroflexi sponge symbionts were related to central energy and carbon converting pathways, amino acid and fatty acid metabolism, and respiration. Clade-specific metabolic features included a massively expanded genomic repertoire for carbohydrate degradation in Anaerolineae and Caldilineae genomes, but only amino acid utilization by SAR202. While Anaerolineae and Caldilineae import cofactors and vitamins, SAR202 genomes harbor genes encoding components involved in cofactor biosynthesis. A number of features relevant to symbiosis were further identified, including CRISPR-Cas systems, eukaryote-like repeat proteins, and secondary metabolite gene clusters. Chloroflexi symbionts were visualized in the sponge extracellular matrix at ultrastructural resolution by the fluorescence in situ hybridization-correlative light and electron microscopy (FISH-CLEM) method. Carbohydrate degradation potential was reported previously for &quot;Candidatus Poribacteria&quot; and SAUL, typical symbionts of HMA sponges, and we propose here that HMA sponge symbionts collectively engage in degradation of dissolved organic matter, both labile and recalcitrant. Thus, sponge microbes may not only provide nutrients to the sponge host, but they may also contribute to dissolved organic matter (DOM) recycling and primary productivity in reef ecosystems via a pathway termed the sponge loop. IMPORTANCEChloroflexi represent a widespread, yet enigmatic bacterial phylum with few cultivated members. We used metagenomic and single-cell genomic approaches to characterize the functional gene repertoire of Chloroflexi symbionts in marine sponges. The results of this study suggest clade-specific metabolic specialization and that Chloroflexi symbionts have the genomic potential for dissolved organic matter (DOM) degradation from seawater. Considering the abundance and dominance of sponges in many benthic environments, we predict that the role of sponge symbionts in biogeochemical cycles is larger than previously thought.},
}
@article {pmid30636240,
year = {2018},
author = {Kamińska, E},
title = {[The role of emollients in atopic dermatitis in children].},
journal = {Developmental period medicine},
volume = {22},
number = {4},
pages = {396-403},
pmid = {30636240},
issn = {1428-345X},
abstract = {Atopic dermatitis is a chronic inflammatory disease characterized by recurrent flares, intense itching, erythema, dry skin resulting from skin barrier defects, and staphylococcal infections. Multiple factors may affect the skin`s normal barrier function, including filaggrin gene mutations, immune dysregulation, altered skin microbiome, altered lipids in stratum corneum, or deficiency of antimicrobial peptides AMPs. The disease mainly affects children, causing a considerable impact on the quality of their life; its first manifestations occur with up to 90% of cases before the age of 5. For years emollients have been known as oily substances used to treat rough, scaling, xerotic conditions to make skin flexible and soft. Recently, we have learned that emollients can also moisten and hydrate dry skin, so the terms &quot;emollient&quot; and &quot;moisturizer&quot; are often used interchangeably. According to current management guidelines on atopic dermatitis prepared by dermatological societies, long-term emollient application direct to the skin and as bath additives are the basic therapy of atopic dermatitis. Emollients may be used in monotherapy or - in the flares - in conjunction with topical corticosteroids or calcineurin inhibitors. Clinical trials proved that regular emollient application moistens and hydrates the skin and helps the skin maintain a defensive barrier effect as well as reduces the amount of topical corticosteroids needed for atopic eczema in infants, children and adult patients. The results of trials and long clinical experience proved that emollients are safe and effective in patients with atopic dermatitis. This paper presents information based on recent knowledge concerning emollients: an overview of emollient components, their properties, mechanism of action, and the role they play in atopic eczema, as well as the results of clinical trials performed in children with atopic dermatitis.},
}
@article {pmid30636005,
year = {2019},
author = {Untersmayr, E and Bax, HJ and Bergmann, C and Bianchini, R and Cozen, W and Gould, HJ and Hartmann, K and Josephs, DH and Levi-Schaffer, F and Penichet, ML and O'Mahony, L and Poli, A and Redegeld, F and Roth-Walter, F and Turner, MC and Vangelista, L and Karagiannis, SN and Jensen-Jarolim, E},
title = {AllergoOncology: microbiota in allergy and cancer - an EAACI position paper.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.13718},
pmid = {30636005},
issn = {1398-9995},
abstract = {The microbiota can play important roles in the development of human immunity and the establishment of immune homeostasis. Lifestyle factors including diet, hygiene, and exposure to viruses or bacteria, and medical interventions with antibiotics or anti-ulcer medications, regulate phylogenetic variability and the quality of cross-talk between innate and adaptive immune cells via mucosal and skin epithelia. More recently, microbiota and their composition have been linked to protective effects for health. Imbalance, however, has been linked to immune-related diseases such as allergy and cancer, characterized by impaired, or exaggerated immune tolerance, respectively. In this AllergoOncology position paper, we focus on the increasing evidence defining the microbiota composition as a key determinant of immunity and immune tolerance, linked to the risk for development of allergic and malignant diseases. We discuss novel insights into the role of microbiota in disease and patient responses to treatments in cancer and in allergy. These may highlight opportunities to improve patient outcomes with medical interventions supported through a restored microbiome. This article is protected by copyright. All rights reserved.},
}
@article {pmid30635612,
year = {2019},
author = {Pak, HH and Cummings, NE and Green, CL and Brinkman, JA and Yu, D and Tomasiewicz, JL and Yang, SE and Boyle, C and Konon, EN and Ong, IM and Lamming, DW},
title = {The Metabolic Response to a Low Amino Acid Diet is Independent of Diet-Induced Shifts in the Composition of the Gut Microbiome.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {67},
doi = {10.1038/s41598-018-37177-3},
pmid = {30635612},
issn = {2045-2322},
abstract = {Obesity and type 2 diabetes are increasing in prevalence around the world, and there is a clear need for new and effective strategies to promote metabolic health. A low protein (LP) diet improves metabolic health in both rodents and humans, but the mechanisms that underlie this effect remain unknown. The gut microbiome has recently emerged as a potent regulator of host metabolism and the response to diet. Here, we demonstrate that a LP diet significantly alters the taxonomic composition of the gut microbiome at the phylum level, altering the relative abundance of Actinobacteria, Bacteroidetes, and Firmicutes. Transcriptional profiling suggested that any impact of the microbiome on liver metabolism was likely independent of the microbiome-farnesoid X receptor (FXR) axis. We therefore tested the ability of a LP diet to improve metabolic health following antibiotic ablation of the gut microbiota. We found that a LP diet promotes leanness, increases energy expenditure, and improves glycemic control equally well in mice treated with antibiotics as in untreated control animals. Our results demonstrate that the beneficial effects of a LP diet on glucose homeostasis, energy balance, and body composition are unlikely to be mediated by diet-induced changes in the taxonomic composition of the gut microbiome.},
}
@article {pmid30635384,
year = {2019},
author = {Chen, YM and Chiang, YC and Tseng, TY and Wu, HY and Chen, YY and Wu, CH and Chiu, CH},
title = {Molecular and Functional Analysis of the Type IV Pilus Gene Cluster in Streptococcus sanguinis SK36.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02788-18},
pmid = {30635384},
issn = {1098-5336},
abstract = {Streptococcus sanguinis, dominant in the oral microbiome, is the only known streptococcal species possessing a pil gene cluster for the biosynthesis of type IV pili (Tfp). Although this cluster is commonly present in the genome of S. sanguinis, most of the strains do not express Tfp-mediated twitching motility. Thus, this study was designed to investigate the biological functions encoded by the cluster in the twitching-negative strain, S. sanguinis SK36. We found that the cluster was transcribed as an operon, with three promoters located 5' to the cluster, and one in the intergenic region between SSA_2307 and SSA_2305. Studies using promoter-cat fusion strains revealed that the transcription of the cluster was mainly driven by the distal 5' promoter, which is located more than 800 bases 5' to the first gene of the cluster, SSA_2318. Optimal expression of the cluster occurred at the early-stationary growth phase in a CcpA-dependent manner, although a CcpA-binding consensus is absent in the promoter region. Expression of the cluster resulted in a short hair-like surface structure under transmission electron microscopy. Deletion of the putative pilin genes (SSA_2313-2315) abolished the biosynthesis of this structure and significantly reduced the adherence of SK36 to HeLa and SCC-4 cells. Mutations in the pil genes down-regulated biofilm formation by S. sanguinis SK36. Taken together, the results demonstrate that Tfp of SK36 are important for host cell adherence, but not for motility, and that expression of the pil cluster is subject to complex regulation.IMPORTANCEThe proteins and assembly machinery of the type IV pili (Tfp) are conserved throughout bacteria and archaea, and yet, the function of this surface structure differs from species to species, and even strain to strain. As seen in Streptococcus sanguinis SK36, the expression of the Tfp gene cluster results in a hair-like surface structure that is much shorter than the typical Tfp. This pilus is essential for the adherence of SK36, but is not involved in motility. Being a member of the highly diverse dental biofilm, perhaps S. sanguinis could more effectively utilize this structure to adhere to host cells and to interact with other microbes within the same niche.},
}
@article {pmid30635376,
year = {2019},
author = {Feng, S and McLellan, SL},
title = {Highly specific sewage-derived Bacteroides qPCR assays target sewage polluted waters.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02696-18},
pmid = {30635376},
issn = {1098-5336},
abstract = {The identification of sewage contamination in water has primarily relied on detection of the human Bacteroides using markers within the V2 region of the 16S ribosomal RNA (rRNA) gene. Despite establishment of multiple assays that target the HF183 cluster (i.e., Bacteroides dorei) and other Bacteroides organisms (e.g., Bacteroides thetaiotomicron), the potential for more human-associated markers in this genus has not been explored in depth. We examined Bacteroides population structure in sewage and animal hosts across the V4V5 and V6 hypervariable regions. Using near full-length cloned sequences, we identified the sequences in the V4V5 and V6 hypervariable regions that are linked to the HF183 marker in V2 region and found these sequences were present in multiple animals. In addition, the V4V5 and V6 regions contained human fecal marker sequences for organisms that were independent of HF183 cluster. The most abundant Bacteroides in untreated sewage was not human associated but pipe derived. Two TaqMan qPCR assays were developed targeting the V4V5 and V6 regions of this organism. Validation studies using fecal samples from seven animal hosts (n=76) and uncontaminated water samples (n=30) demonstrated their high specificity for sewage. Freshwater Bacteroides were also identified in uncontaminated water samples, demonstrating that measures of total Bacteroides do not reflect fecal pollution. Comparison of two previously described human Bacteroides assays (HB and HF183/BacR287) in municipal wastewater influent and sewage contaminated urban water samples produced identical results, illustrating they target the same organism. Detection of sewage-derived Bacteroides provided an independent measure of sewage-impacted waters.IMPORTANCEBacteroides are major member of the gut microbiota and host-specific organisms within this genus have been used extensively to gain information on pollution sources. This study provides a broad view of the population structure of Bacteroides within sewage to contextualize the well-studied HF183 marker for a human-associated Bacteroides The study also delineates host-specific sequence patterns across multiple hypervariable regions of the 16S rRNA gene to improve our ability to use sequence data to assess water quality. Here, we demonstrate that regions downstream of the HF183 marker are non-specific, but other potential human-associated markers are present. Further, we show the most abundant Bacteroides in sewage is free-living, rather than host associated, and specifically found in sewage. Quantitative PCR assays that target organism specific to sewer pipes offer measures that are independent of the human microbiome for identifying sewage pollution in water.},
}
@article {pmid30634900,
year = {2019},
author = {Kromann, S and Hvidtfeldt, A and Boye, M and Sørensen, DB and Jørgensen, S and Nielsen, JP and Olsen, RH},
title = {In vitro synergy of sertraline and tetracycline cannot be reproduced in pigs orally challenged with a tetracycline resistant Escherichia coli.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {12},
doi = {10.1186/s12866-018-1383-5},
pmid = {30634900},
issn = {1471-2180},
support = {4184-00512//Danish Council of Independent Research/ ; },
abstract = {BACKGROUND: Antimicrobial helper-compounds may reverse antimicrobial resistance. Sertraline, a antidepressant drug, has been suggested as a tetracycline helper-compound. Tetracycline is the preferred antimicrobial for treatment of enteric diseases in pigs. This study is the first to evaluate the potency of sertraline as a tetracycline adjuvant in pigs.<br><br>METHODS: Forty-eight nursery pigs were divided into four treatment groups: Tetracycline, sertraline, tetracycline/sertraline or un-medicated control. Fecal and ileal samples were obtained before treatment, 48 h and nine days after five days of treatment, respectively. Colony forming units (CFU) of tetracycline resistant coliforms in each sample (ileal or fecal) and CFU of an orally inoculated tetracycline-resistant strain of Escherichia coli were determined at each sampling point. The microbiome of fecal and ileal and samples was analyzed by sequencing of the 16S V3-V4 region.<br><br>RESULTS: The results did not provide evidence that sertraline in combination with tetracycline has any impact on tetracycline resistant bacteria in either fecal or ileum samples, while in the tetracycline treated group of pigs, an increase in the prevalence of a tetracycline resistant indicator strain of Escherichia coli shortly after ended five-day treatment was observed. The ileal samples obtained shortly after ended treatment showed treatment-associated changes in the composition of the microbiota in the groups of pigs treated with tetracycline (+/-) sertraline. While tetracycline treatment increased the abundance in the reads of E. coli, sertraline/tetracycline treatment led to increased abundances of Streptococcus spp. and decreased abundances of Lactobacillus spp. However, all observed differences (on CFU counts and microbiota composition) between groups shortly after treatment had diminished in less than two weeks after last treatment day.<br><br>CONCLUSIONS: Sertraline (+/-) tetracycline treatment did not reduce the long-term level of tetracycline-resistant bacteria in the feces or small intestine contents of piglets compared to the un-medicated control group of pigs. The result of this study reflects the importance of in vivo studies for confirmation of the antimicrobial helper-compound potential of an in vitro active compound.},
}
@article {pmid30634649,
year = {2019},
author = {Tröscher-Mußotter, J and Tilocca, B and Stefanski, V and Seifert, J},
title = {Analysis of the Bacterial and Host Proteins along and across the Porcine Gastrointestinal Tract.},
journal = {Proteomes},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/proteomes7010004},
pmid = {30634649},
issn = {2227-7382},
support = {microP//Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg/ ; },
abstract = {Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different porcine gastrointestinal tract sections were analyzed by metaproteomics to obtain a deeper insight into the functions of bacterial groups with concomitant analyses of host proteins. Firmicutes (Prevotellaceae) dominated mucosa and digesta samples, followed by Bacteroidetes. Actinobacteria and Proteobacteria were much higher in abundance in mucosa compared to digesta samples. Functional profiling reveals the presence of core functions shared between digesta and mucosa samples. Protein abundances of energy production and conversion were higher in mucosa samples, whereas in digesta samples more proteins were involved in lipid transport and metabolism; short-chain fatty acids production were detected. Differences were also highlighted between sections, with the small intestine appearing more involved in carbohydrate transport and metabolism than the large intestine. Thus, this study produced the first functional analyses of the porcine GIT biology, discussing the findings in relation to expected bacterial and host functions.},
}
@article {pmid30633104,
year = {2019},
author = {Nicholson, SE and Burmeister, DM and Johnson, TR and Zou, Y and Lai, Z and Scroggins, S and DeRosa, M and Jonas, RB and Merrill, DR and Zhu, C and Newton, LM and Stewart, RM and Schwacha, MG and Jenkins, DH and Eastridge, BJ},
title = {A PROSPECTIVE STUDY IN SEVERELY INJURED PATIENTS REVEALS AN ALTERED GUT MICROBIOME IS ASSOCIATED WITH TRANSFUSION VOLUME.},
journal = {The journal of trauma and acute care surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/TA.0000000000002201},
pmid = {30633104},
issn = {2163-0763},
abstract = {BACKGROUND: Traumatic injury can lead to a compromised intestinal epithelial barrier and inflammation. While alterations in the gut microbiome of critically injured patients may influence clinical outcomes, the impact of trauma on gut microbial composition is unknown. Our objective was to determine if the gut microbiome is altered in severely injured patients and begin to characterize changes in the gut microbiome due to time and therapeutic intervention.<br><br>METHODS: We conducted a prospective, observational study in adult patients (n=72) sustaining severe injury admitted to a Level I Trauma Center. Healthy volunteers (n=13) were also examined. Fecal specimens were collected on admission to the Emergency Department (ED) and at 3, 7, 10, and 13 (±2) days following injury. Microbial DNA was isolated for 16s rRNA sequencing, and α- and β-diversity were estimated, according to taxonomic classification against the Greengenes database.<br><br>RESULTS: The gut microbiome of trauma patients was altered on admission (i.e., within 30 minutes following injury) compared to healthy volunteers. Patients with an unchanged gut microbiome on admission were transfused more RBCs than those with an altered gut microbiome (p<0.001). Although the gut microbiome started to return to a β-diversity profile similar to that of healthy volunteers over time, it remained different from healthy controls. Alternatively, α-diversity initially increased post-injury, but subsequently decreased during the hospitalization. Injured patients on admission had a decreased abundance of traditionally beneficial microbial phyla (e.g., Firmicutes) with a concomitant decrease in opportunistic phyla (e.g., Proteobacteria) compared to healthy controls (p< 0.05). Large amounts of blood products and RBCs were both associated with higher α-diversity (p<0.001) and a β-diversity clustering closer to healthy controls.<br><br>CONCLUSIONS: The human gut microbiome changes early after trauma and may be aided by early massive transfusion. Ultimately, the gut microbiome of trauma patients may provide valuable diagnostic and therapeutic insight for the improvement of outcomes post-injury.<br><br>LEVEL OF EVIDENCE: Level III STUDY TYPE: Prognostic and Epidemiological.},
}
@article {pmid30632609,
year = {2019},
author = {Hamada, T and Nowak, JA and Milner, DA and Song, M and Ogino, S},
title = {Integration of microbiology, molecular pathology, and epidemiology: a new paradigm to explore the pathogenesis of microbiome-driven neoplasms.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.5236},
pmid = {30632609},
issn = {1096-9896},
abstract = {Molecular pathological epidemiology (MPE) is an integrative transdisciplinary field that addresses heterogeneous effects of exogenous and endogenous factors (collectively termed &quot;exposures&quot;), including microorganisms, on disease occurrence and consequence utilising molecular pathological signatures of the disease. In parallel with the paradigm of precision medicine, findings from MPE research can provide aetiological insights into tailored strategies of disease prevention and treatment. Due to the availability of molecular pathological tests on tumours, the MPE approach has been utilised predominantly in research on cancers including breast, lung, prostate, and colorectal carcinomas. Mounting evidence indicates that the microbiome (inclusive of viruses, bacteria, fungi, and parasites) plays an important role in a variety of human diseases including neoplasms. An alteration of the microbiome may be not only a cause of neoplasia but also an informative biomarker that indicates or mediates the association of an epidemiological exposure with health conditions and outcomes. To adequately educate and train investigators in this emerging area, we herein propose the integration of microbiology into the MPE model (termed &quot;microbiology-MPE&quot;), which can improve our understanding of the complex interactions of environment, tumour cells, the immune system, and microbes in the tumour microenvironment during the carcinogenic process. Using this approach, we can examine how lifestyle factors, dietary patterns, medications, environmental exposures, and germline genetics influence cancer development and progression through impacting the microbial communities in the human body. Further integration of other disciplines (e.g. pharmacology, immunology, nutrition) into microbiology-MPE would expand this developing research frontier. With the advent of high-throughput next-generation sequencing technologies, researchers now have increasing access to large-scale metagenomics as well as other omics data (e.g. genomics, epigenomics, proteomics, and metabolomics) in population-based research. The integrative field of microbiology-MPE will open new opportunities for personalised medicine and public health.},
}
@article {pmid30632438,
year = {2019},
author = {Moutinho, BD and Baima, JP and Rigo, FF and Saad-Hossne, R and Rodrigues, J and Romeiro, FG and Sassaki, LY},
title = {Fecal microbiota transplantation in refractory ulcerative colitis - a case report.},
journal = {The Journal of international medical research},
volume = {},
number = {},
pages = {300060518821790},
doi = {10.1177/0300060518821790},
pmid = {30632438},
issn = {1473-2300},
abstract = {Studies comparing gut microbiota profiles of inflammatory bowel disease (IBD) patients have shown several changes in microbiota composition, with marked reduction of local biodiversity relative to that of healthy controls. Modulation of the bacterial community is a promising strategy to reduce the proportion of harmful microorganisms and increase the proportion of beneficial bacteria; this is expected to prevent or treat IBD. The exact mechanism of fecal microbiota transplantation (FMT) remains unknown; however, replacing the host microbiota can reestablish gut microbial composition and function in IBD patients. The present report describes an ulcerative colitis patient who underwent FMT. A 17-year-old male with moderate to severe clinical activity, which was refractory to mesalazine, azathioprine, and infliximab, underwent FMT as alternative therapy. The patient exhibited clinical improvement after the procedure; however, the symptoms returned. A second FMT was performed 8 months after the first procedure, but the patient did not improve. In conclusion, despite the FMT failure observed in this patient, the procedure is a promising therapeutic option for IBD patients, and more in-depth studies of this method are needed.},
}
@article {pmid30632421,
year = {2019},
author = {Kolilekas, L and Papiris, S and Bouros, D},
title = {Existing and emerging treatments for idiopathic pulmonary fibrosis.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2019.1568244},
pmid = {30632421},
issn = {1747-6356},
abstract = {INTRODUCTION: Idiopathic pulmonary fibrosis (IPF) is a progressive and invariable fatal interstitial lung disease. Current antifibrotic treatment halts disease progression but do not cure the disease itself. In the last decade, a substantial understanding in disease pathobiological mechanisms led to the development of numerous clinical trials testing promising pharmacologic agents. Areas covered: In this review, we summarize and discuss current and emerging pharmacological therapies for IPF and highlight the potential of different promising investigational compounds in phase II-IV trials with positive or pending results. Expert commentary: Existing therapies for IPF slow disease progression and recent advances in understanding IPF complex pathogenesis unfolded multiple new possible therapeutic targets. A relevant number of promising clinical trials targeted specific biologic pathways, are ongoing or upcoming, but we are far away from a definitive cure of IPF soon. An 'oncologic approach' via tailoring medicine could be a realistic therapeutic intervention that may improve expectancy and quality of life in IPF.},
}
@article {pmid30632250,
year = {2019},
author = {Zhou, YX and Fuentes-Creollo, G and Ponce, F and Langley, SA and Jen, KY and Celniker, SE and Mao, JH and Snijders, AM},
title = {No difference in 4-nitroquinoline induced tumorigenesis between germ-free and colonized mice.},
journal = {Molecular carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1002/mc.22972},
pmid = {30632250},
issn = {1098-2744},
abstract = {Variations in oral bacterial communities have been linked to oral cancer suggesting that the oral microbiome is an etiological factor that can influence oral cancer development. The 4-nitroquinoline 1-oxide (4-NQO)-induced murine oral and esophageal cancer model is frequently used to assess the effects of preventive and/or therapeutic agents. We used this model to assess the impact of the microbiome on tumorigenesis using axenic (germ-free) and conventionally housed mice. Increased toxicity was observed in germ-free mice, however, no difference in tumor incidence, multiplicity and size was observed. Transcriptional profiling of liver tissue from germ-free and conventionally housed mice identified 254 differentially expressed genes including ten cytochrome p450 enzymes, the largest family of phase-1 drug metabolizing enzymes in the liver. Gene ontology revealed that differentially expressed genes were enriched for liver steatosis, inflammation and oxidative stress in livers of germ-free mice. Our observations emphasize the importance of the microbiome in mediating chemical toxicity at least in part by altering host gene expression. Studies on the role of the microbiome in chemical-induced cancer using germ-free animal models should consider the potential difference in dose due to the microbiome-mediated changes in host metabolizing capacity, which might influence the ability to draw conclusions especially for tumor induction models that are dose dependent. This article is protected by copyright. All rights reserved.},
}
@article {pmid30632097,
year = {2019},
author = {Xu, H and Li, H},
title = {Acne, the Skin Microbiome, and Antibiotic Treatment.},
journal = {American journal of clinical dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s40257-018-00417-3},
pmid = {30632097},
issn = {1179-1888},
support = {R01GM099530//National Institutes of Health/ ; 81673087//National Natural Science Foundation of China/ ; 81502739//National Natural Science Foundation of China/ ; 81703148//National Natural Science Foundation of China/ ; CIFMS 2016-I2M-1-003//Chinese Academy of Medical Sciences/ ; 2016ZX320014//Innovation Research on Critical Diseases/ ; },
abstract = {Acne vulgaris is a chronic skin disorder involving hair follicles and sebaceous glands. Multiple factors contribute to the disease, including skin microbes. The skin microbiome in the follicle is composed of a diverse group of microorganisms. Among them, Propionibacterium acnes and Malassezia spp. have been linked to acne development through their influence on sebum secretion, comedone formation, and inflammatory response. Antibiotics targeting P. acnes have been the mainstay in acne treatment for the past four decades. Among them, macrolides, clindamycin, and tetracyclines are the most widely prescribed. As antibiotic resistance becomes an increasing concern in clinical practice, understanding the skin microbiome associated with acne and the effects of antibiotic use on the skin commensals is highly relevant and critical to clinicians. In this review, we summarize recent studies of the composition and dynamics of the skin microbiome in acne and the effects of antibiotic treatment on skin microbes.},
}
@article {pmid30631436,
year = {2018},
author = {Grainger, J and Daw, R and Wemyss, K},
title = {Systemic instruction of cell-mediated immunity by the intestinal microbiome.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {},
doi = {10.12688/f1000research.14633.1},
pmid = {30631436},
issn = {2046-1402},
abstract = {Recent research has shed light on the plethora of mechanisms by which the gastrointestinal commensal microbiome can influence the local immune response in the gut (in particular, the impact of the immune system on epithelial barrier homeostasis and ensuring microbial diversity). However, an area that is much less well explored but of tremendous therapeutic interest is the impact the gut microbiome has on systemic cell-mediated immune responses. In this commentary, we highlight some key studies that are beginning to broadly examine the different mechanisms by which the gastrointestinal microbiome can impact the systemic immune compartment. Specifically, we discuss the effects of the gut microbiome on lymphocyte polarisation and trafficking, tailoring of resident immune cells in the liver, and output of circulating immune cells from the bone marrow. Finally, we explore contexts in which this new understanding of long-range effects of the gut microbiome can have implications, including cancer therapies and vaccination.},
}
@article {pmid30631320,
year = {2018},
author = {Ghosh, D and Bernstein, JA and Khurana Hershey, GK and Rothenberg, ME and Mersha, TB},
title = {Leveraging Multilayered &quot;Omics&quot; Data for Atopic Dermatitis: A Road Map to Precision Medicine.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2727},
doi = {10.3389/fimmu.2018.02727},
pmid = {30631320},
issn = {1664-3224},
abstract = {Atopic dermatitis (AD) is a complex multifactorial inflammatory skin disease that affects ~280 million people worldwide. About 85% of AD cases begin in childhood, a significant portion of which can persist into adulthood. Moreover, a typical progression of children with AD to food allergy, asthma or allergic rhinitis has been reported (&quot;allergic march&quot; or &quot;atopic march&quot;). AD comprises highly heterogeneous sub-phenotypes/endotypes resulting from complex interplay between intrinsic and extrinsic factors, such as environmental stimuli, and genetic factors regulating cutaneous functions (impaired barrier function, epidermal lipid, and protease abnormalities), immune functions and the microbiome. Though the roles of high-throughput &quot;omics&quot; integrations in defining endotypes are recognized, current analyses are primarily based on individual omics data and using binary clinical outcomes. Although individual omics analysis, such as genome-wide association studies (GWAS), can effectively map variants correlated with AD, the majority of the heritability and the functional relevance of discovered variants are not explained or known by the identified variants. The limited success of singular approaches underscores the need for holistic and integrated approaches to investigate complex phenotypes using trans-omics data integration strategies. Integrating omics layers (e.g., genome, epigenome, transcriptome, proteome, metabolome, lipidome, exposome, microbiome), which often have complementary and synergistic effects, might provide the opportunity to capture the flow of information underlying AD disease manifestation. Overlapping genes/candidates derived from multiple omics types include FLG, SPINK5, S100A8, and SERPINB3 in AD pathogenesis. Overlapping pathways include macrophage, endothelial cell and fibroblast activation pathways, in addition to well-known Th1/Th2 and NFkB activation pathways. Interestingly, there was more multi-omics overlap at the pathway level than gene level. Further analysis of multi-omics overlap at the tissue level showed that among 30 tissue types from the GTEx database, skin and esophagus were significantly enriched, indicating the biological interconnection between AD and food allergy. The present work explores multi-omics integration and provides new biological insights to better define the biological basis of AD etiology and confirm previously reported AD genes/pathways. In this context, we also discuss opportunities and challenges introduced by &quot;big omics data&quot; and their integration.},
}
@article {pmid30631318,
year = {2018},
author = {Shao, L and Ling, Z and Chen, D and Liu, Y and Yang, F and Li, L},
title = {Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3166},
doi = {10.3389/fmicb.2018.03166},
pmid = {30631318},
issn = {1664-302X},
abstract = {Early detection and effective interventions for liver cirrhosis (LC) remain an urgent unmet clinical need. Inspired from intestinal disorders in LC patients, we investigated the associations between gut microbiome and disease progression based on a raw metagenomic dataset of 47 healthy controls, 49 compensated, and 46 decompensated LC patients from our previous study, and a metabolomic dataset of urine samples from the same controls/patients using ultra-performance liquid chromatography/mass spectrophotometry system. It was found that the combination and relative abundance of gut microbiome, the inter-microbiome regulatory networks, and the microbiome-host correlation patterns varied during disease progression. The significant reduction of bacteria involved in fermentation of plant cell wall polysaccharides and resistant starch (such as Alistipes sp. HG5, Clostridium thermocellum) contributed to the reduced supply of energy sources, the disorganized self-feeding and cross-feeding networks and the thriving of some opportunistic pathogens in genus Veillonella. The marked decrease of butyrate-producing bacteria and increase of Ruminococcus gnavus implicated in degradation of elements from the mucus layer provided an explanation for the impaired intestinal barrier function and systematic inflammation in LC patients. Our results pave the way for further developments in early detection and intervention of LC targeting on gut microbiome.},
}
@article {pmid30631136,
year = {2018},
author = {Ho, TTB and Groer, MW and Kane, B and Yee, AL and Torres, BA and Gilbert, JA and Maheshwari, A},
title = {Enteric dysbiosis and fecal calprotectin expression in premature infants.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41390-018-0254-y},
pmid = {30631136},
issn = {1530-0447},
abstract = {BACKGROUND: Premature infants often develop enteric dysbiosis with a preponderance of Gammaproteobacteria, which has been related to adverse clinical outcomes. We investigated the relationship between increasing fecal Gammaproteobacteria and mucosal inflammation, measured by fecal calprotectin (FC).<br><br>METHODS: Stool samples were collected from very-low-birth weight (VLBW) infants at ≤2, 3, and 4 weeks' postnatal age. Fecal microbiome was surveyed using polymerase chain reaction amplification of the V4 region of 16S ribosomal RNA, and FC was measured by enzyme immunoassay.<br><br>RESULTS: We enrolled 45 VLBW infants (gestation 27.9 ± 2.2 weeks, birth weight 1126 ± 208 g) and obtained stool samples at 9.9 ± 3, 20.7 ± 4.1, and 29.4 ± 4.9 days. FC was positively correlated with the genus Klebsiella (r = 0.207, p = 0.034) and its dominant amplicon sequence variant (r = 0.290, p = 0.003), but not with the relative abundance of total Gammaproteobacteria. Klebsiella colonized the gut in two distinct patterns: some infants started with low Klebsiella abundance and gained these bacteria over time, whereas others began with very high Klebsiella abundance.<br><br>CONCLUSION: In premature infants, FC correlated with relative abundance of a specific pathobiont, Klebsiella, and not with that of the class Gammaproteobacteria. These findings indicate a need to define dysbiosis at genera or higher levels of resolution.},
}
@article {pmid30631088,
year = {2019},
author = {Bergelson, J and Mittelstrass, J and Horton, MW},
title = {Characterizing both bacteria and fungi improves understanding of the Arabidopsis root microbiome.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {24},
doi = {10.1038/s41598-018-37208-z},
pmid = {30631088},
issn = {2045-2322},
abstract = {Roots provide plants mineral nutrients and stability in soil; while doing so, they come into contact with diverse soil microbes that affect plant health and productivity. Despite their ecological and agricultural relevance, the factors that shape the root microbiome remain poorly understood. We grew a worldwide panel of replicated Arabidopsis thaliana accessions outdoors and over winter to characterize their root-microbial communities. Although studies of the root microbiome tend to focus on bacteria, we found evidence that fungi have a strong influence on the structure of the root microbiome. Moreover, host effects appear to have a stronger influence on plant-fungal communities than plant-bacterial communities. Mapping the host genes that affect microbiome traits identified a priori candidate genes with roles in plant immunity; the root microbiome also appears to be strongly affected by genes that impact root and root hair development. Our results suggest that future analyses of the root microbiome should focus on multiple kingdoms, and that the root microbiome is shaped not only by genes involved in defense, but also by genes involved in plant form and physiology.},
}
@article {pmid30630481,
year = {2019},
author = {Kenyon, CR and Delva, W and Brotman, RM},
title = {Differential sexual network connectivity offers a parsimonious explanation for population-level variations in the prevalence of bacterial vaginosis: a data-driven, model-supported hypothesis.},
journal = {BMC women's health},
volume = {19},
number = {1},
pages = {8},
doi = {10.1186/s12905-018-0703-0},
pmid = {30630481},
issn = {1472-6874},
abstract = {BACKGROUND: The prevalence of bacterial vaginosis (BV) and vaginal microbiota types varies dramatically between different populations around the world. Understanding what underpins these differences is important, as high-diversity microbiotas associated with BV are implicated in adverse pregnancy outcomes and enhanced susceptibility to and transmission of sexually transmitted infections.<br><br>MAIN TEXT: We hypothesize that these variations in the vaginal microbiota can, in part, be explained by variations in the connectivity of sexual networks. We argue: 1) Couple-level data suggest that BV-associated bacteria can be sexually transmitted and hence high sexual network connectivity would be expected to promote the spread of BV-associated bacteria. Epidemiological studies have found positive associations between indicators of network connectivity and the prevalence of BV; 2) The relationship between BV prevalence and STI incidence/prevalence can be parsimoniously explained by differential network connectivity; 3) Studies from other mammals are generally supportive of the association between network connectivity and high-diversity vaginal microbiota.<br><br>CONCLUSION: To test this hypothesis, we propose a combination of empirical and simulation-based study designs.},
}
@article {pmid30630325,
year = {2018},
author = {Dudík, B and Sepová, HK and Bilková, A},
title = {Inflammatory bowel disease: factors involved in pathogenesis.},
journal = {Ceska a Slovenska farmacie : casopis Ceske farmaceuticke spolecnosti a Slovenske farmaceuticke spolecnosti},
volume = {67},
number = {3},
pages = {95-100},
pmid = {30630325},
issn = {1210-7816},
abstract = {The incidence of inflammatory bowel disease (IBD) in developed countries increases every year. The aetiology is still not completely understood and its clarification is a key prerequisite for effective prophylaxis and therapy. IBD is most-likely caused by a combination of several factors: environmental, genetic, immunological, and disruption of intestinal microbiota composition - dysbiosis. &quot;Westernization&quot; of lifestyle and urbanization seem to be among the most serious environmental factors. The pathogenesis is also influenced by the imbalance between the TH1 and TH2 cellular response and the expression of genes involved in T cell response and immunodeficiency. Last but not least, the worldwide overuse of antimicrobial drugs depletes the microbiome, which has a direct impact on the development of the dysbiosis. The subject of this review is a detailed characterization of the above-mentioned factors involved in the onset and development of IBD. Key words: gut microbiota inflammatory bowel disease immunopathogenesis dysbiosis.},
}
@article {pmid30630301,
year = {2018},
author = {Kim, K and Castro, EJT and Shim, H and Advincula, JVG and Kim, YW},
title = {Differences Regarding the Molecular Features and Gut Microbiota Between Right and Left Colon Cancer.},
journal = {Annals of coloproctology},
volume = {34},
number = {6},
pages = {280-285},
doi = {10.3393/ac.2018.12.17},
pmid = {30630301},
issn = {2287-9714},
support = {2017R1D1A3B03032301//National Research Foundation of Korea/ ; },
abstract = {For many years, developmental and physiological differences have been known to exist between anatomic segments of the colorectum. Because of different outcomes, prognoses, and clinical responses to chemotherapy, the distinction between right colon cancer (RCC) and left colon cancer (LCC) has gained attention. Furthermore, variations in the molecular features and gut microbiota between right and LCCs have recently been a hot research topic. CpG island methylator phenotype-high, microsatellite instability-high colorectal cancers are more likely to occur on the right side whereas tumors with chromosomal instability have been detected in approximately 75% of LCC patients and 30% of RCC patients. The mutation rates of oncogenes and tumor suppressor genes also differ between RCC and LCC patients. Biofilm is more abundant in RCC patients than LLC patients, as are Prevotella, Selenomonas, and Peptostreptococcus. Conversely, Fusobacterium, Escherichia/Shigella, and Leptotrichia are more abundant in LCC patients compared to RCC patients. Distinctive characteristics are apparent in terms of molecular features and gut microbiota between right and LCC. However, how or to what extent these differences influence diverging oncologic outcomes remains unclear. Further clinical and translational studies are needed to elucidate the causative relationship between primary tumor location and prognosis.},
}
@article {pmid30629725,
year = {2019},
author = {Balasubramanian, S and Osburne, MS and BrinJones, H and Tai, AK and Leong, JM},
title = {Prophage induction, but not production of phage particles, is required for lethal disease in a microbiome-replete murine model of enterohemorrhagic E. coli infection.},
journal = {PLoS pathogens},
volume = {15},
number = {1},
pages = {e1007494},
doi = {10.1371/journal.ppat.1007494},
pmid = {30629725},
issn = {1553-7374},
abstract = {Enterohemorrhagic Escherichia coli (EHEC) colonize intestinal epithelium by generating characteristic attaching and effacing (AE) lesions. They are lysogenized by prophage that encode Shiga toxin 2 (Stx2), which is responsible for severe clinical manifestations. As a lysogen, prophage genes leading to lytic growth and stx2 expression are repressed, whereas induction of the bacterial SOS response in response to DNA damage leads to lytic phage growth and Stx2 production both in vitro and in germ-free or streptomycin-treated mice. Some commensal bacteria diminish prophage induction and concomitant Stx2 production in vitro, whereas it has been proposed that phage-susceptible commensals may amplify Stx2 production by facilitating successive cycles of infection in vivo. We tested the role of phage induction in both Stx production and lethal disease in microbiome-replete mice, using our mouse model encompassing the murine pathogen Citrobacter rodentium lysogenized with the Stx2-encoding phage Φstx2dact. This strain generates EHEC-like AE lesions on the murine intestine and causes lethal Stx-mediated disease. We found that lethal mouse infection did not require that Φstx2dact infect or lysogenize commensal bacteria. In addition, we detected circularized phage genomes, potentially in the early stage of replication, in feces of infected mice, confirming that prophage induction occurs during infection of microbiota-replete mice. Further, C. rodentium (Φstx2dact) mutants that do not respond to DNA damage or express stx produced neither high levels of Stx2 in vitro or lethal infection in vivo, confirming that SOS induction and concomitant expression of phage-encoded stx genes are required for disease. In contrast, C. rodentium (Φstx2dact) mutants incapable of prophage genome excision or of packaging phage genomes retained the ability to produce Stx in vitro, as well as to cause lethal disease in mice. Thus, in a microbiome-replete EHEC infection model, lytic induction of Stx-encoding prophage is essential for lethal disease, but actual phage production is not.},
}
@article {pmid30629579,
year = {2019},
author = {Miranda-CasoLuengo, R and Lu, J and Williams, EJ and Miranda-CasoLuengo, AA and Carrington, SD and Evans, ACO and Meijer, WG},
title = {Delayed differentiation of vaginal and uterine microbiomes in dairy cows developing postpartum endometritis.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0200974},
doi = {10.1371/journal.pone.0200974},
pmid = {30629579},
issn = {1932-6203},
abstract = {Bacterial overgrowth in the uterus is a normal event after parturition. In contrast to the healthy cow, animals unable to control the infection within 21 days after calving develop postpartum endometritis. Studies on the Microbial Ecology of the bovine reproductive tract have focused on either vaginal or uterine microbiomes. This is the first study that compares both microbiomes in the same animals. Terminal Restriction Fragment Length Polymorphism of the 16S rRNA gene showed that despite large differences associated to individuals, a shared community exist in vagina and uterus during the postpartum period. The largest changes associated with development of endometritis were observed at 7 days postpartum, a time when vaginal and uterine microbiomes were most similar. 16S rRNA pyrosequencing of the vaginal microbiome at 7 days postpartum showed at least three different microbiome types that were associated with later development of postpartum endometritis. All three microbiome types featured reduced bacterial diversity. Taken together, the above findings support a scenario where disruption of the compartmentalization of the reproductive tract during parturition results in the dispersal and mixing of the vaginal and uterine microbiomes, which subsequently are subject to differentiation. This differentiation was observed early postpartum in the healthy cow. In contrast, loss of bacterial diversity and dominance of the microbiome by few bacterial taxa were related to a delayed succession at 7DPP in cows that at 21 DPP or later were diagnosed with endometritis.},
}
@article {pmid30629190,
year = {2019},
author = {Marcial-Coba, MS and Knøchel, S and Nielsen, DS},
title = {Low-moisture food matrices as probiotic carriers.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnz006},
pmid = {30629190},
issn = {1574-6968},
abstract = {To exert a beneficial effect on the host, adequate doses of probiotics must be administered and maintaining their viability until consumption is thus essential. Dehydrated probiotics exhibit enhanced long-term viability and can be incorporated into low-moisture food matrices which also possess high stability at refrigeration and ambient temperature. However, several factors associated with the desiccation process, the physicochemical properties of the matrix and the storage conditions can affect probiotic survival. In the near future, an increased demand for probiotics based on functionally dominant members of the gut microbiome ('next-generation probiotics', NGP) is expected. NGPs are very sensitive to oxygen and efficient encapsulation protocols are needed. Strategies to improve the viability of traditional probiotics and particularly of NGPs involve the selection of a suitable carrier as well as proper desiccation and protection techniques. Dried probiotic microcapsules may constitute an alternative to improve the microbial viability not only during storage but also upper gastrointestinal tract passage. Here we review the main dehydration techniques that are applied in the industry as well as the potential stresses associated with the desiccation process and storage. Finally, low- or intermediate-moisture food matrices suitable as carriers of traditional as well as NGPs will be discussed.},
}
@article {pmid30629185,
year = {2019},
author = {Stewart, CJ and Mansbach, JM and Ajami, NJ and Petrosino, JF and Zhu, Z and Liang, L and Camargo, CA and Hasegawa, K},
title = {Serum metabolome is associated with nasopharyngeal microbiota and disease severity among infants with bronchiolitis.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiz021},
pmid = {30629185},
issn = {1537-6613},
abstract = {Background: Emerging evidence suggests relations of nasopharyngeal metabolome and microbiota with bronchiolitis severity. However, the influence of host systemic metabolism on disease pathobiology remains unclear. We aimed to examine metabolome profiles and their association with higher severity, defined by use of positive pressure ventilation (PPV), in infants hospitalized for bronchiolitis.<br><br>Methods: In 140 infants with bronchiolitis, metabolomic profiling was performed on serum: n=70 in the training dataset and n=70 independent samples in the test dataset. We also profiled the nasopharyngeal airway microbiota and examined its association with the serum metabolites.<br><br>Results: Serum metabolome profiles differed by bronchiolitis severity (P<0.001). In total, 20 metabolites in the training dataset were significantly associated with the risk of PPV and 18 metabolites remained significant following adjustment for confounders (FDR<0.10). Phosphatidylcholine metabolites were associated with higher risks of PPV use, while metabolites from the plasmalogen sub-pathway were associated with lower risks. The test dataset validated these findings (FDR<0.05). Streptococcus abundance was positively associated with metabolites that are associated with higher risks of PPV.<br><br>Conclusions: Serum metabolomic signatures were associated with both the nasopharyngeal microbiota and bronchiolitis severity. Our findings advance research into the complex interrelations between airway microbiome, host systemic response, and pathobiology of bronchiolitis.},
}
@article {pmid30629027,
year = {2019},
author = {Vick, AD and Hery, DN and Markowiak, SF and Brunicardi, FC},
title = {Closing the Disparity in Pancreatic Cancer Outcomes: A Closer Look at Nonmodifiable Factors and Their Potential Use in Treatment.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000001238},
pmid = {30629027},
issn = {1536-4828},
abstract = {OBJECTIVES: African Americans (AAs) have disproportionately higher incidence and lower survival rates from pancreatic cancer compared with whites. Historically, this disparity has been attributed to modifiable risk factors. Recent studies suggest that nonmodifiable aspects may also play an important role. We review these new contributions as potential targets for closing the disparity.<br><br>METHODS: A PubMed search was conducted to review studies of nonmodifiable elements contributing to pancreatic cancer disparities in AAs.<br><br>RESULTS: Several nonmodifiable risks are associated with the racial disparity in pancreatic cancer. SSTR5 P335L, Kaiso, and KDM4/JMJD2A demonstrate differential racial expression, increasing their potential as therapeutic targets. Many social determinants of health and their associations with diabetes, obesity, and the microbiome are partially modifiable risk factors that significantly contribute to outcomes in minorities. Barriers to progress include the low minority inclusion in research studies.<br><br>CONCLUSIONS: Genomics, epigenetics, the microbiome, and social determinants of health are components that contribute to the pancreatic cancer disparity in AAs. These factors can be researched, targeted, and modified to improve mortality rates. Closing the disparity in pancreatic cancer will require an integrated approach of personalized medicine, increased minority recruitment to studies, and advanced health care/education access.},
}
@article {pmid30628788,
year = {2019},
author = {Xue, J and Lai, Y and Chi, L and Tu, P and Leng, J and Liu, CW and Ru, H and Lu, K},
title = {Serum metabolomics reveals that gut microbiome perturbation mediates metabolic disruption induced by arsenic exposure in mice.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.8b00697},
pmid = {30628788},
issn = {1535-3907},
abstract = {Arsenic contamination in drinking water has been a worldwide health concern for decades. Except for being a well-recognized carcinogen, arsenic exposure has also been linked with diabetes, neurological effects, and cardiovascular diseases. Recently, increasing evidence have indicated that gut microbiome is an important risk factor in modulating the development of diseases. In the present study, we aim to investigate the role of gut microbiome perturbation in arsenic-induced diseases by coupling a mass spectrometry-based metabolomics approach and an animal model with altered gut microbiome induced by bacterial infection. Serum metabolic profiling has revealed that gut microbiome perturbation and arsenic exposure induced the dramatic changes of numerous metabolite pathways, including fatty acid metabolism, phospholipids, sphingolipids, cholesterols, and tryptophan metabolism, which were not or less disrupted when gut microbiome stays normal. In summary, this study suggested that gut microbiome perturbation can exacerbate or cause the metabolic disorders induced by arsenic exposure.},
}
@article {pmid30627872,
year = {2019},
author = {Wang, Q and Wang, K and Wu, W and Giannoulatou, E and Ho, JWK and Li, L},
title = {Host and microbiome multi-omics integration: applications and methodologies.},
journal = {Biophysical reviews},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12551-018-0491-7},
pmid = {30627872},
issn = {1867-2450},
support = {81330011, 81330014, 81790631, 81790633, 81570512, and 81121002//National Natural Science Foundation of China/ ; 81721091//Science Fund for Creative Research Groups/ ; 100848//National Heart Foundation of Australia/ ; 101204//National Heart Foundation of Australia/ ; },
abstract = {The study of the microbial community-the microbiome-associated with a human host is a maturing research field. It is increasingly clear that the composition of the human's microbiome is associated with various diseases such as gastrointestinal diseases, liver diseases and metabolic diseases. Using high-throughput technologies such as next-generation sequencing and mass spectrometry-based metabolomics, we are able to comprehensively sequence the microbiome-the metagenome-and associate these data with the genomic, epigenomics, transcriptomic and metabolic profile of the host. Our review summarises the application of integrating host omics with microbiome as well as the analytical methods and related tools applied in these studies. In addition, potential future directions are discussed.},
}
@article {pmid30627823,
year = {2019},
author = {Brandstetter, S and Toncheva, AA and Niggel, J and Wolff, C and Gran, S and Seelbach-Göbel, B and Apfelbacher, C and Melter, M and Kabesch, M and , },
title = {KUNO-Kids birth cohort study: rationale, design, and cohort description.},
journal = {Molecular and cellular pediatrics},
volume = {6},
number = {1},
pages = {1},
doi = {10.1186/s40348-018-0088-z},
pmid = {30627823},
issn = {2194-7791},
support = {HEALS:603964//EU/ ; SYSINFLAME: 01ZX1306E//Bundesministerium für Bildung, Wissenschaft, Forschung und Technologie (DE)/ ; },
abstract = {BACKGROUND: Birth cohort studies can contribute substantially to the understanding of health and disease - in childhood and over the life course. The KUNO-Kids birth cohort study was established to investigate various aspects of child health, using novel omics technologies in a systems medicine approach.<br><br>RESULTS: After 3 years of recruitment, 2515 infants and their families have joined the study. Parents with higher education are overrepresented as in many other birth cohorts and are more likely to complete follow-up assessments via self-report questionnaires. The vast majority of participants consented to clinical examinations of their child and to the non-invasive collection of diverse biosamples, which were processed specifically for their integrated use in omics technology covering genomics, epigenomics, transcriptomics, metabolomics, and microbiome analyses of the skin, oral cavity, and stool.<br><br>CONCLUSIONS: The data and diverse biomaterial collected in the KUNO-Kids birth cohort study will provide extensive opportunities for investigating child health and its determinants in a holistic approach. The combination of a broad range of research questions in one study will allow for a cost-effective use of biomaterial and omics results and for a comprehensive analysis of biological and social determinants of health and disease. Aiming for low attrition and ensuring participants' long-term commitment will be crucial to fully exploit the potential of the study.},
}
@article {pmid30627762,
year = {2019},
author = {Treichel, NS and Prevoršek, Z and Mrak, V and Kostrić, M and Vestergaard, G and Foesel, B and Pfeiffer, S and Stres, B and Schöler, A and Schloter, M},
title = {Effect of the Nursing Mother on the Gut Microbiome of the Offspring During Early Mouse Development.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-019-01317-7},
pmid = {30627762},
issn = {1432-184X},
abstract = {The development of the gut microbiome is influenced by several factors. It is acquired during and after birth and involves both maternal and environmental factors as well as the genetic disposition of the offspring. However, it is unclear if the microbiome development is directly triggered by the mode of delivery and very early contact with the mother or mostly at later stages of initial development mainly by breast milk provided by the mother. To investigate to what extent the gut microbiome composition of the offspring is determined by the nursing mother, providing breast milk, compared to the birth mother during early development, a cross-fostering experiment involving two genetically different mouse lines was developed, being prone to be obese or lean, respectively. The microbiome of the colon was analyzed by high-throughput 16S rRNA gene sequencing, when the mice were 3 weeks old. The nursing mother affected both α- and β-diversity of the offspring's gut microbiome and shaped its composition. Especially bacterial families directly transferred by breast milk, like Streptococcaceae, or families which are strongly influenced by the quality of the breast milk like Rikenellaceae, showed a strong response. The core microbiome transferred from the obese nursing mother showed a higher robustness in comparison to the microbiome transferred from the lean nursing mother. Overall, the nursing mother impacts the gut microbial composition of the offspring during early development and might play an important role for health and disease of the animals at later stages of life.},
}
@article {pmid30627668,
year = {2018},
author = {Fenker, DE and McDaniel, CT and Panmanee, W and Panos, RJ and Sorscher, EJ and Sabusap, C and Clancy, JP and Hassett, DJ},
title = {A Comparison between Two Pathophysiologically Different yet Microbiologically Similar Lung Diseases: Cystic Fibrosis and Chronic Obstructive Pulmonary Disease.},
journal = {International journal of respiratory and pulmonary medicine},
volume = {5},
number = {2},
pages = {},
doi = {10.23937/2378-3516/1410098},
pmid = {30627668},
issn = {2378-3516},
abstract = {Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are chronic pulmonary diseases that affect ~70,000 and 251 million individuals worldwide, respectively. Although these two diseases have distinctly different pathophysiologies, both cause chronic respiratory insufficiency that erodes quality of life and causes significant morbidity and eventually death. In both CF and COPD, the respiratory microbiome plays a major contributing role in disease progression and morbidity. Pulmonary pathogens can differ dramatically during various stages of each disease and frequently cause acute worsening of lung function due to disease exacerbation. Despite some similarities, outcome and timing/type of exacerbation can also be quite different between CF and COPD. Given these clinical distinctions, both patients and physicians should be aware of emerging therapeutic options currently being offered or in development for the treatment of lung infections in individuals with CF and COPD. Although interventions are available that prolong life and mitigate morbidity, neither disorder is curable. Both acute and chronic pulmonary infections contribute to an inexorable downward course and may trigger exacerbations, culminating in loss of lung function or respiratory failure. Knowledge of the pulmonary pathogens causing these infections, their clinical presentation, consequences, and management are, therefore, critical. In this review, we compare and contrast CF and COPD, including underlying causes, general outcomes, features of the lung microbiome, and potential treatment strategies.},
}
@article {pmid30627520,
year = {2019},
author = {Pugazhendhi, A and Kumar, G and Sivagurunathan, P},
title = {Microbiome involved in anaerobic hydrogen producing granules: A mini review.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {e00301},
doi = {10.1016/j.btre.2018.e00301},
pmid = {30627520},
issn = {2215-017X},
abstract = {This mini review overviewed the latest updates on the anaerobic hydrogen fermentation using the granulation technology and the microbiome involved in the process. Additionally, the implication of various reactor design and their microbial changes were compared and provided the new insights on the role of microbiomes for rapid granules formation and long term stable operation in a continuous mode operation. The information provided in this communication would help to understand the key role of microbiomes and their importance in anaerobic hydrogen producing granular systems.},
}
@article {pmid30626617,
year = {2019},
author = {Rowan-Nash, AD and Korry, BJ and Mylonakis, E and Belenky, P},
title = {Cross-Domain and Viral Interactions in the Microbiome.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {83},
number = {1},
pages = {},
doi = {10.1128/MMBR.00044-18},
pmid = {30626617},
issn = {1098-5557},
abstract = {SUMMARYThe importance of the microbiome to human health is increasingly recognized and has become a major focus of recent research. However, much of the work has focused on a few aspects, particularly the bacterial component of the microbiome, most frequently in the gastrointestinal tract. Yet humans and other animals can be colonized by a wide array of organisms spanning all domains of life, including bacteria and archaea, unicellular eukaryotes such as fungi, multicellular eukaryotes such as helminths, and viruses. As they share the same host niches, they can compete with, synergize with, and antagonize each other, with potential impacts on their host. Here, we discuss these major groups making up the human microbiome, with a focus on how they interact with each other and their multicellular host.},
}
@article {pmid30626002,
year = {2019},
author = {Rechenberger, J and Samaras, P and Jarzab, A and Behr, J and Frejno, M and Djukovic, A and Sanz, J and González-Barberá, EM and Salavert, M and López-Hontangas, JL and Xavier, KB and Debrauwer, L and Rolain, JM and Sanz, M and Garcia-Garcera, M and Wilhelm, M and Ubeda, C and Kuster, B},
title = {Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.},
journal = {Proteomes},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/proteomes7010002},
pmid = {30626002},
issn = {2227-7382},
support = {031L0089//Bundesministerium für Bildung und Forschung/ ; },
abstract = {The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.},
}
@article {pmid30625189,
year = {2019},
author = {Sanctuary, MR and Kain, JN and Chen, SY and Kalanetra, K and Lemay, DG and Rose, DR and Yang, HT and Tancredi, DJ and German, JB and Slupsky, CM and Ashwood, P and Mills, DA and Smilowitz, JT and Angkustsiri, K},
title = {Pilot study of probiotic/colostrum supplementation on gut function in children with autism and gastrointestinal symptoms.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210064},
doi = {10.1371/journal.pone.0210064},
pmid = {30625189},
issn = {1932-6203},
abstract = {Over half of all children with autism spectrum disorders (ASD) have gastrointestinal (GI) co-morbidities including chronic constipation, diarrhea, and irritable bowel syndrome. The severity of these symptoms has been correlated with the degree of GI microbial dysbiosis. The study objective was to assess tolerability of a probiotic (Bifidobacterium infantis) in combination with a bovine colostrum product (BCP) as a source of prebiotic oligosaccharides and to evaluate GI, microbiome and immune factors in children with ASD and GI co-morbidities. This pilot study is a randomized, double blind, controlled trial of combination treatment (BCP + B. infantis) vs. BCP alone in a cross-over study in children ages 2-11 with ASD and GI co-morbidities (n = 8). This 12-week study included 5 weeks of probiotic-prebiotic supplementation, followed by a two-week washout period, and 5 weeks of prebiotic only supplementation. The primary outcome of tolerability was assessed using validated questionnaires of GI function and atypical behaviors, along with side effects. Results suggest that the combination treatment is well-tolerated in this cohort. The most common side effect was mild gassiness. Some participants on both treatments saw a reduction in the frequency of certain GI symptoms, as well as reduced occurrence of particular aberrant behaviors. Improvement may be explained by a reduction in IL-13 and TNF-α production in some participants. Although limited conclusions can be drawn from this small pilot study, the results support the need for further research into the efficacy of these treatments.},
}
@article {pmid30625134,
year = {2019},
author = {Lee, KH and Gordon, A and Shedden, K and Kuan, G and Ng, S and Balmaseda, A and Foxman, B},
title = {The respiratory microbiome and susceptibility to influenza virus infection.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0207898},
doi = {10.1371/journal.pone.0207898},
pmid = {30625134},
issn = {1932-6203},
abstract = {Influenza is a major cause of morbidity and mortality worldwide. However, vaccine effectiveness has been low to moderate in recent years and vaccine coverage remains low, especially in low- and middle-income countries. Supplementary methods of prevention should be explored to reduce the high burden of influenza. A potential target is the respiratory tract microbiome, complex microbial communities which envelop the respiratory epithelium and play an important role in shaping host immunity. Using a household transmission study, we examined whether the nose/throat microbiota was associated with influenza susceptibility among participants exposed to influenza virus in the household. Further, we characterized changes in the nose/throat microbiota to explore whether community stability was influenced by influenza virus infection. Using a generalized linear mixed effects model, we found a nasal/oropharyngeal community state type (CST) associated with decreased susceptibility to influenza. The CST was rare and transitory among young children but a prevalent and stable CST among adults. Using boosting and linear mixed effects models, we found associations between the nose/throat microbiota and influenza also existed at the taxa level, specifically with the relative abundance of Alloprevotella, Prevotella, and Bacteroides oligotypes. We found high rates of change between bacterial community states among both secondary cases and household contacts who were not infected during follow up. Further work is needed to separate the effect of influenza virus infection from the considerable short-term changes that occur even in the absence of virus. Lastly, age was strongly associated with susceptibility to influenza and the nose/throat bacterial community structure. Although additional studies are needed to determine causality, our results suggest the nose/throat microbiome may be a potential target for reducing the burden of influenza.},
}
@article {pmid30625111,
year = {2019},
author = {Doonan, J and Denman, S and Pachebat, JA and McDonald, JE},
title = {Genomic analysis of bacteria in the Acute Oak Decline pathobiome.},
journal = {Microbial genomics},
volume = {},
number = {},
pages = {},
doi = {10.1099/mgen.0.000240},
pmid = {30625111},
issn = {2057-5858},
abstract = {The UK's native oak is under serious threat from Acute Oak Decline (AOD). Stem tissue necrosis is a primary symptom of AOD and several bacteria are associated with necrotic lesions. Two members of the lesion pathobiome, Brenneria goodwinii and Gibbsiella quercinecans, have been identified as causative agents of tissue necrosis. However, additional bacteria including Lonsdalea britannica and Rahnella species have been detected in the lesion microbiome, but their role in tissue degradation is unclear. Consequently, information on potential genome-encoded mechanisms for tissue necrosis is critical to understand the role and mechanisms used by bacterial members of the lesion pathobiome in the aetiology of AOD. Here, the whole genomes of bacteria isolated from AOD-affected trees were sequenced, annotated and compared against canonical bacterial phytopathogens and non-pathogenic symbionts. Using orthologous gene inference methods, shared virulence genes that retain the same function were identified. Furthermore, functional annotation of phytopathogenic virulence genes demonstrated that all studied members of the AOD lesion microbiota possessed genes associated with phytopathogens. However, the genome of B. goodwinii was the most characteristic of a necrogenic phytopathogen, corroborating previous pathological and metatranscriptomic studies that implicate it as the key causal agent of AOD lesions. Furthermore, we investigated the genome sequences of other AOD lesion microbiota to understand the potential ability of microbes to cause disease or contribute to pathogenic potential of organisms isolated from this complex pathobiome. The role of these members remains uncertain but some such as G. quercinecans may contribute to tissue necrosis through the release of necrotizing enzymes and may help more dangerous pathogens activate and realize their pathogenic potential or they may contribute as secondary/opportunistic pathogens with the potential to act as accessory species for B. goodwinii. We demonstrate that in combination with ecological data, whole genome sequencing provides key insights into the pathogenic potential of bacterial species whether they be phytopathogens, part-contributors or stimulators of the pathobiome.},
}
@article {pmid30624596,
year = {2019},
author = {Yadav, D and Dutta, A and Mande, SS},
title = {OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsy045},
pmid = {30624596},
issn = {1756-1663},
abstract = {Many microbiome studies employ reference-based operational taxonomic unit (OTU)-picking methods, which in general, rely on databases cataloguing reference OTUs identified through clustering full-length 16S rRNA genes. Given that the rate of accumulation of mutations are not uniform throughout the length of a 16S rRNA gene across different taxonomic clades, results of OTU identification or taxonomic classification obtained using 'short-read' sequence queries (as generated by next-generation sequencing platforms) can be inconsistent and of suboptimal accuracy. De novo OTU clustering results too can significantly vary depending upon the hypervariable region (V-region) targeted for sequencing. As a consequence, comparison of microbiomes profiled in different scientific studies becomes difficult and often poses a challenge in analysing new findings in context of prior knowledge. The OTUX approach of reference-based OTU-picking proposes to overcome these limitations by using 'customized' OTU reference databases, which can cater to different sets of short-read sequences corresponding to different 16S V-regions. The results obtained with OTUX-approach (which are in terms of OTUX-OTU identifiers) can also be 'mapped back' or represented in terms of other OTU database identifiers/taxonomy, e.g. Greengenes, thus allowing for easy cross-study comparisons. Validation with simulated datasets indicates more efficient, accurate, and consistent taxonomic classifications obtained using OTUX-approach, as compared with conventional methods.},
}
@article {pmid30624285,
year = {2019},
author = {Dehner, C and Fine, R and Kriegel, MA},
title = {The microbiome in systemic autoimmune disease: mechanistic insights from recent studies.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000000574},
pmid = {30624285},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: The resident bacterial communities and the host immune system have coevolved for millennia. However, recent changes in modern societies have disrupted this coevolutionary homeostasis and contributed to a rise in immune-mediated conditions. The purpose of this review is to provide an overview of recently elucidated mechanisms of how certain taxa within the bacterial microbiome propagate autoimmunity.<br><br>RECENT FINDINGS: Interactions between the bacterial microbiome with innate and adaptive immune cells propagate autoreactivity, chronic inflammation, and tissue damage in susceptible hosts. These interactions contribute to autoimmune diseases such as rheumatoid arthritis or systemic lupus erythematosus, which are the focus of this review. Recent findings suggest that autoimmune manifestations in genetically susceptible individuals can arise through cross-reactivity with commensal orthologs of autoantigens or commensal-mediated posttranslational modification of autoantigens. Physiologic responses to gut, oral, or skin commensal bacteria can thus be misdirected toward such autoantigens in susceptible hosts. In addition, recent studies highlight that a breach of the gut barrier and translocation of commensal bacteria to non-gut organs can trigger several autoimmune pathways that can be prevented by commensal vaccination or dietary interventions.<br><br>SUMMARY: Complex host-microbiota interactions contribute to systemic autoimmunity outside the gut. On a molecular level, posttranslational modification of, and cross-reactivity with, autoantigens represent mechanisms of how the microbiota mediates autoimmunity. On a cellular level, translocation of live gut bacteria across a dysfunctional gut barrier allows for direct interactions with immune and tissue cells, instigating autoimmunity systemically.},
}
@article {pmid30624175,
year = {2019},
author = {Sloan, TJ and Turton, JC and Tyson, J and Musgrove, A and Fleming, VM and Lister, MM and Loose, MW and Sockett, RE and Diggle, M and Game, FL and Jeffcoate, W},
title = {Examining diabetic heel ulcers through an ecological lens: microbial community dynamics associated with healing and infection.},
journal = {Journal of medical microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1099/jmm.0.000907},
pmid = {30624175},
issn = {1473-5644},
abstract = {PURPOSE: While some micro-organisms, such as Staphylococcus aureus, are clearly implicated in causing tissue damage in diabetic foot ulcers (DFUs), our knowledge of the contribution of the entire microbiome to clinical outcomes is limited. We profiled the microbiome of a longitudinal sample series of 28 people with diabetes and DFUs of the heel in an attempt to better characterize the relationship between healing, infection and the microbiome.<br><br>METHODOLOGY: In total, 237 samples were analysed from 28 DFUs, collected at fortnightly intervals for 6 months or until healing. Microbiome profiles were generated by 16S rRNA gene sequence analysis, supplemented by targeted nanopore sequencing.Result/Key findings. DFUs which failed to heal during the study period (20/28, 71.4 %) were more likely to be persistently colonized with a heterogeneous community of micro-organisms including anaerobes and Enterobacteriaceae (log-likelihood ratio 9.56, P=0.008). During clinically apparent infection, a reduction in the diversity of micro-organisms in a DFU was often observed due to expansion of one or two taxa, with recovery in diversity at resolution. Modelling of the predicted species interactions in a single DFU with high diversity indicated that networks of metabolic interactions may exist that contribute to the formation of stable communities.<br><br>CONCLUSION: Longitudinal profiling is an essential tool for improving our understanding of the microbiology of chronic wounds, as community dynamics associated with clinical events can only be identified by examining changes over multiple time points. The development of complex communities, particularly involving Enterobacteriaceae and strict anaerobes, may be contributing to poor outcomes in DFUs and requires further investigation.},
}
@article {pmid30624087,
year = {2019},
author = {Jung, C and Brubaker, L},
title = {The etiology and management of recurrent urinary tract infections in postmenopausal women.},
journal = {Climacteric : the journal of the International Menopause Society},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/13697137.2018.1551871},
pmid = {30624087},
issn = {1473-0804},
abstract = {Urinary tract infections (UTIs) are one of the most common infections and affect up to 50% of women in their lifetime, with almost half of these women experiencing a recurrence in 6-12 months. Menopause predisposes women to recurrent UTI (rUTI), as normally lower levels of estrogen lead to changes in the urogenital epithelium and subsequently urogenital microbiome. The recently discovered urobiome is now known to have different compositions in both healthy and unhealthy bladders, including a role in the pathophysiology of rUTI, and may be a therapeutic target for prevention and treatment options for rUTI. In postmenopausal women with frequent UTI, the diagnosis of acute UTI should be made using a combination of the symptom assessment and urine diagnostic studies. The choice of UTI antibiotic should include consideration of efficacy, collateral effects, and side-effects. Some women may be candidates for self-start therapy, in which the patient accurately recognizes her UTI symptoms and then starts previously prescribed antibiotics. A large component of the management of women with rUTI is prevention. Urobiome research for bladder health and disease is a young field of investigation with significant potential to improve care for postmenopausal women affected by rUTI through novel, evidence-based prevention and treatment strategies.},
}
@article {pmid30623484,
year = {2019},
author = {Zhai, J and Knox, K and Twigg, HL and Zhou, H and Zhou, JJ},
title = {Exact variance component tests for longitudinal microbiome studies.},
journal = {Genetic epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/gepi.22185},
pmid = {30623484},
issn = {1098-2272},
support = {DMS-1645093//National Science Foundation/ ; GM105785//National Institute of General Medical Sciences/ ; GM053275//National Institute of General Medical Sciences/ ; HG006139//National Human Genome Research Institute/ ; K01DK106116//National Institute of Diabetes and Digestive and Kidney Diseases/ ; New Investigator Award//Arizona Biomedical Research Commission/ ; },
abstract = {In metagenomic studies, testing the association between microbiome composition and clinical outcomes translates to testing the nullity of variance components. Motivated by a lung human immunodeficiency virus (HIV) microbiome project, we study longitudinal microbiome data by using variance component models with more than two variance components. Current testing strategies only apply to models with exactly two variance components and when sample sizes are large. Therefore, they are not applicable to longitudinal microbiome studies. In this paper, we propose exact tests (score test, likelihood ratio test, and restricted likelihood ratio test) to (a) test the association of the overall microbiome composition in a longitudinal design and (b) detect the association of one specific microbiome cluster while adjusting for the effects from related clusters. Our approach combines the exact tests for null hypothesis with a single variance component with a strategy of reducing multiple variance components to a single one. Simulation studies demonstrate that our method has a correct type I error rate and superior power compared to existing methods at small sample sizes and weak signals. Finally, we apply our method to a longitudinal pulmonary microbiome study of HIV-infected patients and reveal two interesting genera Prevotella and Veillonella associated with forced vital capacity. Our findings shed light on the impact of the lung microbiome on HIV complexities. The method is implemented in the open-source, high-performance computing language Julia and is freely available at https://github.com/JingZhai63/VCmicrobiome.},
}
@article {pmid30623278,
year = {2019},
author = {Friedrich, AW},
title = {Control of hospital acquired infections and antimicrobial resistance in Europe: the way to go.},
journal = {Wiener medizinische Wochenschrift (1946)},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10354-018-0676-5},
pmid = {30623278},
issn = {1563-258X},
support = {202085//EU/InterregVA/ ; },
abstract = {One of the major challenges for modern medicine is our ageing society and an increased level of immunocompromised hosts. More invasive and intensive medical interventions will increase the number of healthcare-associated infections (HCAI), which means infection that occur because of or in concomitance, but in any case, during or after healthcare interventions. Such infections are caused usually endogenously from microbial components of the patient's own microbiome. Usually, the microorganisms of the microbiome show a natural resistance against a few antibiotics. Due to selection processes and epidemic transmission of specific clones, microorganisms that have become resistant to multiple antibiotics become part of the patient's microbiome and can subsequently cause infections that are difficult or even impossible to treat. The kind of infections that will occur depends on diverse factors. Already today, according to Cassini et al., 2,609,911 new cases of HCAI occur every year in the European Union and European Economic Area (EU/EEA). The cumulative burden of the six HAIs was estimated at 501 disability-adjusted life years (DALYs) per 100,000 general population each year in the EU/EEA. In a recent publication, 426,277 healthcare-associated infections caused by antimicrobial resistant microorganisms were calculated to occur in the EU every year. Attributable deaths in the EU due to antimicrobial resistant microorganisms were estimated to be 33,110 per year. We know that we cannot prevent all HCAI. Because medical innovations will allow for an increased number of novel treatments that will comprise abiotic materials, microorganisms will adapt to this environment and enhance the risk for new HCAI. The challenge for the future will not be to try to prevent all infections, as some of them will remain unavoidable, but to prevent the occurrence of non-treatable microorganisms that would make unavoidable infections additionally untreatable. That means that we need to reflect on how we organize infection prevention, diagnostics and control. While patients with classical infectious diseases present with infectious diseases (ID)-specific symptoms, patients with HCAI present usually with another underlying disease. HCAI are therefore perceived as a secondary damage not following classical clinical and epidemiological rules. However, more recently we have to consider how we should react to HCAI and antimicrobial resistance (AMR) as they are quite different in epidemiology and transmission behavior than classical infectious diseases. Today, the prevalence of AMR is rising all over Europe. Although good success has been seen in many countries, methicillin-resistant Staphylococcus aureus (MRSA) remains an important challenge for many countries. In addition to MRSA, multidrug-resistant Escherichia coli and carbapenem-resistant Enterobacteriaceae are becoming a problem of public health importance. Furthermore, we need to focus more on implementation of known infection prevention measures than trying to solve the problem by observing and describing it. However, in addition to medical factors such as antibiotic use, hand hygiene etc., we tend to forget that there are factors behind these factors that have a major influence and are found in the structures of our different healthcare systems. We need to look more at the context before we try to implement prevention measures and need to learn from each other. A common goal to tackle carbapenem-resistant Enterobacteriaceae (CRE) by 2030 would be an important step to foster collaboration across Europe. As the current funding and remmuneration system does not sufficiently support prevention of HCAI and AMR, it is time for the development of a less production- but more prevention-economic financing system for clinical microbiology and infection control.},
}
@article {pmid30623233,
year = {2019},
author = {Kim, JY and Kim, EM and Yi, MH and Lee, J and Lee, S and Hwang, Y and Yong, D and Sohn, WM and Yong, TS},
title = {Chinese liver fluke Clonorchis sinensis infection changes the gut microbiome and increases probiotic Lactobacillus in mice.},
journal = {Parasitology research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00436-018-6179-x},
pmid = {30623233},
issn = {1432-1955},
support = {NRF-2016R1A2B4016194//National Research Foundation of Korea/ ; 2011-0012166//National Research Foundation of Korea/ ; },
abstract = {Chinese liver fluke Clonorchis sinensis changes the host's immune system. Recently, it has been reported that helminths including C. sinensis can ameliorate immune-related diseases such as allergy. In addition, recent studies showed that helminth infection can alleviate immune-mediated disorders by altering the gut microbiome. However, changes in the gut microbiome due to C. sinensis have not been reported yet. In this study, changes in the gut microbiome of C57BL/6 mice infected with C. sinensis metacercariae were evaluated over time. Stool was analyzed by 16S rRNA amplicon analysis using high-throughput sequencing technology. There was no apparent difference in species richness and diversity between the infected and control groups. However, the composition of the microbiome was different between the infected and control groups at 20 days and 30 days post-infection, and the difference disappeared at 50 days post-infection. In particular, this microbiome alteration was associated with a change in the relative abundance of genus Lactobacillus and the probiotic Lactobacillus species that are known to have an immune-modulation role in immune-mediated diseases.},
}
@article {pmid30623080,
year = {2018},
author = {Borges, LGDA and Giongo, A and Pereira, LM and Trindade, FJ and Gregianini, TS and Campos, FS and Ghedin, E and da Veiga, ABG},
title = {Comparison of the nasopharynx microbiome between influenza and non-influenza cases of severe acute respiratory infections: A pilot study.},
journal = {Health science reports},
volume = {1},
number = {6},
pages = {e47},
doi = {10.1002/hsr2.47},
pmid = {30623080},
issn = {2398-8835},
abstract = {Aims: Influenza A virus (IAV) can cause severe acute respiratory infection (SARI), and disease outcome may be associated with changes in the microbiome of the nasopharynx. This is a pilot study to characterize the microbiome of the nasopharynx in patients hospitalized with SARI, infected and not infected by IAV.<br><br>Methods and Results: Using target sequencing of the 16S rRNA gene, we assessed the bacterial community of nasopharyngeal aspirate samples and compared the microbiome of patients infected with IAV with the microbiome of patients who were negative for IAV. We observed differences in the relative abundance of Proteobacteria and Firmicutes between SARI patients, with Streptococcus being enriched and Pseudomonas underrepresented in IAV patients compared with patients who were not infected with IAV.<br><br>Conclusion: Pseudomonas taxon seems to be in high frequency on the nasopharynx of SARI patients with non-IAV infection and might present a negative association with Streptococcus taxon. Microbial profile appears to be different between SARI patients infected or not infected with IAV.},
}
@article {pmid30622561,
year = {2018},
author = {Lee, SH and Joo, NS and Kim, KM and Kim, KN},
title = {The Therapeutic Effect of a Multistrain Probiotic on Diarrhea-Predominant Irritable Bowel Syndrome: A Pilot Study.},
journal = {Gastroenterology research and practice},
volume = {2018},
number = {},
pages = {8791916},
doi = {10.1155/2018/8791916},
pmid = {30622561},
issn = {1687-6121},
abstract = {Backgrounds: Recent studies suggest that diarrhea-predominant irritable bowel syndrome (IBS) is associated with intestinal bacterial microflora, colonic inflammation, and small intestinal bacterial overgrowth (SIBO). The purpose of this study was to evaluate the effect of a multistrain probiotic intake on these associated factors in patients with diarrhea-predominant IBS.<br><br>Methods: The recruited volunteers were adults who were diagnosed with diarrhea-predominant IBS according to the Rome III criteria. After 8 weeks of probiotic ingestion, changes in gastrointestinal symptoms, fecal microbiome, SIBO, and fecal calprotectin were determined.<br><br>Results: There was an increase in beneficial bacteria (41.2 ± 16.8% vs. 53.7 ± 15.3%, P = 0.018) and a decrease in harmful bacteria (13.0 ± 13.9% vs. 4.7 ± 4.0%, P = 0.010) in the microbial stool analysis. The SIBO prevalence also decreased at the end of treatment. However, the average levels of fecal calprotectin showed a decreasing tendency, without reaching statistical significance (364.4 ± 729.1 mg/kg vs. 200.9 ± 347.6 mg/kg, P = 0.375).<br><br>Conclusion: Treatment with a multistrain probiotic for 8 weeks led to significant increases in beneficial bacteria in the gut as well as the improvement of gastrointestinal symptoms. This study is registered at the Clinical Research Information Service (KCT0002906).},
}
@article {pmid30622429,
year = {2018},
author = {Belizário, JE and Faintuch, J and Garay-Malpartida, M},
title = {Gut Microbiome Dysbiosis and Immunometabolism: New Frontiers for Treatment of Metabolic Diseases.},
journal = {Mediators of inflammation},
volume = {2018},
number = {},
pages = {2037838},
doi = {10.1155/2018/2037838},
pmid = {30622429},
issn = {1466-1861},
abstract = {Maintenance of healthy human metabolism depends on a symbiotic consortium among bacteria, archaea, viruses, fungi, and host eukaryotic cells throughout the human gastrointestinal tract. Microbial communities provide the enzymatic machinery and the metabolic pathways that contribute to food digestion, xenobiotic metabolism, and production of a variety of bioactive molecules. These include vitamins, amino acids, short-chain fatty acids (SCFAs), and metabolites, which are essential for the interconnected pathways of glycolysis, the tricarboxylic acid/Krebs cycle, oxidative phosphorylation (OXPHOS), and amino acid and fatty acid metabolism. Recent studies have been elucidating how nutrients that fuel the metabolic processes impact on the ways immune cells, in particular, macrophages, respond to different stimuli under physiological and pathological conditions and become activated and acquire a specialized function. The two major inflammatory phenotypes of macrophages are controlled through differential consumption of glucose, glutamine, and oxygen. M1 phenotype is triggered by polarization signal from bacterial lipopolysaccharide (LPS) and Th1 proinflammatory cytokines such as interferon-γ, TNF-α, and IL-1β, or both, whereas M2 phenotype is triggered by Th2 cytokines such as interleukin-4 and interleukin-13 as well as anti-inflammatory cytokines, IL-10 and TGFβ, or glucocorticoids. Glucose utilization and production of chemical mediators including ATP, reactive oxygen species (ROS), nitric oxide (NO), and NADPH support effector activities of M1 macrophages. Dysbiosis is an imbalance of commensal and pathogenic bacteria and the production of microbial antigens and metabolites. It is now known that the gut microbiota-derived products induce low-grade inflammatory activation of tissue-resident macrophages and contribute to metabolic and degenerative diseases, including diabetes, obesity, metabolic syndrome, and cancer. Here, we update the potential interplay of host gut microbiome dysbiosis and metabolic diseases. We also summarize on advances on fecal therapy, probiotics, prebiotics, symbiotics, and nutrients and small molecule inhibitors of metabolic pathway enzymes as prophylactic and therapeutic agents for metabolic diseases.},
}
@article {pmid30622302,
year = {2019},
author = {Nishida, AH and Ochman, H},
title = {A great-ape view of the gut microbiome.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41576-018-0085-z},
pmid = {30622302},
issn = {1471-0064},
abstract = {Humans assemble a specialized microbiome from a world teeming with diverse microorganisms. Comparison to the microbiomes of great apes provides a dimension that is indispensable to understanding how these microbial communities form, function and change. This evolutionary perspective exposes not only how human gut microbiomes have been shaped by our great-ape heritage but also the features that make humans unique, as exemplified by an expansive loss of bacterial and archaeal diversity and the identification of microbial lineages that have co-diversified with their hosts.},
}
@article {pmid30622298,
year = {2019},
author = {Bernard, NJ},
title = {Dietary modulation of the microbiome as therapy.},
journal = {Nature reviews. Rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41584-019-0165-2},
pmid = {30622298},
issn = {1759-4804},
}
@article {pmid30622186,
year = {2019},
author = {Maseda, D and Zackular, JP and Trindade, B and Kirk, L and Roxas, JL and Rogers, LM and Washington, MK and Du, L and Koyama, T and Viswanathan, VK and Vedantam, G and Schloss, PD and Crofford, LJ and Skaar, EP and Aronoff, DM},
title = {Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate Clostridium difficile Colitis while Dysregulating the Inflammatory Response.},
journal = {mBio},
volume = {10},
number = {1},
pages = {},
doi = {10.1128/mBio.02282-18},
pmid = {30622186},
issn = {2150-7511},
abstract = {Clostridium difficile infection (CDI) is a major public health threat worldwide. The use of nonsteroidal anti-inflammatory drugs (NSAIDs) is associated with enhanced susceptibility to and severity of CDI; however, the mechanisms driving this phenomenon have not been elucidated. NSAIDs alter prostaglandin (PG) metabolism by inhibiting cyclooxygenase (COX) enzymes. Here, we found that treatment with the NSAID indomethacin prior to infection altered the microbiota and dramatically increased mortality and the intestinal pathology associated with CDI in mice. We demonstrated that in C. difficile-infected animals, indomethacin treatment led to PG deregulation, an altered proinflammatory transcriptional and protein profile, and perturbed epithelial cell junctions. These effects were paralleled by increased recruitment of intestinal neutrophils and CD4+ cells and also by a perturbation of the gut microbiota. Together, these data implicate NSAIDs in the disruption of protective COX-mediated PG production during CDI, resulting in altered epithelial integrity and associated immune responses.IMPORTANCEClostridium difficile infection (CDI) is a spore-forming anaerobic bacterium and leading cause of antibiotic-associated colitis. Epidemiological data suggest that use of nonsteroidal anti-inflammatory drugs (NSAIDs) increases the risk for CDI in humans, a potentially important observation given the widespread use of NSAIDs. Prior studies in rodent models of CDI found that NSAID exposure following infection increases the severity of CDI, but mechanisms to explain this are lacking. Here we present new data from a mouse model of antibiotic-associated CDI suggesting that brief NSAID exposure prior to CDI increases the severity of the infectious colitis. These data shed new light on potential mechanisms linking NSAID use to worsened CDI, including drug-induced disturbances to the gut microbiome and colonic epithelial integrity. Studies were limited to a single NSAID (indomethacin), so future studies are needed to assess the generalizability of our findings and to establish a direct link to the human condition.},
}
@article {pmid30621760,
year = {2018},
author = {Gerner, SM and Rattei, T and Graf, AB},
title = {Assessment of urban microbiome assemblies with the help of targeted in silico gold standards.},
journal = {Biology direct},
volume = {13},
number = {1},
pages = {22},
doi = {10.1186/s13062-018-0225-6},
pmid = {30621760},
issn = {1745-6150},
support = {Call 19-19 Project UrbanMetagenApp//MA23/ ; },
abstract = {BACKGROUND: Microbial communities play a crucial role in our environment and may influence human health tremendously. Despite being the place where human interaction is most abundant we still know little about the urban microbiome. This is highlighted by the large amount of unclassified DNA reads found in urban metagenome samples. The only in silico approach that allows us to find unknown species, is the assembly and classification of draft genomes from a metagenomic dataset. In this study we (1) investigate the applicability of an assembly and binning approach for urban metagenome datasets, and (2) develop a new method for the generation of in silico gold standards to better understand the specific challenges of such datasets and provide a guide in the selection of available software.<br><br>RESULTS: We applied combinations of three assembly (Megahit, SPAdes and MetaSPAdes) and three binning tools (MaxBin, MetaBAT and CONCOCT) to whole genome shotgun datasets from the CAMDA 2017 Challenge. Complex in silico gold standards with a simulated bacterial fraction were generated for representative samples of each surface type and city. Using these gold standards, we found the combination of SPAdes and MetaBAT to be optimal for urban metagenome datasets by providing the best trade-off between the number of high-quality genome draft bins (MIMAG standards) retrieved, the least amount of misassemblies and contamination. The assembled draft genomes included known species like Propionibacterium acnes but also novel species according to respective ANI values.<br><br>CONCLUSIONS: In our work, we showed that, even for datasets with high diversity and low sequencing depth from urban environments, assembly and binning-based methods can provide high-quality genome drafts. Of vital importance to retrieve high-quality genome drafts is sequence depth but even more so a high proportion of the bacterial sequence fraction too achieve high coverage for bacterial genomes. In contrast to read-based methods relying on database knowledge, genome-centric methods as applied in this study can provide valuable information about unknown species and strains as well as functional contributions of single community members within a sample. Furthermore, we present a method for the generation of sample-specific highly complex in silico gold standards.<br><br>REVIEWERS: This article was reviewed by Craig Herbold, Serghei Mangul and Yana Bromberg.},
}
@article {pmid30621755,
year = {2018},
author = {Osmanovic, D and Kessler, DA and Rabin, Y and Soen, Y},
title = {Darwinian selection of host and bacteria supports emergence of Lamarckian-like adaptation of the system as a whole.},
journal = {Biology direct},
volume = {13},
number = {1},
pages = {24},
doi = {10.1186/s13062-018-0224-7},
pmid = {30621755},
issn = {1745-6150},
support = {1902/12//Israel Science Foundation/ ; 2015619//United States - Israel Binational Science Foundation/ ; 40663//John Templeton Foundation/ ; },
abstract = {BACKGROUND: The relatively fast selection of symbiotic bacteria within hosts and the potential transmission of these bacteria across generations of hosts raise the question of whether interactions between host and bacteria support emergent adaptive capabilities beyond those of germ-free hosts.<br><br>RESULTS: To investigate possibilities for emergent adaptations that may distinguish composite host-microbiome systems from germ-free hosts, we introduce a population genetics model of a host-microbiome system with vertical transmission of bacteria. The host and its bacteria are jointly exposed to a toxic agent, creating a toxic stress that can be alleviated by selection of resistant individuals and by secretion of a detoxification agent (&quot;detox&quot;). We show that toxic exposure in one generation of hosts leads to selection of resistant bacteria, which in turn, increases the toxic tolerance of the host's offspring. Prolonged exposure to toxin over many host generations promotes anadditional form of emergent adaptation due to selection of hosts based on detox produced by their bacterial community as a whole (as opposed to properties of individual bacteria).<br><br>CONCLUSIONS: These findings show that interactions between pure Darwinian selections of host and its bacteria can give rise to emergent adaptive capabilities, including Lamarckian-like adaptation of the host-microbiome system.<br><br>REVIEWERS: This article was reviewed by Eugene Koonin, Yuri Wolf and Philippe Huneman.},
}
@article {pmid30621600,
year = {2019},
author = {Imhann, F and Van der Velde, KJ and Barbieri, R and Alberts, R and Voskuil, MD and Vich Vila, A and Collij, V and Spekhorst, LM and der Sloot Kwj, V and Peters, V and Van Dullemen, HM and Visschedijk, MC and Eam, F and Swertz, MA and Dijkstra, G and Weersma, RK},
title = {The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.},
journal = {BMC gastroenterology},
volume = {19},
number = {1},
pages = {5},
doi = {10.1186/s12876-018-0917-5},
pmid = {30621600},
issn = {1471-230X},
support = {016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 92.003.577//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; CD14-04//Maag Lever Darm Stichting (NL)/ ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients.<br><br>CONSTRUCTION AND CONTENT: We initiated the 1000IBD project (https://1000ibd.org) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.<br><br>UTILITY AND DISCUSSION: All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models.<br><br>CONCLUSIONS: We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.},
}
@article {pmid30620802,
year = {2017},
author = {Vaziri, ND and Suematsu, Y and Shimomura, A and Vaziri, ND},
title = {[Uremic toxins and gut micro biome].},
journal = {Nihon Jinzo Gakkai shi},
volume = {59},
number = {4},
pages = {535-544},
pmid = {30620802},
issn = {0385-2385},
abstract = {In the past, little attention had been paid to the intestine and its microbial flora as a potential source of systemic inflammation in chronic kidney disease(CKD). Systemic inflammation plays a central role in progression of CKD and its cardiovascular and various other complications. The gastrointestinal tract houses a large community of microbes that have a symbiotic relationship with the host. The normal microbial flora protects the host against pathogenic microorganisms. It also contributes to the energy metabolism, micronutrient homeostasis and nitrogen bal- ance. Recent studies have revealed significant changes in the composition and function of the microbial flora in CKD patients and animals. These changes are driven by altered intestinal bio- chemical environment caused by: I-heavy influx of urea and uric acid from body fluids into the gastrointestinal tract, II- restrictions of potassium-rich food including fruits and vegetables which as the main source of indigestible complex carbohydrates are the essential nutrients for the guts' symbiotic microbial com- munity, and III- various medications such as phosphate binders, antibiotics etc. Together the changes in intestinal milieu and the resultant microbial dysbiosis play a major role in systemic inflammation and uremic toxicity by several mechanisms : I-generation of several microbial derived uremic toxins such as indoxyl sulfate, p-cresol sulfate and trimethylamine-N-oxide etc. II-reduction of microbial derived micronutrients such a short chain fatty acids (SCFA) which are the main source of nutrients for colonocytes. This is caused by diminished substrates (indigestible complex carbohydrates) which leads to depletion of SCFA-making bacteria. In addition, III-Disruption of the intestinal epithelial barrier by ammonia and ammonium hydroxide generated from hydrolysis of urea by urease-possessing microbial species which are common complications of CKD, and bowel ischemia caused by excessive use of diuretics (in CKD patients) and aggressive ultrafiltration by hemodialysis (in ESRD patients) can impair gastrointestinal epithelial barrier. The resulting breakdown of the gut epithelial barrier (tight junction complex) leads to influx of endotoxin, microbial fragments, and other noxious luminal products in the sub-epithelial tissue and systemic circulation leading to local and systemic inflammation and oxidative stress which are the major cause of morbidity and mortality in CKD population. This review is intended to provide an overview of the effects of CKD on the gut microbiome and intestinal epithelial barrier structure and the potential interventions aimed at mitigating these abnormalities.},
}
@article {pmid30620405,
year = {2019},
author = {Flowers, SA and Baxter, NT and Ward, KM and Kraal, AZ and McInnis, MG and Schmidt, TM and Ellingrod, VL},
title = {Effects of Atypical Antipsychotic Treatment and Resistant Starch Supplementation on Gut Microbiome Composition in a Cohort of Patients with Bipolar Disorder or Schizophrenia.},
journal = {Pharmacotherapy},
volume = {},
number = {},
pages = {},
doi = {10.1002/phar.2214},
pmid = {30620405},
issn = {1875-9114},
abstract = {STUDY OBJECTIVE: Previous studies have identified shifts in gut microbiota associated with atypical antipsychotic (AAP) treatment, which may link AAPs to metabolic burden. Dietary prebiotics such as resistant starch may be beneficial in obesity and glucose regulation, but little is known mechanistically about its ability to modify gut microbiota in AAP-treated individuals. This investigation was undertaken to mechanistically delineate the effects of AAP treatment and resistant starch supplementation on gut microbiota in a psychiatric population.<br><br>DESIGN: Cross-sectional cohort study.<br><br>SETTING: The study was performed in an outpatient setting.<br><br>PATIENTS: Thirty-seven adults with a diagnosis of bipolar disorder or schizophrenia who were treated with an AAP (clozapine, olanzapine, risperidone, quetiapine, or ziprasidone [21 patients]) or lithium and/or lamotrigine (16 patients) for at least 6 months.<br><br>INTERVENTION: Patients in the AAP group received raw unmodified potato starch (resistant starch) daily for 14 days.<br><br>MEASUREMENTS AND MAIN RESULTS: Of the 37 patients, the mean ± SD age was 52.2 ± 12.5 years, and 57% were male. The primary outcome was gut microbiome DNA composition. Microbiome DNA obtained from stool samples from all patients was subject to 16S rRNA gene sequencing before and during resistant starch supplementation. Inter- and Intragroup microbial diversity measures were performed by permutational multivariate analysis of variance and Inverse Simpson Diversity Index, respectively. Differentially abundant organisms were detected by using linear discriminant analysis effect size. Although no significant difference in overall microbiota composition was detected at baseline between AAP users and nonusers, non-AAP users showed increased fractional representation of Alistipes. AAP-treated females exhibited decreased diversity compared with non-AAP-treated females. Although the microbiome of AAP-treated patients varied with resistant starch administration, an increased abundance of the Actinobacteria phylum was observed.<br><br>CONCLUSION: These data suggest that AAP treatment is associated with measurable differences in gut microbiota, particularly in female AAP-treated patients in whom reduced species richness was observed. Additionally, variable microbiome responses to resistant starch supplementation were seen, with a significant increase in starch degraders. This article is protected by copyright. All rights reserved.},
}
@article {pmid30620398,
year = {2019},
author = {Huang, SF and Yang, YY and Chou, KT and Fung, CP and Wang, FD and Su, WJ},
title = {Systemic proinflammation after Mycobacterium tuberculosis infection was correlated to the gut microbiome in HIV-uninfected humans.},
journal = {European journal of clinical investigation},
volume = {},
number = {},
pages = {e13068},
doi = {10.1111/eci.13068},
pmid = {30620398},
issn = {1365-2362},
abstract = {BACKGROUND: The dysbiosis of gut microbiome and interaction with host immunity after Mycobacterium tuberculosis (MTB) infection are under-investigation. We had found fatigue symptom concurrent with dysbiosis by decreasing the ratio of Firmicutes to Bacteroidetes (F/B ratio) in active tuberculosis (TB). The study aims to assess the inflammatory biomarkers and their interaction with gut microbiome in active TB and latent TB infection before starting anti-TB regimens.<br><br>MATERIALS AND METHOD: Interleukin-1 beta (IL-1B), IL-4, IL-6, IL-10, CD3+, CD4+, CD8+ T cells, and interferon-gamma (IFN-γ) releasing assay (IGRA) were measured in 25 active TB patients, 32 LTBI subjects, and 23 healthy controls (HC). Gut microbiome profiles were obtained using 16S rRNA MiSeq sequencing method.<br><br>RESULTS: The leukocytosis (7008±383 cell/cum, p<0.05), increase in IL-6 (229.7±104μg/dL, p<0.05), and decrease in IL-4 (0.27μg/dL±0.1, p<0.05) were presented in active TB. The proportion of polymorphic neutrophil (PMN) in peripheral blood was positively related to the relative abundance of Bacteroidetes in LTBI and active TB (R2 =0.23, p<0.05). The F/B ratio was positively related to the detectable IL-1B in TB (R2 =0.97, p<0.01) and to the IL-4 in LTBI (R2 =0.27, p<0.05). In LTBI, the relative abundances of Coriobacteriales was positively related to the secretion of IFN-gamma against TB antigens more likely associated with of CD4+ T cell (R2 =0.42, p<0.05).<br><br>CONCLUSION: In active TB, dysbiosis with higher relative abundances of Bacteroidetes in stool and low F/B ratio was related to systemic proinflammation. In LTBI, dose-response relationship between peripheral PMN and relative abundances of Bacteroidetes was remained but not lead to systemic inflammation. This article is protected by copyright. All rights reserved.},
}
@article {pmid30620146,
year = {2019},
author = {Rossi, GA and Morelli, P and Galietta, LJ and Colin, AA},
title = {Airway microenvironment alterations and pathogen growth in cystic fibrosis.},
journal = {Pediatric pulmonology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ppul.24246},
pmid = {30620146},
issn = {1099-0496},
support = {//Ricerca Corrente, Italian Ministry of Health/ ; },
abstract = {Cystic Fibrosis Transmembrane Regulator (CFTR) dysfunction is associated with epithelial cell vulnerability and with dysregulation of the local inflammatory responses resulting in excessive airway neutrophilic inflammation and pathogen growth. In combination with impaired mucociliary clearance, and dysregulation of defense function, bacterial infection follows with eventual airway damage and remodeling. Because of these inherent vulnerabilities, viral infections are also more severe and prolonged and appear to render the airway even more prone to bacterial infection. Airway acidity, deficient nitric oxide production and increased iron concentrations, further enhance the airway milieu's susceptibility to infection. Novel diagnostic techniques of the airway microbiome elucidate the coexistence of an array of non-virulent taxa beyond the recognized virulent organisms, predominantly Pseudomonas aeruginosa. The complex interplay between these two bacterial populations, including upregulation of virulence genes and utilization of mucin as a nutrient source, modulates the action of pathogens, modifies the CF airway milieu and contributes to the processes leading to airway derangement. The review provides an update on recent advances of the complex mechanisms that render the CF airway vulnerable to inflammation, infection and ultimately structural damage, the key pathogenetic elements of CF. The recent contributions on CF pathogenesis will hopefully help in identifying new prophylactic measures and therapeutic targets for this highly destructive disorder.},
}
@article {pmid30619992,
year = {2019},
author = {Sharpton, SR and Yong, GJM and Terrault, NA and Lynch, SV},
title = {Gut Microbial Metabolism and Nonalcoholic Fatty Liver Disease.},
journal = {Hepatology communications},
volume = {3},
number = {1},
pages = {29-43},
doi = {10.1002/hep4.1284},
pmid = {30619992},
issn = {2471-254X},
abstract = {The gut microbiome, the multispecies community of microbes that exists in the gastrointestinal tract, encodes several orders of magnitude more functional genes than the human genome. It also plays a pivotal role in human health, in part due to metabolism of environmental, dietary, and host-derived substrates, which produce bioactive metabolites. Perturbations to the composition and associated metabolic output of the gut microbiome have been associated with a number of chronic liver diseases, including nonalcoholic fatty liver disease (NAFLD). Here, we review the rapidly evolving suite of next-generation techniques used for studying gut microbiome composition, functional gene content, and bioactive products and discuss relationships with the pathogenesis of NAFLD.},
}
@article {pmid30619868,
year = {2018},
author = {Ried, K and Travica, N and Sali, A},
title = {The Effect of Kyolic Aged Garlic Extract on Gut Microbiota, Inflammation, and Cardiovascular Markers in Hypertensives: The GarGIC Trial.},
journal = {Frontiers in nutrition},
volume = {5},
number = {},
pages = {122},
doi = {10.3389/fnut.2018.00122},
pmid = {30619868},
issn = {2296-861X},
abstract = {Background: Previous research suggests Kyolic-aged-garlic-extract to be effective in reducing blood pressure in a large proportion of hypertensive patients similar to first-line standard antihypertensive medication. High blood pressure has been linked to gut dysbiosis, with a significant decrease in microbial richness and diversity in hypertensives compared to normotensives. Furthermore, gut dysbiosis has been associated with increased inflammatory status and risk of cardiovascular events. Objective: To assess the effect of Kyolic aged GARlic extract on Gut microbiota, Inflammation, and Cardiovascular markers, including blood pressure, pulse wave velocity and arterial stiffness. Methods: A total of 49 participants with uncontrolled hypertension completed a double-blind randomized placebo-controlled trial of 12-weeks, investigating the effect of daily intake of aged-garlic-extract (1.2 g containing 1.2 mg S-allylcysteine) or placebo on blood pressure, pulse wave velocity and arterial stiffness, inflammatory markers, and gut microbiota. Results: Mean blood pressure was significantly reduced by 10 ± 3.6 mmHg systolic and 5.4 ± 2.3 mmHg diastolic compared to placebo. Vitamin B12 status played a role in responsiveness to garlic on blood pressure in 17% of patients. Garlic significantly lowered central blood pressure, pulse pressure and arterial stiffness (p < 0.05). Trends observed in inflammatory markers TNF-α and IL-6 need to be confirmed in larger trials. Furthermore, aged-garlic-extract improved gut microbiota, evident by higher microbial richness and diversity with a marked increase in Lactobacillus and Clostridia species after 3 months of supplementation. Conclusions: Kyolic-aged-garlic-extract is effective in reducing blood pressure in patients with uncontrolled hypertension, and has the potential to improve arterial stiffness, inflammation, and gut microbial profile. Aged-garlic-extract is highly tolerable with a high safety profile as a stand-alone or adjunctive antihypertensive treatment, with multiple benefits for cardiovascular health. Trial Registration: Australian New Zealand Clinical Trial Registry ACTRN12616000185460 (https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=370096).},
}
@article {pmid30619860,
year = {2018},
author = {Guerreiro, CS and Calado, Â and Sousa, J and Fonseca, JE},
title = {Diet, Microbiota, and Gut Permeability-The Unknown Triad in Rheumatoid Arthritis.},
journal = {Frontiers in medicine},
volume = {5},
number = {},
pages = {349},
doi = {10.3389/fmed.2018.00349},
pmid = {30619860},
issn = {2296-858X},
abstract = {Growing experimental and clinical evidence suggests that a chronic inflammatory response induced by gut dysbiosis can critically contribute to the development of rheumatic diseases, including rheumatoid arthritis (RA). Of interest, an adherence to a Mediterranean diet has been linked to a reduction in mortality and morbidity in patients with inflammatory diseases. Diet and intestinal microbiota are modifying factors that may influence intestinal barrier strength, functional integrity, and permeability regulation. Intestinal microbiota may play a crucial role in RA pathogenesis, but up to now no solid data has clarified a mechanistic relationship between gut microbiota and the development of RA. Nonetheless, microbiota composition in subjects with RA differs from that of controls and this altered microbiome can be partially restored after prescribing disease modifying antirheumatic drugs. High levels of Prevotella copri and similar species are correlated with low levels of microbiota previously associated with immune regulating properties. In addition, some nutrients can alter intestinal permeability and thereby influence the immune response without a known impact on the microbiota. However, critical questions remain to be elucidated, such as the way microbiome fluctuates in relation to diet, and how disease activity may be influenced by changes in diet, microbiota or diet-intestinal microbiota equilibrium.},
}
@article {pmid30619787,
year = {2018},
author = {Torsten, M and Aaron, L},
title = {Microbial Transglutaminase Is Immunogenic and Potentially Pathogenic in Pediatric Celiac Disease.},
journal = {Frontiers in pediatrics},
volume = {6},
number = {},
pages = {389},
doi = {10.3389/fped.2018.00389},
pmid = {30619787},
issn = {2296-2360},
abstract = {The enzyme microbial transglutaminase is heavily used in the food processing industries to ameliorate food qualities and elongate the products' shelf life. As a protein's glue, it cross-links gliadin peptides, creating neo-complexes that are immunogenic and potentially pathogenic to celiac disease communities. Even lacking sequence identity, it imitates functionally the endogenous tissue transglutaminase, known to be the autoantigen of celiac disease and representing an undisputable key player in celiac disease initiation and progress. The present review expend on the enzyme characteristics, exogenous intestinal sources, its cross-linking avidity to gluten or gliadin, turning naïve protein to immunogenic ones. Several observation on microbial transglutaminase cross linked complexes immunogenicity in celiac patients are reviewed and its pathogenicity is summarized. Warnings on its potential risks for the gluten dependent conditions are highlighted. When substantiated, it might represent a new environmental factor of celiac disease genesis. It is hoped that the presented knowledge will encourage further research to explore the mechanism and the pathogenic pathways taken by the gliadin cross linked enzyme in driving celiac disease.},
}
@article {pmid30619779,
year = {2018},
author = {Hu, YL and Pang, W and Huang, Y and Zhang, Y and Zhang, CJ},
title = {The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {433},
doi = {10.3389/fcimb.2018.00433},
pmid = {30619779},
issn = {2235-2988},
abstract = {Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.},
}
@article {pmid30619776,
year = {2018},
author = {Drall, KM and Tun, HM and Kozyrskyj, AL},
title = {Commentary: The Influence of Proton Pump Inhibitors on the Fecal Microbiome of Infants with Gastroesophageal Reflux-A Prospective Longitudinal Interventional Study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {430},
doi = {10.3389/fcimb.2018.00430},
pmid = {30619776},
issn = {2235-2988},
}
@article {pmid30619773,
year = {2018},
author = {Zhu, C and Yuan, C and Ao, S and Shi, X and Chen, F and Sun, X and Zheng, S},
title = {The Predictive Potentiality of Salivary Microbiome for the Recurrence of Early Childhood Caries.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {423},
doi = {10.3389/fcimb.2018.00423},
pmid = {30619773},
issn = {2235-2988},
abstract = {The aim of this study was to investigate the variation of the salivary microbiota in the recurrence of early childhood caries (ECC), and to explore and verify the potential microbial indicators of ECC recurrence. Saliva samples from kindergarten children were tracked every 6 months for 1 year. Finally, in total 28 children and 84 samples were placed on the analysis phase: 7 children with ECC recurrence made up the ECC-recurrence (ER) group, 6 children without ECC recurrence constituted the non-ECC-recurrence (NER) group, and 15 children who kept ECC-free were set as the ECC-free (EF) group. DNA amplicons of the V3-V4 hypervariable region of the bacterial 16S rDNA were generated and sequencing was performed using Illumina MiSeq PE250 platform. No statistically significant differences of the Shannon indices were found in both cross-sectional and longitudinal comparisons. Furthermore, both principal coordinates analysis (PCoA) and heatmap plots demonstrated that the salivary microbial community structure might have potentiality to predict ECC recurrence at an early phase. The relative abundance of Fusobacterium, Prevotella, Leptotrichia, and Capnocytophaga differed significantly between the ER and NER groups at baseline. The values of area under the curve (AUC) of the four genera and their combined synthesis in the prediction for ECC recurrence were 0.857, 0.833, 0.786, 0.833, and 0.952, respectively. The relative abundance of Fusobacterium, Prevotella, Leptotrichia, and Capnocytophaga and their combination showed satisfactory accuracy in the prediction for ECC recurrence, indicating that salivary microbiome had predictive potentiality for recurrence of this disease. These findings might facilitate more effective strategy to be taken in the management of the recurrence of ECC.},
}
@article {pmid30619438,
year = {2018},
author = {Yu, P and Hochholdinger, F},
title = {The Role of Host Genetic Signatures on Root-Microbe Interactions in the Rhizosphere and Endosphere.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1896},
doi = {10.3389/fpls.2018.01896},
pmid = {30619438},
issn = {1664-462X},
abstract = {Microbiomes inhabiting plants are crucial for plant productivity and well-being. A plethora of interactions between roots, microbiomes, and soil shapes the self-organization of the microbial community associated with the root system. The rhizosphere (i.e., the soil close to the root surface) and endosphere (i.e., all inner root tissues) are critical interfaces for the exchange of resources between roots and the soil environment. In recent years, next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes in the endosphere and interactions between roots and microbes at the root-soil interfaces. Genetic factors such as species and genotype of host plants are the driving force of microbial community differentiation and composition. In this mini-review, we will survey the role of these factors on plant-microbe interactions by highlighting the results of next-generation genomic and transcriptomic studies in the rhizosphere and endosphere of land plants. Moreover, environmental factors such as geography and soil type shape the microbiome. Relationships between the root-associated microbiome, architectural variations and functional switches within the root system determine the health and fitness of the whole plant system. A detailed understanding of plant-microbe interactions is of fundamental agricultural importance and significance for crop improvement by plant breeding.},
}
@article {pmid30619323,
year = {2018},
author = {Vossen, ARJV and van der Zee, HH and Prens, EP},
title = {Hidradenitis Suppurativa: A Systematic Review Integrating Inflammatory Pathways Into a Cohesive Pathogenic Model.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2965},
doi = {10.3389/fimmu.2018.02965},
pmid = {30619323},
issn = {1664-3224},
abstract = {Background: The pathogenesis of hidradenitis suppurativa (HS) is not fully understood. This systematic review examined the latest evidence for molecular inflammatory pathways involved in HS as a chronic inflammatory skin disease. Methods: A systematic literature search was performed in PubMed/Medline and EMBASE from January 2013 through September 2017, according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA). Findings on HS pathogenesis were also compared with those of other immune-mediated inflammatory diseases (IMIDs) in a non-systematic review. In addition, current therapeutic options for HS are briefly discussed on the basis of the findings for the inflammatory pathways involved in HS. Results: A total of 32 eligible publications were identified by the systematic search; these were supplemented with three additional publications. The extracted data indicated that four key themes underlie the pathogenesis of HS and related syndromic conditions. First, nicastrin (NCSTN) and PSTPIP1 mutations are directly associated with auto-inflammatory disease. Secondly, the up-regulation of several cytokines including tumor necrosis factor-α and T helper-17/interleukin-23 are connected to auto-inflammatory mechanisms in the pathogenesis of HS. Thirdly, the microbiome of lesional skin differs significantly vs. normal-appearing skin. Fourthly, HS risk is enhanced through physiological and environmental factors such as smoking, obesity, and mechanical friction. There is significant overlap between the pathogenesis of HS, its syndromic forms and other IMIDs, particularly with respect to aberrations in the innate immune response. Conclusions: The evidence presented in this review supports HS as an auto-inflammatory skin disorder associated with alterations in the innate immune system. Based on these most recent data, an integrative viewpoint is presented on the pathogenesis of HS. Current management strategies on HS consist of anti-inflammatory therapies, surgical removal of chronic lesions, and lifestyle changes such as smoking cessation and weight loss. As large gaps remain in the understanding of the pathogenesis of HS, further research is warranted to ultimately improve the management and treatment of patients with HS and related syndromic conditions.},
}
@article {pmid30619299,
year = {2018},
author = {Satitsuksanoa, P and Jansen, K and Głobińska, A and van de Veen, W and Akdis, M},
title = {Regulatory Immune Mechanisms in Tolerance to Food Allergy.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2939},
doi = {10.3389/fimmu.2018.02939},
pmid = {30619299},
issn = {1664-3224},
abstract = {Oral tolerance can develop after frequent exposure to food allergens. Upon ingestion, food is digested into small protein fragments in the gastrointestinal tract. Small food particles are later absorbed into the human body. Interestingly, some of these ingested food proteins can cause allergic immune responses, which can lead to food allergy. So far it has not been completely elucidated how these proteins become immunogenic and cause food allergies. In contrast, oral tolerance helps to prevent the pathologic reactions against different types of food antigens from animal or plant origin. Tolerance to food is mainly acquired by dendritic cells, epithelial cells in the gut, and the gut microbiome. A subset of CD103+ DCs is capable of inducing T regulatory cells (Treg cells) that express anti-inflammatory cytokines. Anergic T cells also contribute to oral tolerance, by reducing the number of effector cells. Similar to Treg cells, B regulatory cells (Breg cells) suppress effector T cells and contribute to the immune tolerance to food allergens. Furthermore, the human microbiome is an essential mediator in the induction of oral tolerance or food allergy. In this review, we outline the current understanding of regulatory immune mechanisms in oral tolerance. The biological changes reflecting early consequences of immune stimulation with food allergens should provide useful information for the development of novel therapeutic treatments.},
}
@article {pmid30619274,
year = {2018},
author = {Thofte, O and Su, YC and Brant, M and Littorin, N and Duell, BL and Alvarado, V and Jalalvand, F and Riesbeck, K},
title = {EF-Tu From Non-typeable Haemophilus influenzae Is an Immunogenic Surface-Exposed Protein Targeted by Bactericidal Antibodies.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2910},
doi = {10.3389/fimmu.2018.02910},
pmid = {30619274},
issn = {1664-3224},
abstract = {Non-typeable Haemophilus influenzae (NTHi), a commensal organism in pre-school children, is an opportunistic pathogen causing respiratory tract infections including acute otitis media. Adults suffering from chronic obstructive pulmonary disease (COPD) are persistently colonized by NTHi. Previous research has suggested that, in some bacterial species, the intracellular elongation factor thermo-unstable (EF-Tu) can moonlight as a surface protein upon host encounter. The aim of this study was to determine whether EF-Tu localizes to the surface of H. influenzae, and if such surface-associated EF-Tu is a target for bactericidal antibodies. Using flow cytometry, transmission immunoelectron microscopy, and epitope mapping, we demonstrated that EF-Tu is exposed at the surface of NTHi, and identified immunodominant epitopes of this protein. Rabbits immunized with whole-cell NTHi produced significantly more immunoglobulin G (IgG) directed against EF-Tu than against the NTHi outer membrane proteins D and F as revealed by enzyme-linked immunosorbent assays. Chemical cleavage of NTHi EF-Tu by cyanogen bromide (CNBr) followed by immunoblotting showed that the immunodominant epitopes were located within the central and C-terminal regions of the protein. Peptide epitope mapping by dot blot analysis further revealed four different immunodominant peptide sequences; EF-Tu41-65, EF-Tu161-185, EF-Tu221-245, and EF-Tu281-305. These epitopes were confirmed to be surface-exposed and accessible by peptide-specific antibodies in flow cytometry. We also analyzed whether antibodies raised against NTHi EF-Tu cross-react with other respiratory tract pathogens. Anti-EF-Tu IgG significantly detected EF-Tu on unencapsulated bacteria, including the Gram-negative H. parainfluenzae, H. haemolyticus, Moraxella catarrhalis and various Gram-positive Streptococci of the oral microbiome. In contrast, considerably less EF-Tu was observed at the surface of encapsulated bacteria including H. influenzae serotype b (Hib) and Streptococcus pneumoniae (e.g., serotype 3 and 4). Removal of the capsule, as exemplified by Hib RM804, resulted in increased EF-Tu surface density. Finally, anti-NTHi EF-Tu IgG promoted complement-dependent bacterial killing of NTHi and other unencapsulated Gram-negative bacteria as well as opsonophagocytosis of Gram-positive bacteria. In conclusion, our data demonstrate that NTHi EF-Tu is surface-exposed and recognized by antibodies mediating host innate immunity against NTHi in addition to other unencapsulated respiratory tract bacteria.},
}
@article {pmid30619246,
year = {2018},
author = {Dahl, Å},
title = {Pollen Lipids Can Play a Role in Allergic Airway Inflammation.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2816},
doi = {10.3389/fimmu.2018.02816},
pmid = {30619246},
issn = {1664-3224},
abstract = {In seed plants, pollen grains carry the male gametes to female structures. They are frequent in the ambient air, and cause airway inflammation in one out of four persons in the population. This was traditionally attributed to soluble glycoproteins, leaking into the nasal mucosa or the conjunctiva, and able to bind antibodies. It is now more and more recognized that also other immunomodulating compounds are present. Lipids bind to Toll-like and PPARγ receptors belonging to antigen-presenting cells in the mammal immune system, activate invariant Natural Killer T-cells, and are able to induce a Type 2 reaction in effector cells. They may also mimic lipid mediators from mammal mast cells. Pollen grains have a rich lipodome of their own. Among the lipids that have been associated with an atopic reaction are saturated and unsaturated fatty acids, glycophospholipids, sphingolipids, sterols, and oxylipids, as well as lipopolysaccharides from the microbiome on the pollen surface. Lipids can be ligands to allergenic proteins.},
}
@article {pmid30619215,
year = {2018},
author = {Han, M and Yang, P and Zhong, C and Ning, K},
title = {The Human Gut Virome in Hypertension.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3150},
doi = {10.3389/fmicb.2018.03150},
pmid = {30619215},
issn = {1664-302X},
abstract = {Objectives: Previous studies have reported that the gut microbiome has an important link with the development of hypertension. Though previous researches have focused on the links of gut bacteria with hypertension, little has been known about the linkage of gut viruses to hypertension and the development of hypertension, largely due to the lack of data mining tools for such investigation. In this work, we have analyzed 196 fecal metagenomic data related to hypertension aiming to profile the gut virome and link the gut virome to pre-hypertension and hypertension. Design: Here, we have applied a statistically sound method for mining of gut virome data and linking gut virome to hypertension. We characterized the viral composition and bacterial composition of 196 samples, identified the viral-type of each sample and linked gut virome to hypertension. Results: We stratified these 196 fecal samples into two viral-types and selected 32 viruses as the biomarkers for these groups. We found that viruses could have a superior resolution and discrimination power than bacteria for differentiation of healthy samples and pre-hypertension samples, as well as hypertension samples. Moreover, as to the co-occurrence networks linking viruses and bacteria, we found increasingly pervasive virus-bacteria linkages from healthy people to pre-hypertension people to hypertension patients. Conclusion: Overall, our results have shown ample indications of the link between human gut virome and hypertension, and could help provide microbial solutions toward early diagnoses of hypertension.},
}
@article {pmid30619212,
year = {2018},
author = {Coretti, L and Paparo, L and Riccio, MP and Amato, F and Cuomo, M and Natale, A and Borrelli, L and Corrado, G and Comegna, M and Buommino, E and Castaldo, G and Bravaccio, C and Chiariotti, L and Berni Canani, R and Lembo, F},
title = {Gut Microbiota Features in Young Children With Autism Spectrum Disorders.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3146},
doi = {10.3389/fmicb.2018.03146},
pmid = {30619212},
issn = {1664-302X},
abstract = {Proliferation and/or depletion of clusters of specific bacteria regulate intestinal functions and may interfere with neuro-immune communication and behavior in patients with autism spectrum disorder (ASD). Consistently, qualitative and quantitative alteration of bacterial metabolites may functionally affect ASD pathophysiology. Up to date, age-restricted cohort studies, that may potentially help to identify specific microbial signatures in ASD, are lacking. We investigated the gut microbiota (GM) structure and fecal short chain fatty acids (SCFAs) levels in a cohort of young children (2-4 years of age) with ASD, with respect to age-matched neurotypical healthy controls. Strong increase of Bacteroidetes and Proteobacteria and decrease of Actinobacteria was observed in these patients. Among the 91 OTUs whose relative abundance was altered in ASD patients, we observed a striking depletion of Bifidobacterium longum, one of the dominant bacteria in infant GM and, conversely, an increase of Faecalibacterium prausnitzii, a late colonizer of healthy human gut and a major butyrate producer. High levels of F. prausnitzii were associated to increase of fecal butyrate levels within normal range, and over representation of KEGG functions related to butyrate production in ASD patients. Here we report unbalance of GM structure with a shift in colonization by gut beneficial bacterial species in ASD patients as off early childhood.},
}
@article {pmid30619206,
year = {2018},
author = {Guo, M and Chen, J and Li, Q and Fu, Y and Fan, G and Ma, J and Peng, L and Zeng, L and Chen, J and Wang, Y and Lee, SM},
title = {Dynamics of Gut Microbiome in Giant Panda Cubs Reveal Transitional Microbes and Pathways in Early Life.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3138},
doi = {10.3389/fmicb.2018.03138},
pmid = {30619206},
issn = {1664-302X},
abstract = {Adult giant pandas (Ailuropoda melanoleuca) express transitional characteristics in that they consume bamboos, despite their carnivore-like digestive tracts. Their genome contains no cellulolytic enzymes; therefore, understanding the development of the giant panda gut microbiome, especially in early life, is important for decoding the rules underlying gut microbial formation, inheritance and dietary transitions. With deep metagenomic sequencing, we investigated the gut microbiomes of two newborn giant panda brothers and their parents living in Macao, China, from 2016 to 2017. Both giant panda cubs exhibited progressive increases in gut microbial richness during growth, particularly from the 6th month after birth. Enterobacteriaceae dominated the gut microbial compositions in both adult giant pandas and cubs. A total of 583 co-abundance genes (CAGs) and about 79 metagenomic species (MGS) from bacteria or viruses displayed significant changes with age. Seven genera (Shewanella, Oblitimonas, Helicobacter, Haemophilus, Aeromonas, Listeria, and Fusobacterium) showed great importance with respect to gut microbial structural determination in the nursing stage of giant panda cubs. Furthermore, 10 orthologous gene functions and 44 pathways showed significant changes with age. Of the significant pathways, 16 from Escherichia, Klebsiella, Propionibacterium, Lactobacillus, and Lactococcus displayed marked differences between parents and their cubs at birth, while 29 pathways from Escherichia, Campylobacter and Lactobacillus exhibited significant increase in cubs from 6 to 9 months of age. In addition, oxidoreductases, transferases, and hydrolases dominated the significantly changed gut microbial enzymes during the growth of giant panda cubs, while few of them were involved in cellulose degradation. The findings indicated diet-stimulated gut microbiome transitions and the important role of Enterobacteriaceae in the guts of giant panda in early life.},
}
@article {pmid30619199,
year = {2018},
author = {Yan, Q and Li, X and Ma, B and Zou, Y and Wang, Y and Liao, X and Liang, J and Mi, J and Wu, Y},
title = {Different Concentrations of Doxycycline in Swine Manure Affect the Microbiome and Degradation of Doxycycline Residue in Soil.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3129},
doi = {10.3389/fmicb.2018.03129},
pmid = {30619199},
issn = {1664-302X},
abstract = {Antibiotic residues that enter the soil through swine manure could disturb the number, community structure and functions of microbiota which could also degrade antibiotics in soil. Five different concentrations of doxycycline (DOX) incorporated into swine manure were added to soil to explore the effects of DOX on microbiota in soil and degradation itself. The results showed that the soil microbiome evolved an adaptation to the soil containing DOX by generating resistance genes. Moreover, some of the organisms within the soil microbiome played crucial roles in the degradation of DOX. The average degradation half-life of DOX in non-sterile groups was 13.85 ± 0.45 days, which was significantly shorter than the 29.26 ± 0.98 days in the group with sterilized soil (P < 0.01), indicating that the soil microbiome promoted DOX degradation. DOX addition affected the number of tetracycline resistance genes, depending on the type of gene and the DOX concentration. Among these genes, tetA, tetM, tetW, and tetX had significantly higher copy numbers when the concentration of DOX was higher. In contrast, a lower concentration of DOX had an inhibitory effect on tetG. At the same time, the microbial compositions were affected by the initial concentration of DOX and the different experimental periods. The soil chemical indicators also affected the microbial diversity changes, mainly because some microorganisms could survive in adversity and become dominant bacterial groups, such as the genera Vagococcus and Enterococcus (which were associated with electrical conductivity) and Caldicoprobacter spp. (which were positively correlated with pH). Our study mainly revealed soil microbiota and DOX degradation answered differently under variable concentrations of DOX mixed with swine manure in soil.},
}
@article {pmid30619188,
year = {2018},
author = {Xiao, J and Chen, L and Yu, Y and Zhang, X and Chen, J},
title = {A Phylogeny-Regularized Sparse Regression Model for Predictive Modeling of Microbial Community Data.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3112},
doi = {10.3389/fmicb.2018.03112},
pmid = {30619188},
issn = {1664-302X},
abstract = {Fueled by technological advancement, there has been a surge of human microbiome studies surveying the microbial communities associated with the human body and their links with health and disease. As a complement to the human genome, the human microbiome holds great potential for precision medicine. Efficient predictive models based on microbiome data could be potentially used in various clinical applications such as disease diagnosis, patient stratification and drug response prediction. One important characteristic of the microbial community data is the phylogenetic tree that relates all the microbial taxa based on their evolutionary history. The phylogenetic tree is an informative prior for more efficient prediction since the microbial community changes are usually not randomly distributed on the tree but tend to occur in clades at varying phylogenetic depths (clustered signal). Although community-wide changes are possible for some conditions, it is also likely that the community changes are only associated with a small subset of &quot;marker&quot; taxa (sparse signal). Unfortunately, predictive models of microbial community data taking into account both the sparsity and the tree structure remain under-developed. In this paper, we propose a predictive framework to exploit sparse and clustered microbiome signals using a phylogeny-regularized sparse regression model. Our approach is motivated by evolutionary theory, where a natural correlation structure among microbial taxa exists according to the phylogenetic relationship. A novel phylogeny-based smoothness penalty is proposed to smooth the coefficients of the microbial taxa with respect to the phylogenetic tree. Using simulated and real datasets, we show that our method achieves better prediction performance than competing sparse regression methods for sparse and clustered microbiome signals.},
}
@article {pmid30619179,
year = {2018},
author = {Regier, Y and Komma, K and Weigel, M and Pulliainen, AT and Göttig, S and Hain, T and Kempf, VAJ},
title = {Microbiome Analysis Reveals the Presence of Bartonella spp. and Acinetobacter spp. in Deer Keds (Lipoptena cervi).},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3100},
doi = {10.3389/fmicb.2018.03100},
pmid = {30619179},
issn = {1664-302X},
abstract = {The deer ked (Lipoptena cervi) is distributed in Europe, North America, and Siberia and mainly infests cervids as roe deer, fallow deer, and moose. From a one health perspective, deer keds occasionally bite other animals or humans and are a potential vector for Bartonella schoenbuchensis. This bacterium belongs to a lineage of ruminant-associated Bartonella spp. and is suspected to cause dermatitis and febrile diseases in humans. In this study, we analyzed the microbiome from 130 deer keds collected from roe deer, fallow deer and humans in the federal states of Hesse, Baden-Wuerttemberg, and Brandenburg, Germany. Endosymbiontic Arsenophonus spp. and Bartonella spp. represented the biggest portion (~90%) of the microbiome. Most Bartonella spp. (n = 93) were confirmed to represent B. schoenbuchensis. In deer keds collected from humans, no Bartonella spp. were detected. Furthermore, Acinetobacter spp. were present in four samples, one of those was confirmed to represent A. baumannii. These data suggest that deer keds harbor only a very narrow spectrum of bacteria which are potentially pathogenic for animals of humans.},
}
@article {pmid30619148,
year = {2018},
author = {Zhang, H and Hua, R and Zhang, B and Zhang, X and Yang, H and Zhou, X},
title = {Serine Alleviates Dextran Sulfate Sodium-Induced Colitis and Regulates the Gut Microbiota in Mice.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3062},
doi = {10.3389/fmicb.2018.03062},
pmid = {30619148},
issn = {1664-302X},
abstract = {Serine alleviates inflammatory responses and is beneficial for gut health; however, whether it exerts any effects on ulcerative colitis or regulates intestinal microbiota remains unknown. We investigated the effects of serine supplementation on colonic morphology, inflammation, and microbiota composition in dextran sulfate sodium (DSS)-induced colitis model in mice. Acute colitis was induced through the oral intake of 3.5% DSS in water for 7 days. Mice with acute colitis were divided into two groups; The DSS and Ser-treated groups were rectally administrated with PBS or 1% (w/v) serine (40 mg/kg body weight) for 7 days. The results showed that serine decreased the disease activity index, as well as myeloperoxidase, eosinophil peroxidase, and proinflammatory cytokine concentrations in colonic tissue, while serine improved colonic morphology and inhibited cell apoptosis in colitis mice. In addition, 16S rRNA phylogenetic sequencing revealed a shift in bacterial community composition, and changes in microbiota functional profiles following serine supplementation, although no significant difference in α-diversity analysis was observed. The effects of serine supplementation helped on the recovery of major perturbations to macrobiotic functions, such as amino acids metabolism; tissue replication and repair; and cell growth and death. Serine might have great potential for the renewal of colonic tissue in DSS-induced colitis.},
}
@article {pmid30619140,
year = {2018},
author = {Mavrodi, OV and Jung, CM and Eberly, JO and Hendry, SV and Namjilsuren, S and Biber, PD and Indest, KJ and Mavrodi, DV},
title = {Rhizosphere Microbial Communities of Spartina alterniflora and Juncus roemerianus From Restored and Natural Tidal Marshes on Deer Island, Mississippi.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3049},
doi = {10.3389/fmicb.2018.03049},
pmid = {30619140},
issn = {1664-302X},
abstract = {The U. S. Gulf of Mexico is experiencing a dramatic increase in tidal marsh restoration actions, which involves planting coastal areas with smooth cordgrass (Spartina alterniflora) and black needlerush (Juncus roemerianus) for erosion control and to provide habitat for fish and wildlife. It can take decades for sedimentary cycles in restored marshes to approach reference conditions, and the contribution of the sediment microbial communities to these processes is poorly elucidated. In this study, we addressed this gap by comparing rhizosphere microbiomes of S. alterniflora and J. roemerianus from two restored marshes and a natural reference marsh located at Deer Island, MS. Our results revealed that plants from the restored and reference areas supported similar microbial diversity indicating the rapid colonization of planted grasses with indigenous soil microbiota. Although close in composition, the microbial communities from the three studied sites differed significantly in the relative abundance of specific taxa. The observed differences are likely driven by the host plant identity and properties of sediment material used for the creation of restored marshes. Some of the differentially distributed groups of bacteria include taxa involved in the cycling of carbon, nitrogen, and sulfur, and may influence the succession of vegetation at the restored sites to climax condition. We also demonstrated that plants from the restored and reference sites vary in the frequency of culturable rhizobacteria that exhibit traits commonly associated with the promotion of plant growth and suppression of phytopathogenic fungi. Our findings will contribute to the establishment of benchmarks for the assessment of the outcome of coastal restoration projects in the Gulf of Mexico and better define factors that affect the long-term resiliency of tidal marshes and their vulnerability to climate change.},
}
@article {pmid30619134,
year = {2018},
author = {Porcar, M and Louie, KB and Kosina, SM and Van Goethem, MW and Bowen, BP and Tanner, K and Northen, TR},
title = {Microbial Ecology on Solar Panels in Berkeley, CA, United States.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3043},
doi = {10.3389/fmicb.2018.03043},
pmid = {30619134},
issn = {1664-302X},
abstract = {Solar panels can be found practically all over the world and represent a standard surface that can be colonized by microbial communities that are resistant to harsh environmental conditions, including high irradiation, temperature fluctuations and desiccation. These properties make them not only ideal sources of stress-resistant bacteria, but also standard devices to study the microbial communities and their colonization process from different areas of Earth. We report here a comprehensive description of the microbial communities associated with solar panels in Berkeley, CA, United States. Cultivable bacteria were isolated to characterize their adhesive capabilities, and UV- and desiccation-resistance properties. Furthermore, a parallel culture-independent metagenomic and metabolomic approach has allowed us to gain insight on the taxonomic and functional nature of these communities. Metagenomic analysis was performed using the Illumina HiSeq2500 sequencing platform, revealing that the bacterial population of the Berkeley solar panels is composed mainly of Actinobacteria, Bacteroidetes and Proteobacteria, as well as lower amounts of Deinococcus-Thermus and Firmicutes. Furthermore, a clear predominance of Hymenobacter sp. was also observed. A functional analysis revealed that pathways involved in the persistence of microbes on solar panels (i.e., stress response, capsule development, and metabolite repair) and genes assigned to carotenoid biosynthesis were common to all metagenomes. On the other hand, genes involved in photosynthetic pathways and general autotrophic subsystems were rare, suggesting that these pathways are not critical for persistence on solar panels. Metabolomics was performed using a liquid chromatography tandem mass spectrometry (LC-MS/MS) approach. When comparing the metabolome of the solar panels from Berkeley and from Valencia (Spain), a very similar composition in polar metabolites could be observed, although some metabolites appeared to be differentially represented (for example, trigonelline, pantolactone and 5-valerolactone were more abundant in the samples from Valencia than in the ones from Berkeley). Furthermore, triglyceride metabolites were highly abundant in all the solar panel samples, and both locations displayed similar profiles. The comparison of the taxonomic profile of the Californian solar panels with those previously described in Spain revealed striking similarities, highlighting the central role of both selective pressures and the ubiquity of microbial populations in the colonization and establishment of microbial communities.},
}
@article {pmid30619117,
year = {2018},
author = {López-García, A and Pineda-Quiroga, C and Atxaerandio, R and Pérez, A and Hernández, I and García-Rodríguez, A and González-Recio, O},
title = {Comparison of Mothur and QIIME for the Analysis of Rumen Microbiota Composition Based on 16S rRNA Amplicon Sequences.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3010},
doi = {10.3389/fmicb.2018.03010},
pmid = {30619117},
issn = {1664-302X},
abstract = {Background: Microbiome studies need to analyze massive sequencing data, which requires the use of sophisticated bioinformatics pipelines. Up to date, several tools are available, although the literature is scarce on studies that compare the performance of different bioinformatics pipelines on rumen microbiota when 16S rRNA amplicons are analyzed. The impact of the pipeline on the outcome of the results is also unknown, mainly in terms of the output from studies using these tools as an intermediate phenotype (pseudophenotypes). This study compares two commonly used software (Quantitative Insights Into Microbial Ecology) (QIIME) and mothur, and two microbial gene data bases (GreenGenes and SILVA) for 16S rRNA gene analysis, using metagenome read data collected from rumen content of a cohort of dairy cows. Results: We compared the relative abundance (RA) of the identified OTUs at the genus level. Both tools presented a high degree of agreement at identifying the most abundant genera: Bifidobacterium, Butyrivibrio, Methanobrevibacter, Prevotella, and Succiniclasticum (RA > 1%), regardless the database. There were no statistical differences between mothur and QIIME (P > 0.05) at estimating the overall RA of the most abundant (RA > 10%) genera, either using SILVA or GreenGenes. However, differences were found at RA < 10% (P < 0.05) when using GreenGenes as database, with mothur assigning OTUs to a larger number of genera and in larger RA for these less frequent microorganisms. With this database mothur resulted in larger richness (P < 0.05), more favorable rarefaction curves and a larger analytic sensitivity. These differences caused significant and relevant differences between tools at identifying the dissimilarity of microbiotas between pairs of animals. However, these differences were attenuated, but not erased, when SILVA was used as the reference database. Conclusion: The findings showed that the SILVA database seemed a preferred reference dataset for classifying OTUs from rumen microbiota. If this database was used, both QIIME and mothur produced comparable richness and diversity, and also in the RA of most common rumen microbes. However, important differences were found for less common microorganisms which impacted on the beta diversity calculated between pipelines. This may have relevant implications at studying global rumen microbiota.},
}
@article {pmid30619112,
year = {2018},
author = {Deng, H and Yang, S and Zhang, Y and Qian, K and Zhang, Z and Liu, Y and Wang, Y and Bai, Y and Fan, H and Zhao, X and Zhi, F},
title = {Bacteroides fragilis Prevents Clostridium difficile Infection in a Mouse Model by Restoring Gut Barrier and Microbiome Regulation.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2976},
doi = {10.3389/fmicb.2018.02976},
pmid = {30619112},
issn = {1664-302X},
abstract = {Clostridium difficile is currently the leading cause of nosocomial infection. Antibiotics remain the first-line therapy for C. difficile-associated diseases (CDAD), despite the risks of resistance promotion and further gut microbiota perturbation. Notably, the abundance of Bacteroides fragilis was reported to be significantly decreased in CDAD patients. This study aimed to clarify the prophylactic effects of B. fragilis strain ZY-312 in a mouse model of C. difficile infection (CDI). The CDI mouse model was successfully created using C. difficile strain VPI 10463 spores, as confirmed by lethal diarrhea (12.5% survival rate), serious gut barrier disruption, and microbiota disruption. CDI model mice prophylactically treated with B. fragilis exhibited significantly higher survival rates (100% in low dosage group, 87.5% in high dosage group) and improved clinical manifestations. Histopathological analysis of colon and cecum tissue samples revealed an intact gut barrier with strong ZO-1 and Muc-2 expression. The bacterial diversity and relative abundance of gut microbiota were significantly improved. Interestingly, the relative abundance of Akkermansia muciniphila was positively correlated with B. fragilis treatment. In vitro experiments showed that B. fragilis inhibited C. difficile adherence, and attenuated the decrease in CDI-induced transepithelial electrical resistance, ZO-1 and MUC-2 loss, and apoptosis, suggesting that B. fragilis protected against CDI possibly by resisting pathogen colonization and improving gut barrier integrity and functions. In summary, B. fragilis exerted protective effects on a CDI mouse model by modulating gut microbiota and alleviating barrier destruction, thereby relieving epithelial stress and pathogenic colitis triggered by C. difficile. This study provides an alternative preventative measure for CDI and lays the foundations for further investigations of the relationships among opportunistic pathogens, commensal microbiota, and the gut barrier.},
}
@article {pmid30619105,
year = {2018},
author = {Gannesen, AV and Lesouhaitier, O and Racine, PJ and Barreau, M and Netrusov, AI and Plakunov, VK and Feuilloley, MGJ},
title = {Regulation of Monospecies and Mixed Biofilms Formation of Skin Staphylococcus aureus and Cutibacterium acnes by Human Natriuretic Peptides.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2912},
doi = {10.3389/fmicb.2018.02912},
pmid = {30619105},
issn = {1664-302X},
abstract = {Staphylococcus aureus and Cutibacterium acnes are common representatives of the human skin microbiome. However, when these bacteria are organized in biofilm, they could be involved in several skin disorders such as acne or psoriasis. They inhabit in hollows of hair follicles and skin glands, where they form biofilms. There, they are continuously exposed to human hormones, including human natriuretic peptides (NUPs). We first observed that the atrial natriuretic peptide (ANP) and the C-type natriuretic peptide (CNP) have a strong effect S. aureus and C. acnes biofilm formation on the skin. These effects are significantly dependent on the aero-anaerobic conditions and temperature. We also show that both ANP and CNP increased competitive advantages of C. acnes toward S. aureus in mixed biofilm. Because of their temperature-dependent effects, NUPs appear to act as a thermostat, allowing the skin to modulate bacterial development in normal and inflammatory conditions. This is an important step toward understanding how human neuroendocrine systems can regulate the cutaneous microbial community and should be important for applications in fundamental sciences, medicine, dermatology, and cosmetology.},
}
@article {pmid30618841,
year = {2018},
author = {Huitzil, S and Sandoval-Motta, S and Frank, A and Aldana, M},
title = {Modeling the Role of the Microbiome in Evolution.},
journal = {Frontiers in physiology},
volume = {9},
number = {},
pages = {1836},
doi = {10.3389/fphys.2018.01836},
pmid = {30618841},
issn = {1664-042X},
abstract = {There is undeniable evidence showing that bacteria have strongly influenced the evolution and biological functions of multicellular organisms. It has been hypothesized that many host-microbial interactions have emerged so as to increase the adaptive fitness of the holobiont (the host plus its microbiota). Although this association has been corroborated for many specific cases, general mechanisms explaining the role of the microbiota in the evolution of the host are yet to be understood. Here we present an evolutionary model in which a network representing the host adapts in order to perform a predefined function. During its adaptation, the host network (HN) can interact with other networks representing its microbiota. We show that this interaction greatly accelerates and improves the adaptability of the HN without decreasing the adaptation of the microbial networks. Furthermore, the adaptation of the HN to perform several functions is possible only when it interacts with many different bacterial networks in a specialized way (each bacterial network participating in the adaptation of one function). Disrupting these interactions often leads to non-adaptive states, reminiscent of dysbiosis, where none of the networks the holobiont consists of can perform their respective functions. By considering the holobiont as a unit of selection and focusing on the adaptation of the host to predefined but arbitrary functions, our model predicts the need for specialized diversity in the microbiota. This structural and dynamical complexity in the holobiont facilitates its adaptation, whereas a homogeneous (non-specialized) microbiota is inconsequential or even detrimental to the holobiont's evolution. To our knowledge, this is the first model in which symbiotic interactions, diversity, specialization and dysbiosis in an ecosystem emerge as a result of coevolution. It also helps us understand the emergence of complex organisms, as they adapt more easily to perform multiple tasks than non-complex ones.},
}
@article {pmid30618559,
year = {2018},
author = {Van Dyken, P and Lacoste, B},
title = {Impact of Metabolic Syndrome on Neuroinflammation and the Blood-Brain Barrier.},
journal = {Frontiers in neuroscience},
volume = {12},
number = {},
pages = {930},
doi = {10.3389/fnins.2018.00930},
pmid = {30618559},
issn = {1662-4548},
abstract = {Metabolic syndrome, which includes diabetes and obesity, is one of the most widespread medical conditions. It induces systemic inflammation, causing far reaching effects on the body that are still being uncovered. Neuropathologies triggered by metabolic syndrome often result from increased permeability of the blood-brain-barrier (BBB). The BBB, a system designed to restrict entry of toxins, immune cells, and pathogens to the brain, is vital for proper neuronal function. Local and systemic inflammation induced by obesity or type 2 diabetes mellitus can cause BBB breakdown, decreased removal of waste, and increased infiltration of immune cells. This leads to disruption of glial and neuronal cells, causing hormonal dysregulation, increased immune sensitivity, or cognitive impairment depending on the affected brain region. Inflammatory effects of metabolic syndrome have been linked to neurodegenerative diseases. In this review, we discuss the effects of obesity and diabetes-induced inflammation on the BBB, the roles played by leptin and insulin resistance, as well as BBB changes occurring at the molecular level. We explore signaling pathways including VEGF, HIFs, PKC, Rho/ROCK, eNOS, and miRNAs. Finally, we discuss the broader implications of neural inflammation, including its connection to Alzheimer's disease, multiple sclerosis, and the gut microbiome.},
}
@article {pmid30618372,
year = {2019},
author = {Christensen, E},
title = {[The gut microbiome is important in chronic liver disease].},
journal = {Ugeskrift for laeger},
volume = {181},
number = {2},
pages = {},
pmid = {30618372},
issn = {1603-6824},
abstract = {There is increasing evidence of gut dysbiosis being a significant factor in the development and progression of important chronic liver diseases including non-alcoholic steatohepatitis (NASH), alcoholic liver disease, primary sclerosing cholangitis and cirrhosis. Dysbiotic microbiota and their toxic metabolites translocate across the gut epithelium via the portal vein and cause damage to the liver. In NASH, alcohol-producing gut bacteria may be critical for its development. Therapeutic measures to normalise the gut microbiota with diet, probiotics or transplantation of normal microbiota seem to have a beneficial effect.},
}
@article {pmid30618262,
year = {2019},
author = {Williams, B and Weber, KM and Chlipala, G and Evans, C and Morack, R and French, A},
title = {HIV status does not affect rectal microbiome composition, diversity or stability over time: A Chicago Women's Interagency HIV Study (WIHS).},
journal = {AIDS research and human retroviruses},
volume = {},
number = {},
pages = {},
doi = {10.1089/AID.2018.0250},
pmid = {30618262},
issn = {1931-8405},
abstract = {It remains unclear whether differences in gut microbiota noted between HIV infected and uninfected individuals are driven by HIV or sexual behavior. We evaluated rectal swab microbiota of HIV-infected and uninfected women with similar demographic, neighborhood and diet characteristics enrolled in the Chicago Women's Interagency HIV Study (WIHS). DNA was amplified for sequencing of fragments of bacterial small subunit (SSU or 16S) ribosomal RNA (rRNA) genes. HIV infected and uninfected women did not differ by Shannon diversity index (p=0.14), NMDS plot of Bray-Curtis indices (p=0.488, r=0.0027) or copy number of individual taxa. Both groups demonstrated marked microbiome stability over time (p=0.889).},
}
@article {pmid30618044,
year = {2019},
author = {Kan, JM and Cowan, CSM and Ooi, CY and Kasparian, NA},
title = {What can the gut microbiome teach us about the connections between child physical and mental health? A systematic review.},
journal = {Developmental psychobiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/dev.21819},
pmid = {30618044},
issn = {1098-2302},
support = {101229//National Heart Foundation of Australia Future Leader Fellowship/ ; APP1081001//National Health and Medical Research Council/ ; //Harkness Fellowship in Health Care Policy &amp; Practice/ ; GutMIND 797592//Marie Skłodowska-Curie Grant Agreement/ ; //UNSW Medicine Neuroscience, Mental Health and Addictions Theme and SPHERE Mindgardens Clinical Academic Groups seed grant scheme/ ; },
abstract = {A deeper understanding of the gut-brain axis is of significance in pediatrics, given the influential role of early childhood experiences and exposures in shaping the microbiome, and health, across the life course. This systematic review synthesized evidence on the connection between the gut microbiome and mental health in children with physical illness. Six electronic databases were systematically searched and data extracted according to the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines. Of 1,476 identified articles, 11 articles reporting on nine unique studies (all randomized controlled trials) were included. Most studies examined the gut microbiome in infants with colic, while the remaining studies investigated outcomes in children aged 1 day to 18 years at risk for atopic dermatitis or irritable bowel syndrome. Baseline and postintervention gut microbiome differences varied across studies. Findings on psychological functioning also varied, with only half of the captured studies showing a positive effect of intervention on psychological well-being. Only two studies analyzed the association between the gut microbiome and psychological outcomes, each with a different pattern of results. As the field moves forward, it will be critical to gain a better understanding of the microbiome characteristics that influence mental health outcomes in pediatric populations.},
}
@article {pmid30617347,
year = {2019},
author = {Peters, JM and Koo, BM and Patino, R and Heussler, GE and Hearne, CC and Qu, J and Inclan, YF and Hawkins, JS and Lu, CHS and Silvis, MR and Harden, MM and Osadnik, H and Peters, JE and Engel, JN and Dutton, RJ and Grossman, AD and Gross, CA and Rosenberg, OS},
title = {Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0327-z},
pmid = {30617347},
issn = {2058-5276},
abstract = {The vast majority of bacteria, including human pathogens and microbiome species, lack genetic tools needed to systematically associate genes with phenotypes. This is the major impediment to understanding the fundamental contributions of genes and gene networks to bacterial physiology and human health. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a versatile method of blocking gene expression using a catalytically inactive Cas9 protein (dCas9) and programmable single guide RNAs, has emerged as a powerful genetic tool to dissect the functions of essential and non-essential genes in species ranging from bacteria to humans1-6. However, the difficulty of establishing effective CRISPRi systems across bacteria is a major barrier to its widespread use to dissect bacterial gene function. Here, we establish 'Mobile-CRISPRi', a suite of CRISPRi systems that combines modularity, stable genomic integration and ease of transfer to diverse bacteria by conjugation. Focusing predominantly on human pathogens associated with antibiotic resistance, we demonstrate the efficacy of Mobile-CRISPRi in gammaproteobacteria and Bacillales Firmicutes at the individual gene scale, by examining drug-gene synergies, and at the library scale, by systematically phenotyping conditionally essential genes involved in amino acid biosynthesis. Mobile-CRISPRi enables genetic dissection of non-model bacteria, facilitating analyses of microbiome function, antibiotic resistances and sensitivities, and comprehensive screens for host-microorganism interactions.},
}
@article {pmid30617224,
year = {2019},
author = {Lo, BC and Shin, SB and Canals Hernaez, D and Refaeli, I and Yu, HB and Goebeler, V and Cait, A and Mohn, WW and Vallance, BA and McNagny, KM},
title = {IL-22 Preserves Gut Epithelial Integrity and Promotes Disease Remission during Chronic Salmonella Infection.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {},
number = {},
pages = {},
doi = {10.4049/jimmunol.1801308},
pmid = {30617224},
issn = {1550-6606},
abstract = {The cytokine IL-22 is rapidly induced at barrier surfaces where it regulates host-protective antimicrobial immunity and tissue repair but can also enhance disease severity in some chronic inflammatory settings. Using the chronic Salmonella gastroenteritis model, Ab-mediated neutralization of IL-22 impaired intestinal epithelial barrier integrity and, consequently, exaggerated expression of proinflammatory cytokines. As disease normally resolved, neutralization of IL-22 caused luminal narrowing of the cecum-a feature reminiscent of fibrotic strictures seen in Crohn disease patients. Corresponding to the exaggerated immunopathology caused by IL-22 suppression, Salmonella burdens in the gut were reduced. This enhanced inflammation and pathogen clearance was associated with alterations in gut microbiome composition, including the overgrowth of Bacteroides acidifaciens Our findings thus indicate that IL-22 plays a protective role by limiting infection-induced gut immunopathology but can also lead to persistent pathogen colonization.},
}
@article {pmid30617004,
year = {2019},
author = {Arredondo-Hernandez, R and Orduña-Estrada, P and Lopez-Vidal, Y and Ponce de Leon-Rosales, S},
title = {Clostridium Difficile Infection: An Immunological Conundrum.},
journal = {Archives of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arcmed.2018.11.002},
pmid = {30617004},
issn = {1873-5487},
abstract = {The lack of comprehensive understanding of the way immunity backfires on incidence and complications has made Clostridium difficile infection (CDI), the infectious disease of our times, as evidenced by in the parallel course it follows along epidemic of chronic degenerative diseases. Within these ailments, if as suspected the main effect of Clostridium difficile A and B toxins depends on inflammation, then aberrant immune function due to antibiotics would explain IBD triggering after treatment but also, the higher incidence and mortality surrounding disorders that are inflammatory and/or that show abatement of neutrophils. This review will discuss severity of the disease in terms of challenges to immunity during the progression of acute illness. We will identify the common signals in the communication between microbiota and inflammatory cells, as well as the sequestration of the regulatory network by Clostridium difficile, which leads to tissue damage and prevents its elimination from intestinal lumen.},
}
@article {pmid30616668,
year = {2019},
author = {Karimian, F and Vatandoost, H and Rassi, Y and Maleki-Ravasan, N and Mohebali, M and Shirazi, MH and Koosha, M and Choubdar, N and Oshaghi, MA},
title = {Aerobic midgut microbiota of sand fly vectors of zoonotic visceral leishmaniasis from northern Iran, a step toward finding potential paratransgenic candidates.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {10},
doi = {10.1186/s13071-018-3273-y},
pmid = {30616668},
issn = {1756-3305},
support = {28646//Tehran University of Medical Sciences and Health Services/ ; },
abstract = {BACKGROUND: Leishmaniasis is caused by Leishmania parasites and is transmitted to humans through the bite of infected sand flies. Development of Leishmania to infective metacyclic promastigotes occurs within the sand fly gut where the gut microbiota influences development of the parasite. Paratransgenesis is a new control method in which symbiotic bacteria are isolated, transformed and reintroduced into the gut through their diet to express anti-parasitic molecules. In the present study, the midgut microbiota of three sand fly species from a steppe and a mountainous region of northern Iran, where zoonotic visceral leishmaniasis (ZVL) is endemic, was investigated.<br><br>METHODS: Briefly, adult female sand flies was collected during summer 2015 and, after dissection, the bacterial composition of the guts were analyzed using a culture-dependent method. Bacterial DNA from purified colonies was extracted to amplify the 16S rRNA gene which was then sequenced.<br><br>RESULTS: Three ZVL sand fly vectors including Phlebotomus major, P. kandelakii and P. halepensis were found in the highlighted regions. In total, 39 distinct aerobic bacterial species were found in the sand fly midguts. The sand fly microbiota was dominated by Proteobacteria (56.4%) and Firmicutes (43.6%). Bacterial richness was significantly higher in the steppe region than in the mountainous region (32 vs 7 species). Phlebotomus kandelakii, the most important ZVL vector in the study area, had the highest bacterial richness among the three species. Bacillus subtilis and Pantoea agglomerans were isolated from the guts of the sand flies; these are already used for the paratransgenesis of sand flies and mosquitoes, respectively.<br><br>CONCLUSIONS: The existence of B. subtilis and P. agglomerans in the ZVL vectors and other sand fly species studied so far suggests that these two bacterial species are potential candidates for paratransgenic approach to prevent ZVL transmission. Further research needs to test the possible relationship between the gut microbiome richness and the vector competence of the ZVL vectors.},
}
@article {pmid30616666,
year = {2019},
author = {Regier, Y and Komma, K and Weigel, M and Kraiczy, P and Laisi, A and Pulliainen, AT and Hain, T and Kempf, VAJ},
title = {Combination of microbiome analysis and serodiagnostics to assess the risk of pathogen transmission by ticks to humans and animals in central Germany.},
journal = {Parasites &amp; vectors},
volume = {12},
number = {1},
pages = {11},
doi = {10.1186/s13071-018-3240-7},
pmid = {30616666},
issn = {1756-3305},
support = {1369-354//Robert Koch Institut, Berlin/ ; SFB-TR84 TRR 84/2 2014//Deutsche Forschungsgemeinschaft/ ; 01ZX16004C//BMBF CAPSyS/ ; None//Deutsches Zentrum für Infektionsforschung/ ; 295296, 2016-2020//Academy of Finland/ ; Junior group leader grant, 2015-2018//Sigrid Juséliuksen Säätiö/ ; SFB-TR84 project B08 (TRR 84/3 2018)//Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Arthropod-borne diseases remain a major health-threat for humans and animals worldwide. To estimate the distribution of pathogenic agents and especially Bartonella spp., we conducted tick microbiome analysis and determination of the infection status of wild animals, pets and pet owners in the state of Hesse, Germany.<br><br>RESULTS: In total, 189 engorged ticks collected from 163 animals were tested. Selected ticks were analyzed by next generation sequencing (NGS) and confirmatory PCRs, blood specimens of 48 wild animals were analyzed by PCR to confirm pathogen presence and sera of 54 dogs, one cat and 11 dog owners were analyzed by serology. Bartonella spp. were detected in 9.5% of all ticks and in the blood of 17 roe deer. Further data reveal the presence of the human and animal pathogenic species of genera in the family Spirochaetaceae (including Borrelia miyamotoi and Borrelia garinii), Bartonella spp. (mainly Bartonella schoenbuchensis), Rickettsia helvetica, Francisella tularensis and Anaplasma phagocytophilum in ticks. Co-infections with species of several genera were detected in nine ticks. One dog and five dog owners were seropositive for anti-Bartonella henselae-antibodies and one dog had antibodies against Rickettsia conorii.<br><br>CONCLUSIONS: This study provides a snapshot of pathogens circulating in ticks in central Germany. A broad range of tick-borne pathogens are present in ticks, and especially in wild animals, with possible implications for animal and human health. However, a low incidence of Bartonella spp., especially Bartonella henselae, was detected. The high number of various detected pathogens suggests that ticks might serve as an excellent sentinel to detect and monitor zoonotic human pathogens.},
}
@article {pmid30616583,
year = {2019},
author = {Caputo, M and Zoch-Lesniak, B and Karch, A and Vital, M and Meyer, F and Klawonn, F and Baillot, A and Pieper, DH and Mikolajczyk, RT},
title = {Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {1},
doi = {10.1186/s12866-018-1372-8},
pmid = {30616583},
issn = {1471-2180},
abstract = {BACKGROUND: Little is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants' nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers.<br><br>RESULTS: For our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection.<br><br>CONCLUSIONS: Our findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection.},
}
@article {pmid30616384,
year = {2019},
author = {Christoff, AP and Sereia, AF and Hernandes, C and de Oliveira, LF},
title = {Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {},
number = {},
pages = {1535370218821857},
doi = {10.1177/1535370218821857},
pmid = {30616384},
issn = {1535-3699},
abstract = {IMPACT STATEMENT: Research concerning the microbiome of indoor environments like hospitals, houses or buildings could have several implications for human health. Today, there is an ongoing shift in the paradigm of microbial analysis, from single isolated bacterial samples to entire microbiome profiles using high-throughput DNA sequencing methods. The use of sequencing methods in several studies has revealed an unprecedented microbial diversity in indoor environments, leading to a larger comprehension of the entire microbiome context. Here, we present a review of these microbiome studies using high-throughput DNA sequencing, including some new approaches and ideas that can be broadly applied in microbial tracking and epidemiological surveillance of indoor environments.},
}
@article {pmid30615894,
year = {2019},
author = {Bajic, P and Wolfe, AJ and Gupta, GN},
title = {The Urinary Microbiome: Implications in Bladder Cancer Pathogenesis and Therapeutics.},
journal = {Urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urology.2018.12.034},
pmid = {30615894},
issn = {1527-9995},
abstract = {Recent investigation has proven that the bladder is not sterile. However, the implications of this finding in the pathophysiology and management of urothelial cell carcinoma have not been fully described. In this review, we summarize the literature relating to the urinary and gastrointestinal microbiomes in the context of urothelial cell carcinoma. The bladder microbiome may relate to urothelial cell carcinoma pathogenesis/progression, act as a non-invasive and modifiable urinary biomarker and have implications in treatment using immunotherapy agents such as intravesical Bacillus Calmette Guerin. Investigators should continue to optimize techniques to characterize this intriguing new area of human health.},
}
@article {pmid30615657,
year = {2019},
author = {Lyman, CC and Holyoak, GR and Meinkoth, K and Wieneke, X and Chillemi, KA and DeSilva, U},
title = {Canine endometrial and vaginal microbiomes reveal distinct and complex ecosystems.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0210157},
doi = {10.1371/journal.pone.0210157},
pmid = {30615657},
issn = {1932-6203},
abstract = {The objective of this study was to characterize the normal microbiome of healthy canine vagina and endometrium and to determine the effect of the stage of estrous, on the resident microbiome. Cranial vaginal swabs and uterine biopsy samples were collected from twenty-five bitches in five different stages of estrous at elective ovariohysterectomy (OVH). Over 4 million reads of the V4 region of 16S rDNA gene were obtained and used for further analyses. A total of 317 genera belonging to 24 known phyla were identified. The endometrium was higher in bacterial diversity while the vagina was higher in richness. Proteobacteria, Bacteroidetes and Firmicutes were the most abundant phyla observed across all samples. Hydrotalea, Ralstonia, and Fusobacterium accounted for nearly 60% of the OTUs identified in the vagina while organisms identified in the endometrium were more evenly distributed. Pseudomonas, Staphylococcus, and Corynebacterium were the prominent genera in the endometrium. The microbiome of the endometrium was distinctly different from that of the vagina. There was large animal-to-animal variation. Other than the vaginal microbiome of bitches in estrus (i.e. in heat), there were no distinct clustering of the organisms based on the stage of estrous. These findings establish the presence of a resident microbiome of the endometrium throughout all stages of estrous cycle.},
}
@article {pmid30613807,
year = {2018},
author = {O'Sullivan, V and Madrid-Gambin, F and Alegra, T and Gibbons, H and Brennan, L},
title = {Impact of Sample Storage on the NMR Fecal Water Metabolome.},
journal = {ACS omega},
volume = {3},
number = {12},
pages = {16585-16590},
doi = {10.1021/acsomega.8b01761},
pmid = {30613807},
issn = {2470-1343},
abstract = {The study of the fecal metabolome is an important area of research to better understand the human gut microbiome and its impact on human health and diseases. However, there is a lack of work in examining the impact of storage and processing conditions on the metabolite levels of fecal water. Furthermore, there is no universal protocol used for the storage of fecal samples and preparation of fecal water. The objective of the current study was to examine the impact of different storage conditions on fecal samples prior to metabolite extraction. Fecal samples obtained from nine healthy individuals were processed under different conditions: (1) fresh samples prepared immediately after collection, (2) fecal samples stored at 4 °C for 24 h prior to processing, and (3) fecal samples stored at -80 °C for 24 h prior to processing. All samples were analyzed using NMR spectroscopy, multivariate statistical analysis, and repeated measures ANOVA. Samples which were frozen at -80 °C prior to extraction of the metabolites exhibited an increase in the number of metabolites including branched-chain amino acids, aromatic amino acids, and tricarboxylic acid cycle intermediates. Storage of fecal samples at 4 °C ensured higher fidelity to freshly processed samples leading to the recommendation that fecal samples should not be frozen prior to extraction of fecal water. Furthermore, the work highlights the need to standardize sample storage of fecal samples to allow for the accurate study of the fecal metabolome.},
}
@article {pmid30613620,
year = {2018},
author = {Tincati, C and Ancona, G and Marchetti, G},
title = {The fecal microbiome directly drives immune activation in HIV infection.},
journal = {Annals of translational medicine},
volume = {6},
number = {Suppl 1},
pages = {S45},
doi = {10.21037/atm.2018.09.66},
pmid = {30613620},
issn = {2305-5839},
}
@article {pmid30613388,
year = {2018},
author = {Platsidaki, E and Dessinioti, C},
title = {Recent advances in understanding Propionibacterium acnes (Cutibacterium acnes) in acne.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {},
doi = {10.12688/f1000research.15659.1},
pmid = {30613388},
issn = {2046-1402},
abstract = {The skin commensal Propionibacterium acnes, recently renamed Cutibacterium acnes, along with the other major pathophysiological factors of increased seborrhea, hyperkeratinization of the pilosebaceous unit, and inflammation, has long been implicated in the pathogenesis of acne. Recent advances have contributed to our understanding of the role of P. acnes in acne. Although there are no quantitative differences in P. acnes of the skin of patients with acne compared with controls, the P. acnes phylogenic groups display distinct genetic and phenotypic characteristics, P. acnes biofilms are more frequent in acne, and different phylotypes may induce distinct immune responses in acne. P. acnes plays a further important role in the homeostasis of the skin's microbiome, interacting with other cutaneous commensal or pathogenic microorganisms such as Staphylococcus epidermidis, Streptococcus pyogenes, and Pseudomonas species. In the era of increasing antimicrobial resistance, the selection of acne treatment targeting P. acnes and the prevention of antibiotic resistance play a key role in improving outcomes in acne patients and public health.},
}
@article {pmid30613378,
year = {2018},
author = {Lee, SJ},
title = {Recent advances in managing lower urinary tract infections.},
journal = {F1000Research},
volume = {7},
number = {},
pages = {},
doi = {10.12688/f1000research.16245.1},
pmid = {30613378},
issn = {2046-1402},
abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections. Traditionally, all symptomatic UTIs are tested and treated. The use of antibiotics has resulted in an antibiotic resistance crisis, and we have limited options for managing UTIs. Currently, we live in the era of antimicrobial resistance and may live in other eras like the era of the microbiome. New insights might provide an opportunity to prevent the overuse and misuse of antibiotics and could enable the development of innovate managing strategies.},
}
@article {pmid30612664,
year = {2019},
author = {Nakajima, S and Nomura, T and Common, J and Kabashima, K},
title = {Insights into atopic dermatitis gained from genetically defined mouse models.},
journal = {The Journal of allergy and clinical immunology},
volume = {143},
number = {1},
pages = {13-25},
doi = {10.1016/j.jaci.2018.11.014},
pmid = {30612664},
issn = {1097-6825},
abstract = {Atopic dermatitis (AD) is characterized by severe pruritus and recurrent eczema with a chronic disease course. Impaired skin barrier function, hyperactivated TH2 cell-type inflammation, and pruritus-induced scratching contribute to the disease pathogenesis of AD. Skin microbial alterations complicate the pathogenesis of AD further. Mouse models are a powerful tool to analyze such intricate pathophysiology of AD, with a caution that anatomy and immunology of the skin differ between human subjects and mice. Here we review recent understanding of AD etiology obtained using mouse models, which address the epidermal barrier, skin microbiome, TH2 immune response, and pruritus.},
}
@article {pmid30612189,
year = {2019},
author = {Ruusunen, A and Rocks, T and Jacka, F and Loughman, A},
title = {The gut microbiome in anorexia nervosa: relevance for nutritional rehabilitation.},
journal = {Psychopharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00213-018-5159-2},
pmid = {30612189},
issn = {1432-2072},
abstract = {Rapidly accumulating evidence supports the important role of gut microbiome in the regulation of mood, behaviour, appetite, gastrointestinal symptomology, and nutrient metabolism. These are all core features frequently altered in individuals with anorexia nervosa (AN). Current treatment recommendations for AN support the use of high-calorie diets as an essential part of nutritional rehabilitation, commonly achieved by elevating the fat content of the diet. However, in contrast to this approach, there is accumulating evidence suggesting the importance of balanced, high-fibre diets on the gut microbiome. Studies have demonstrated profound differences in the microbial composition of underweight people with AN and those of normal- or overweight individuals. Specific alterations vary widely between studies. It is thus far unclear to what extent the observed differences are brought on by iatrogenic effects of nutritional rehabilitation or the disorder itself. To date, only two studies have investigated the changes in the intestinal microbiota during nutritional rehabilitation and corresponding weight restoration. These studies suggest that the gut microbiome of AN patients was different to healthy controls both prior and following nutritional rehabilitation, though it is noted that these states were associated with lower and higher nutritional intakes, respectively. There is a clear need for further investigation regarding the effects of nutritional rehabilitation on the gut microbiome. Such research would provide insights into the potential role of gut microbiome in modulating the pathophysiology of AN and inform future treatment strategies.},
}
@article {pmid30612185,
year = {2019},
author = {Murphy, AE and Kolkmeyer, R and Song, B and Anderson, IC and Bowen, J},
title = {Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-01312-4},
pmid = {30612185},
issn = {1432-184X},
support = {OCE 1062882//National Science Foundation/ ; OCE 1233801//National Science Foundation/ ; LTER 0080381//National Science Foundation/ ; NA10OAR4170085//Virginia Sea Grant, Virginia Institute of Marine Science/ ; },
abstract = {Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.},
}
@article {pmid30611442,
year = {2019},
author = {Ramos, GP and Papadakis, KA},
title = {Mechanisms of Disease: Inflammatory Bowel Diseases.},
journal = {Mayo Clinic proceedings},
volume = {94},
number = {1},
pages = {155-165},
doi = {10.1016/j.mayocp.2018.09.013},
pmid = {30611442},
issn = {1942-5546},
abstract = {Inflammatory bowel diseases (IBDs), represented by Crohn disease and ulcerative colitis, are associated with major morbidity in Western countries and with increasing incidence in the developing world. Although analysis of the genome of patients with IBD, especially through genome-wide association studies, has unraveled multiple pathways involved in IBD pathogenesis, only part of IBD heritability has been explained by genetic studies. This finding has revealed that environmental factors also play a major role in promoting intestinal inflammation, mostly through their effects in the composition of the microbiome. However, in order for microbial dysbiosis to result in uncontrolled intestinal inflammation, the intestinal barrier formed by intestinal epithelial cells and the innate immune system should also be compromised. Finally, activation of the immune system depends on the working balance between effector and regulatory cells present in the intestinal mucosa, which have also been found to be dysregulated in this patient population. Therefore, IBD pathogenesis is a result of the interplay of genetic susceptibility and environmental impact on the microbiome that through a weakened intestinal barrier will lead to inappropriate intestinal immune activation. In this article, we will review the mechanisms proposed to cause IBD from the genetic, environmental, intestinal barrier, and immunologic perspectives.},
}
@article {pmid30611307,
year = {2019},
author = {Sirová, D and Bárta, J and Šimek, K and Posch, T and Pech, J and Stone, J and Borovec, J and Adamec, L and Vrba, J},
title = {Correction to: Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {4},
doi = {10.1186/s40168-018-0617-y},
pmid = {30611307},
issn = {2049-2618},
abstract = {AbstractFollowing publication of the original article [1], the author reported an error in Fig. 3.},
}
@article {pmid30611306,
year = {2019},
author = {Koppejan, H and Jansen, DTSL and Hameetman, M and Thomas, R and Toes, REM and van Gaalen, FA},
title = {Altered composition and phenotype of mucosal-associated invariant T cells in early untreated rheumatoid arthritis.},
journal = {Arthritis research &amp; therapy},
volume = {21},
number = {1},
pages = {3},
doi = {10.1186/s13075-018-1799-1},
pmid = {30611306},
issn = {1478-6362},
support = {115142//The Innovative Medicines Initiative Joint Undertaking/ ; FP7/2007-2013//Seventh Framework Programme/ ; NA//European Federation of Pharmaceutical Industries and Associations/ ; 15-2-401//Reumafonds/ ; },
abstract = {BACKGROUND: Mucosal-associated invariant T (MAIT) cells are innate-like T cells that recognise bacterial metabolites presented by MHC class I-related protein 1 (MR1). Bacterial dysbiosis has been implicated in auto-inflammatory disease development. We investigated MAIT cells in early, untreated rheumatoid arthritis (RA) and spondyloarthritis (SpA) patients.<br><br>METHODS: Blood and synovial fluid mononuclear cells obtained from patients (SpA/RA) and controls were stimulated with fixed Escherichia coli to provide MAIT ligand. Cells were analysed by flow cytometry and MAIT cells were identified by MR1-5-OP-RU tetramers. Synovial biopsies were studied by confocal microscopy.<br><br>RESULTS: Peripheral and synovial CD3+ MR1-tet+ MAIT cell frequencies were comparable in all groups. MAIT cells were detected in RA and SpA synovium based on CD3, CD161 and Vα7.2 expression. Peripheral RA MAIT cells were mostly CD4+ (controls 8.3%, SpA 12.3%, RA 52.6%; p < 0.001) and CD161 expression was strongly reduced (control mean fluorescence intensity (MFI) = 2348, SpA MFI = 2219, RA MFI = 226; p < 0.001). MAIT cells were hyporesponsive, shown by minimal upregulation of CD25 and CD69 to E. coli stimulation (control, CD25 MFI = 177, CD69 MFI = 1307; SpA, CD25 MFI = 95, CD69 MFI = 1257; RA, CD25 MFI = 0, CD69 MFI = 467; p < 0.001 and p = 0.01 respectively).<br><br>CONCLUSION: In early untreated RA patients, the peripheral MAIT cell composition was altered, with reduced levels of CD161 expression, and cells were hyporesponsive to stimulation. MAIT cell dysfunction may provide a link between the microbiome and development of RA.},
}
@article {pmid30611275,
year = {2019},
author = {Simpson, T and Deleuil, S and Echeverria, N and Komanduri, M and Macpherson, H and Suo, C and Gondalia, S and Fard, MT and Pipingas, A and Scholey, A and Stough, C},
title = {The Australian Research Council Longevity Intervention (ARCLI) study protocol (ANZCTR12611000487910) addendum: neuroimaging and gut microbiota protocol.},
journal = {Nutrition journal},
volume = {18},
number = {1},
pages = {1},
doi = {10.1186/s12937-018-0428-9},
pmid = {30611275},
issn = {1475-2891},
support = {DP1093825//Australian Research Council Discovery/ ; DP1093825//Australian Research Council Discovery/ ; },
abstract = {BACKGROUND: The Australian Research Council Longevity Intervention (ARCLI) was designed to investigate the effects of two active supplements, Pycnogenol and Bacopa monnieri (CDRI08) on cognitive performance in a cohort of elderly participants. An additional antioxidant supplement has been included into the trial. A neuroimaging component has also been added to the ARCLI study to investigate the neurochemical biomarkers of oxidative stress in vivo, as well as structural and functional changes associated with ageing and oxidative stress. Faecal biomarkers of gut microflora will also be analysed to investigate if gut microbiota are associated with domains of cognition (e.g., attention, processing speed, memory), mood or other ARCLI outcome variables. The aim of this paper is to update the published methods of the ARCLI clinical trial before it is completed, and data analysis commences.<br><br>METHODS: ARCLI is a randomised, placebo controlled, double-blind, now 4-arm clinical trial including neuroimaging and gut microflora sub-studies. Along with the demographic, haematological, mood, cardiovascular and cognitive assessments described in the initial protocol, 80 eligible participants from the overall study pool of ~ 400 will be recruited into the neuroimaging study and undergo scans at baseline, 3 months and 12 months. Proton magnetic resonance spectroscopy, resting state functional connectivity and arterial spin labelled perfusion sequences are neuroimaging techniques included for each MRI visit in the study. Similarly, approximately 300 participants from the main study pool will be recruited to provide faecal samples at baseline, 3 months and 12 months so that the gut microbiome can be studied.<br><br>DISCUSSION: ARCLI is 12-month intervention study, currently underway with a group of older adults, investigating a range of outcomes and their association with ageing. The additional measurements in the ARCLI trial will further the understanding of the underlying mechanisms associated with healthy ageing and may provide insights into novel preventative therapeutic strategies for maintaining cognitive and brain health into old age.<br><br>TRIAL REGISTRATION: Australia and New Zealand Clinical Trials Register (ANZCTR): ACTRN12611000487970 .},
}
@article {pmid30610862,
year = {2019},
author = {Hvas, CL and Jørgensen, SMD and Jørgensen, SP and Storgaard, M and Lemming, L and Hansen, MM and Erikstrup, C and Dahlerup, JF},
title = {Fecal Microbiota Transplantation is Superior to Fidaxomicin for Treatment of Recurrent Clostridium difficile Infection.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2018.12.019},
pmid = {30610862},
issn = {1528-0012},
abstract = {BACKGROUND &amp; AIMS: Fecal microbiota transplantation (FMT) is recommended for treatment of recurrent Clostridium difficile infection (rCDI). We performed a single-center, randomized trial to compare the effects of FMT with those of fidaxomicin and vancomycin.<br><br>METHODS: We studied consecutive adults with rCDI seen at a gastroenterology clinic in Denmark, from April 5, 2016 through June 10, 2018. Patients were randomly assigned to a group that received FMT, applied by colonoscopy or nasojejunal tube after 4-10 days of vancomycin (125 mg 4 times daily; FMTv; n = 24), 10 days of fidaxomicin (200 mg twice daily; n = 24), or 10 days of vancomycin (125 mg 4 times daily; n = 16). Patients who had recurrence of CDI following this course of treatment and patients who could not be randomly assigned to groups were offered rescue FMTv. The primary outcome was combined clinical resolution and a negative result from a PCR test for Clostridium difficile (CD) toxin 8 weeks following the allocated treatment. Secondary endpoints included clinical resolution at week 8.<br><br>RESULTS: All 64 patients received their assigned treatment. The combination of clinical resolution and negative results from the test for CD were observed in 17 patients with FMTv (71%), 8 patients given fidaxomicin (33%), and 3 patients given vancomycin (19%) (P for FMTv vs fidaxomicin = .009; P for FMTv vs vancomycin = .001; P for fidaxomicin vs vancomycin = .31). Clinical resolution was observed in 22 patients given FMTv (92%), 10 patients given fidaxomicin (42%), and 3 patients given vancomycin (19%) (P = .0002; P < .0001; P = .13). Results did not differ significantly between patients who received FMTv as their initial therapy and patients who received rescue FMTv. There was 1 serious adverse event that might have been related to FMTv.<br><br>CONCLUSIONS: In a randomized trial of patients with rCDI, we found the combination of vancomycin and FMT to be superior to fidaxomicin or vancomycin, based on endpoints of clinical and microbiological resolution or clinical resolution alone. ClinicalTrials.gov no: NCT02743234. EudraCT j.no: 2015-003004-24.},
}
@article {pmid30610454,
year = {2019},
author = {Shukla, G and Kamboj, S and Sharma, B},
title = {Comparative Analysis of Antigiardial Potential of Heat Inactivated and Probiotic Protein of Probiotic Lactobacillus rhamnosus GG in Murine Giardiasis.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12602-018-9506-8},
pmid = {30610454},
issn = {1867-1314},
abstract = {The present study was designed to envisage the antigiardial efficacy of killed probiotic and probiotic protein (PP) of Lactobacillus rhamnosus GG in murine giardiasis. Experimentally, it was observed that animal administered either with probiotic protein emulsified with adjuvant (PP(E) + Giardia) or killed probiotic (killed probiotic (i/p) + Giardia) had significantly reduced Giardia cycle with respect to observed severity and duration of giardiasis compared with Giardia-infected mice. Further, it was found that animals belonging to PP(E) + Giardia and killed probiotic (i/p) + Giardia had significantly high levels of antigiardial IgA antibody and nitric oxide both in serum and in intestinal fluid compared with Giardia-infected and counter control mice. Histopathologyically, also animals belonging to PP(E) + Giardia and killed probiotic (i/p) + Giardia animals had intact mucosal epithelium lining, basal crypts, and normal villi along with increased goblet cells compared with severe microvillus atrophy, vacuolated epithelial cells, and ileitis in Giardia-infected mice. This is the first-ever study to demonstrate that prior administration of either killed probiotics or probiotic protein of effective probiotic reduced both the severity and the duration of giardiasis mainly by modulating the gut microbiome and morphology along with mucosal immunity, but animals belonging to PP(E) + Giardia had better response than killed probiotic (i/p) + Giardia suggesting that probiotic components do have adjuvant potential and may be used as the vaccine candidate for gastrointestinal diseases.},
}
@article {pmid30609941,
year = {2019},
author = {Zhong, H and Penders, J and Shi, Z and Ren, H and Cai, K and Fang, C and Ding, Q and Thijs, C and Blaak, EE and Stehouwer, CDA and Xu, X and Yang, H and Wang, J and Wang, J and Jonkers, DMAE and Masclee, AAM and Brix, S and Li, J and Arts, ICW and Kristiansen, K},
title = {Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {2},
doi = {10.1186/s40168-018-0608-z},
pmid = {30609941},
issn = {2049-2618},
support = {ID0E5LAG8456//European Foundation for the Study of Diabetes (DE)/ ; ID0EGNAG8457//Netherlands Asthma Foundation/ ; ID0EQOAG8458//Shenzhen Municipal Government of China/ ; ID0E1PAG8459//ZonMW/JPI HDHL Intestinal Microbiomics/ ; ID0EERAG8460//Stichting Astma Bestrijding/ ; ID0E1PAG8461//Dutch Biobanking and Biomolecular Resources Infrastructure (BBMRI-NL)/ ; ID0E1PAG8462//Netherlands Asthma Foundation/ ; },
abstract = {BACKGROUND: The gut microbiota evolves from birth and is in early life influenced by events such as birth mode, type of infant feeding, and maternal and infant antibiotics use. However, we still have a gap in our understanding of gut microbiota development in older children, and to what extent early events and pre-school lifestyle modulate the composition of the gut microbiota, and how this impinges on whole body metabolic regulation in school-age children.<br><br>RESULTS: Taking advantage of the KOALA Birth Cohort Study, a long-term prospective birth cohort in the Netherlands with extensive collection of high-quality host metadata, we applied shotgun metagenomics sequencing and systematically investigated the gut microbiota of children at 6-9 years of age. We demonstrated an overall adult-like gut microbiota in the 281 Dutch school-age children and identified 3 enterotypes dominated by the genera Bacteroides, Prevotella, and Bifidobacterium, respectively. Importantly, we found that breastfeeding duration in early life and pre-school dietary lifestyle correlated with the composition and functional competences of the gut microbiota in the children at school age. The correlations between pre-school dietary lifestyle and metabolic phenotypes exhibited a striking enterotype dependency. Thus, an inverse correlation between high dietary fiber consumption and low plasma insulin levels was only observed in individuals with the Bacteroides and Prevotella enterotypes, but not in Bifidobacterium enterotype individuals in whom the gut microbiota displayed overall lower microbial gene richness, alpha-diversity, functional potential for complex carbohydrate fermentation, and butyrate and succinate production. High total fat consumption and elevated plasma free fatty acid levels in the Bifidobacterium enterotype are associated with the co-occurrence of Streptococcus.<br><br>CONCLUSIONS: Our work highlights the persistent effects of breastfeeding duration and pre-school dietary lifestyle in affecting the gut microbiota in school-age children and reveals distinct compositional and functional potential in children according to enterotypes. The findings underscore enterotype-specific links between the host metabolic phenotypes and dietary patterns, emphasizing the importance of microbiome-based stratification when investigating metabolic responses to diets. Future diet intervention studies are clearly warranted to examine gut microbe-diet-host relationships to promote knowledge-based recommendations in relation to improving metabolic health in children.},
}
@article {pmid30609922,
year = {2019},
author = {Tsai, YL and Lin, TL and Chang, CJ and Wu, TR and Lai, WF and Lu, CC and Lai, HC},
title = {Probiotics, prebiotics and amelioration of diseases.},
journal = {Journal of biomedical science},
volume = {26},
number = {1},
pages = {3},
doi = {10.1186/s12929-018-0493-6},
pmid = {30609922},
issn = {1423-0127},
support = {CORPD1F0013//Chang Gung Memorial Hospital/ ; CMRPD1F0123//Chang Gung Memorial Hospital/ ; 107-2321-B-182-002//Ministry of Science and Technology, Taiwan/ ; MOST 107-3017-F-182-001//Ministry of Science and Technology, Taiwan/ ; },
abstract = {Dysbiosis of gut microbiota is closely related to occurrence of many important chronic inflammations-related diseases. So far the traditionally prescribed prebiotics and probiotics do not show significant impact on amelioration of these diseases in general. Thus the development of next generation prebiotics and probiotics designed to target specific diseases is urgently needed. In this review, we first make a brief introduction on current understandings of normal gut microbiota, microbiome, and their roles in homeostasis of mucosal immunity and gut integrity. Then, under the situation of microbiota dysbiosis, development of chronic inflammations in the intestine occurs, leading to leaky gut situation and systematic chronic inflammation in the host. These subsequently resulted in development of many important diseases such as obesity, type 2 diabetes mellitus, liver inflammations, and other diseases such as colorectal cancer (CRC), obesity-induced chronic kidney disease (CKD), the compromised lung immunity, and some on brain/neuro disorders. The strategy used to optimally implant the effective prebiotics, probiotics and the derived postbiotics for amelioration of the diseases is presented. While the effectiveness of these agents seems promising, additional studies are needed to establish recommendations for most clinical settings.},
}
@article {pmid30609875,
year = {2019},
author = {Waseem, H and Jameel, S and Ali, J and Saleem Ur Rehman, H and Tauseef, I and Farooq, U and Jamal, A and Ali, MI},
title = {Contributions and Challenges of High Throughput qPCR for Determining Antimicrobial Resistance in the Environment: A Critical Review.},
journal = {Molecules (Basel, Switzerland)},
volume = {24},
number = {1},
pages = {},
doi = {10.3390/molecules24010163},
pmid = {30609875},
issn = {1420-3049},
abstract = {Expansion in whole genome sequencing and subsequent increase in antibiotic resistance targets have paved the way of high throughput qPCR (HT-qPCR) for analyzing hundreds of antimicrobial resistance genes (ARGs) in a single run. A meta-analysis of 51 selected studies is performed to evaluate ARGs abundance trends over the last 7 years. WaferGenTM SmartChip is found to be the most widely used HT-qPCR platform among others for evaluating ARGs. Up till now around 1000 environmental samples (excluding biological replicates) from different parts of the world have been analyzed on HT-qPCR. Calculated detection frequency and normalized ARGs abundance (ARGs/16S rRNA gene) reported in gut microbiome studies have shown a trend of low ARGs as compared to other environmental matrices. Disparities in the HT-qPCR data analysis which are causing difficulties to researchers in precise interpretation of results have been highlighted and a possible way forward for resolving them is also suggested. The potential of other amplification technologies and point of care or field deployable devices for analyzing ARGs have also been discussed in the review. Our review has focused on updated information regarding the role, current status and future perspectives of HT-qPCR in the field of antimicrobial resistance.},
}
@article {pmid30609850,
year = {2019},
author = {Vivarelli, S and Salemi, R and Candido, S and Falzone, L and Santagati, M and Stefani, S and Torino, F and Banna, GL and Tonini, G and Libra, M},
title = {Gut Microbiota and Cancer: From Pathogenesis to Therapy.},
journal = {Cancers},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/cancers11010038},
pmid = {30609850},
issn = {2072-6694},
abstract = {Cancer is a multifactorial pathology and it represents the second leading cause of death worldwide. In the recent years, numerous studies highlighted the dual role of the gut microbiota in preserving host's health. Gut resident bacteria are able to produce a number of metabolites and bioproducts necessary to protect host's and gut's homeostasis. Conversely, several microbiota subpopulations may expand during pathological dysbiosis and therefore produce high levels of toxins capable, in turn, to trigger both inflammation and tumorigenesis. Importantly, gut microbiota can interact with the host either modulating directly the gut epithelium or the immune system. Numerous gut populating bacteria, called probiotics, have been identified as protective against the genesis of tumors. Given their capability of preserving gut homeostasis, probiotics are currently tested to help to fight dysbiosis in cancer patients subjected to chemotherapy and radiotherapy. Most recently, three independent studies show that specific gut resident species may potentiate the positive outcome of anti-cancer immunotherapy. The highly significant studies, uncovering the tight association between gut microbiota and tumorigenesis, as well as gut microbiota and anti-cancer therapy, are here described. The role of the Lactobacillus rhamnosus GG (LGG), as the most studied probiotic model in cancer, is also reported. Overall, according to the findings here summarized, novel strategies integrating probiotics, such as LGG, with conventional anti-cancer therapies are strongly encouraged.},
}
@article {pmid30608907,
year = {2019},
author = {Naskali, E and Dettmer, K and Oefner, PJ and Pereira, PAB and Krohn, K and Auvinen, P and Ranki, A and Kluger, N},
title = {Serotonin and tryptophan metabolites, autoantibodies and gut microbiome in APECED.},
journal = {Endocrine connections},
volume = {},
number = {},
pages = {},
doi = {10.1530/EC-18-0513},
pmid = {30608907},
issn = {2049-3614},
abstract = {OBJECTIVE: Intestinal autoimmunity with gastrointestinal (GI) dysfunction has been shown in patients with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). Patients lack entero-endocrine (EE) cells and have circulating autoantibodies (Aabs) against critical enzymes in serotonin (5-HT) biosynthesis.<br><br>DESIGN: We sought to determine serum levels of 5- HT, tryptophan (Trp) metabolites, and L-DOPA in 37 Finnish APECED patients, and to correlate their abundance with the presence of TPH and AADC Aabs, GI dysfunction and depressive symptoms. We also performed an exploratory analysis of the gut microbiome.<br><br>METHODS: Serum 5-HT, L-DOPA, and Trp metabolite levels were determined by liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). TPH and AADC Aabs were measured by ELISA. Depression was assessed with a structured RBDI questionnaire. The V3-V4 regions of the bacterial 16S rRNA gene were sequenced for gut microbiome exploration.<br><br>RESULTS: Serum 5-HT levels were significantly decreased (130 ± 131 nmol/L versus 686 ± 233 nmol/L, p < 0.0001) in APECED patients with TPH-1 (±AADC) Aabs compared to controls and patients with only AADC Aabs. Reduced 5-HT levels correlated with constipation. The genus Escherichia/Shigella was overrepresented in the intestinal microbiome. No correlation between serum Trp, 5-HT or L-DOPA levels and the RBDI total score, fatigue or sleep disorders was found.<br><br>CONCLUSIONS: This exploratory study found low serum levels of 5-HT to be associated with constipation and the presence of TPH-1 and AADC Aabs, but not with symptoms of depression. Hence, serum 5-HT, TPH1 and AADC Aabs should be determined in APECED patients presenting with GI symptoms.},
}
@article {pmid30608429,
year = {2019},
author = {Yomota, M and Yanagawa, N and Sakai, F and Yamada, Y and Sekiya, N and Ohashi, K and Okamura, T},
title = {Association between chronic bacterial airway infection and prognosis of bronchiolitis obliterans syndrome after hematopoietic cell transplantation.},
journal = {Medicine},
volume = {98},
number = {1},
pages = {e13951},
doi = {10.1097/MD.0000000000013951},
pmid = {30608429},
issn = {1536-5964},
abstract = {Bronchiolitis obliterans syndrome (BOS) is a rare pulmonary complication of hematopoietic stem cell transplantation (HSCT) with high mortality. Chronic bacterial airway infection (CAI) causes exacerbation and progression of several airway diseases, and bacterial airway colonization was shown to be associated with BOS after lung transplantation.We assessed the association between CAI and clinical course in patients with BOS after HSCT. This retrospective study included 910 patients undergoing allogeneic HSCT between 2005 and 2013 at our institution. BOS diagnosis was reevaluated according to the 2014 US National Institutes of Health criteria. Sputum and bronchial lavage culture results, pulmonary function, and survival were compared between patients with and without CAI.Median follow-up was 974.5 (261.5-2748.5) days. BOS was diagnosed in 27 (3.0%) patients, including 18 males. Median age at BOS diagnosis was 45 (40.5-58) years. Nine patients had ≥2 positive sputum cultures for bacteria or one positive bronchial lavage culture for nontuberculous mycobacteria (CAI+), whereas 9 patients had negative sputum/bronchial lavage culture or only one positive sputum culture (CAI-). Median change in forced expiratory volume in 1 s within 6 months after BOS diagnosis and overall survival were significantly worse in CAI+ patients than in CAI- patients (-250 vs +260 mL, P = .002, and 1340 days vs not reached, P = .04, respectively). No other factors including patient demographics or transplant protocol affected prognosis. There were no differences in clinical characteristics of patients with and without CAI, except for the time from transplantation to BOS diagnosis (214 vs 768 days for CAI+ and CAI-, respectively; P = .02).CAI was associated with worse outcomes in patients with BOS after HSCT. Further prospective studies should assess the association between the airway microbiome and changes in pulmonary function after HSCT to improve prognosis.},
}
@article {pmid30607442,
year = {2019},
author = {Klimek, L and Wollenberg, B and Guntinas-Lichius, O and Pfaar, O and Koennecke, M},
title = {[Reasons for the development of allergies in children].},
journal = {HNO},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00106-018-0595-1},
pmid = {30607442},
issn = {1433-0458},
abstract = {Allergies are one of the most common chronic diseases in childhood, contributing to a tremendous medical and economical burden in health care systems of most industrialized countries. The development of allergies is dependent on a complex interaction of-among others-environmental factors, nutrition, genetic and epigenetic mechanisms as well as the microbiome. These diverse factors can influence early life immune regulation including innate and adaptive immune mechanisms in a complex fashion. In case of any Childhood allergies have increased significantly in past decades. In addition to environmental factors and nutrition, genetic and epigenetic mechanisms as well as the microbiome of children play an important role. Of relevance is the way in which these diverse factors influence early immune development of the innate and adaptive immune systems of children. Their complex regulation is decisive for whether or not a child develops an allergy that manifests in most cases as atopic dermatitis, bronchial asthma, or allergic rhino conjunctivitis, or whether a child develops an immune tolerance. These influences can begin prenatally, already setting the course for later immune system development and occurrence of disease.},
}
@article {pmid30607012,
year = {2019},
author = {Silverman, GJ},
title = {The microbiome in SLE pathogenesis.},
journal = {Nature reviews. Rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41584-018-0152-z},
pmid = {30607012},
issn = {1759-4804},
}
@article {pmid30606975,
year = {2018},
author = {Toyota, K and Shirai, S},
title = {Growing Interest in Microbiome Research Unraveling Disease Suppressive Soils against Plant Pathogens.},
journal = {Microbes and environments},
volume = {33},
number = {4},
pages = {345-347},
doi = {10.1264/jsme2.ME3304rh},
pmid = {30606975},
issn = {1347-4405},
}
@article {pmid30606811,
year = {2019},
author = {Vitetta, L and Chen, J and Clarke, S},
title = {The vermiform appendix: an immunological organ sustaining a microbiome inoculum.},
journal = {Clinical science (London, England : 1979)},
volume = {133},
number = {1},
pages = {1-8},
doi = {10.1042/CS20180956},
pmid = {30606811},
issn = {1470-8736},
abstract = {The hominoid vermiform appendix has been characterized as a diverticulum of the caecum and describes an entity at the juxtaposition of the colon in the confluence of tanias. The independent development of the lymphoid follicle centres of the appendix is progressed at birth in the presence of the intestinal commensal microbiome, an obligatory prompt for the diversification of intestinal and extra-intestinal mucosal immunological tissue. In the vermiform appendix, this activity is centred on further developing the inventory of primary antibodies and the maturation of T- and B-lymphocyte cells in the follicles within the lymphoid tissue. Furthermore, the columnar epithelia, enterocytes and goblet cells comprise the complement of cells that occupy the lamina propria and muscularis mucosae of the vermiform appendix's mucosa, while macrophages and an abundance of immunoglobulin A and immunoglobulin G generating plasma cells seed the lamina propria Intraepithelial immune cells consisting predominantly of specific CD8+ T regulatory lymphocytes occupy sites in the appendix analogous to those present in the intestinal epithelia of the caecal colon. The complement of bacterial genera concealed in the vermiform appendix is posited extant as a biofilm inoculum of the intestinal commensal microbiome. This facilitates re-inoculation of the proximal colon and to a lesser degree the terminal ilium post an intestinal perturbation such as occurs with daily lifestyle stressors, dietary choices and the short-term administration of antibiotics rather than an infectious fulminant colitis. A plausible appreciation results of the importance of multiple immunological aspects of a healthy vermiform appendix and the provision of a commensal biofilm to the gut that repairs a dysbiotic microbiome contributing to balancing intestinal pro- and anti-inflammatory activity for maintaining homeostasis in the gut. Since the composition of the gut microbiome can vary over the short-term and long-term, it is plausible that the appendix inoculum may be instrumental in maintaining the intestinal microbiome.},
}
@article {pmid30606403,
year = {2019},
author = {Gong, J and Noel, S and Pluznick, JL and Hamad, ARA and Rabb, H},
title = {Gut Microbiota-Kidney Cross-Talk in Acute Kidney Injury.},
journal = {Seminars in nephrology},
volume = {39},
number = {1},
pages = {107-116},
doi = {10.1016/j.semnephrol.2018.10.009},
pmid = {30606403},
issn = {1558-4488},
abstract = {The recent surge in research on the intestinal microbiota has greatly changed our understanding of human biology. Significant technical advances in DNA sequencing analysis and its application to metagenomics and metatranscriptomics has profoundly enhanced our ability to quantify and track complex microbial communities and to begin understanding their impact on human health and disease. This has led to a better understanding of the relationships between the intestinal microbiome and renal physiology/pathophysiology. In this review, we discuss the interactions between intestinal microbiota and kidney. We focus on select aspects including the intestinal barrier, immunologic and soluble mediators of microbiome effects, and effects of dysbiosis on acute kidney injury. Relevant studies on microbiome changes in other renal diseases are highlighted. We also introduce potential mechanisms of intervention with regard to gut microbiota in renal diseases.},
}
@article {pmid30605818,
year = {2018},
author = {Wang, D and Yan, S and Yan, J and Teng, M and Meng, Z and Li, R and Zhou, Z and Zhu, W},
title = {Effects of triphenyl phosphate exposure during fetal development on obesity and metabolic dysfunctions in adult mice: Impaired lipid metabolism and intestinal dysbiosis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {246},
number = {},
pages = {630-638},
doi = {10.1016/j.envpol.2018.12.053},
pmid = {30605818},
issn = {1873-6424},
abstract = {Previous in vitro studies have implied that triphenyl phosphate (TPHP) may act as an obesogen. However, its specific contributions to the progression of obesity and related metabolic diseases are still unclear in vivo in mice. In this study, we evaluated the effects of in utero and lactational exposure to three doses of TPHP (10, 100, and 1000 μg/kg BW) on obesity and metabolic dysfunctions in adult male mice fed a low-fat diet (LFD) or high-fat diet (HFD), by examining body weight, liver weight, histopathology, blood biochemistry, gene expression, and gut microbiota compositions and metabolic functions. Results showed that TPHP exposure led to increased body weight, liver weight, fat mass, hepatic steatosis, impaired glucose homeostasis, and insulin resistance, and mRNA levels of genes involved in lipid metabolism, especially lipogenesis and lipid accumulation, were significantly altered by TPHP treatment. Gas chromatography-mass spectrometry (GC-MS) analysis further supported the changes in fatty acid composition. Intestinal flora measurements by 16S rRNA gene sequencing and 1H NMR based fecal metabolomics indicated that TPHP treatment modulated gut microbiome composition and influenced host-gut co-metabolism, especially for bile acids and short chain fatty acids (SCFAs). These results suggest that fetal exposure to TPHP can promote the development of obesity and metabolic dysfunctions in adult mice.},
}
@article {pmid30605512,
year = {2019},
author = {Awany, D and Allali, I and Chimusa, ER},
title = {Tantalizing dilemma in risk prediction from disease scoring statistics.},
journal = {Briefings in functional genomics},
volume = {},
number = {},
pages = {},
doi = {10.1093/bfgp/ely040},
pmid = {30605512},
issn = {2041-2657},
abstract = {Over the past decade, human host genome-wide association studies (GWASs) have contributed greatly to our understanding of the impact of host genetics on phenotypes. Recently, the microbiome has been recognized as a complex trait in host genetic variation, leading to microbiome GWAS (mGWASs). For these, many different statistical methods and software tools have been developed for association mapping. Applications of these methods and tools have revealed several important findings; however, the establishment of causal factors and the direction of causality in the interactive role between human genetic polymorphisms, the microbiome and the host phenotypes are still a huge challenge. Here, we review disease scoring approaches in host and mGWAS and their underlying statistical methods and tools. We highlight the challenges in pinpointing the genetic-associated causal factors in host and mGWAS and discuss the role of multi-omic approach in disease scoring statistics that may provide a better understanding of human phenotypic variation by enabling further system biological experiment to establish causality.},
}
@article {pmid30604388,
year = {2019},
author = {Osman, AEG and Luke, JJ},
title = {The Impact of the Fecal Microbiome on Cancer Immunotherapy.},
journal = {BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy},
volume = {},
number = {},
pages = {},
doi = {10.1007/s40259-018-0328-8},
pmid = {30604388},
issn = {1179-190X},
support = {W81XWH-17-1-0265//U.S. Department of Defense/ ; },
abstract = {Recent advances in culture-free methods of studying the human microbiome, coupled with strong bioinformatics tools, have provided new insights on the role of the human microbiome in health and disease. The human gut, in particular, houses a vast number and diverse variety of microbes. A plethora of evidence has demonstrated the significant effects of the gut microbiome on local and systemic immunity. Studies in hematopoietic stem cell transplantation recipients provided early evidence of the involvement of the gut microbiome in the development of graft-versus-host disease and its related mortality. Cancer immunotherapy and checkpoint inhibitors, in particular, harness the power of the host's immune system to fight a range of malignancies. Resistance to immunotherapy and fatal immune-related adverse events both continue to be challenges in the field. The role of the human gut microbiome in affecting the response to immunotherapy was recently uncovered through a series of preclinical and clinical studies. The evidence presented in these studies provides tremendous potential for gut microbes to be used for biomarker development and therapeutic intervention trials.},
}
@article {pmid30604186,
year = {2019},
author = {Gao, W and Salzwedel, AP and Carlson, AL and Xia, K and Azcarate-Peril, MA and Styner, MA and Thompson, AL and Geng, X and Goldman, BD and Gilmore, JH and Knickmeyer, RC},
title = {Gut microbiome and brain functional connectivity in infants-a preliminary study focusing on the amygdala.},
journal = {Psychopharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00213-018-5161-8},
pmid = {30604186},
issn = {1432-2072},
support = {DA042988//National Institutes of Health/ ; DA043678//National Institutes of Health/ ; NS088975//National Institutes of Health/ ; DA043171//National Institutes of Health/ ; MH070890//National Institutes of Health/ ; HD053000//National Institutes of Health/ ; MH092335//National Institutes of Health/ ; MH104330//National Institutes of Health/ ; },
abstract = {Recently, there has been a surge of interest in the possibility that microbial communities inhabiting the human gut could affect cognitive development and increase risk for mental illness via the &quot;microbiome-gut-brain axis.&quot; Infancy likely represents a critical period for the establishment of these relationships, as it is the most dynamic stage of postnatal brain development and a key period in the maturation of the microbiome. Indeed, recent reports indicate that characteristics of the infant gut microbiome are associated with both temperament and cognitive performance. The neural circuits underlying these relationships have not yet been delineated. To address this gap, resting-state fMRI scans were acquired from 39 1-year-old human infants who had provided fecal samples for identification and relative quantification of bacterial taxa. Measures of alpha diversity were generated and tested for associations with measures of functional connectivity. Primary analyses focused on the amygdala as manipulation of the gut microbiota in animal models alters the structure and neurochemistry of this brain region. Secondary analyses explored functional connectivity of nine canonical resting-state functional networks. Alpha diversity was significantly associated with functional connectivity between the amygdala and thalamus and between the anterior cingulate cortex and anterior insula. These regions play an important role in processing/responding to threat. Alpha diversity was also associated with functional connectivity between the supplementary motor area (SMA, representing the sensorimotor network) and the inferior parietal lobule (IPL). Importantly, SMA-IPL connectivity also related to cognitive outcomes at 2 years of age, suggesting a potential pathway linking gut microbiome diversity and cognitive outcomes during infancy. These results provide exciting new insights into the gut-brain axis during early human development and should stimulate further studies into whether microbiome-associated changes in brain circuitry influence later risk for psychopathology.},
}
@article {pmid30604012,
year = {2019},
author = {Tyagi, A and Singh, B and Billekallu Thammegowda, NK and Singh, NK},
title = {Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome.},
journal = {Archives of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00203-018-1615-y},
pmid = {30604012},
issn = {1432-072X},
support = {YSS/2014/000269//Science and Engineering Research Board/ ; },
abstract = {Gut microbiota of freshwater carp (Labeo rohita) was investigated by shotgun metagenomics to understand its taxonomic composition and functional capabilities. With the presence of 36 phyla, 326 families and 985 genera, the fish gut microbiota was found to be quite diverse in nature. However, at the phylum level, more than three-fourths of gut microbes belonged to Proteobacteria. Very low prevalence of commonly used probiotic bacteria (Bacillus, Lactobacillus, Streptococcus, and Lactococcus) in fish gut suggested the need to search for alternative probiotics for aquaculture use. Biosynthesis pathways were found to be the most dominant (51%) followed by degradation (39%), energy metabolism (4%) and fermentation (2%). In conformity with herbivorous feeding habit of L. rohita, gut microbiome also had pathways for the degradation of cellulose, hemicellulose, chitin, pectin, starch, and other complex carbohydrates. High prevalence of Actinobacteria and antibiotic biosynthesis pathways in the fish gut microbiome indicated its potential for bioprospecting of potentially novel natural antibiotics. Fifty-one different types of antibiotic resistance genes (ARGs) belonging to 15 antimicrobial resistance (AMR) gene families and conferring resistance against 24 antibiotic types were detected in fish gut. Some of the ARGs for multi-drug resistance were also found to be located on sequences of plasmid origin. The presence of pathogenic bacteria and ARGs on plasmid sequences suggested the potential risk due to horizontal gene transfer in the confined gut environment. The role of ARGs in fish gut microbiome needs further investigations.},
}
@article {pmid30603692,
year = {2018},
author = {Vijayashree Priyadharsini, J and Smiline Girija, AS and Paramasivam, A},
title = {An insight into the emergence of Acinetobacter baumannii as an oro-dental pathogen and its drug resistance gene profile - An in silico approach.},
journal = {Heliyon},
volume = {4},
number = {12},
pages = {e01051},
doi = {10.1016/j.heliyon.2018.e01051},
pmid = {30603692},
issn = {2405-8440},
abstract = {Background: Acinetobacter baumannii, a potential nosocomial pathogen has stealthily gained entry into the oral cavity. Their association with other pathogens like Pseudomonas aeruginosa in chronic and aggressive periodontitis cases is well documented. The magnitude of problem caused by A.baumannii could be attributed to resistance genes acquired by the organism. Since the microbiome of oral cavity is heterogeneous and complex, the transfer of genes from multidrug resistant A.baumannii may be a serious threat in infection control and management. In view of this fact, the present study aims to categorize and characterize drug resistant genes present in each of the 19 genomes of Acinetobacter Sp. selected for the study.<br><br>Methods: About 19 genome sequences of Acinetobacter spp. with the predominance of different strains of A.baumannii was genotyped using in silico restriction digestion and pulse field gel electrophoresis (PFGE). Further, the prevalence of common drug resistant genes in the genome of various Acinetobacter spp. was recorded using in silico PCR analysis.<br><br>Results: Based on the PFGE pattern, phylogenetic tree was constructed and the genomes were clustered into 6 genotypes. Genotype 4 (n = 8; 42.10%) and 5 (n = 6; 31.57%) were predominant, followed by genotypes 2 (n = 2; 10.52%), 1, 3 and 6 (n = 1; 5.26%). Three species were excluded from the list since they were negative for most of the drug resistant genes tested. Prevalence of drug resistant genes in each of the 16 genomes analysed found oxa-51, ISAba 1 and ADC 1 to be the major genes found in A.baumannii. Acinetobacter spp. belonging to genotypes 4 and 5 were found to harbour 6-10 and 2-8 potential drug resistant genes respectively.<br><br>Conclusion: The present study showed cluster of multi-drug resistant genes in genomes analysed, thus, warranting the need for antibiotic surveillance, alternate therapeutic measures and development of novel antimicrobials. An extensive study on the genes conferring drug resistance in this pathogen will open new avenues for battling the entry and spread of this pathogen in vulnerable patient groups.},
}
@article {pmid30603107,
year = {2018},
author = {Vesty, A and Gear, K and Biswas, K and Radcliff, FJ and Taylor, MW and Douglas, RG},
title = {Microbial and inflammatory-based salivary biomarkers of head and neck squamous cell carcinoma.},
journal = {Clinical and experimental dental research},
volume = {4},
number = {6},
pages = {255-262},
doi = {10.1002/cre2.139},
pmid = {30603107},
issn = {2057-4347},
abstract = {Head and neck squamous cell carcinoma (HNSCC) patients often present with poor oral health, making it difficult to assess the relationship between oral microbes, inflammation, and carcinoma. This study investigates salivary microbes and inflammatory cytokines as biomarkers for HNSCC, with consideration of oral health. Saliva was collected from 30 participants, including 14 HNSCC patients and 16 participants representing both dentally compromised and healthy individuals. Bacterial and fungal communities were analyzed based on 16S rRNA gene and ITS1 amplicon sequencing, respectively, and concentrations of inflammatory cytokines were quantified using a cytometric bead array, with flow cytometry. Diversity-based analyses revealed that the bacterial communities of HNSCC patients were significantly different to those of the healthy control group but not the dentally compromised patients. Fungal communities were dominated by Candida, irrespective of cohort, with Candida albicans comprising ≥96% of fungal sequences in most HNSCC patients. Significantly higher concentrations of interleukin (IL)-1β and IL-8 were detected in HNSCC and dentally compromised patients, when independently compared with healthy controls. IL-1β and IL-8 concentrations were significantly positively correlated with the abundance of C. albicans. Our findings suggest that salivary microbial and inflammatory biomarkers of HNSCC are influenced by oral health.},
}
@article {pmid30602581,
year = {2019},
author = {Hall, RJ and Flanagan, LA and Bottery, MJ and Springthorpe, V and Thorpe, S and Darby, AC and Wood, AJ and Thomas, GH},
title = {A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet.},
journal = {mBio},
volume = {10},
number = {1},
pages = {},
doi = {10.1128/mBio.02106-18},
pmid = {30602581},
issn = {2150-7511},
abstract = {The tsetse fly is the insect vector for the Trypanosoma brucei parasite, the causative agent of human African trypanosomiasis. The colonization and spread of the trypanosome correlate positively with the presence of a secondary symbiotic bacterium, Sodalis glossinidius The metabolic requirements and interactions of the bacterium with its host are poorly understood, and herein we describe a metabolic model of S. glossinidius metabolism. The model enabled the design and experimental verification of a defined medium that supports S. glossinidius growth ex vivo This has been used subsequently to analyze in vitro aspects of S. glossinidius metabolism, revealing multiple unique adaptations of the symbiont to its environment. Continued dependence on a sugar, and the importance of the chitin monomer N-acetyl-d-glucosamine as a carbon and energy source, suggests adaptation to host-derived molecules. Adaptation to the amino acid-rich blood diet is revealed by a strong dependence on l-glutamate as a source of carbon and nitrogen and by the ability to rescue a predicted l-arginine auxotrophy. Finally, the selective loss of thiamine biosynthesis, a vitamin provided to the host by the primary symbiont Wigglesworthia glossinidia, reveals an intersymbiont dependence. The reductive evolution of S. glossinidius to exploit environmentally derived metabolites has resulted in multiple weaknesses in the metabolic network. These weaknesses may become targets for reagents that inhibit S. glossinidius growth and aid the reduction of trypanosomal transmission.IMPORTANCE Human African trypanosomiasis is caused by the Trypanosoma brucei parasite. The tsetse fly vector is of interest for its potential to prevent disease spread, as it is essential for T. brucei life cycle progression and transmission. The tsetse's mutualistic endosymbiont Sodalis glossinidius has a link to trypanosome establishment, providing a disease control target. Here, we describe a new, experimentally verified model of S. glossinidius metabolism. This model has enabled the development of a defined growth medium that was used successfully to test aspects of S. glossinidius metabolism. We present S. glossinidius as uniquely adapted to life in the tsetse, through its reliance on the blood diet and host-derived sugars. Additionally, S. glossinidius has adapted to the tsetse's obligate symbiont Wigglesworthia glossinidia by scavenging a vitamin it produces for the insect. This work highlights the use of metabolic modeling to design defined growth media for symbiotic bacteria and may provide novel inhibitory targets to block trypanosome transmission.},
}
@article {pmid30602481,
year = {2019},
author = {Winston McPherson, G and Long, T and Salipante, SJ and Rongitsch, JA and Hoffman, NG and Stephens, K and Penewit, K and Greene, DN},
title = {The Vaginal Microbiome of Transgender Men.},
journal = {Clinical chemistry},
volume = {65},
number = {1},
pages = {199-207},
doi = {10.1373/clinchem.2018.293654},
pmid = {30602481},
issn = {1530-8561},
abstract = {BACKGROUND: Hormonal changes influence the composition of vaginal flora, which is directly related to the health of an individual. Transgender men prescribed testosterone experience a vaginal hormone composition that differs from cisgender women. To the author's knowledge, there are no clinical studies evaluating the influence that testosterone administration has on the vaginal microbiome.<br><br>METHODS: Vaginal swabs were self-collected by a cohort of self-identified healthy transgender men prescribed testosterone for at least 1 year (n = 28) and from cisgender women who were used as the comparator (n = 8). Participants completed a questionnaire to indicate the mode and dose of testosterone administration, sexual history, and vaginal health. Serum was collected for hormone analysis. Bacterial community profiles were assessed with broad-range PCR primers targeting the V3-V4 hypervariable region of the 16S bacterial rRNA, next-generation sequencing, and analysis by phylogenetic placement.<br><br>RESULTS: Compared to cisgender women, the vaginal floras of transgender men were less likely to have Lactobacillus as their primary genus. Intravaginal estrogen administration was positively associated with the presence of Lactobacillus in transgender men (P = 0.045). Transgender men had a significantly increased relative abundance of >30 species and a significantly higher α diversity (P = 0.0003). The presence of Lactobacillus was significantly associated with a lower α diversity index (P = 0.017).<br><br>CONCLUSIONS: The vaginal microbiome of transgender men who were assigned a female sex at birth and use testosterone may differ from that of cisgender women. Intravaginal estrogen administration may reduce these differences by promoting colonization with Lactobacillus species and decreasing α diversity.},
}
@article {pmid30602371,
year = {2019},
author = {Buret, AG and Motta, JP and Allain, T and Ferraz, J and Wallace, JL},
title = {Pathobiont release from dysbiotic gut microbiota biofilms in intestinal inflammatory diseases: a role for iron?.},
journal = {Journal of biomedical science},
volume = {26},
number = {1},
pages = {1},
doi = {10.1186/s12929-018-0495-4},
pmid = {30602371},
issn = {1423-0127},
support = {183-681-2011, 413888-2012//Natural Sciences and Engineering Research Council of Canada/ ; 12033//Canadian Institutes of Health Research/Canada ; 20142017//Crohn's and Colitis Canada/ ; PCOFUND-GA-2013-609398//AgreenSkillsPlus/ ; },
abstract = {Gut microbiota interacting with an intact mucosal surface are key to the maintenance of homeostasis and health. This review discusses the current state of knowledge of the biofilm mode of growth of these microbiota communities, and how in turn their disruptions may cause disease. Beyond alterations of relative microbial abundance and diversity, the aim of the review is to focus on the disruptions of the microbiota biofilm structure and function, the dispersion of commensal bacteria, and the mechanisms whereby these dispersed commensals may become pathobionts. Recent findings have linked iron acquisition to the expression of virulence factors in gut commensals that have become pathobionts. Causal studies are emerging, and mechanisms common to enteropathogen-induced disruptions, as well as those reported for Inflammatory Bowel Disease and colo-rectal cancer are used as examples to illustrate the great translational potential of such research. These new observations shed new light on our attempts to develop new therapies that are able to protect and restore gut microbiota homeostasis in the many disease conditions that have been linked to microbiota dysbiosis.},
}
@article {pmid30602367,
year = {2019},
author = {Chen, YY and Chen, DQ and Chen, L and Liu, JR and Vaziri, ND and Guo, Y and Zhao, YY},
title = {Microbiome-metabolome reveals the contribution of gut-kidney axis on kidney disease.},
journal = {Journal of translational medicine},
volume = {17},
number = {1},
pages = {5},
doi = {10.1186/s12967-018-1756-4},
pmid = {30602367},
issn = {1479-5876},
support = {81673578//National Natural Science Foundation of China/ ; 81603271//National Natural Science Foundation of China/ ; 81872985//National Natural Science Foundation of China/ ; },
abstract = {Dysbiosis represents changes in composition and structure of the gut microbiome community (microbiome), which may dictate the physiological phenotype (health or disease). Recent technological advances and efforts in metagenomic and metabolomic analyses have led to a dramatical growth in our understanding of microbiome, but still, the mechanisms underlying gut microbiome-host interactions in healthy or diseased state remain elusive and their elucidation is in infancy. Disruption of the normal gut microbiota may lead to intestinal dysbiosis, intestinal barrier dysfunction, and bacterial translocation. Excessive uremic toxins are produced as a result of gut microbiota alteration, including indoxyl sulphate, p-cresyl sulphate, and trimethylamine-N-oxide, all implicated in the variant processes of kidney diseases development. This review focuses on the pathogenic association between gut microbiota and kidney diseases (the gut-kidney axis), covering CKD, IgA nephropathy, nephrolithiasis, hypertension, acute kidney injury, hemodialysis and peritoneal dialysis in clinic. Targeted interventions including probiotic, prebiotic and symbiotic measures are discussed for their potential of re-establishing symbiosis, and more effective strategies for the treatment of kidney diseases patients are suggested. The novel insights into the dysbiosis of the gut microbiota in kidney diseases are helpful to develop novel therapeutic strategies for preventing or attenuating kidney diseases and complications.},
}
@article {pmid30602276,
year = {2018},
author = {Stebel, R and Svačinka, R and Vojtilová, L and Freibergerová, M and Husa, P},
title = {Fecal bacteriotherapy in the treatment of Clostridium difficile infection.},
journal = {Epidemiologie, mikrobiologie, imunologie : casopis Spolecnosti pro epidemiologii a mikrobiologii Ceske lekarske spolecnosti J.E. Purkyne},
volume = {67},
number = {3},
pages = {104-109},
pmid = {30602276},
issn = {1210-7913},
abstract = {AIM: Using a prospective analysis to assess the success of faecal bacteriotherapy (FBT) in antibiotic-associated colitis due to Clostridium difficile. To analyse whether any of the factors according to which the treated patients can be categorized has a statistically significant effect on the therapeutic outcome.<br><br>MATERIALS AND METHODS: During the 2-year study period (2015-2016), 71 patients received FBT. After treatment, the patients were followed up by means of clinic visits or by phone. If colitis did not recur within eight weeks of follow-up, the treatment was considered successful.<br><br>RESULTS: The overall success rate was 76%, with statistically insignificant decline in recurrences. Subgroup analysis did not show any statistically significant difference in the success rate between the routes of administration, i.e. through a naso-enteral feeding tube and rectal enema. Likewise, there were no statistically significant differences in the success rate between the types of prior antibiotic therapy or between using fresh and cryo-stored stool suspension. No unexpected adverse event or lethality occurred during the study period.<br><br>CONCLUSIONS: Faecal bacteriotherapy is a successful and safe therapeutic alternative for recurrent C. difficile infections.},
}
@article {pmid30602220,
year = {2018},
author = {Takajo, T and Tomita, K and Tsuchihashi, H and Enomoto, S and Tanichi, M and Toda, H and Okada, Y and Furuhashi, H and Sugihara, N and Wada, A and Horiuchi, K and Inaba, K and Hanawa, Y and Shibuya, N and Shirakabe, K and Higashiyama, M and Kurihara, C and Watanabe, C and Komoto, S and Nagao, S and Kimura, K and Miura, S and Shimizu, K and Hokari, R},
title = {Depression Promotes the Onset of Irritable Bowel Syndrome through Unique Dysbiosis in Rats.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl18296},
pmid = {30602220},
issn = {2005-1212},
abstract = {Background/Aims: Although studies using conventional animal models have shown that specific stressors cause irritable bowel syndrome (IBS), it is unclear whether depression itself causes IBS. Our aim was to establish a rat model to determine if depression itself promotes the onset of IBS and to elucidate the role of gut microbiota in brain-gut axis pathogenesis during coincident depression and IBS.<br><br>Methods: Rat models of depression were induced using our shuttle box method of learned helplessness. Visceral hypersensitivity was evaluated by colorectal distension (CRD) to diagnose IBS. Gut microbiota compositions were analyzed using high-throughput sequencing. In the subanalysis of rats without depression-like symptoms, rats with posttraumatic stress disorder (PTSD) were also examined.<br><br>Results: The threshold value of CRD in depressed rats was significantly lower than that in control rats. Microbial community analysis of cecal microbiota showed that the relative abundance of Clostridiales incertae sedis, the most prevalent microbe, was significantly lower in depressed rats than in control rats. The distribution pattern of the microbiota clearly differed between depressed rats and control rats. Neither visceral hypersensitivity nor the composition of gut microbiota was altered in rats with PTSD-like phenotypes.<br><br>Conclusions: Our rat model of depression is useful for clarifying the effect of depression on IBS and suggests that depression itself, rather than specific stressors, promotes the onset of IBS. Further, we provided evidence that various psychiatric diseases, viz. depression and PTSD, are associated with unique gut microbiota profiles, which could differentially affect the onset and progression of coincident IBS.},
}
@article {pmid30601862,
year = {2019},
author = {Thornbury, M and Sicheri, J and Slaine, P and Getz, LJ and Finlayson-Trick, E and Cook, J and Guinard, C and Boudreau, N and Jakeman, D and Rohde, J and McCormick, C},
title = {Characterization of novel lignocellulose-degrading enzymes from the porcupine microbiome using synthetic metagenomics.},
journal = {PloS one},
volume = {14},
number = {1},
pages = {e0209221},
doi = {10.1371/journal.pone.0209221},
pmid = {30601862},
issn = {1932-6203},
abstract = {Plant cell walls are composed of cellulose, hemicellulose, and lignin, collectively known as lignocellulose. Microorganisms degrade lignocellulose to liberate sugars to meet metabolic demands. Using a metagenomic sequencing approach, we previously demonstrated that the microbiome of the North American porcupine (Erethizon dorsatum) is replete with genes that could encode lignocellulose-degrading enzymes. Here, we report the identification, synthesis and partial characterization of four novel genes from the porcupine microbiome encoding putative lignocellulose-degrading enzymes: β-glucosidase, α-L-arabinofuranosidase, β-xylosidase, and endo-1,4-β-xylanase. These genes were identified via conserved catalytic domains associated with cellulose- and hemicellulose-degradation. Phylogenetic trees were created for each of these putative enzymes to depict genetic relatedness to known enzymes. Candidate genes were synthesized and cloned into plasmid expression vectors for inducible protein expression and secretion. The putative β-glucosidase fusion protein was efficiently secreted but did not permit Escherichia coli (E. coli) to use cellobiose as a sole carbon source, nor did the affinity purified enzyme cleave p-Nitrophenyl β-D-glucopyranoside (p-NPG) substrate in vitro over a range of physiological pH levels (pH 5-7). The putative hemicellulose-degrading β-xylosidase and α-L-arabinofuranosidase enzymes also lacked in vitro enzyme activity, but the affinity purified endo-1,4-β-xylanase protein cleaved a 6-chloro-4-methylumbelliferyl xylobioside substrate in acidic and neutral conditions, with maximal activity at pH 7. At this optimal pH, KM, Vmax, and kcat were determined to be 32.005 ± 4.72 μM, 1.16x10-5 ± 3.55x10-7 M/s, and 94.72 s-1, respectively. Thus, our pipeline enabled successful identification and characterization of a novel hemicellulose-degrading enzyme from the porcupine microbiome. Progress towards the goal of introducing a complete lignocellulose-degradation pathway into E. coli will be accelerated by combining synthetic metagenomic approaches with functional metagenomic library screening, which can identify novel enzymes unrelated to those found in available databases.},
}
@article {pmid30600366,
year = {2019},
author = {Xu, J and Huang, G and Nagy, T and Teng, Q and Guo, TL},
title = {Sex-dependent effects of bisphenol A on type 1 diabetes development in non-obese diabetic (NOD) mice.},
journal = {Archives of toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00204-018-2379-5},
pmid = {30600366},
issn = {1432-0738},
support = {R21ES24487//National Institutes of Health/ ; R41AT009523//National Institutes of Health (US)/ ; },
abstract = {Type 1 diabetes (T1D) is an autoimmune disease caused by immune-mediated pancreatic β-cell destruction. The endocrine disrupting chemical bisphenol A (BPA) has widespread human exposure and can modulate immune function and the gut microbiome (GMB), which may contribute to the increasing T1D incidence worldwide. It was hypothesized that BPA had sex-dependent effects on T1D by modulating immune homeostasis and GMB. Adult female and male non-obese diabetic (NOD) mice were orally administered BPA at environmentally relevant doses (30 or 300 µg/kg). Antibiotic-treated adult NOD females were exposed to 0 or 30 µg/kg BPA. BPA accelerated T1D development in females, but delayed males from T1D. Consistently, females had a shift towards pro-inflammation (e.g., increased macrophages and Bacteroidetes), while males had increases in anti-inflammatory immune factors and a decrease in both anti- and pro-inflammatory GMB. Although bacteria altered during sub-acute BPA exposure differed from bacteria altered from chronic BPA exposure in both sexes, the GMB profile was consistently pro-inflammatory in females, while males had a general decrease of both anti- and pro-inflammatory gut microbes. However, treatment of females with the antibiotic vancomycin failed to prevent BPA-induced glucose intolerance, suggesting changes in Gram-positive bacteria were not a primary mechanism. In conclusion, BPA exposure was found to have sex dimorphic effects on T1D with detrimental effects in females, and immunomodulation was identified as the primary mechanism.},
}
@article {pmid30600139,
year = {2018},
author = {Spinler, JK and Karri, V and Hirschi, KD},
title = {Planting the Microbiome.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2018.12.001},
pmid = {30600139},
issn = {1878-4380},
abstract = {Plant-derived microRNAs stabilized by species-specific lipid nanoparticles mediate interkingdom communication through bacterial intermediates and impact consumer health. Ingested by distinct gut bacteria, these microRNA-containing particles alter bacterial gene expression to affect host immunity. This three-kingdom interplay provides compelling approaches for health-directed dietary interventions for consumers.},
}
@article {pmid30586752,
year = {2018},
author = {Bartolomaeus, H and Balogh, A and Yakoub, M and Homann, S and Markó, L and Höges, S and Tsvetkov, D and Krannich, A and Wundersitz, S and Avery, EG and Haase, N and Kräker, K and Hering, L and Maase, M and Kusche-Vihrog, K and Grandoch, M and Fielitz, J and Kempa, S and Gollasch, M and Zhumadilov, Z and Kozhakhmetov, S and Kushugulova, A and Eckardt, KU and Dechend, R and Rump, LC and Forslund, SK and Müller, DN and Stegbauer, J and Wilck, N},
title = {The Short-Chain Fatty Acid Propionate Protects from Hypertensive Cardiovascular Damage.},
journal = {Circulation},
volume = {},
number = {},
pages = {},
doi = {10.1161/CIRCULATIONAHA.118.036652},
pmid = {30586752},
issn = {1524-4539},
abstract = {BACKGROUND: Arterial hypertension and its organ sequelae show characteristics of T cell mediated inflammatory diseases. Experimental anti-inflammatory therapies have been shown to ameliorate hypertensive end-organ damage. Recently, the CANTOS study targeting interleukin-1β demonstrated that anti-inflammatory therapy reduces cardiovascular risk. The gut microbiome plays pivotal role in immune homeostasis and cardiovascular health. Short-chain fatty acids (SCFA) are produced from dietary fiber by gut bacteria and affect host immune homeostasis. Here, we investigated effects of the SCFA propionate in two different mouse models of hypertensive cardiovascular damage.<br><br>METHODS: To investigate the effect of SCFA on hypertensive cardiac damage and atherosclerosis, wild-type NMRI (WT) or ApoE-/- deficient mice received propionate (200mM) or control in the drinking water. To induce hypertension, WT mice were infused with Angiotensin (Ang)II (1.44mg/kg/d s.c.) for 14 days. To accelerate the development of atherosclerosis, ApoE-/- mice were infused with AngII (0.72mg/kg/d s.c.) for 28 days. Cardiac damage and atherosclerosis were assessed using histology, echocardiography, in vivo electrophysiology, immunofluorescence, and flow cytometry. Blood pressure was measured by radiotelemetry. Regulatory T cell (Treg) depletion using PC61 antibody was used to examine the mode of action of propionate.<br><br>RESULTS: Propionate significantly attenuated cardiac hypertrophy, fibrosis, vascular dysfunction, and hypertension in both models. Susceptibility to cardiac ventricular arrhythmias was significantly reduced in propionate-treated AngII-infused WT mice. Aortic atherosclerotic lesion area was significantly decreased in propionate-treated ApoE-/-. Systemic inflammation was mitigated by propionate treatment, quantified as a reduction in splenic effector memory T cell frequencies and splenic T helper 17 cells in both models, and a decrease in local cardiac immune cell infiltration in WT mice. Cardioprotective effects of propionate were abrogated in Treg-depleted AngII-infused mice, suggesting the effect is Treg-dependent.<br><br>CONCLUSIONS: Our data emphasize an immune-modulatory role of SCFAs and their importance for cardiovascular health. The data suggest that lifestyle modifications leading to augmented SCFA production could be a beneficial non-pharmacological preventive strategy for patients with hypertensive cardiovascular disease.},
}
@article {pmid30599284,
year = {2018},
author = {Johnston, J and Hoggard, M and Biswas, K and Astudillo-García, C and Radcliff, FJ and Mahadevan, M and Douglas, RG},
title = {Pathogen reservoir hypothesis investigated by analyses of the adenotonsillar and middle ear microbiota.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {118},
number = {},
pages = {103-109},
doi = {10.1016/j.ijporl.2018.12.030},
pmid = {30599284},
issn = {1872-8464},
abstract = {INTRODUCTION: Adenotonsillar and middle ear diseases result in some of the most frequently performed operations in the pediatric population worldwide. The pathogen reservoir hypothesis (PRH) suggests that the adenoids act as a reservoir of bacteria which play a potential pathogenic role in otitis media. Evidence supporting this hypothesis is limited. This study sought to comprehensively determine and compare associations between the adenotonsillar and middle ear bacterial microbiota within individual patients via next-generation sequencing and microbial network analyses.<br><br>METHODS: Bacterial 16S rRNA gene-targeted amplicon sequencing was used to determine the bacterial composition of ten pediatric patients undergoing adenotonsillectomy and ventilation tube insertion for otitis media with effusion. At the time of surgery, swabs were taken from the adenoid surface, tonsil crypts and middle ear clefts (through the myringotomy incision).<br><br>RESULTS: The most abundant sequences within the bacterial community at genus level across all anatomical sites were Fusobacterium, Haemophilus, Neisseria, and Porphyromonas. There was an observable difference in the relative abundance of bacterial communities, with a higher proportion of Haemophilus and Moraxella in the adenoid when compared with the middle ear. Furthermore, only one module (consisting of 4 bacterial OTUs) from one patient was identified through microbial network analyses to be significantly associated between middle ear and adenoid. In addition, microbial network analysis revealed that the adenoid and tonsil microbiota share greater similarity than do the adenoid and middle ear.<br><br>CONCLUSION: The results of this study suggest that the adenoid microenvironment does not correlate to the middle ear microenvironment. A future study at the species level, and over time, is required to further investigate whether the differing relationship between the microbiota of the adenoid and middle ear rejects the pathogen reservoir hypothesis.},
}
@article {pmid30598769,
year = {2018},
author = {Gomola, CE and McKay, JK and Wallenstein, MD and Wagg, C and O'Brien, MJ},
title = {Within-species trade-offs in plant-stimulated soil enzyme activity and growth, flowering, and seed size.},
journal = {Ecology and evolution},
volume = {8},
number = {23},
pages = {11717-11724},
doi = {10.1002/ece3.4623},
pmid = {30598769},
issn = {2045-7758},
abstract = {Soil microbial communities affect species demographic rates of plants. In turn, plants influence the composition and function of the soil microbiome, potentially resulting in beneficial feedbacks that alter their fitness and establishment. For example, differences in the ability to stimulate soil enzyme activity among plant lineages may affect plant growth and reproduction. We used a common garden study to test differences in plant-stimulated soil enzyme activity between lineages of the same species across developmental stages. Lineages employed different strategies whereby growth, days to flowering and seed size traded-off with plant-stimulated soil enzyme activity. Specifically, the smaller seeded lineage stimulated more enzyme activity at the early stage of development and flowered earlier while the larger seeded lineage sustained lower but consistent enzyme activity through development. We suggest that these lineages, which are both successful invaders, employ distinct strategies (a colonizer and a competitor) and differ in their influence on soil microbial activity. Synthesis. The ability to influence the soil microbial community by plants may be an important trait that trades off with growth, flowering, and seed size for promoting plant establishment, reproduction, and invasion.},
}
@article {pmid30598734,
year = {2019},
author = {Cieplik, F and Zaura, E and Brandt, BW and Buijs, MJ and Buchalla, W and Crielaard, W and Laine, ML and Deng, DM and Exterkate, RAM},
title = {Microcosm biofilms cultured from different oral niches in periodontitis patients.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1551596},
doi = {10.1080/20022727.2018.1551596},
pmid = {30598734},
issn = {2000-2297},
abstract = {Objective: Periodontal diseases are triggered by dysbiotic microbial biofilms. Therefore, it is essential to develop appropriate biofilm models. Aim of the present study was to culture microcosm biofilms inoculated from different niches in periodontitis patients and compare their microbial composition to those inoculated from subgingival plaque. Methods: Saliva, subgingival plaque, tongue and tonsils were sampled in five periodontitis patients to serve as inocula for culturing biofilms in vitro in an active attachment model. Biofilms were grown for 14 or 28 d and analyzed for their microbial composition by 16S rDNA sequencing. Results: As classified by HOMD, all biofilms were dominated by periodontitis-associated taxa, irrespective which niche had been used for inoculation. There was a low similarity between 14 d biofilms and their respective inocula (Bray-Curtis similarity 0.26), while biofilms cultured for 14 and 28 d shared high similarity (0.69). Principal components analysis showed much stronger clustering per patient than per niche indicating that the choice of patients may be more crucial than choice of the respective niches in these patients. Conclusion: Saliva, tongue scrapings or tonsil swabs may represent sufficient alternative inocula for growing microcosm biofilms resembling periodontitis-associated microbial communities in cases when sampling subgingival plaque is not possible.},
}
@article {pmid30598732,
year = {2019},
author = {Ramage, G and O'Donnell, L and Sherry, L and Culshaw, S and Bagg, J and Czesnikiewicz-Guzik, M and Brown, C and McKenzie, D and Cross, L and MacInnes, A and Bradshaw, D and Varghese, R and Gomez Pereira, P and Jose, A and Sanyal, S and Robertson, D},
title = {Impact of frequency of denture cleaning on microbial and clinical parameters - a bench to chairside approach.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1538437},
doi = {10.1080/20002297.2018.1538437},
pmid = {30598732},
issn = {2000-2297},
abstract = {Objective: Robust scientific and clinical evidence of how to appropriately manage denture plaque is lacking. This two-part study (i) developed an in vitro model of denture plaque removal, and (ii) assessed effectiveness of these approaches in a randomised clinical trial. Method: (i) a complex denture plaque model was developed using the dominant microbial genera from a recent microbiome analyses. Biofilms formed on polymethylmethacrylate were brushed daily with a wet toothbrush, then either treated daily for 5 days or only on Days 1 and 5 with Polident® denture cleanser tablets (3 min soaking). Quantitative and qualitative microbiological assessments were performed. (ii), an examiner-blind, randomised, crossover study of complete maxillary denture wearers was performed (n = 19). Either once-daily for 7 days or on Day 7 only, participants soaked dentures for 15 min using Corega® denture cleansing tables, then brushed. Denture plaque microbiological assessment used sterilized filter paper discs. Results: The in vitro model showed daily cleaning with denture cleanser plus brushing significantly reduced microbial numbers compared to intermittent denture cleaning with daily brushing (p < 0.001). The clinical component of the study showed a statistically significant reduction in denture plaque microbial numbers in favour of daily versus weekly treatment (aerobic bacteria p = 0.0144). Both in vitro and in vivo studies showed that denture plaque biofilm composition were affected by different treatment arms. Conclusions: This study demonstrated that daily denture cleansing regimens are superior to intermittent denture cleansing, and that cleansing regimens can induce denture plaque compositional changes. Clinicaltrials.gov registration: NCT02780661.},
}
@article {pmid30598729,
year = {2019},
author = {Fechney, JM and Browne, GV and Prabhu, N and Irinyi, L and Meyer, W and Hughes, T and Bockmann, M and Townsend, G and Salehi, H and Adler, CJ},
title = {Preliminary study of the oral mycobiome of children with and without dental caries.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1536182},
doi = {10.1080/20002297.2018.1536182},
pmid = {30598729},
issn = {2000-2297},
abstract = {Children's oral health is in a dire state, with dental decay (caries) being one of the most common chronic diseases. While the role of bacteria in the oral microbiome and dental caries is established, the contribution of fungi is relatively unknown. We assessed the oral mycobiome in childhood (n = 17), to determine if the composition of fungi varies between children with and without caries. Oral mycobiome composition was assessed by using Illumina MiSeq to sequence the ITS2 region, which was amplified from dental plaque. This revealed that the oral mycobiome in the investigated children contained 46 fungal species. Candida albicans was the most abundant species and was ubiquitous in all samples, indicating this species may not be involved in caries development as previously suggested. While the overall diversity of fungi was similar, independent of caries status (p > 0.05), we found caries influenced the abundance of specific fungi. Children without caries had a significantly higher abundance of 17 species compared to children with caries, which had three enriched species (p < 0.001). While the differentially abundant species between health and caries may be specific to an Australian population, our findings indicate the mycobiome plays a role in oral health.},
}
@article {pmid30598728,
year = {2019},
author = {Rafeek, R and Carrington, CVF and Gomez, A and Harkins, D and Torralba, M and Kuelbs, C and Addae, J and Moustafa, A and Nelson, KE},
title = {Xylitol and sorbitol effects on the microbiome of saliva and plaque.},
journal = {Journal of oral microbiology},
volume = {11},
number = {1},
pages = {1536181},
doi = {10.1080/20002297.2018.1536181},
pmid = {30598728},
issn = {2000-2297},
abstract = {Chewing gum containing xylitol may help prevent caries by reducing levels of mutans streptococci (MS) and lactobacilli in saliva and plaque. Very little is known about other species which are possibly beneficial to oral health. In this study, we employed high-throughput sequencing of the 16S rRNA gene to profile microbial communities of saliva and plaque following short-term consumption of xylitol and sorbitol containing chewing gum. Participants (n = 30) underwent a washout period and were randomly assigned to one of two groups. Each group chewed either xylitol or sorbitol gum for three weeks, before undergoing a second four-week washout period after which they switched to the alternate gum for three weeks. Analysis of samples collected before and after each intervention identified distinct plaque and saliva microbial communities that altered dependent on the order in which gum treatments were given. Neither the xylitol nor sorbitol treatments significantly affected the bacterial composition of plaque. Lactobacilli were undetected and the number of Streptococcus mutans sequence reads was very low and unaffected by either xylitol or sorbitol. However, sorbitol affected several other streptococcal species in saliva including increasing the abundance of S. cristatus, an oral commensal shown to inhibit bacteria associated with chronic periodontitis.},
}
@article {pmid30598701,
year = {2018},
author = {Antão, EM and Vincze, S and Hanke, R and Klimmek, L and Suchecka, K and Lübke-Becker, A and Wieler, LH},
title = {Antibiotic resistance, the 3As and the road ahead.},
journal = {Gut pathogens},
volume = {10},
number = {},
pages = {52},
doi = {10.1186/s13099-018-0280-7},
pmid = {30598701},
issn = {1757-4749},
abstract = {Antibiotic resistance is by far one of the most important health threats of our time. Only a global concerted effort of several disciplines based on the One-Health concept will help in slowing down this process and potentially mitigate the ruin of healthcare we have come to enjoy. In this review, we attempt to summarize the most basic and important topics that serve as good information tools to create Awareness. The Availability of antibiotics or the lack thereof is another significant factor that must be given thought, and finally because antibiotic resistance is a problem that will not go away, it is important to have Alternatives. Together, we have the 3As, essential concepts, in dealing with this growing and complex problem.},
}
@article {pmid30598508,
year = {2018},
author = {Guo, Y and Crnkovic, CM and Won, KJ and Yang, X and Lee, JR and Orjala, J and Lee, H and Jeong, H},
title = {Commensal gut bacteria convert the immunosuppressant tacrolimus to less potent metabolites.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {},
number = {},
pages = {},
doi = {10.1124/dmd.118.084772},
pmid = {30598508},
issn = {1521-009X},
abstract = {Tacrolimus exhibits low and variable drug exposure after oral dosing, but the contributing factors remain unclear. Based on our recent report showing a positive correlation between fecal abundance of Faecalibacterium prausnitzii and oral tacrolimus dose in kidney transplant patients, we tested whether F. prausnitzii and other gut abundant bacteria are capable of metabolizing tacrolimus. Incubation of F. prausnitzii with tacrolimus led to production of two compounds (the major one named M1), which was not observed upon tacrolimus incubation with hepatic microsomes. Isolation, purification, and structure elucidation using mass spectrometry and nuclear magnetic resonance spectroscopy indicated that M1 is a C-9 keto-reduction product of tacrolimus. Pharmacological activity testing using human peripheral blood mononuclear cells demonstrated that M1 is 15-fold less potent than tacrolimus as an immunosuppressant. Screening of 22 gut bacteria species revealed that most Clostridiales bacteria are extensive tacrolimus metabolizers. Tacrolimus conversion to M1 was verified in fresh stool samples from two healthy adults. M1 was also detected in the stool samples from kidney transplant recipients who had been taking tacrolimus orally. Together, this study presents gut bacteria metabolism as a previously unrecognized elimination route of tacrolimus, potentially contributing to the low and variable tacrolimus exposure after oral dosing.},
}
@article {pmid30598099,
year = {2018},
author = {Abe, K and Hirayama, M and Ohno, K and Shimamura, T},
title = {A latent allocation model for the analysis of microbial composition and disease.},
journal = {BMC bioinformatics},
volume = {19},
number = {Suppl 19},
pages = {519},
doi = {10.1186/s12859-018-2530-6},
pmid = {30598099},
issn = {1471-2105},
abstract = {BACKGROUND: Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large number of zeros, which makes it difficult to analyze in case-control studies. Most existing approaches either add a small number called a pseudo-count or use probability models such as the multinomial and Dirichlet-multinomial distributions to explain the excess zero counts, which may produce unnecessary biases and impose a correlation structure taht is unsuitable for microbiome data.<br><br>RESULTS: The purpose of this article is to develop a new probabilistic model, called BERnoulli and MUltinomial Distribution-based latent Allocation (BERMUDA), to address these problems. BERMUDA enables us to describe the differences in bacteria composition and a certain disease among samples. We also provide a simple and efficient learning procedure for the proposed model using an annealing EM algorithm.<br><br>CONCLUSION: We illustrate the performance of the proposed method both through both the simulation and real data analysis. BERMUDA is implemented with R and is available from GitHub (https://github.com/abikoushi/Bermuda).},
}
@article {pmid30598081,
year = {2018},
author = {Chen, HM and Chen, CC and Chen, CC and Wang, SC and Wang, CL and Huang, CH and Liou, JS and Liu, TW and Peng, HL and Lin, FM and Liu, CY and Weng, SL and Cheng, CJ and Hung, YF and Liao, CC and Huang, HD},
title = {Gut microbiome changes in overweight male adults following bowel preparation.},
journal = {BMC genomics},
volume = {19},
number = {Suppl 10},
pages = {904},
doi = {10.1186/s12864-018-5285-6},
pmid = {30598081},
issn = {1471-2164},
abstract = {BACKGROUND: Human gut microbiome has an essential role in human health and disease. Although the major dominant microbiota within individuals have been reported, the change of gut microbiome caused by external factors, such as antibiotic use and bowel cleansing, remains unclear. We conducted this study to investigate the change of gut microbiome in overweight male adults after bowel preparation, where none of the participants had been diagnosed with any systemic diseases.<br><br>METHODS: A total of 20 overweight, male Taiwanese adults were recruited, and all participants were omnivorous. The participants provided fecal samples and blood samples at three time points: prior to bowel preparation, 7 days after colonoscopy, and 28 days after colonoscopy. The microbiota composition in fecal samples was analyzed using 16S ribosome RNA gene amplicon sequencing.<br><br>RESULTS: Our results demonstrated that the relative abundance of the most dominant bacteria hardly changed from prior to bowel preparation to 28 days after colonoscopy. Using the ratio of Prevotella to the sum of Prevotella and Bacteroides in the fecal samples at baseline, the participants were separated into two groups. The fecal samples of the Type 1 group was Bacteroides-dominant, and that of the Type 2 group was Prevotella-dominant with a noticeable presence Bacteroides. Bulleidia appears more in the Type 1 fecal samples, while Akkermensia appears more in the Type 2 fecal samples. Of each type, the gut microbial diversity differed slightly among the three collection times. Additionally, the Type 2 fecal microbiota was temporarily susceptible to bowel cleansing. Predictive functional analysis of microbial community reveals that their activities for the mineral absorption metabolism and arachidonic acid metabolism differed significantly between the two types. Depending on their fecal type, the variance of triglycerides and C-reactive protein also differed between the two types of participants.<br><br>CONCLUSIONS: Depending upon the fecal type, the microbial diversity and the predictive functional modules of microbial community differed significantly after bowel preparation. In addition, blood biochemical markers presented somewhat associated with fecal type. Therefore, our results might provide some insights as to how knowledge of the microbial community could be used to promote health through personalized clinical treatment.},
}
@article {pmid30598080,
year = {2018},
author = {Chen, HM and Chang, TH and Lin, FM and Liang, C and Chiu, CM and Yang, TL and Yang, T and Huang, CY and Cheng, YN and Chang, YA and Chang, PY and Weng, SL},
title = {Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis.},
journal = {BMC genomics},
volume = {19},
number = {Suppl 10},
pages = {876},
doi = {10.1186/s12864-018-5284-7},
pmid = {30598080},
issn = {1471-2164},
abstract = {BACKGROUND: One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the &quot;normal&quot; vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel criteria and Nugent score test are widely used for diagnosing BV; however, these tests are based on different criteria, and so may indicate distinct changes in the vaginal microbial community. Nevertheless, few studies have compared the results of these test against metagenomics analysis.<br><br>METHODS: Vaginal flora samples from 77 participants were classified according to the Amsel criteria and Nugent score test. The microbiota composition was analyzed using 16S ribosome RNA gene amplicon sequencing. Bioinformatics analysis and multivariate statistical analysis were used to evaluate the microbial diversity and function.<br><br>RESULTS: Only 3 % of the participants diagnosed BV negative using the Amsel criteria (A-) were BV-positive according to the Nugent score test (N+), while over half of the BV-positive patients using the Amsel criteria (A+) were BV-negative according to the Nugent score test (N-). Thirteen genera showed significant differences in distribution among BV status defined by BV tests (e.g., A - N-, A + N- and A + N+). Variations in the four most abundant taxa, Lactobacillus, Gardnerella, Prevotella, and Escherichia, were responsible for most of this dissimilarity. Furthermore, vaginal microbial diversity differed significantly among the three groups classified by the Nugent score test (N-, N+, and intermediate flora), but not between the Amsel criteria groups. Numerous predictive microbial functions, such as bacterial chemotaxis and bacterial invasion of epithelial cells, differed significantly among multiple BV test, but not between the A- and A+ groups.<br><br>CONCLUSIONS: Metagenomics analysis can greatly expand our current understanding of vaginal microbial diversity in health and disease. Metagenomics profiling may also provide more reliable diagnostic criteria for BV testing.},
}
@article {pmid30598019,
year = {2018},
author = {Frati, F and Salvatori, C and Incorvaia, C and Bellucci, A and Di Cara, G and Marcucci, F and Esposito, S},
title = {The Role of the Microbiome in Asthma: The Gut⁻Lung Axis.},
journal = {International journal of molecular sciences},
volume = {20},
number = {1},
pages = {},
doi = {10.3390/ijms20010123},
pmid = {30598019},
issn = {1422-0067},
support = {WAidid2018_02//World Association of Infectious Diseases and Immunologcal Disorders/ ; },
abstract = {Asthma is one of the most common chronic respiratory diseases worldwide. It affects all ages but frequently begins in childhood. Initiation and exacerbations may depend on individual susceptibility, viral infections, allergen exposure, tobacco smoke exposure, and outdoor air pollution. The aim of this review was to analyze the role of the gut⁻lung axis in asthma development, considering all asthma phenotypes, and to evaluate whether microbe-based therapies may be used for asthma prevention. Several studies have confirmed the role of microbiota in the regulation of immune function and the development of atopy and asthma. These clinical conditions have apparent roots in an insufficiency of early life exposure to the diverse environmental microbiota necessary to ensure colonization of the gastrointestinal and/or respiratory tracts. Commensal microbes are necessary for the induction of a balanced, tolerogenic immune system. The identification of commensal bacteria in both the gastroenteric and respiratory tracts could be an innovative and important issue. In conclusion, the function of microbiota in healthy immune response is generally acknowledged, and gut dysbacteriosis might result in chronic inflammatory respiratory disorders, particularly asthma. Further investigations are needed to improve our understanding of the role of the microbiome in inflammation and its influence on important risk factors for asthma, including tobacco smoke and host genetic features.},
}
@article {pmid30597319,
year = {2018},
author = {Meng, L and Sun, T and Li, M and Saleem, M and Zhang, Q and Wang, C},
title = {Soil-applied biochar increases microbial diversity and wheat plant performance under herbicide fomesafen stress.},
journal = {Ecotoxicology and environmental safety},
volume = {171},
number = {},
pages = {75-83},
doi = {10.1016/j.ecoenv.2018.12.065},
pmid = {30597319},
issn = {1090-2414},
abstract = {The herbicide &quot;fomesafen&quot; causes phytotoxicity to the rotational wheat crop and may reduce its yield. Considering that biochar may improve remediation and biophysical conditions of the contaminated soil environments to benefit plant growth. Here, we investigated the impacts of three levels of the wheat straw-derived biochar (1%, 2%, and 4% (w/w)) on growth, physiological properties, and rhizosphere microbial communities of the wheat (Triticum aestivum) seedlings under the fomesafen stress using high-throughput sequencing. The results showed that biochar amended into soil significantly reduced the uptake of wheat to fomesafen and thereby eliminate its toxicity to wheat seedlings. Moreover, biochar increased the abundance and diversity of plant beneficial bacterial and fungal taxa in the rhizosphere of wheat seedlings. Compared with the three addition amounts, amendment with 2% of biochar has the best effects to reduce the toxicity of fomesafen on wheat seedlings and maintain the balance of soil microbial community structure in soil contaminated with fomesafen (1.0 mg kg-1). Overall, our results suggest that the level of biochar application influences the structure and diversity of soil microbiome (and mycobiome) and plant performance under abiotic stress conditions.},
}
@article {pmid30597136,
year = {2018},
author = {Yang, I and Knight, AK and Dunlop, AL and Corwin, EJ},
title = {Characterizing the Subgingival Microbiome of Pregnant African American Women.},
journal = {Journal of obstetric, gynecologic, and neonatal nursing : JOGNN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jogn.2018.12.003},
pmid = {30597136},
issn = {1552-6909},
abstract = {OBJECTIVE: To generate preliminary data about the subgingival microbiome of pregnant African American women to calculate power for a future larger study and to explore associations among the microbiome, periodontal inflammation, and preterm birth.<br><br>DESIGN: Comparative descriptive pilot study design.<br><br>SETTING: Urban area in the southeastern United States.<br><br>PARTICIPANTS: Thirty-four African American women in the third trimester of pregnancy.<br><br>METHODS: Based on visual assessment, participants were placed in two groups: healthy gingiva and gingivitis. Saliva samples were analyzed for interleukin-1 β (IL-1β), matrix metalloproteinase-8 (MMP-8), and C-reactive protein (CRP). DNA was extracted from subgingival plaque samples, and amplicons of the fourth hypervariable region were sequenced.<br><br>RESULTS: We found no differences in overall microbiome diversity between the healthy gingiva (n = 22) and the gingivitis (n = 12) groups although significant differences were found among the bacterial taxa present. The gingivitis group had greater levels of salivary IL-1β and MMP-8, whereas CRP was not different between groups. Overall microbiome diversity was positively associated with the CRP level. We found no significant relationships among the subgingival microbiome, periodontal inflammation, and preterm birth.<br><br>CONCLUSION: Gingivitis in pregnancy did not appear to shift the overall composition or diversity of the subgingival microbiome although differences in several bacterial taxa suggest that inflamed gingiva in pregnant women are associated with a disruption in the stability of the subgingival microbiome. A correlation between the abundance of bacteria and CRP also suggests an association between the microbiome and systemic inflammation. These findings provide support for future research about how the oral microbiome and progression of periodontal disease in pregnant women link with adverse pregnancy outcomes.},
}
@article {pmid30596380,
year = {2018},
author = {Broom, LJ and Kogut, MH},
title = {The role of the gut microbiome in shaping the immune system of chickens.},
journal = {Veterinary immunology and immunopathology},
volume = {204},
number = {},
pages = {44-51},
doi = {10.1016/j.vetimm.2018.10.002},
pmid = {30596380},
issn = {1873-2534},
abstract = {Most animals are colonised by at least as many microbial cells as somatic cells, potentially comprising at least 100 times more genes within just the gut microbiota than the host itself. It is, therefore, evident that such a conglomeration can have a profound effect on various bodily systems, particularly the (gut) immune system. Chickens are major providers of efficiently produced protein for humans but also harbour common foodborne pathogens and are susceptible to significant and costly diseases, making a thorough understanding of the influence of the gut microbiome on the immune system very pertinent. Major colonisation of the chicken intestine occurs after hatch and this, along with subsequent microbiota composition and activity, are influenced by numerous host and environmental factors, such that each individual has a unique microbiome signature. However, both extreme (e.g. germ free) and more subtle (e.g. diet changes) microbiome modifications can profoundly impact the development of the gut immune system, particularly adaptive immune apparatus and function. This review will consider the influence of the chicken gut microbiome on immune system development, the implications of this relationship in terms of disease susceptibility, vaccine response, optimal health and productivity, and thus exogenous approaches to positively shape microbiome-immune system interactions.},
}
@article {pmid30596004,
year = {2018},
author = {Dowd, JB and Renson, A},
title = {&quot;Under the Skin&quot; and into the Gut: Social Epidemiology of the Microbiome.},
journal = {Current epidemiology reports},
volume = {5},
number = {4},
pages = {432-441},
doi = {10.1007/s40471-018-0167-7},
pmid = {30596004},
issn = {2196-2995},
abstract = {Purpose of the Review: As the science of the microbiome advances, social epidemiologists can contribute to understanding how the broader social environment shapes the microbiome over the life course. This review summarizes current research and describes potential mechanisms of the social epidemiology of the microbiome.<br><br>Recent Findings: Most existing literature linking the social environment and the microbiome comes from animal models, focused on the impact of social interactions and psychosocial stress. Suggestive evidence of the importance of early life exposures, health behaviors, and the built environment also point to the importance of the social environment for the microbiome in humans.<br><br>Summary: Social epidemiology as a field is well poised to contribute expertise in theory and measurement of the broader social environment to this new area, and to consider both the upstream and downstream mechanisms by which this environment gets &quot;under the skin&quot; and &quot;into the gut.&quot; As population-level microbiome data becomes increasingly available, we encourage investigation of the multi-level determinants of the microbiome and how the microbiome may link the social environment and health.},
}
@article {pmid30595998,
year = {2018},
author = {Jacob, S and Dötsch, A and Knoll, S and Köhler, HR and Rogall, E and Stoll, D and Tisler, S and Huhn, C and Schwartz, T and Zwiener, C and Triebskorn, R},
title = {Does the antidiabetic drug metformin affect embryo development and the health of brown trout (Salmo trutta f. fario)?.},
journal = {Environmental sciences Europe},
volume = {30},
number = {1},
pages = {48},
doi = {10.1186/s12302-018-0179-4},
pmid = {30595998},
issn = {2190-4707},
abstract = {Background: Due to the rising number of type 2 diabetes patients, the antidiabetic drug, metformin is currently among those pharmaceuticals with the highest consumption rates worldwide. Via sewage-treatment plants, metformin enters surface waters where it is frequently detected in low concentrations (µg/L). Since possible adverse effects of this substance in aquatic organisms have been insufficiently explored to date, the aim of this study was to investigate the impact of metformin on health and development in brown trout (Salmo trutta f. fario) and its microbiome.<br><br>Results: Brown trout embryos were exposed to 0, 1, 10, 100 and 1000 µg/L metformin over a period from 48 days post fertilisation (dpf) until 8 weeks post-yolk sac consumption at 7 °C (156 dpf) and 11 °C (143 dpf). Chemical analyses in tissues of exposed fish showed the concentration-dependent presence of metformin in the larvae. Mortality, embryonic development, body length, liver tissue integrity, stress protein levels and swimming behaviour were not influenced. However, compared to the controls, the amount of hepatic glycogen was higher in larvae exposed to metformin, especially in fish exposed to the lowest metformin concentration of 1 µg/L, which is environmentally relevant. At higher metformin concentrations, the glycogen content in the liver showed a high variability, especially for larvae exposed to 1000 µg/L metformin. Furthermore, the body weight of fish exposed to 10 and 100 µg/L metformin at 7 °C and to 1 µg/L metformin at 11 °C was decreased compared with the respective controls. The results of the microbiome analyses indicated a shift in the bacteria distribution in fish exposed to 1 and 10 µg/L metformin at 7 °C and to 100 µg/L metformin at 11 °C, leading to an increase of Proteobacteria and a reduction of Firmicutes and Actinobacteria.<br><br>Conclusions: Overall, weight reduction and the increased glycogen content belong to the described pharmaceutical effects of the drug in humans, but this study showed that they also occur in brown trout larvae. The impact of a shift in the intestinal microbiome caused by metformin on the immune system and vitality of the host organism should be the subject of further research before assessing the environmental relevance of the pharmaceutical.},
}
@article {pmid30595970,
year = {2018},
author = {Villa, NY and McFadden, G},
title = {Virotherapy as Potential Adjunct Therapy for Graft-Vs-Host Disease.},
journal = {Current pathobiology reports},
volume = {6},
number = {4},
pages = {247-263},
doi = {10.1007/s40139-018-0186-6},
pmid = {30595970},
issn = {2167-485X},
abstract = {Purpose of Review: This review discusses the pathophysiology, risk factors, and the advances in the prevention or treatment of graft-vs-host disease (GvHD) by exploiting adjunct virotherapy. In addition, nonviral adjunct therapeutic options for the prevention of GvHD in the context of allogeneic hematopoietic stem cell transplantation (allo-HSCT) are discussed. The role of oncolytic viruses to treat different HSCT-eligible hematological cancers is also considered and correlated with the issue of GvHD in the context of allo-HSCT.<br><br>Recent Findings: Emerging therapies focused on the prevention or treatment of GvHD include the use of regulatory T cells (Tregs), mesenchymal stem cells (MSCs), microbiome manipulation, B cell inhibitors, among others. Our lab and others have reported that an oncolytic DNA virus from the Poxviridae family, called myxoma virus (MYXV), not only exhibits oncolytic activity against various hematologic malignancies like multiple myeloma (MM) or acute myeloid leukemia (AML) but also, in addition, ex vivo MYXV treatment of human allogeneic-bone marrow transplants (allo-BMT), or allo-peripheral blood mononuclear cell (allo-PBMC) transplants can abrogate GvHD in xenografted mice without impairing graft-vs-tumor (GvT) effects against residual cancer. To date, this is the first and the only oncolytic virus with a dual potential of mediating oncolysis against a residual cancer target and also inhibiting or preventing GvHD following allo-HSCT.<br><br>Summary: This review discusses how oncolytic virotherapy can be applied as a potential adjunct therapy for the potential treatment of GvHD. In addition, we highlight major emerging nonviral therapies currently studied for the treatment or prevention of GvHD. We also review the emerging oncolytic virotherapies against different hematological cancers currently eligible for allo-HSCT and highlight the potential role of the oncolytic virus MYXV to decrease GvHD while maintaining or enhancing the positive benefits of GvT.},
}
@article {pmid30595952,
year = {2018},
author = {Dinwiddie, DL and Denson, JL and Kennedy, JL},
title = {Role of the Airway Microbiome in Respiratory Infections and Asthma in Children.},
journal = {Pediatric allergy, immunology, and pulmonology},
volume = {31},
number = {4},
pages = {236-240},
doi = {10.1089/ped.2018.0958},
pmid = {30595952},
issn = {2151-321X},
abstract = {The respiratory tract can be colonized with bacterial, fungal, and viral microorganisms, and the whole of the microbiota, their genes, and the surrounding environment is collectively termed the microbiome. Increasing evidence indicates that the respiratory microbiome has an important role in respiratory health and disease and is both impacted by and potentially contributes to the severity of symptomatic respiratory viral infections and asthma in children. A deeper understanding of the complex interactions between bacteria, viruses, and the host will provide further comprehension into the drivers and mechanisms of respiratory health and disease and will impart opportunities for clinical therapies.},
}
@article {pmid30595552,
year = {2018},
author = {Wu, P and Sun, P and Nie, K and Zhu, Y and Shi, M and Xiao, C and Liu, H and Liu, Q and Zhao, T and Chen, X and Zhou, H and Wang, P and Cheng, G},
title = {A Gut Commensal Bacterium Promotes Mosquito Permissiveness to Arboviruses.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2018.11.004},
pmid = {30595552},
issn = {1934-6069},
abstract = {Mosquitoes are hematophagous vectors that can acquire human viruses in their intestinal tract. Here, we define a mosquito gut commensal bacterium that promotes permissiveness to arboviruses. Antibiotic depletion of gut bacteria impaired arboviral infection of a lab-adapted Aedes aegypti mosquito strain. Reconstitution of individual cultivable gut bacteria in antibiotic-treated mosquitoes identified Serratia marcescens as a commensal bacterium critical for efficient arboviral acquisition. S. marcescens facilitates arboviral infection through a secreted protein named SmEnhancin, which digests membrane-bound mucins on the mosquito gut epithelia, thereby enhancing viral dissemination. Field Aedes mosquitoes positive for S. marcescens were more permissive to dengue virus infection than those free of S. marcescens. Oral introduction of S. marcescens into field mosquitoes that lack this bacterium rendered these mosquitoes highly susceptible to arboviruses. This study defines a commensal-driven mechanism that contributes to vector competence, and extends our understanding of multipartite interactions among hosts, the gut microbiome, and viruses.},
}
@article {pmid30594321,
year = {2018},
author = {Vazquez, F and Fernández-Blázquez, A and García, B},
title = {Vaginosis. Vaginal microbiota.},
journal = {Enfermedades infecciosas y microbiologia clinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eimc.2018.11.009},
pmid = {30594321},
issn = {1578-1852},
abstract = {The latest advances in the vaginal microbiome and molecular diagnosis of bacterial vaginosis have allowed for a better knowledge of this entity, characterising aspects of its pathogenesis and the establishment of the vaginal biolayer, the models and new theories of its aetiology, how it is transmitted, with it being considered nowadays as a probable sexually transmitted infection, the separation of other entities such as aerobic vaginosis, its molecular diagnosis and treatment with new molecules to prevent frequent relapses. This entity and the study of the vaginal microbiome have made it possible to consider these infections as a polymicrobial syndrome, putting an end to the dogma: one microorganism, one disease. In addition, a lesser-known entity such as aerobic vaginosis and the methods for its detection are updated.},
}
@article {pmid30594143,
year = {2018},
author = {Ignasiak, K and Maxwell, A},
title = {Oxytetracycline reduces the diversity of tetracycline-resistance genes in the Galleria mellonella gut microbiome.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {228},
doi = {10.1186/s12866-018-1377-3},
pmid = {30594143},
issn = {1471-2180},
support = {BB/J004656/1//Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {BACKGROUND: Clinically-relevant multidrug resistance is sometimes present in bacteria not exposed to human-made antibiotics, in environments without extreme selective pressures, such as the insect gut. The use of antibiotics on naïve microbiomes often leads to decreased microbe diversity and increased antibiotic resistance.<br><br>RESULTS: Here we investigate the impact of antibiotics on the insect gut microbiome by identifying tetracycline-resistance genes in the gut bacteria of greater wax moth (Galleria mellonella) larvae, feeding on artificial food containing oxytetracycline. We determined that G. mellonella can be raised on artificial food for over five generations and that the insects tolerate low doses of antibiotics in their diets, but doses of oxytetracycline higher than sub-inhibitory lead to early larval mortality. In our experiments, greater wax moth larvae had a sparse microbiome, which is consistent with previous findings. Additionally, we determined that the microbiome of G. mellonella larvae not exposed to antibiotics carries a number of tetracycline-resistance genes and some of that diversity is lost upon exposure to strong selective pressure.<br><br>CONCLUSIONS: We show that G. mellonella larvae can be raised on artificial food, including antibiotics, for several generations and that the microbiome can be sampled. We show that, in the absence of antibiotics, the insect gut microbiome can maintain a diverse pool of tetracycline-resistance genes. Selective pressure, from exposure to the antibiotic oxytetracycline, leads to microbiome changes and alteration in the tetracycline-resistance gene pool.},
}
@article {pmid30593419,
year = {2019},
author = {Liptak, R and Gromova, B and Maronek, M and Gardlik, R},
title = {Reverse phenotype transfer via fecal microbial transplantation in inflammatory bowel disease.},
journal = {Medical hypotheses},
volume = {122},
number = {},
pages = {41-44},
doi = {10.1016/j.mehy.2018.10.017},
pmid = {30593419},
issn = {1532-2777},
abstract = {Inflammatory bowel disease (IBD) is characterized by a disbalance in the composition of intestinal microbiota. It is not clear whether such dysbiosis is a cause or a consequence of a disease state. Fecal microbiota transplantation (FMT) from a healthy donor to a patient or diseased animal is a valuable tool for targeted modification of microbiome leading to therapeutic response. Positive effect has been shown in therapy of a number of gastrointestinal as well as non-gastrointestinal diseases. In addition, FMT has been successfully used to transfer the diseased phenotype form a donor with the disease to a healthy recipient. However, targeted modification of the microbiome before the onset of colitis has not been shown previously. Based on our preliminary results, we propose the hypothesis of so called reverse phenotype transfer in IBD. This term describes the phenomenon, in which the transplantation of gut microbiota from a donor more sensitive to IBD to a healthy recipient leads to resistance of the recipient to IBD and vice versa. Mice that received FMT from donors with severe colitis have shown improved colitis score compared with mice that received FMT from donors more resistant to development of colitis. Such reverse phenotype transfer has broad implications, especially in terms of preventive medicine. However, detailed mechanisms need to be elucidated to conclude the validity of the phenomenon.},
}
@article {pmid30592890,
year = {2018},
author = {Semenikhina, VF and Rozhkova, IV and Begunova, AV and Fedorova, TV and Shirshova, TI},
title = {[Development of biotechnology of fermented milk product with Lactobacillus reuteri LR1 and the evaluation of its functional property in experiment in vitro and in vivo].},
journal = {Voprosy pitaniia},
volume = {87},
number = {5},
pages = {52-62},
doi = {10.24411/0042-8833-2018-10053},
pmid = {30592890},
issn = {0042-8833},
support = {project № 16-16-00094//Russian Science Foundation/ ; },
abstract = {In this article the biotechnology of the dairy product based on the probiotic strain of Lactobacillus reuteri LR1 is presented. The following conditions of milk fermentation were screened: fermentation by monoculture of Lactobacillus reuteri LR1, fermentation by monoculture of Lactobacillus reuteri LR1 with addition of yeast extract as growth-promoting factor, and combined fermentation by Lactobacillus reuteri LR1, Lactobacillus helveticus NK1 and Streptococcus thermophilus (HTC). It had been demonstrated that after 8 hours of cultivation the number of Lactobacillus reuteri LR1 cells in the monoculture with introduced yeast extract was up to 5,9×108 CFU/cm3 whereas cell count for the monoculture without yeast extract introduction was 1,6×107 CFU/cm3. The optimized biotechnological parameters of the dairy product fermentation, which provided the required Lactobacillus reuteri LR1 cell count, were as follows: Lactobacillus reuteri LR1 starter dosage of 6%, HTC starter dosage of 3-4%, fermentation temperature of 37±1 °C, and fermentation duration of 6 hours. The developed product possessed an apparent antagonistic activity against test-cultures of such pathogenic and opportunistic microorganisms as E. coli ATCC 25922, Salmonella typhimurium, Staphylococcus aureus ATCC 6538 and Klebsiella pneumoniae. The survival of the test-cultures cultivated with the obtained dairy product on the first cultivation day was from 36 to 46% and on the second - from 8 to 20%, in comparison with the pure test-cultures. The investigation of the functional properties of the obtained dairy product was carried out by the single-factor experiment with the albino Wistar rat-stock (initial body weight 160±10 g, n=10 in each group). Its positive effect on the rats' microbiome composition and lipid exchange indices has been demonstrated. It had been shown that the administration of the obtained dairy product in the rats' diet (5 ml per day per os) during 30 days didn't cause any abnormalities in the health status and behavior of the laboratory animals of spf-category. The number and distribution of leucocytes and lymphocytes, and granulocytes in all rats' populations (intact, control and treatment) were within the normal range. Upon the introduction of the developed dairy product into the rats' diet, the increased levels of bifidobacteria, lactic acid bacteria and typical for normal rats' microflora enterobacteria were observed in the rats' microbiome. As for the biochemical indices that characterize rats' lipid metabolism, the rats consuming fermented dairy products (control and treatment) demonstrated statistically significant reduction of blood serum cholesterol level compared to the intact rat group; additionally the rats consuming the developed in this study dairy product (treatment) demonstrated statistically significant reduction of blood serum triglyceride level compared to the intact rats. Utilized in this study Lactobacillus reuteri LR1 is the first strain that was purified in Russia and characterized as useful for manufacturing of the probiotic food products, since currently only Lactobacillus reuteri strains of foreign origin can be seen on the market.},
}
@article {pmid30592644,
year = {2018},
author = {Pala, L and Nezi, L and De Pas, T and Pennacchioli, E and Cocorocchio, E and Ferrucci, P and Conforti, F and Goldhirsch, A},
title = {Sex Differences in Efficacy and Toxicity of Systemic Cancer Treatments: Role of the Microbiome.},
journal = {Journal of clinical oncology : official journal of the American Society of Clinical Oncology},
volume = {},
number = {},
pages = {JCO1801270},
doi = {10.1200/JCO.18.01270},
pmid = {30592644},
issn = {1527-7755},
}
@article {pmid30592451,
year = {2019},
author = {Hersh, CP and Adcock, IM and Celedón, JC and Cho, MH and Christiani, DC and Himes, BE and Kaminski, N and Mathias, RA and Meyers, DA and Quackenbush, J and Redline, S and Steiling, KA and Tabor, HK and Tobin, MD and Wurfel, MM and Yang, IV and Koppelman, GH},
title = {High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report.},
journal = {Annals of the American Thoracic Society},
volume = {16},
number = {1},
pages = {1-16},
doi = {10.1513/AnnalsATS.201810-716WS},
pmid = {30592451},
issn = {2325-6621},
abstract = {High-throughput, &quot;next-generation&quot; sequencing methods are now being broadly applied across all fields of biomedical research, including respiratory disease, critical care, and sleep medicine. Although there are numerous review articles and best practice guidelines related to sequencing methods and data analysis, there are fewer resources summarizing issues related to study design and interpretation, especially as applied to common, complex, nonmalignant diseases. To address these gaps, a single-day workshop was held at the American Thoracic Society meeting in May 2017, led by the American Thoracic Society Section on Genetics and Genomics. The aim of this workshop was to review the design, analysis, interpretation, and functional follow-up of high-throughput sequencing studies in respiratory, critical care, and sleep medicine research. This workshop brought together experts in multiple fields, including genetic epidemiology, biobanking, bioinformatics, and research ethics, along with physician-scientists with expertise in a range of relevant diseases. The workshop focused on application of DNA and RNA sequencing research in common chronic diseases and did not cover sequencing studies in lung cancer, monogenic diseases (e.g., cystic fibrosis), or microbiome sequencing. Participants reviewed and discussed study design, data analysis and presentation, interpretation, functional follow-up, and reporting of results. This report summarizes the main conclusions of the workshop, specifically addressing the application of these methods in respiratory, critical care, and sleep medicine research. This workshop report may serve as a resource for our research community as well as for journal editors and reviewers of sequencing-based manuscript submissions in our research field.},
}
@article {pmid30592383,
year = {2018},
author = {van Dijkhuizen, EHP and Del Chierico, F and Malattia, C and Russo, A and Pires Marafon, D and Ter Haar, NM and Magni-Manzoni, S and Vastert, SJ and Dallapiccola, B and Prakken, B and Martini, A and De Benedetti, F and Putignani, L and , },
title = {Microbiome analytics of the gut microbiota in juvenile idiopathic arthritis patients: an observational, longitudinal cohort study.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.40827},
pmid = {30592383},
issn = {2326-5205},
abstract = {OBJECTIVES: To assess the composition of gut microbiota in Italian and Dutch juvenile idiopathic arthritis (JIA) patients at baseline, in inactive disease and persistent activity, compared to healthy controls.<br><br>METHODS: In a prospective, multicenter, observational cohort study, fecal samples were collected of 78 Italian and 21 Dutch treatment-naïve JIA patients at baseline with less than 6 months disease duration and compared to 107 geography-matched samples of healthy children. Furthermore, 44 follow up samples in inactive disease and 25 in persistent activity were analyzed. Gut microbiota composition was determined by 16S rRNA-based-metagenomics. The α- and β-diversity were computed, and log-ratios of relative abundance were compared between patients and healthy controls using random forest models and logistic regression.<br><br>RESULTS: Italian baseline samples showed reduced richness compared to healthy controls (p <0.001). Random forest distinguished Italian baseline samples from controls and suggested differences between Dutch samples and controls (area under the curve >0.99 and 0.71, respectively). Mainly the Operational Taxonomic Units (OTUs) Erysipelotrichaceae (increased in patients), Allobaculum (decreased) and Faecalibacterium prausnitzii (increased) showed different relative abundance in Italian baseline samples compared to controls after controlling for multiple comparisons. Some OTUs differed between Dutch samples and healthy controls, but no evidence remained after controlling for multiple comparisons. No differences were found in paired analysis between Italian baseline and inactive disease samples.<br><br>CONCLUSIONS: We found evidence for dysbiosis in JIA patients. Only patient/control status, age and geographical origin appeared to be drivers of the microbiota profiles, regardless of disease activity stage, inflammation and autoimmunity markers. This article is protected by copyright. All rights reserved.},
}
@article {pmid30591731,
year = {2018},
author = {Crofts, TS and Wang, B and Spivak, A and Gianoulis, TA and Forsberg, KJ and Gibson, MK and Johnsky, LA and Broomall, SM and Rosenzweig, CN and Skowronski, EW and Gibbons, HS and Sommer, MOA and Dantas, G},
title = {Publisher Correction: Shared strategies for β-lactam catabolism in the soil microbiome.},
journal = {Nature chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41589-018-0208-z},
pmid = {30591731},
issn = {1552-4469},
abstract = {In the version of the article originally published, the x axis of the graph in Fig. 4d was incorrectly labeled as &quot;Retention time (min)&quot;. It should read &quot;Reaction time (min)&quot;. The 'deceased' footnote was also formatted incorrectly when published. The footnote text itself should include the name of co-author Tara A. Gianoulis in addition to the previous link to her name in the author list through footnote number 10. The errors have been corrected in the HTML and PDF versions of the article.},
}
@article {pmid30591685,
year = {2018},
author = {de la Cuesta-Zuluaga, J and Mueller, NT and Álvarez-Quintero, R and Velásquez-Mejía, EP and Sierra, JA and Corrales-Agudelo, V and Carmona, JA and Abad, JM and Escobar, JS},
title = {Higher Fecal Short-Chain Fatty Acid Levels Are Associated with Gut Microbiome Dysbiosis, Obesity, Hypertension and Cardiometabolic Disease Risk Factors.},
journal = {Nutrients},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/nu11010051},
pmid = {30591685},
issn = {2072-6643},
support = {K01HL141589//National Heart, Lung, and Blood Institute/ ; P30DK072488//Mid-Atlantic Nutrition Obesity Research Center/ ; NA//Foundation for Gender Specific Medicine/ ; },
abstract = {Fiber fermentation by gut microbiota yields short-chain fatty acids (SCFAs) that are either absorbed by the gut or excreted in feces. Studies are conflicting as to whether SCFAs are beneficial or detrimental to cardiometabolic health, and how gut microbiota associated with SCFAs is unclear. In this study of 441 community-dwelling adults, we examined associations of fecal SCFAs, gut microbiota diversity and composition, gut permeability, and cardiometabolic outcomes, including obesity and hypertension. We assessed fecal microbiota by 16S rRNA gene sequencing, and SCFA concentrations by gas chromatography/mass spectrometry. Fecal SCFA concentrations were inversely associated with microbiota diversity, and 70 unique microbial taxa were differentially associated with at least one SCFA (acetate, butyrate or propionate). Higher SCFA concentrations were associated with a measure of gut permeability, markers of metabolic dysregulation, obesity and hypertension. Microbial diversity showed association with these outcomes in the opposite direction. Associations were significant after adjusting for measured confounders. In conclusion, higher SCFA excretion was associated with evidence of gut dysbiosis, gut permeability, excess adiposity, and cardiometabolic risk factors. Studies assessing both fecal and circulating SCFAs are needed to test the hypothesis that the association of higher fecal SCFAs with obesity and cardiometabolic dysregulation is due to less efficient SCFA absorption.},
}
@article {pmid30591521,
year = {2018},
author = {Kolodziejczyk, AA and Zheng, D and Shibolet, O and Elinav, E},
title = {The role of the microbiome in NAFLD and NASH.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.15252/emmm.201809302},
pmid = {30591521},
issn = {1757-4684},
abstract = {Nonalcoholic fatty liver disease (NAFLD) is the hepatic manifestation of cardiometabolic syndrome, which often also includes obesity, diabetes, and dyslipidemia. It is rapidly becoming the most prevalent liver disease worldwide. A sizable minority of NAFLD patients develop nonalcoholic steatohepatitis (NASH), which is characterized by inflammatory changes that can lead to progressive liver damage, cirrhosis, and hepatocellular carcinoma. Recent studies have shown that in addition to genetic predisposition and diet, the gut microbiota affects hepatic carbohydrate and lipid metabolism as well as influences the balance between pro-inflammatory and anti-inflammatory effectors in the liver, thereby impacting NAFLD and its progression to NASH In this review, we will explore the impact of gut microbiota and microbiota-derived compounds on the development and progression of NAFLD and NASH, and the unexplored factors related to potential microbiome contributions to this common liver disease.},
}
@article {pmid30591184,
year = {2018},
author = {Dutton, JS and Hinman, SS and Kim, R and Wang, Y and Allbritton, NL},
title = {Primary Cell-Derived Intestinal Models: Recapitulating Physiology.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2018.12.001},
pmid = {30591184},
issn = {1879-3096},
abstract = {The development of physiologically relevant intestinal models fueled by breakthroughs in primary cell-culture methods has enabled successful recapitulation of key features of intestinal physiology. These advances, paired with engineering methods, for example incorporating chemical gradients or physical forces across the tissues, have yielded ever more sophisticated systems that enhance our understanding of the impact of the host microbiome on human physiology as well as on the genesis of intestinal diseases such as inflammatory bowel disease and colon cancer. In this review we highlight recent advances in the development and usage of primary cell-derived intestinal models incorporating monolayers, organoids, microengineered platforms, and macrostructured systems, and discuss the expected directions of the field.},
}
@article {pmid30591021,
year = {2018},
author = {Jenkins, SV and Vang, KB and Gies, A and Griffin, RJ and Jun, SR and Nookaew, I and Dings, RPM},
title = {Sample storage conditions induce post-collection biases in microbiome profiles.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {227},
doi = {10.1186/s12866-018-1359-5},
pmid = {30591021},
issn = {1471-2180},
support = {P20GM103625//National Institute of General Medical Sciences/ ; },
abstract = {BACKGROUND: Here we investigated the influence of different stabilization and storage strategies on the quality and composition of the fecal microbial community. Namely, same-day isolated murine DNA was compared to samples stored for 1 month in air at ambient temperature, with or without preservative buffers (i.e. EDTA and lysis buffer), different temperatures (i.e. 4 °C, - 20 °C, and - 80 °C), and hypoxic conditions.<br><br>RESULTS: Only storage in lysis buffer significantly reduced DNA content, yet without integrity loss. Storage in EDTA affected alpha diversity the most, which was also reflected in cluster separation. Distinct changes were also seen in the phyla and bacterial species abundance per storage strategy. Metabolic function analysis showed 22 pathways not significantly affected by storage conditions, whereas the tyrosine metabolism pathway was significantly changed in all strategies except by EDTA.<br><br>CONCLUSION: Each long-term storage strategy introduced a unique post-collection bias, which is important to take into account when interpreting data.},
}
@article {pmid30590511,
year = {2018},
author = {Lee, KH and Coull, BA and Moscicki, AB and Paster, BJ and Starr, JR},
title = {Bayesian variable selection for multivariate zero-inflated models: Application to microbiome count data.},
journal = {Biostatistics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/biostatistics/kxy067},
pmid = {30590511},
issn = {1468-4357},
abstract = {Microorganisms play critical roles in human health and disease. They live in diverse communities in which they interact synergistically or antagonistically. Thus for estimating microbial associations with clinical covariates, such as treatment effects, joint (multivariate) statistical models are preferred. Multivariate models allow one to estimate and exploit complex interdependencies among multiple taxa, yielding more powerful tests of exposure or treatment effects than application of taxon-specific univariate analyses. Analysis of microbial count data also requires special attention because data commonly exhibit zero inflation, i.e., more zeros than expected from a standard count distribution. To meet these needs, we developed a Bayesian variable selection model for multivariate count data with excess zeros that incorporates information on the covariance structure of the outcomes (counts for multiple taxa), while estimating associations with the mean levels of these outcomes. Though there has been much work on zero-inflated models for longitudinal data, little attention has been given to high-dimensional multivariate zero-inflated data modeled via a general correlation structure. Through simulation, we compared performance of the proposed method to that of existing univariate approaches, for both the binary (&quot;excess zero&quot;) and count parts of the model. When outcomes were correlated the proposed variable selection method maintained type I error while boosting the ability to identify true associations in the binary component of the model. For the count part of the model, in some scenarios the univariate method had higher power than the multivariate approach. This higher power was at a cost of a highly inflated false discovery rate not observed with the proposed multivariate method. We applied the approach to oral microbiome data from the Pediatric HIV/AIDS Cohort Oral Health Study and identified five (of 44) species associated with HIV infection.},
}
@article {pmid30589960,
year = {2018},
author = {Cai, Y and Liu, W and Lin, Y and Zhang, S and Zou, B and Xiao, D and Lin, L and Zhong, Y and Zheng, H and Liao, Q and Xie, Z},
title = {Compound polysaccharides ameliorate experimental colitis by modulating gut microbiota composition and function.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.14583},
pmid = {30589960},
issn = {1440-1746},
abstract = {BACKGROUND AND AIM: Inflammatory bowel disease (IBD) results from a dysregulated immune response to intestinal microbial flora in individuals with genetic predisposition(s). This study aimed to determine the effects of compound polysaccharides (CP) containing yam polysaccharide and inulin on the rat model of colitis induced by 2,4,6-trinitrobenzenesulfonic acid (TNBS) and to explain the mechanism in terms of gut microbiota composition and function.<br><br>METHODS: Male SD rats were divided into three groups: the control group, the model group and the CP group. Disease activity index (DAI), serum myeloperoxidase (MPO) level and the composition and function of gut microbiota were analyzed.<br><br>RESULTS: The data in the study showed CP reduced inflammation in the rat model of colitis induced by TNBS and ameliorated the experimental colitis. The results also indicated that CP not only reversed TNBS-induced gut dysbiosis-indexed by increased short-chain fatty acids-producing bacteria, lactic acid-producing bacteria and decreased Bacteroides, Proteobacteria as well as sulfate-reducing bacteria, but also restored the dysregulated microbiota function of colitic rats into a normal condition, including an improvement on basic metabolism and a reduction on oxidative stress, cell motility, signal transduction, xenobiotics biodegradation and metabolism as well as pathogenesis processes.<br><br>CONCLUSIONS: CP ameliorated the experimental colitis of rats induced by TNBS by modulating the gut microbiota composition and function profiles, which makes it possible to be used as prebiotic agents to treat gut dysbiosis in colitis individuals.},
}
@article {pmid30588757,
year = {2018},
author = {Ren, J and Hu, D and Mao, Y and Yang, H and Liao, W and Xu, W and Ge, P and Zhang, H and Sang, X and Lu, X and Zhong, S},
title = {Alteration in gut microbiota caused by time-restricted feeding alleviate hepatic ischaemia reperfusion injury in mice.},
journal = {Journal of cellular and molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcmm.14069},
pmid = {30588757},
issn = {1582-4934},
support = {2016-I2M-1-001//CAMS Innovation Fund for Medical Sciences/ ; 2015AA020303//National High-tech R&amp;D Program/ ; },
abstract = {Time-restricted feeding (TRF), that is, no caloric intake for 14-16 hours each day leads to favourable nutritional outcomes. This study is the first to investigate TRF through a surgical perspective verifying its efficacy against liver ischaemia reperfusion (I/R) injury. We randomly assigned 100 10-week-old wild-type male C57BL/6 mice into two feeding regimens: TRF and ad libitum access to food. Main outcomes were evaluated at 6, 12 and 24 hours post-I/R surgery after 12 weeks of intervention. TRF group demonstrated minor liver injury via histological study; lower serum levels of liver enzymes, glucose and lipids; higher concentrations of free fatty acid and β-hydroxybutyrate; decreased oxidative stress and inflammatory biomarkers; as well as less severe cell apoptosis and proliferation. Further exploration indicated better gut microenvironment and intestinal epithelial tight junction function. TRF employed its positive influence on a wide spectrum of biochemical pathways and ultimately revealed protective effect against hepatic I/R injury possibly through adjusting the gut microbiota. The results referred to a strong indication of adopting better feeding pattern for surgical patients.},
}
@article {pmid30588567,
year = {2018},
author = {Wei, F and Wu, Q and Hu, Y and Huang, G and Nie, Y and Yan, L},
title = {Conservation metagenomics: a new branch of conservation biology.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11427-018-9423-3},
pmid = {30588567},
issn = {1869-1889},
abstract = {Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade, increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology, nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.},
}
@article {pmid30588486,
year = {2018},
author = {Duscher, AA and Conesa, A and Bishop, M and Vroom, MM and Zubizarreta, SD and Foster, JS},
title = {Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity.},
journal = {NPJ microgravity},
volume = {4},
number = {},
pages = {25},
doi = {10.1038/s41526-018-0060-1},
pmid = {30588486},
issn = {2373-8065},
abstract = {For long-duration space missions, it is critical to maintain health-associated homeostasis between astronauts and their microbiome. To achieve this goal it is important to more fully understand the host-symbiont relationship under the physiological stress conditions of spaceflight. To address this issue we examined the impact of a spaceflight analog, low-shear-modeled microgravity (LSMMG), on the transcriptome of the mutualistic bacterium Vibrio fischeri. Cultures of V. fischeri and a mutant defective in the global regulator Hfq (∆hfq) were exposed to either LSMMG or gravity conditions for 12 h (exponential growth) and 24 h (stationary phase growth). Comparative transcriptomic analysis revealed few to no significant differentially expressed genes between gravity and the LSMMG conditions in the wild type or mutant V. fischeri at exponential or stationary phase. There was, however, a pronounced change in transcriptomic profiles during the transition between exponential and stationary phase growth in both V. fischeri cultures including an overall decrease in gene expression associated with translational activity and an increase in stress response. There were also several upregulated stress genes specific to the LSMMG condition during the transition to stationary phase growth. The ∆hfq mutants exhibited a distinctive transcriptome profile with a significant increase in transcripts associated with flagellar synthesis and transcriptional regulators under LSMMG conditions compared to gravity controls. These results indicate the loss of Hfq significantly influences gene expression under LSMMG conditions in a bacterial symbiont. Together, these results improve our understanding of the mechanisms by which microgravity alters the physiology of beneficial host-associated microbes.},
}
@article {pmid30588210,
year = {2018},
author = {Swain Ewald, HA and Ewald, PW},
title = {Natural Selection, The Microbiome, and Public Health.},
journal = {The Yale journal of biology and medicine},
volume = {91},
number = {4},
pages = {445-455},
pmid = {30588210},
issn = {1551-4056},
abstract = {The microbiome is composed of hundreds of interacting species that have co-evolved with the host and alterations in microbiome composition have been associated with health and disease. Insights from evolutionary ecology may aid efforts to ameliorate microbiome-associated diseases. One step toward this goal involves recognition that the idea of commensalism has been applied too broadly to human/microbe symbioses. Commensalism is most accurately viewed on a symbiosis continuum as a dividing line that separates a spectrum of mutualisms of decreasing positive interdependence from parasitisms of increasing severity. Insights into the evolution of the gut microbial symbiosis continuum will help distinguish between human actions that will advance or hinder health. Theory and research indicate that a major benefit of mutualistic microbes will be protection against pathogens. Mismatches between current and ancestral diets may disfavor mutualists, resulting in microbiome effects on health problems, including obesity, diabetes, autism, and childhood allergy. Evolutionary theory indicates that mutualisms will be favored when symbionts depend on resources that are not used by the host. These resources, which are referred to as human-inaccessible microbiota-accessible carbohydrates (HIMACs), can be supplied naturally through diet. Public health interventions need to consider the position of gut microbes on the mutualist-parasite continuum and the specific associations between prebiotics, such as HIMACs, and the mutualists they support. Otherwise interventions may fail to restore the match between human adaptations, diet, and microbiome function and may thereby fail to improve health and even inadvertently promote illness.},
}
@article {pmid30587804,
year = {2018},
author = {Ugarelli, K and Laas, P and Stingl, U},
title = {The Microbial Communities of Leaves and Roots Associated with Turtle Grass (Thalassia testudinum) and Manatee Grass (Syringodium filliforme) are Distinct from Seawater and Sediment Communities, but Are Similar between Species and Sampling Sites.},
journal = {Microorganisms},
volume = {7},
number = {1},
pages = {},
doi = {10.3390/microorganisms7010004},
pmid = {30587804},
issn = {2076-2607},
support = {Hatch project FLA-FTL-005631//U.S. Department of Agriculture/ ; },
abstract = {Seagrasses are vital members of coastal systems, which provide several important ecosystem services such as improvement of water quality, shoreline protection, and serving as shelter, food, and nursery to many species, including economically important fish. They also act as a major carbon sink and supply copious amounts of oxygen to the ocean. A decline in seagrasses has been observed worldwide, partly due to climate change, direct and indirect human activities, diseases, and increased sulfide concentrations in the coastal porewaters. Several studies have shown a symbiotic relationship between seagrasses and their microbiome. For instance, the sulfur, nitrogen, and carbon cycles are important biochemical pathways that seem to be linked between the plant and its microbiome. The microbiome presumably also plays a key role in the health of the plant, for example in oxidizing phyto-toxic sulfide into non-toxic sulfate, or by providing protection for seagrasses from pathogens. Two of the most abundant seagrasses in Florida include Thalassiatestudinum (turtle grass) and Syringodium filliforme (manatee grass), yet there is little data on the composition of the microbiome of these two genera. In this study, the microbial composition of the phyllosphere and rhizosphere of Thalassia testudinum and Syringodium filiforme were compared to water and sediment controls using amplicon sequencing of the V4 region of the 16S rRNA gene. The microbial composition of the leaves, roots, seawater, and sediment differ from one another, but are similar between the two species of seagrasses.},
}
@article {pmid30586952,
year = {2018},
author = {Oh, HJ and Kim, JH and Bae, JM and Kim, HJ and Cho, NY and Kang, GH},
title = {Prognostic Impact of Fusobacterium nucleatum Depends on Combined Tumor Location and Microsatellite Instability Status in Stage II/III Colorectal Cancers Treated with Adjuvant Chemotherapy.},
journal = {Journal of pathology and translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.4132/jptm.2018.11.29},
pmid = {30586952},
issn = {2383-7837},
abstract = {Background: This study aimed to investigate the prognostic impact of intratumoral Fusobacterium nucleatum in colorectal cancer (CRC) treated with adjuvant chemotherapy.<br><br>Materials and Methods: F. nucleatum DNA was quantitatively measured in a total of 593 CRC tissues retrospectively collected from surgically resected specimens of stage III or high-risk stage II CRC patients who had received curative surgery and subsequent oxaliplatin-based adjuvant chemotherapy (either FOLFOX or CAPOX). Each case was classified into one of the three categories: F. nucleatum‒high, ‒low, or ‒negative.<br><br>Results: No significant differences in survival were observed between the F. nucleatum‒high and ‒low/negative groups in the 593 CRCs (p=.671). Subgroup analyses according to tumor location demonstrated that disease-free survival was significantly better in F. nucleatum‒high than in ‒low/negative patients with non-sigmoid colon cancer (including cecal, ascending, transverse, and descending colon cancers; n=219; log-rank p=.026). In multivariate analysis, F. nucleatum was determined to be an independent prognostic factor in non-sigmoid colon cancers (hazard ratio, 0.42; 95% confidence interval, 0.18 to 0.97; p=.043). Furthermore, the favorable prognostic effect of F. nucleatum‒high was observed only in a non-microsatellite instability-high (non-MSI-high) subset of non-sigmoid colon cancers (log-rank p=0.014), but not in a MSI-high subset (log-rank p=0.844), suggesting that the combined status of tumor location and MSI may be a critical factor for different prognostic impacts of F. nucleatum in CRCs treated with adjuvant chemotherapy.<br><br>Conclusion: Intratumoral F. nucleatum load is a potential prognostic factor in a non-MSI-high/non-sigmoid/non-rectal cancer subset of stage II/III CRCs treated with oxaliplatin-based adjuvant chemotherapy.},
}
@article {pmid30586799,
year = {2019},
author = {Muñoz, X and Barreiro, E and Bustamante, V and Lopez-Campos, JL and González-Barcala, FJ and Cruz, MJ},
title = {Diesel exhausts particles: Their role in increasing the incidence of asthma. Reviewing the evidence of a causal link.},
journal = {The Science of the total environment},
volume = {652},
number = {},
pages = {1129-1138},
doi = {10.1016/j.scitotenv.2018.10.188},
pmid = {30586799},
issn = {1879-1026},
abstract = {Exposure to air pollutants has been correlated with an increase in the severity of asthma and in the exacerbation of pre-existing asthma. However, whether or not environmental pollution can cause asthma remains a controversial issue. The present review analyzes the current scientific evidence of the possible causal link between diesel exhaust particles (DEP), the solid fraction of the complex mixture of diesel exhaust, and asthma. The mechanisms that influence the expression and development of asthma are complex. In children prolonged exposure to pollutants such as DEPs may increase asthma prevalence. In adults, this causal relation is less clear, probably because of the heterogeneity of the studies carried out. There is also evidence of physiological mechanisms by which DEPs can cause asthma. The most frequently described interactions between cellular responses and DEP are the induction of pulmonary oxidative stress and inflammation and the activation of receptors of the bronchial epithelium such as toll-like receptors or increases in Th2 and Th17 cytokines, which generally orchestrate the asthmatic response. Others support indirect mechanisms through epigenetic changes, pulmonary microbiome modifications, or the interaction of DEP with environmental antigens to enhance their activity. However, in spite of this evidence, more studies are needed to assess the harmful effects of pollution - not only in the short term in the form of increases in the rate of exacerbations, but in the medium and long term as well, as a possible trigger of the disease.},
}
@article {pmid30586168,
year = {2018},
author = {Ziesemer, KA and Ramos-Madrigal, J and Mann, AE and Brandt, BW and Sankaranarayanan, K and Ozga, AT and Hoogland, M and Hofman, CA and Salazar-García, DC and Frohlich, B and Milner, GR and Stone, AC and Aldenderfer, M and Lewis, CM and Hofman, CL and Warinner, C and Schroeder, H},
title = {The efficacy of whole human genome capture on ancient dental calculus and dentin.},
journal = {American journal of physical anthropology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ajpa.23763},
pmid = {30586168},
issn = {1096-8644},
support = {319209//H2020 European Research Council/ ; 649307DK-TAF 5662//Horizon 2020 Framework Programme/ ; BCS 1516633, BCS-1528698//National Science Foundation/ ; },
abstract = {OBJECTIVES: Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques.<br><br>MATERIALS AND METHODS: Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in-solution hybridization capture and high-throughput sequencing.<br><br>RESULTS: Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four-fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on-target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum-level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off-target sequences in human genome-enriched calculus libraries may still be useful for oral microbiome reconstruction.<br><br>DISCUSSION: While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.},
}
@article {pmid30585838,
year = {2018},
author = {Rochling, FA and Catron, HA},
title = {Intestinal failure-associated liver disease: causes, manifestations and therapies.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOG.0000000000000503},
pmid = {30585838},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: The goal of this review is to provide updates on the causes, manifestations and therapies IFALD in adults with an emphasis on recent discoveries on pathways of pathogenesis and interventions to reduce the incidence of IFALD.<br><br>RECENT FINDINGS: IFALD is a multifactorial complication of long-term home parenteral therapy. Although exact pathways are unknown, altered bile acid metabolism, microbiome dysbiosis impact on the gut-liver axis and soybean-based lipid formulations are major drivers of IFALD development.<br><br>SUMMARY: IFALD contributes to morbidity and mortality in patients on parenteral nutrition. Proactive management by a multidisciplinary team has led to improved outcomes in at-risk patients. Attention to early treatment and prevention of sepsis, introduction of nonsoybean based lipid formulations, surgical procedures such as step enteroplasties and, potentially, microbiome dysbiosis are considerations in IFLAD management.},
}
@article {pmid30585426,
year = {2018},
author = {Zhang, M and Gaughan, S and Chang, Q and Chen, H and Lu, G and Wang, X and Xu, L and Zhu, L and Jiang, J},
title = {Age-related changes in the gut microbiota of the Chinese giant salamander (Andrias davidianus).},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e778},
doi = {10.1002/mbo3.778},
pmid = {30585426},
issn = {2045-8827},
support = {2016YFC0503200//National Key Research and Development Program of China/ ; Y6D3041//Technology Foundation for Selected Overseas Chinese Scholar/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)/ ; },
abstract = {The composition of the intestinal microbial community may vary across developmental stages. In this study, we explored how this microbial community shifted along the intestinal tract of the Chinese giant salamander (Andrias davidianus) at various ages. Next-generation sequencing was used to sequence the bacterial 16S rRNA gene from different kind of samples, including the stomach, duodenum, ileum, and rectum. The highest mean relative abundance of the bacterial community in the gastrointestinal tract shifted in relation to age: within the first year, Bacteroidetes (47.76%) dominated the gut microbiome, whereas Proteobacteria was the most dominant at age 2 (32.88%) and age 3 (30.78%), and finally, Firmicutes was the most dominant at age 4 (34.70%). The overall richness of the gut bacterial community also generally increased from age 2 to 4. Hierarchical cluster analysis revealed that the gut microbiome at age 2 had greater variability than that at either age 3 or 4, likely representing a shift in diet from yolk or redworms as a juvenile to shrimp or crab as an adult. As these salamanders develop, their gastrointestinal tracts increase in complexity, and this compartmentalization may also facilitate an increase in microbial gut diversity.},
}
@article {pmid30585199,
year = {2018},
author = {Van Belleghem, JD and Dąbrowska, K and Vaneechoutte, M and Barr, JJ and Bollyky, PL},
title = {Interactions between Bacteriophage, Bacteria, and the Mammalian Immune System.},
journal = {Viruses},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/v11010010},
pmid = {30585199},
issn = {1999-4915},
support = {Transformative Award//Falk Medical Research Trust/ ; },
abstract = {The human body is host to large numbers of bacteriophages (phages)⁻a diverse group of bacterial viruses that infect bacteria. Phage were previously regarded as bystanders that only impacted immunity indirectly via effects on the mammalian microbiome. However, it has become clear that phages also impact immunity directly, in ways that are typically anti-inflammatory. Phages can modulate innate immunity via phagocytosis and cytokine responses, but also impact adaptive immunity via effects on antibody production and effector polarization. Phages may thereby have profound effects on the outcome of bacterial infections by modulating the immune response. In this review we highlight the diverse ways in which phages interact with human cells. We present a computational model for predicting these complex and dynamic interactions. These models predict that the phageome may play important roles in shaping mammalian-bacterial interactions.},
}
@article {pmid30584647,
year = {2018},
author = {Zhang, J and Zhang, F and Zhao, C and Xu, Q and Liang, C and Yang, Y and Wang, H and Shang, Y and Wang, Y and Mu, X and Zhu, D and Zhang, C and Yang, J and Yao, M and Zhang, L},
title = {Dysbiosis of the gut microbiome is associated with thyroid cancer and thyroid nodules and correlated with clinical index of thyroid function.},
journal = {Endocrine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12020-018-1831-x},
pmid = {30584647},
issn = {1559-0100},
support = {31471202//the National Natural Science Foundation of China/ ; 81670822//the National Natural Science Foundation of China/ ; 2016YYSP009//the Shandong Provincial Key Research and Development Program/ ; 2016GNS023//Weihai Technique Extension Project/ ; 17-3-3-10-nsh//Qingdao Key Research Project/ ; tshw20120206//the Taishan Scholars Program of Shandong Province/ ; },
abstract = {PURPOSE: Thyroid cancer and thyroid nodules are the most prevalent form of thyroid endocrine disorder. The balance of gut microbiome is highly crucial for a healthy human body, especially for the immune and endocrine system. However, the relationship between gut microbiome and the thyroid endocrine disorders such as thyroid cancer and thyroid nodules has not been reported yet.<br><br>METHODS: A cohort of 74 patients was recruited for this study. Among them, 20 patients had thyroid cancer, 18 patients had thyroid nodules, and 36 were matched healthy controls. Gut microbiome composition was analyzed by 16S rRNA (16S ribosomal RNA) gene-based sequencing protocol.<br><br>RESULTS: We compared the gut microbiome results of 74 subjects and established the correlation between gut microbiome and thyroid endocrine function for both thyroid cancer and thyroid nodules. The results inferred that alpha and beta diversity were different for patients with thyroid tumor than the healthy controls (p < 0.01). In comparison to healthy controls, the relative abundance of Neisseria (p < 0.001) and Streptococcus (p < 0.001) was significantly higher for thyroid cancer and thyroid nodules. Butyricimonas (p < 0.001) and Lactobacillus (p < 0.001) displayed notably lower relative abundance for thyroid cancer and thyroid nodules, respectively. It was also found that the clinical indexes were correlated with gut microbiome.<br><br>CONCLUSION: Our results indicate that both thyroid cancer and thyroid nodules are associated with the composition of gut microbiome. These results may support further clinical diagnosis to a great extent and help in developing potential probiotics to facilitate the treatment of thyroid cancer and thyroid nodules.},
}
@article {pmid30584534,
year = {2018},
author = {Ranjan, R and Rani, A and Finn, PW and Perkins, DL},
title = {Multiomic Strategies Reveal Diversity and Important Functional Aspects of Human Gut Microbiome.},
journal = {BioMed research international},
volume = {2018},
number = {},
pages = {6074918},
doi = {10.1155/2018/6074918},
pmid = {30584534},
issn = {2314-6141},
abstract = {It is well accepted that dysbiosis of microbiota is associated with disease; however, the biological mechanisms that promote susceptibility or resilience to disease remain elusive. One of the major limitations of previous microbiome studies has been the lack of complementary metatranscriptomic (functional) data to complement the interpretation of metagenomics (bacterial abundance). The purpose of this study was twofold, first to evaluate the bacterial diversity and differential gene expression of gut microbiota using complementary shotgun metagenomics (MG) and metatranscriptomics (MT) from same fecal sample. Second, to compare sequence data using different Illumina platforms and with different sequencing parameters as new sequencers are introduced, and to determine if the data are comparable on different platforms. In this study, we perform ultradeep metatranscriptomic shotgun sequencing for a sample that we previously analyzed with metagenomics shotgun sequencing. We performed sequencing analysis using different Illumina platforms, with different sequencing and analysis parameters. Our results suggest that use of different Illumina platform did not lead to detectable bias in the sequencing data. The analysis of the sample using MG and MT approach shows that some species genes are highly represented in the MT than in the MG, indicating that some species are highly metabolically active. Our analysis also shows that ~52% of the genes in the metagenome are in the metatranscriptome and therefore are robustly expressed. The functions of the low and rare abundance bacterial species remain poorly understood. Our observations indicate that among the low abundant species analyzed in this study some were found to be more metabolically active compared to others, and can contribute distinct profiles of biological functions that may modulate the host-microbiota and bacteria-bacteria interactions.},
}
@article {pmid30584255,
year = {2018},
author = {Li, Y and Guo, Y and Wen, Z and Jiang, X and Ma, X and Han, X},
title = {Weaning Stress Perturbs Gut Microbiome and Its Metabolic Profile in Piglets.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {18068},
doi = {10.1038/s41598-018-33649-8},
pmid = {30584255},
issn = {2045-2322},
abstract = {Weaned piglets are vulnerable to nutritional, physiological, and psychological stressors, leading to abrupt taxonomic and functional shifts in the intestinal microbiome. In this study, an integrated approach combination of 16S rDNA gene sequencing and the mass spectrometry-based metabolomics techniques was used to investigate the effects of weaning stress on intestinal microbial composition and its metabolic profiles of piglets. Three litters of suckling piglets with same parity were chosen. The samples of colonic contents were collected from each selected piglets (weaned day, 3 days after weaned) for microbial and metabolomics analysis. The results showed that Lachnospiraceae, Negativicutes, Selenomonadales, Campylobacterales and other 15 species increased after weaning, while Porphyromonadaceace, Alloprevotella, Barnesiella and Oscillibacter decreased. Based on the function profiles prediction and metabolomic analysis, five key metabolic pathways including Phenylalanine metabolism, Citrate cycle (TCA cycle), Glycolysis or Gluconeogenesis, Propanoate metabolism, Nicotinate and nicotinamide metabolism might be the relevant pathways involved in weaning stress-induced gut microbiota dysbiosis. Taken together, these results indicated that weaning stress not only changed microbial composition and function but altered the microbial metabolic profiles in the intestine, which might provide a new insight in alleviating weaning stress and facilitating disease prevention during the period of weaning in piglets.},
}
@article {pmid30584188,
year = {2018},
author = {Akyol, TY and Niwa, R and Hirakawa, H and Maruyama, H and Sato, T and Suzuki, T and Fukunaga, A and Sato, T and Yoshida, S and Tawaraya, K and Saito, M and Ezawa, T and Sato, S},
title = {Impact of Introduction of Arbuscular Mycorrhizal Fungi on the Root Microbial Community in Agricultural Fields.},
journal = {Microbes and environments},
volume = {},
number = {},
pages = {},
doi = {10.1264/jsme2.ME18109},
pmid = {30584188},
issn = {1347-4405},
abstract = {Arbuscular mycorrhizal (AM) fungi are important members of the root microbiome and may be used as biofertilizers for sustainable agriculture. To elucidate the impact of AM fungal inoculation on indigenous root microbial communities, we used high-throughput sequencing and an analytical pipeline providing fixed operational taxonomic units (OTUs) as an output to investigate the bacterial and fungal communities of roots treated with a commercial AM fungal inoculum in six agricultural fields. AM fungal inoculation significantly influenced the root microbial community structure in all fields. Inoculation changed the abundance of indigenous AM fungi and other fungal members in a field-dependent manner. Inoculation consistently enriched several bacterial OTUs by changing the abundance of indigenous bacteria and introducing new bacteria. Some inoculum-associated bacteria closely interacted with the introduced AM fungi, some of which belonged to the genera Burkholderia, Cellulomonas, Microbacterium, Sphingomonas, and Streptomyces and may be candidate mycorrhizospheric bacteria that contribute to the establishment and/or function of the introduced AM fungi. Inoculated AM fungi also co-occurred with several indigenous bacteria with putative beneficial traits, suggesting that inoculated AM fungi may recruit specific taxa to confer better plant performance. The bacterial families Methylobacteriaceae, Acetobacteraceae, Armatimonadaceae, and Alicyclobacillaceae were consistently reduced by the inoculation, possibly due to changes in the host plant status caused by the inoculum. To the best of our knowledge, this is the first large-scale study to investigate interactions between AM fungal inoculation and indigenous root microbial communities in agricultural fields.},
}
@article {pmid30584187,
year = {2018},
author = {Narihiro, T and Konishi Nobu, M and Hori, T and Aoyagi, T and Sato, Y and Inaba, T and Aizawa, H and Tamaki, H and Habe, H},
title = {Effects of the Wastewater Flow Rate on Interactions between the Genus Nitrosomonas and Diverse Populations in an Activated Sludge Microbiome.},
journal = {Microbes and environments},
volume = {},
number = {},
pages = {},
doi = {10.1264/jsme2.ME18108},
pmid = {30584187},
issn = {1347-4405},
abstract = {The present study characterized the interactions of microbial populations in activated sludge systems during the operational period after an increase in the wastewater flow rate and consequential ammonia accumulation using a 16S rRNA gene sequencing-based network analysis. Two hundred microbial populations accounting for 81.8% of the total microbiome were identified. Based on a co-occurrence analysis, Nitrosomonas-type ammonia oxidizers had one of the largest number of interactions with diverse bacteria, including a bulking-associated Thiothrix organism. These results suggest that an increased flow rate has an impact on constituents by changing ammonia concentrations and also that Nitrosomonas- and Thiothrix-centric responses are critical for ammonia removal and microbial community recovery.},
}
@article {pmid30583753,
year = {2018},
author = {Caux, F},
title = {[What's new in research?].},
journal = {Annales de dermatologie et de venereologie},
volume = {145 Suppl 7},
number = {},
pages = {VIIS17-VIIS23},
doi = {10.1016/S0151-9638(18)31285-7},
pmid = {30583753},
issn = {0151-9638},
abstract = {A traditional lecture given during the annual meeting of the French Society of Dermatology in Paris summarizes the highlights of the scientific literature over the past year. In the current article the selection of the 2017-2018 period retains the following areas of interest: role of microbiome in the response to anti-PD-1 and in autoimmunity, PI3Kδ inhibitors in autoimmune bullous diseases, diagnostic and therapeutic applications of CRISPR/Cas, arrival of CAR-T cells therapy into clinical practice, gene therapy successes, use of targeted therapies in genodermatoses and integration of genetics in primary care. © 2018 Elsevier Masson SAS. All rights reserved.},
}
@article {pmid30583518,
year = {2018},
author = {Baxter, BA and Oppel, RC and Ryan, EP},
title = {Navy Beans Impact the Stool Metabolome and Metabolic Pathways for Colon Health in Cancer Survivors.},
journal = {Nutrients},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/nu11010028},
pmid = {30583518},
issn = {2072-6643},
support = {2016-67001-24538//National Institute of Food and Agriculture/ ; },
abstract = {Colorectal cancer (CRC) is the third leading cause of cancer-related death in the United States and emerging evidence supports that increased consumption of legumes, such as navy beans, can reduce risk. Navy bean consumption was previously shown to modulate host and microbiome metabolism, and this investigation was performed to assess the impact on the human stool metabolome, which includes the presence of navy bean metabolites. This 4-week, randomized-controlled trial with overweight and obese CRC survivors involved consumption of 1 meal and 1 snack daily. The intervention contained 35 g of cooked navy bean or macronutrient matched meals and snacks with 0 g of navy beans for the control group (n = 18). There were 30 statistically significant metabolite differences in the stool of participants that consumed navy bean at day 28 compared to the participants' baseline (p ≤ 0.05) and 26 significantly different metabolites when compared to the control group. Of the 560 total metabolites identified from the cooked navy beans, there were 237 possible navy bean-derived metabolites that were identified in the stool of participants consuming navy beans, such as N-methylpipecolate, 2-aminoadipate, piperidine, and vanillate. The microbial metabolism of amino acids and fatty acids were also identified in stool after 4 weeks of navy bean intake including cadaverine, hydantoin-5 propionic acid, 4-hydroxyphenylacetate, and caprylate. The stool relative abundance of ophthalmate increased 5.25-fold for navy bean consumers that can indicate glutathione regulation, and involving cancer control mechanisms such as detoxification of xenobiotics, antioxidant defense, proliferation, and apoptosis. Metabolic pathways involving lysine, and phytochemicals were also modulated by navy bean intake in CRC survivors. These metabolites and metabolic pathways represent an acute response to increased navy bean intake, which merit further investigation for improving colonic health after long-term consumption.},
}
@article {pmid30583500,
year = {2018},
author = {Connors, J and Dawe, N and Van Limbergen, J},
title = {The Role of Succinate in the Regulation of Intestinal Inflammation.},
journal = {Nutrients},
volume = {11},
number = {1},
pages = {},
doi = {10.3390/nu11010025},
pmid = {30583500},
issn = {2072-6643},
abstract = {Succinate is a metabolic intermediate of the tricarboxylic acid (TCA) cycle within host cells. Succinate is also produced in large amounts during bacterial fermentation of dietary fiber. Elevated succinate levels within the gut lumen have been reported in association with microbiome disturbances (dysbiosis), as well as in patients with inflammatory bowel disease (IBD) and animal models of intestinal inflammation. Recent studies indicate that succinate can activate immune cells via its specific surface receptor, succinate receptor 1(SUCNR1), and enhance inflammation. However, the role of succinate in inflammatory processes within the gut mucosal immune system is unclear. This review includes current literature on the association of succinate with intestinal inflammation and the potential role of succinate⁻SUCNR1 signaling in gut immune functions.},
}
@article {pmid30583059,
year = {2018},
author = {Wang, Y and Li, J and Zachariah, P and Abrams, J and Freedberg, DE},
title = {Relationship between Remote Cholecystectomy and Incident Clostridioides difficile Infection.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2018.12.016},
pmid = {30583059},
issn = {1469-0691},
abstract = {OBJECTIVES: Cholecystectomy (CCY) is associated with increased fecal levels of secondary bile acids. Secondary bile acids confer resistance to Clostridioides difficile infection (CDI, formerly Clostridium difficile infection) in animal studies. This study tested the hypothesis that CCY confers protection against CDI by increasing gut levels of secondary bile acids.<br><br>METHODS: This was a retrospective case control study. Adults hospitalized between January 2010 and June 2017 at our institution were included. CDI cases were defined as a positive stool PCR followed by anti-CDI treatment and were matched 1:1:1 with two controls groups (those who tested negative for CDI and those who were not tested for CDI) by sex, age group, BMI, and antibiotics exposure. CCY was defined as a history of CCY at least 6 months prior to the index C. difficile test or the index admission date in the untested controls. Conditional logistic regression modeling was used to estimate the relationship between remote CCY and risk for CDI.<br><br>RESULTS: The final study population was 7,077 (2,359 CDI cases, 2,359 matched controls without CDI, and 2,359 matched controls not tested for CDI). Rates of remote CCY did not differ among the three groups (14.4% vs. 15.5% vs. 14.2%) and this result was unchanged after adjusting for additional clinical factors (adjusted OR 0.90, 95% CI 0.76-1.06 comparing CDI cases vs. matched controls without CDI; adjusted OR 1.04, 95% CI 0.78-1.39 comparing CDI cases vs. matched controls not tested for CDI).<br><br>CONCLUSIONS: There was no association between remote CCY and risk for CDI.},
}
@article {pmid30582660,
year = {2018},
author = {Hubbard, CJ and Li, B and McMinn, R and Brock, MT and Maignien, L and Ewers, BE and Kliebenstein, D and Weinig, C},
title = {The effect of rhizosphere microbes outweighs host plant genetics in reducing insect herbivory.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.14989},
pmid = {30582660},
issn = {1365-294X},
abstract = {Rhizosphere microbes affect plant performance, including plant resistance against insect herbivores; yet, a direct comparison of the relative influence of rhizosphere microbes vs. plant genetics on herbivory levels and on metabolites related to defense is lacking. In the crucifer Boechera stricta, we tested the effects of rhizosphere microbes and plant population on herbivore resistance, the primary metabolome, and select secondary metabolites. Plant populations differed significantly in the concentrations of 6 glucosinolates (GLS), secondary metabolites known to provide herbivore resistance in the Brassicaceae. The population with lower GLS levels experienced ~60% higher levels of aphid (Myzus persicae) attack; no association was observed between GLS and damage by a second herbivore, flea beetles (Phyllotreta cruciferae). Rhizosphere microbiome (disrupted vs. intact native microbiome) had no effect on plant GLS concentrations. However, aphid number and flea beetle damage were respectively ~3-fold and 7-fold higher among plants grown in the disrupted vs. intact native microbiome treatment. These differences may be attributable to shifts in primary metabolic pathways previously implicated in host defense against herbivores, including increases in pentose and glucoronate interconversion among plants grown with an intact microbiome. Further, native microbiomes with distinct community composition (as estimated from 16s rRNA amplicon sequencing) differed 2-fold in their effect on host plant susceptibility to aphids. The findings suggest that rhizosphere microbes, including distinct native microbiomes, can play a greater role than population in defense against insect herbivores, and act through metabolic mechanisms independent of population. This article is protected by copyright. All rights reserved.},
}
@article {pmid30582649,
year = {2018},
author = {Leclaire, S and Strandh, M and Dell'Ariccia, G and Gabirot, M and Westerdahl, H and Bonadonna, F},
title = {Plumage microbiota covaries with MHC in blue petrels.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.14993},
pmid = {30582649},
issn = {1365-294X},
abstract = {To increase fitness, a wide range of vertebrates preferentially mate with partners that are dissimilar at the Major Histocompatibility Complex (MHC) or that have high MHC diversity. Although MHC often can be assessed through olfactory cues, the mechanism by which MHC genes influence odor is to a large extent unclear. MHC class IIB molecules, that enable recognition and elimination of extracellular bacteria, have been suggested to influence odor indirectly by shaping odor-producing microbiota, i.e. bacterial communities. There is, however, little evidence of the predicted covariation between an animal's MHC genotype and its bacterial communities in scent-producing body surfaces. Here, using high-throughput sequencing, we tested the covariation between MHC class IIB genotypes and feather microbiota in the blue petrel, a seabird with highly developed olfaction that has been suggested to rely on odor cues during an MHC-based mate choice. First, we show that individuals with similar MHC class IIB profiles also have similar bacterial assemblages in their feathers. Then, we show that individuals with low MHC diversity have less diverse feather microbiota and also a reduced abundance of a bacterium of the genus Arsenophonus, a genus where some species are symbionts of avian ectoparasites. Our results, showing that feather microbiota covary with MHC, are consistent with the hypothesis that individual MHC genotype may shape the semiochemical-producing microbiota in birds. This article is protected by copyright. All rights reserved.},
}
@article {pmid30581863,
year = {2018},
author = {Wen, Z and Xie, G and Zhou, Q and Qiu, C and Li, J and Hu, Q and Dai, W and Li, D and Zheng, Y and Wen, F},
title = {Distinct Nasopharyngeal and Oropharyngeal Microbiota of Children with Influenza A Virus Compared with Healthy Children.},
journal = {BioMed research international},
volume = {2018},
number = {},
pages = {6362716},
doi = {10.1155/2018/6362716},
pmid = {30581863},
issn = {2314-6141},
abstract = {Background: Influenza A virus (IAV) has had the highest morbidity globally over the past decade. A growing number of studies indicate that the upper respiratory tract (URT) microbiota plays a key role for respiratory health and that a dysfunctional respiratory microbiota is associated with disease; but the impact of microbiota during influenza is understudied.<br><br>Methods: We recruited 180 children, including 121 IAV patients and 59 age-matched healthy children. Nasopharyngeal (NP) and oropharyngeal (OP) swabs were collected to conduct 16S rDNA sequencing and compare microbiota structures in different individuals.<br><br>Results: Both NP and OP microbiota in IAV patients differed from those in healthy individuals. The NP dominated genera in IVA patients, such as Moraxella, Staphylococcus, Corynebacterium, and Dolosigranulum, showed lower abundance than in healthy children. The Streptococcus significantly enriched in patients' NP and Phyllobacterium could be generally detected in patients' NP microbiota. The most abundant genera in OP microbiota showed a decline tendency in patients, including Streptococcus, Neisseria, and Haemophilus. The URT's bacterial concurrence network changed dramatically in patients. NP and OP samples were clustered into subgroups by different dominant genera; and NP and OP microbiota provided the precise indicators to distinguish IAV patients from healthy children.<br><br>Conclusion: This is the first respiratory microbiome analysis on pediatric IAV infection which reveals distinct NP and OP microbiota in influenza patients. It provides a new insight into IAV research from the microecology aspect and promotes the understanding of IAV pathogenesis.},
}
@article {pmid30581663,
year = {2018},
author = {Mioduchowska, M and Czyż, MJ and Gołdyn, B and Kilikowska, A and Namiotko, T and Pinceel, T and Łaciak, M and Sell, J},
title = {Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6039},
doi = {10.7717/peerj.6039},
pmid = {30581663},
issn = {2167-8359},
abstract = {Bacterial endosymbionts of aquatic invertebrates remain poorly studied. This is at least partly due to a lack of suitable techniques and primers for their identification. We designed a pair of non-degenerate primers which enabled us to amplify a fragment of ca. 500 bp of the 16S rRNA gene from various known bacterial endosymbiont species. By using this approach, we identified four bacterial endosymbionts, two endoparasites and one uncultured bacterium in seven, taxonomically diverse, freshwater crustacean hosts from temporary waters across a wide geographical area. The overall efficiency of our new WOLBSL and WOLBSR primers for amplification of the bacterial 16S rRNA gene was 100%. However, if different bacterial species from one sample were amplified simultaneously, sequences were illegible, despite a good quality of PCR products. Therefore, we suggest using our primers at the first stage of bacterial endosymbiont identification. Subsequently, genus specific primers are recommended. Overall, in the era of next-generation sequencing our method can be used as a first simple and low-cost approach to identify potential microbial symbionts associated with freshwater crustaceans using simple Sanger sequencing. The potential to detected bacterial symbionts in various invertebrate hosts in such a way will facilitate studies on host-symbiont interactions and coevolution.},
}
@article {pmid30581574,
year = {2019},
author = {Angelakis, E and Bachar, D and Yasir, M and Musso, D and Djossou, F and Melenotte, C and Robert, C and Davoust, B and Gaborit, B and Azhar, EI and Bibi, F and Dutour, A and Raoult, D},
title = {Comparison of the gut microbiota of obese individuals from different geographic origins.},
journal = {New microbes and new infections},
volume = {27},
number = {},
pages = {40-47},
doi = {10.1016/j.nmni.2018.11.005},
pmid = {30581574},
issn = {2052-2975},
abstract = {Few studies have examined the interaction of human geography, microbial community structure and obesity. We tested obese adult volunteers from France, Saudi Arabia, French Polynesia and from a traditional population in the village of Trois-Sauts in French Guiana by sequencing the V3-V4 region. We also sequenced homemade fermented cachiri beers that were obtained from the traditional Amazonian population and are highly consumed by this population. We found that French and Saudis had significantly less richness and biodiversity in their gut microbiota than Amazonians and Polynesians (p <0.05). Principle coordinate analysis of the overall composition of the genera communities revealed that the microbiomes of Amazonians clustered independently from the other obese individuals. Moreover, we found that Amazonians presented significantly stricter anaerobic genera than the Saudis, French and Polynesians (p < 0.001). Polynesians presented significantly lower relative abundance of Lactobacillus sp. than French (p 0.01) and Saudis (p 0.05). Treponema berlinense and Treponema succinifaciens were only present in the gut microbiome of Amazonians. The cachiri beers presented significantly more bacterial species in common with the gut microbiome of Amazonians (p < 0.005). Obese individuals with different origins present modifications in their gut microbiota, and we provide evidence that the cachiri beers influenced the gut microbiome of Amazonians.},
}
@article {pmid30581447,
year = {2018},
author = {Chiaiese, P and Corrado, G and Colla, G and Kyriacou, MC and Rouphael, Y},
title = {Renewable Sources of Plant Biostimulation: Microalgae as a Sustainable Means to Improve Crop Performance.},
journal = {Frontiers in plant science},
volume = {9},
number = {},
pages = {1782},
doi = {10.3389/fpls.2018.01782},
pmid = {30581447},
issn = {1664-462X},
abstract = {Plant biostimulants (PBs) attract interest in modern agriculture as a tool to enhance crop performance, resilience to environmental stress, and nutrient use efficiency. PBs encompass diverse organic and inorganic substances (humic acids and protein hydrolysates) as well as prokaryotes (e.g., plant growth promoting bacteria) and eukaryotes such as mycorrhiza and macroalgae (seaweed). Microalgae, which comprise eukaryotic and prokaryotic cyanobacteria (blue-green algae), are attracting growing interest from scientists, extension specialists, private industry and plant growers because of their versatile nature: simple unicellular structure, high photosynthetic efficiency, ability for heterotrophic growth, adaptability to domestic and industrial wastewater, amenability to metabolic engineering, and possibility to yield valuable co-products. On the other hand, large-scale biomass production and harvesting still represent a bottleneck for some applications. Although it is long known that microalgae produce several complex macromolecules that are active on higher plants, their targeted applications in crop science is still in its infancy. This paper presents an overview of the main extraction methods from microalgae, their bioactive compounds, and application methods in agriculture. Mechanisms of biostimulation that influence plant performance, physiology, resilience to abiotic stress as well as the plant microbiome are also outlined. Considering current state-of-the-art, perspectives for future research on microalgae-based biostimulants are discussed, ranging from the development of crop-tailored, highly effective products to their application for increasing sustainability in agriculture.},
}
@article {pmid30581426,
year = {2018},
author = {Morrison, PK and Newbold, CJ and Jones, E and Worgan, HJ and Grove-White, DH and Dugdale, AH and Barfoot, C and Harris, PA and Argo, CM},
title = {The Equine Gastrointestinal Microbiome: Impacts of Age and Obesity.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {3017},
doi = {10.3389/fmicb.2018.03017},
pmid = {30581426},
issn = {1664-302X},
abstract = {Gastrointestinal microbial communities are increasingly being implicated in host susceptibilities to nutritional/metabolic diseases; such conditions are more prevalent in obese and/or older horses. This controlled study evaluated associations between host-phenotype and the fecal microbiome / metabolome. Thirty-five, Welsh Mountain pony mares were studied across 2 years (Controls, n = 6/year, 5-15 years, Body Condition Score (BCS) 4.5-6/9; Obese, n = 6/year, 5-15 years, BCS > 7/9; Aged, n = 6 Year 1; n = 5 Year 2, ≥19 years old). Animals were individually fed the same hay to maintenance (2% body mass as daily dry matter intake) for 2 (aged / obese) or 4 (control), 4-week periods in a randomized study. Outset phenotype was determined (body fat%, markers of insulin sensitivity). Feces were sampled on the final 3 days of hay feeding-periods and communities determined using Next Generation Sequencing of amplified V1-V2 hypervariable regions of bacterial 16S rRNA. Copy numbers for fecal bacteria, protozoa and fungi were similar across groups, whilst bacterial diversity was increased in the obese group. Dominant bacterial phyla in all groups were Bacteroidetes > Firmicutes > Fibrobacter. Significant differences in the bacterial communities of feces were detected between host-phenotype groups. Relative to controls, abundances of Proteobacteria were increased for aged animals and Bacteroidetes, Firmicutes, and Actinobacteria were increased for obese animals. Over 500 bacterial operational taxonomic units (OTUs) differed significantly between host-phenotype groups. No consistent pattern of changes in discriminant OTUs between groups were maintained across groups and between years. The core bacterial populations contained 21 OTUs, 6.7% of recovered sequences. Distance-based Redundancy Analyses separated fecal bacterial communities with respect to markers of obesity and insulin dysregulation, as opposed to age. Host-phenotype had no impact on the apparent digestibility of dietary GE or DM, fecal volatile fatty acid concentrations or the fecal metabolome (FT-IR). The current study demonstrates that host-phenotype has major effects on equine fecal microbial population structure. Changes were predominantly associated with the obese state, confirming an obesity-associated impact in the absence of nutritional differences. Clear biomarkers of animal-phenotype were not identified within either the fecal microbiome or metabolome, suggesting functional redundancy within the gut microbiome and/or metabolome.},
}
@article {pmid30581114,
year = {2018},
author = {Zegarra-Ruiz, DF and El Beidaq, A and Iñiguez, AJ and Lubrano Di Ricco, M and Manfredo Vieira, S and Ruff, WE and Mubiru, D and Fine, RL and Sterpka, J and Greiling, TM and Dehner, C and Kriegel, MA},
title = {A Diet-Sensitive Commensal Lactobacillus Strain Mediates TLR7-Dependent Systemic Autoimmunity.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2018.11.009},
pmid = {30581114},
issn = {1934-6069},
abstract = {Western lifestyle is linked to autoimmune and metabolic diseases, driven by changes in diet and gut microbiota composition. Using Toll-like receptor 7 (TLR7)-dependent mouse models of systemic lupus erythematosus (SLE), we dissect dietary effects on the gut microbiota and find that Lactobacillus reuteri can drive autoimmunity but is ameliorated by dietary resistant starch (RS). Culture of internal organs and 16S rDNA sequencing revealed TLR7-dependent translocation of L. reuteri in mice and fecal enrichment of Lactobacillus in a subset of SLE patients. L. reuteri colonization worsened autoimmune manifestations under specific-pathogen-free and gnotobiotic conditions, notably increasing plasmacytoid dendritic cells (pDCs) and interferon signaling. However, RS suppressed the abundance and translocation of L. reuteri via short-chain fatty acids, which inhibited its growth. Additionally, RS decreased pDCs, interferon pathways, organ involvement, and mortality. Thus, RS exerts beneficial effects in lupus-prone hosts through suppressing a pathobiont that promotes interferon pathways implicated in the pathogenesis of human autoimmunity.},
}
@article {pmid30562580,
year = {2018},
author = {Merello, M and Lotte, L and Gonfrier, S and Eleni Dit Trolli, S and Casagrande, F and Ruimy, R and Bongain, A},
title = {Enterobacteria vaginal colonization among patients with preterm premature rupture of membranes from 24 to 34 weeks of gestation and neonatal infection risk.},
journal = {Journal of gynecology obstetrics and human reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jogoh.2018.12.007},
pmid = {30562580},
issn = {2468-7847},
abstract = {AIM: Premature rupture of membranes (PROM) increases the neonatal morbidity and mortality, because of its association with a high risk of prematurity and infection. The group B streptococcus (GBS) prophylaxis using amoxicillin doesn't seem to be adapted to the emergence of new bacteria found in vaginal samples (VS). Our study aim was to assess, for PROM occurring at 23-34 weeks' gestation (WG), if the presence of ampicillin-resistant enterobacteria in the vaginal microbiome is predictive of an increased risk of early-onset neonatal infection.<br><br>MATERIAL AND METHODS: We conducted a prospective, observational, single-center study at the Nice Academic Hospital (level 3 maternity ward), between March 16, 2014 and May 3, 2015, that evaluated patients with preterm PROM (24-34 WG). Two groups were constituted according to the VS bacteria isolates and the amoxycillin-resistant enterobacteria found. Two groups of newborns were constituted depending on the suspicion of perinatal maternal-fetal bacterial infection (MFI). An intent-to-treat analysis was performed.<br><br>RESULTS: Among the 67 patients included, 12 newborns presented a strong MFI suspicion, 83% of which were associated to the group of patients with untreated or amoxycillin-resistant enterobacteria VS isolates.<br><br>CONCLUSION: Our study showed that vaginal colonization of untreated or amoxycillin-resistant enterobacteria constitutes a major risk factor of neonatal infection.},
}
@article {pmid30389429,
year = {2018},
author = {Cawley, A and Golding, S and Goulsbra, A and Hoptroff, M and Kumaran, S and Marriott, R},
title = {Microbiology insights into boosting salivary defences through the use of enzymes and proteins.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jdent.2018.10.010},
pmid = {30389429},
issn = {1879-176X},
abstract = {OBJECTIVES: To assess the effects of enzymes and proteins in toothpastes to boost salivary defences and reduce oral bacteria growth and viability.<br><br>METHODS: An in vitro study to measure levels of hypothiocyanite in saliva after treatment with a toothpaste containing enzymes and proteins (colorimetric assay). A randomised, crossover in vivo study measuring, with biochemical assays, the effect of a toothpaste containing enzymes and proteins on the levels of hydrogen peroxide and lysozyme in saliva. In vitro studies to measure, using fluorescent dyes, the effects of enzymes and proteins on bacterial membrane integrity. In vitro microbiology studies measuring the effects of enzymes and proteins on planktonic bacterial growth, in vitro studies in single and multispecies biofilms measuring the effect of toothpaste with enzymes and proteins compared to control toothpaste.<br><br>RESULTS: Levels of hypothiocyanite, hydrogen peroxide and lysozyme are boosted after application of a toothpaste containing enzymes and proteins. The enzymes and proteins adversely affect the bacterial membrane integrity in Streptococcus mutans and growth of planktonic S. mutans and Fusobacterium nucleatum. In a single species biofilm model the viability of S. mutans was significantly reduced and in a 7 species biofilm model bacterial viability was reduced for a biofilm grown on a pellicle pre-treated with toothpaste containing enzymes and proteins.<br><br>CONCLUSIONS: The use of a toothpaste containing enzymes and proteins can boost the natural salivary defences by increasing the levels of lysozyme and hydrogen peroxide in vivo and hypothiocyanite in vitro and reduce the growth and viability of oral bacteria in microbiological models.<br><br>CLINICAL SIGNIFICANCE: The subtle effects reported here of enzymes and proteins in toothpastes on oral bacteria are consistent with both the gum health benefits reported for such toothpastes containing enzymes and proteins by Daly [1] and Pedersen [2] and the rebalancing of the oral microbiome reported by Adams [3].},
}
@article {pmid30580412,
year = {2019},
author = {Feye, KM and Ricke, SC},
title = {Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {1918},
number = {},
pages = {213-227},
doi = {10.1007/978-1-4939-9000-9_18},
pmid = {30580412},
issn = {1940-6029},
abstract = {The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.},
}
@article {pmid30580075,
year = {2018},
author = {Cingi, C and Bayar Muluk, N and Scadding, GK},
title = {Will every child have allergic rhinitis soon?.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {118},
number = {},
pages = {53-58},
doi = {10.1016/j.ijporl.2018.12.019},
pmid = {30580075},
issn = {1872-8464},
abstract = {OBJECTIVES: Given the increasing prevalence of AR amongst children, we aimed to review the literature regarding the future of AR in this population.<br><br>METHODS: We searched the PubMed, Google and Proquest Central databases at Kırıkkale University Library. Search terms used were: &quot;allergic rhinitis&quot;, &quot;children&quot;, &quot;paediatric&quot;, &quot;allergy&quot;, &quot;future&quot;, &quot;risk factors&quot;, &quot;treatment&quot;, &quot;pharmacotherapy&quot; and/or &quot;allergen - specific immunotherapy&quot;. With regard to risk factors for allergic rhinitis, the terms &quot;Environmental factors&quot;, &quot;Improved hygiene&quot;, &quot;Increased indoor allergen exposure&quot;, &quot;Farms, villages, worms, and other parasites&quot;, &quot;Environmental toxicants&quot;, &quot;Diet&quot;, &quot;Lifestyle changes&quot;, &quot;Air pollution&quot; and &quot;Climate factors&quot; were searched for. &quot;Prevention of allergic diseases&quot; and &quot;Allergen-specific immunotherapy in the future&quot; were also included in the search.<br><br>RESULTS: AR has a high prevalence and causes considerable morbidity, has associated comorbidity and features specific complications. The principal treatments rely on avoiding the allergens responsible, and administering drug treatment or immunotherapy, which targets specific antigens. Genetic drift does not explain the rising prevalence of allergic disorders, but multifactorial environmental factors are likely culprits. Amongst such environmental factors to consider are the rise in caesarean births, decreases in breast feeding, dietary changes resulting in less fresh produce being consumed, the eradication of intestinal worm infestations, alterations in the way homes are aired and heated, children taking less exercise and being outdoors for shorter periods, whilst also having more contact with pollution.<br><br>CONCLUSION: Barring substantial lifestyle alterations, more and more children are likely to develop AR. It may prove feasible to stop allergy developing in the first place through manipulation of the microbiome, but the exact format such a modification should involve remains to be discovered. Molecular allergological techniques do offer the prospect of more precisely targeted immunotherapy, the sole disease modifier at present. However, at present the complexity and cost of such interventions prevents their widespread use and research in this area is still needed. The majority of children with AR are going to be managed using nasal saline sprays, since they are the most straightforward and least risky alternative for first line treatment.},
}
@article {pmid30579850,
year = {2018},
author = {Robinson, PFM and Pattaroni, C and Cook, J and Gregory, L and Alonso, AM and Fleming, LJ and Lloyd, CM and Bush, A and Marsland, BJ and Saglani, S},
title = {Lower airway microbiota associates with inflammatory phenotype in severe preschool wheeze.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.12.985},
pmid = {30579850},
issn = {1097-6825},
abstract = {CAPSULE SUMMARY: Targeting the lower airway microbiome may provide a novel approach to prevention of preschool wheezing attacks.},
}
@article {pmid30579705,
year = {2018},
author = {Dodiya, HB and Forsyth, CB and Voigt, RM and Engen, PA and Patel, J and Shaikh, M and Green, SJ and Naqib, A and Roy, A and Kordower, JH and Pahan, K and Shannon, KM and Keshavarzian, A},
title = {Chronic stress-induced gut dysfunction exacerbates Parkinson's disease phenotype and pathology in a rotenone-induced mouse model of Parkinson's disease.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbd.2018.12.012},
pmid = {30579705},
issn = {1095-953X},
abstract = {Recent evidence provides support for involvement of the microbiota-gut-brain axis in Parkinson's disease (PD) pathogenesis. We propose that a pro-inflammatory intestinal milieu, due to intestinal hyper-permeability and/or microbial dysbiosis, initiates or exacerbates PD pathogenesis. One factor that can cause intestinal hyper-permeability and dysbiosis is chronic stress which has been shown to accelerate neuronal degeneration and motor deficits in Parkinsonism rodent models. We hypothesized that stress-induced intestinal barrier dysfunction and microbial dysbiosis lead to a pro-inflammatory milieu that exacerbates the PD phenotype in the low-dose oral rotenone PD mice model. To test this hypothesis, mice received unpredictable restraint stress (RS) for 12 weeks, and during the last six weeks mice also received a daily administration of low-dose rotenone (10 mg/kg/day) orally. The initial six weeks of RS caused significantly higher urinary cortisol, intestinal hyperpermeability, and decreased abundance of putative &quot;anti-inflammatory&quot; bacteria (Lactobacillus) compared to non-stressed mice. Rotenone alone (i.e., without RS) disrupted the colonic expression of the tight junction protein ZO-1, increased oxidative stress (N-tyrosine), increased myenteric plexus enteric glial cell GFAP expression and increased α-synuclein (α-syn) protein levels in the colon compared to controls. Restraint stress exacerbated these rotenone-induced changes. Specifically, RS potentiated rotenone-induced effects in the colon including: (1) intestinal hyper-permeability, (2) disruption of tight junction proteins (ZO-1, Occludin, Claudin1), (3) oxidative stress (N-tyrosine), (4) inflammation in glial cells (GFAP + enteric glia cells), (5) α-syn, (6) increased relative abundance of fecal Akkermansia (mucin-degrading Gram-negative bacteria), and (7) endotoxemia. In addition, RS promoted a number of rotenone-induced effects in the brain including: (1) reduced number of resting microglia and a higher number of dystrophic/phagocytic microglia as well as (FJ-C+) dying cells in the substantia nigra (SN), (2) increased lipopolysaccharide (LPS) reactivity in the SN, and (3) reduced dopamine (DA) and DA metabolites (DOPAC, HVA) in the striatum compared to control mice. Our findings support a model in which chronic stress-induced, gut-derived, pro-inflammatory milieu exacerbates the PD phenotype via a dysfunctional microbiota-gut-brain axis.},
}
@article {pmid30579432,
year = {2019},
author = {Rawls, M and Ellis, AK},
title = {The microbiome of the nose.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {122},
number = {1},
pages = {17-24},
doi = {10.1016/j.anai.2018.05.009},
pmid = {30579432},
issn = {1534-4436},
}
@article {pmid30579332,
year = {2018},
author = {Getachew, B and Aubee, JI and Schottenfeld, RS and Csoka, AB and Thompson, KM and Tizabi, Y},
title = {Ketamine interactions with gut-microbiota in rats: relevance to its antidepressant and anti-inflammatory properties.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {222},
doi = {10.1186/s12866-018-1373-7},
pmid = {30579332},
issn = {1471-2180},
support = {R03AA022479//National Institute on Alcohol Abuse and Alcoholism/ ; R21AG047474//National Institute on Aging/ ; },
abstract = {BACKGROUND: Appreciable evidence suggest that dysbiosis in microbiota, reflected in gut microbial imbalance plays a key role in the pathogenesis of neuropsychiatric disorders including depression and inflammatory diseases. Recently, the antidepressant properties of ketamine have gained prominence due to its fast and long lasting effects. Additional uses for ketamine in inflammatory disorders such as irritable bowel syndrome have been suggested. However, ketamine's exact mechanism of action and potential effects on microbiome is not known. Here, we examined the effects of low dose ketamine, known to induce antidepressant effects, on stool microbiome profile in adult male Wistar rats. Animals (5/group) were injected intraperitoneally with ketamine (2.5 mg/kg) or saline, daily for 7 days and sacrificed on day 8 when intestinal stools were collected and stored at - 80 °C. DNA was extracted from the samples and the 16 S rRNA gene-based microbiota analysis was performed using 16S Metagenomics application.<br><br>RESULTS: At genus-level, ketamine strikingly amplified Lactobacillus, Turicibacter and Sarcina by 3.3, 26 and 42 fold, respectively. Conversely, opportunistic pathogens Mucispirillum and Ruminococcus were reduced by approximately 2.6 and 26 fold, respectively, in ketamine group. Low levels of Lactobacillus and Turicibacter are associated with various disorders including depression and administration of certain species of Lactobacillus ameliorates depressive-like behavior in animal models. Hence, some of the antidepressant effects of ketamine might be mediated through its interaction with these gut bacteria. Additionally, high level of Ruminococcus is positively associated with the severity of irritable bowel syndrome (IBS), and some species of Mucispirillum have been associated with intestinal inflammation. Indirect evidence of anti-inflammatory role of Sarcina has been documented. Hence, some of the anti-inflammatory effects of ketamine and its usefulness in specific inflammatory diseases including IBS may be mediated through its interaction with these latter bacteria.<br><br>CONCLUSION: Our data suggest that at least some of the antidepressant and anti-inflammatory effects of daily ketamine treatment for 7 days may be mediated via its interaction with specific gut bacteria. These findings further validate the usefulness of microbiome as a target for therapeutic intervention and call for more detailed investigation of microbiome interaction with central mediators of mood and/or inflammatory disorders.},
}
@article {pmid30579173,
year = {2018},
author = {Robichaud, K and Girard, C and Dagher, D and Stewart, K and Labrecque, M and Hijri, M and Amyot, M},
title = {Local fungi, willow and municipal compost effectively remediate petroleum-contaminated soil in the Canadian North.},
journal = {Chemosphere},
volume = {220},
number = {},
pages = {47-55},
doi = {10.1016/j.chemosphere.2018.12.108},
pmid = {30579173},
issn = {1879-1298},
abstract = {Low energy-input alternatives based on locally available products are needed for treating petroleum-hydrocarbon spills in northern regions. We tested the efficacy of three local biological components (municipal compost, white-rot fungus: Pleurotus ostreatus and willow: Salix planifolia) to remediate diesel-contaminated soils in a subarctic climate (Whitehorse, YT, Canada), and compared their efficacy to natural attenuation and chemical fertilizers (industry standard). After the first growing season, biologically amended treatments (BAT) that contained >2 biological components, had decreased 69-73% of the diesel's F2 fraction (C10-C16), which is more than natural attenuation or fertilizer (48 and 51%). By the third growing season, the BAT dropped below the Canadian Council of Ministers of the Environment's (CCME) Agricultural &amp; Residential/Parkland guideline (<150 mg kg-1) and 86% of willows had survived and developed extensive roots. MiSeq amplicon sequencing of fungal (ITS) and bacterial (16S) rRNA genes showed the BAT's microbial communities were significantly more abundant and diverse. We found 132 bacterial and 35 fungal genera unique to the BAT. Readily-available local biological components such as municipal compost, fungi and willows may provide an effective alternative to applications of imported chemical fertilizers for the bioremediation and revegetation of diesel-contaminated soil in northern environments.},
}
@article {pmid30578881,
year = {2018},
author = {Mahdavinia, M and Rasmussen, HE and Botha, M and Binh Tran, TD and Van den Berg, JP and Sodergren, E and Davis, E and Engen, K and Gray, C and Lunjani, N and Hlela, C and Preite, N and Basera, W and Hobane, L and Watkins, A and Engen, P and Mankahla, A and Gaunt, B and Thomas, F and Tobin, MC and Landay, A and Weinstock, G and Keshavarzian, A and Levin, ME},
title = {Effects of diet on the childhood gut microbiome and its implications for atopic dermatitis.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.11.034},
pmid = {30578881},
issn = {1097-6825},
abstract = {In this study we found that rural South African children had a high relative abundance of Prevotella copri which was linked to diet and protective for AD.},
}
@article {pmid30578857,
year = {2018},
author = {Zhao, W and Ho, HE and Bunyavanich, S},
title = {The Gut Microbiome in Food Allergy.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2018.12.012},
pmid = {30578857},
issn = {1534-4436},
abstract = {OBJECTIVE: To review observational human, murine, and interventional trial studies that have examined the gut microbiome in food allergy, and to provide perspective on future investigations in this field.<br><br>DATA SOURCES: A review of the published literature was performed with PubMed, and clinical studies catalogued at ClinicalTrials.gov were also reviewed.<br><br>STUDY SELECTIONS: The most recent relevant studies, seminal works, and topical clinical trials were selected.<br><br>RESULTS: Gut dysbiosis likely precedes the development of food allergy, and the timing of such dysbiosis is critical. Gut microbiota associated with individual food allergies may be distinct. Murine models support the importance of gut microbiota in shaping immune maturation and tolerance. Gut microbiota may affect food allergy susceptibility by modulating type 2 immunity, influencing immune development and tolerance, regulating basophil populations, and promoting intestinal barrier function. Ongoing and future interventional trials of probiotics, prebiotics, synbiotics, and fecal microbiota transfer will help translate our understanding of the gut microbiome in food allergy to clinical practice. Future work in this area will include deepening of current research foci, as well as expansion of efforts to include the virome, mycobiome, and interactions between the microbiome, host, and environment. Robust and consistent study designs, multi-dimensional profiling, and systems biology approaches will enable this future work.<br><br>CONCLUSION: By advancing research on the microbiome in food allergy, we can further our understanding of food allergy and derive new approaches for its prevention and therapy.},
}
@article {pmid30578461,
year = {2018},
author = {Nobili, V and Mosca, A and Alterio, T and Cardile, S and Putignani, L},
title = {Fighting Fatty Liver Diseases with Nutritional Interventions, Probiotics, Symbiotics, and Fecal Microbiota Transplantation (FMT).},
journal = {Advances in experimental medicine and biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/5584_2018_318},
pmid = {30578461},
issn = {0065-2598},
abstract = {Pediatric obesity is rising worldwide leading the worrying phenomenon of nonalcoholic fatty liver disease (NAFLD) to shift into one of the most frequent causes of chronic liver illness in childhood. Occurrence of NAFLD depends on several factors such as the geographical area and the diagnostic modalities used; overall it ranges between 3% and 10% of pediatric population, increasing up to 70% in patients with metabolic comorbidities (Manco M, Bottazzo G, DeVito R et al, J Am Coll Nutr 27:667-676, 2008).Recent findings have related the intestinal microbiota to a plethora of pathological conditions, including type 2 diabetes (T2D), obesity, and nonalcoholic steatohepatitis (NASH). One of the emerging areas of the study is the link between liver diseases and gut microbiome, which has added new information to the understanding of the so-called gut-liver axis.In order to address the role of gut microbiome in NAFLD onset and progression, it is necessary to &quot;decipher&quot; operational codes for microbiome investigation within the context of advanced laboratory medicine to capture microbiome features and, hence, to address the function of the intestinal microbiome within the gut microbiota-liver axis.Results of these investigations have allowed the beginning of implementing the usage of probiotics and symbiotics in the medical approach of obesity and NAFLD in adults and children. Several randomized clinical trials (RCTs) have been already published on fecal microbiota transplantation (FMT), T2D, NASH, and inflammatory bowel disease (IBD).This review proposes to describe the current state of knowledge on the ways fatty liver diseases can be addressed with nutritional interventions, probiotics, symbiotics, and FMT.},
}
@article {pmid30578265,
year = {2018},
author = {Stubbendieck, RM and May, DS and Chevrette, MG and Temkin, MI and Wendt-Pienkowski, E and Cagnazzo, J and Carlson, CM and Gern, JE and Currie, CR},
title = {Competition among nasal bacteria suggests a role for siderophore-mediated interactions in shaping the human nasal microbiota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02406-18},
pmid = {30578265},
issn = {1098-5336},
abstract = {Resources available in the human nasal cavity are limited. Therefore, to successfully colonize the nasal cavity, bacteria must compete for scarce nutrients. Competition may occur directly through interference (e.g., antibiotics) or indirectly by nutrient sequestration. To investigate the nature of nasal bacterial competition, we performed co-culture inhibition assays between nasal Actinobacteria and Staphylococcus spp. We found that coagulase-negative staphylococci (CoNS) isolates were sensitive to growth inhibition by Actinobacteria but Staphylococcus aureus isolates were resistant to inhibition. Among Actinobacteria, we observed that Corynebacterium spp. were variable in their ability to inhibit CoNS. We sequenced the genomes of ten Corynebacterium spp. isolates, including three Corynebacterium propinquum that strongly inhibited CoNS and seven other Corynebacterium spp. isolates that only weakly inhibited CoNS Using a comparative genomics approach, we found that the C. propinquum genomes were enriched in genes for iron acquisition and encoded a biosynthetic gene cluster (BGC) for siderophore production, absent in the non-inhibitory Corynebacterium spp. genomes. Using a chromeazurol S assay, we confirmed that C. propinquum produced siderophores. We demonstrated that iron supplementation rescued CoNS from inhibition by C. propinquum, suggesting that inhibition was due to iron restriction through siderophore production. Through comparative metabolomics and molecular networking, we identified the siderophore produced by C. propinquum as dehydroxynocardamine. Finally, we confirmed that the dehydroxynocardamine BGC is expressed in vivo by analyzing human nasal metatranscriptomes from the NIH Human Microbiome Project. Together, our results suggest that bacteria produce siderophores to compete for limited available iron in the nasal cavity and improve their fitness.IMPORTANCE Within the nasal cavity, interference competition through antimicrobial production is prevalent. For instance, nasal Staphylococcus spp. strains can inhibit the growth of other bacteria through the production of nonribosomal peptides and ribosomally synthesized and post-translationally modified peptides. In contrast, bacteria engaging in exploitation competition modify the external environment to prevent competitors from growing, usually by depleting access to essential nutrients. As the nasal cavity is a nutrient limited environment, we hypothesized that exploitation competition occurs in this system. We determined that Corynebacterium propinquum produces an iron-chelating siderophore and this iron-sequestering molecule correlates with the ability to inhibit the growth of coagulase-negative staphylococci. Further, we found that the genes required for siderophore production are expressed in vivo Thus, though siderophore production by bacteria is often considered a virulence trait, our work indicates that bacteria may produce siderophores to compete for limited iron in the human nasal cavity.},
}
@article {pmid30578263,
year = {2018},
author = {Wegner, CE and Gaspar, M and Geesink, P and Herrmann, M and Marz, M and Küsel, K},
title = {Biogeochemical regimes in shallow aquifers reflect the metabolic coupling of elements of nitrogen, sulfur and carbon.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02346-18},
pmid = {30578263},
issn = {1098-5336},
abstract = {Near-surface groundwaters are prone to receive (in)organic matter input from their recharge areas and are known to harbour autotrophic microbial communities linked to nitrogen and sulfur metabolism. Here, we use multi-&quot;omic&quot; profiling to gain holistic insights into the turnover of inorganic nitrogen compounds, carbon fixation processes and organic matter processing in groundwater. We sampled microbial biomass from two superimposed aquifers via monitoring wells that follow groundwater flow from its recharge area through differences in hydrogeochemical settings and land use. Functional profiling revealed that groundwater microbiomes are mainly driven by nitrogen (nitrification, denitrification, anammox) and to a lesser extent sulfur cycling (sulfur oxidation and sulfate reduction), dependent on local hydrochemical differences. Surprisingly, the differentiation potential of the groundwater microbiome surpasses that of hydrochemistry for individual monitoring wells. Dominated by few phyla (Bacteroidetes, Proteobacteria, Planctomycetes, Thaumarchaeota), the taxonomic profiling of groundwater metagenomes and metatranscriptomes revealed pronounced differences between merely present microbiome members and those actively participating in community gene expression and biogeochemical cycling. Unexpectedly, we observed a constitutive expression of carbohydrate-active enzymes, encoded by different microbiome members, along with the groundwater flow path. The turnover of organic carbon apparently complements for lithoautotrophic carbon assimilation pathways mainly used by the groundwater microbiome dependent on the availability of oxygen and inorganic electron donors like ammonium.IMPORTANCE: Groundwater is a key resource for drinking water production and irrigation. The interplay between geological setting, hydrochemistry, carbon storage and groundwater microbiome ecosystem functioning is crucial for our understanding of these important ecosystem services. We targeted the encoded and expressed metabolic potential of groundwater microbiomes along an aquifer transect that diversifies in terms of hydrochemistry and land use. Our results showed that the groundwater microbiome has a higher spatial differentiation potential than hydrochemistry.},
}
@article {pmid30578262,
year = {2018},
author = {Griffith, JM and Basting, PJ and Bischof, KM and Wrona, EP and Kunka, KS and Tancredi, AC and Moore, JP and Hyman, MRL and Slonczewski, JL},
title = {Experimental evolution of Escherichia coli K-12 in the presence of PMF uncoupler CCCP selects for mutations affecting PMF-driven drug efflux pumps.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02792-18},
pmid = {30578262},
issn = {1098-5336},
abstract = {Experimental evolution of Escherichia coli K-12 with benzoate, a partial uncoupler of the proton motive force (PMF), selects for mutations that decrease antibiotic resistance. We conducted experimental evolution in the presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP), a strong uncoupler. Cultures were serially diluted daily 1:100 in LBK medium containing 20-150 µM CCCP buffered at pH 6.5 or at pH 8.0. After 1,000 generations, the populations tolerated up to 150 µM CCCP. Sequenced isolates had mutations in mprA (emrR), which downregulates the EmrAB-TolC pump that exports CCCP. A mprA::kanR deletion conferred growth at 60 CCCP, though not at the higher levels resisted by evolved strains (150 µM). Some mprA mutant strains also had point mutations affecting emrA, but deletion of emrA abolished the CCCP resistance. Thus, CCCP-evolved isolates contained additional adaptations. One isolate lacked emrA or mprA mutations but had mutations in cecR (ybiH) whose product upregulates drug pumps YbhG and YbhFSR; and in gadE, which upregulates multidrug pump mdtEF A cecR::kanR deletion conferred partial resistance to CCCP. Other multidrug efflux genes that had mutations include ybhR and acrAB The acrB isolate was sensitive to AcrAB substrates chloramphenicol and tetracycline. Other mutant genes in CCCP-evolved strains include rng (ribonuclease G) and cyaA (adenylate cyclase). Overall, experimental evolution revealed a CCCP-dependent fitness advantage for mutations increasing CCCP efflux via EmrA; and for mutations that may deactivate proton-driven pumps for drugs not present (cecR, gadE, acrAB, ybhR). These results are consistent with our previous report of drug sensitivity associated with evolved benzoate tolerance.IMPORTANCEThe genetic responses of bacteria to depletion of proton motive force (PMF), and their effects on drug resistance, are poorly understood. PMF drives export of many antibiotics, but the energy cost may decrease fitness when antibiotics are absent. Our evolution experiment reveals genetic mechanisms of adaptation to the PMF uncoupler CCCP, including selection for increased CCCP efflux, but also against the expression of PMF-driven pumps for drugs not present. The results have implications for our understanding of the gut microbiome, which experiences high levels of organic acids that decrease PMF.},
}
@article {pmid30578257,
year = {2018},
author = {Mandel, MJ and Broderick, NA and Martens, EC and Guillemin, K},
title = {Reports from a Healthy Community: The 7th Conference on Beneficial Microbes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02562-18},
pmid = {30578257},
issn = {1098-5336},
abstract = {The last two decades have seen an explosion in research about the beneficial microbial communities associated with plants and animals. Initially this explosion was driven by technological advances that enabled explorations of microbiomes on unprecedented scales. Increasingly, the drive is coming from conceptual advances that are the fruit of research investments into experimental systems to probe the functions of these beneficial microbes and their mechanisms of action. The Conference on Beneficial Microbes has been one of the premiere venues for this research. The 7th Conference on Beneficial Microbes was held July 8-11, 2018, at the University of Wisconsin-Madison Memorial Union. The 308 attendees-representing academia, industry, journals, and funding agencies-participated in an intense 4-day meeting encompassing research frontiers in beneficial microbiology and microbiome science.},
}
@article {pmid30577867,
year = {2018},
author = {Griffiths, JA and Mazmanian, SK},
title = {Emerging evidence linking the gut microbiome to neurologic disorders.},
journal = {Genome medicine},
volume = {10},
number = {1},
pages = {98},
doi = {10.1186/s13073-018-0609-3},
pmid = {30577867},
issn = {1756-994X},
abstract = {The gut microbiome contributes to the development and function of the immune, metabolic, and nervous systems. Furthermore, commensal bacteria modulate symptoms and pathology in mouse models of neuropsychiatric and neurodevelopmental diseases. Uncovering mechanisms that are utilized by the microbiome to mediate gut-brain connections may provide novel opportunities to target therapies to the gut in order to treat neurologic disorders.},
}
@article {pmid30577803,
year = {2018},
author = {Chappell, T and Geva, S and Hogan, JM and Huygens, F and Rathnayake, IU and Rudd, S and Kelly, W and Perrin, D},
title = {Rapid analysis of metagenomic data using signature-based clustering.},
journal = {BMC bioinformatics},
volume = {19},
number = {Suppl 20},
pages = {509},
doi = {10.1186/s12859-018-2540-4},
pmid = {30577803},
issn = {1471-2105},
abstract = {BACKGROUND: Sequencing highly-variable 16S regions is a common and often effective approach to the study of microbial communities, and next-generation sequencing (NGS) technologies provide abundant quantities of data for analysis. However, the speed of existing analysis pipelines may limit our ability to work with these quantities of data. Furthermore, the limited coverage of existing 16S databases may hamper our ability to characterise these communities, particularly in the context of complex or poorly studied environments.<br><br>RESULTS: In this article we present the SigClust algorithm, a novel clustering method involving the transformation of sequence reads into binary signatures. When compared to other published methods, SigClust yields superior cluster coherence and separation of metagenomic read data, while operating within substantially reduced timeframes. We demonstrate its utility on published Illumina datasets and on a large collection of labelled wound reads sourced from patients in a wound clinic. The temporal analysis is based on tracking the dominant clusters of wound samples over time. The analysis can identify markers of both healing and non-healing wounds in response to treatment. Prominent clusters are found, corresponding to bacterial species known to be associated with unfavourable healing outcomes, including a number of strains of Staphylococcus aureus.<br><br>CONCLUSIONS: SigClust identifies clusters rapidly and supports an improved understanding of the wound microbiome without reliance on a reference database. The results indicate a promising use for a SigClust-based pipeline in wound analysis and prediction, and a possible novel method for wound management and treatment.},
}
@article {pmid30577738,
year = {2018},
author = {Zhu, X and Shen, X and Jiang, X and Wei, K and He, T and Ma, Y and Liu, J and Hu, X},
title = {Nonlinear expression and visualization of nonmetric relationships in genetic diseases and microbiome data.},
journal = {BMC bioinformatics},
volume = {19},
number = {Suppl 20},
pages = {505},
doi = {10.1186/s12859-018-2537-z},
pmid = {30577738},
issn = {1471-2105},
abstract = {BACKGROUND: The traditional methods of visualizing high-dimensional data objects in low-dimensional metric spaces are subject to the basic limitations of metric space. These limitations result in multidimensional scaling that fails to faithfully represent non-metric similarity data.<br><br>RESULTS: Multiple maps t-SNE (mm-tSNE) has drawn much attention due to the construction of multiple mappings in low-dimensional space to visualize the non-metric pairwise similarity to eliminate the limitations of a single metric map. mm-tSNE regularization combines the intrinsic geometry between data points in a high-dimensional space. The weight of data points on each map is used as the regularization parameter of the manifold, so the weights of similar data points on the same map are also as close as possible. However, these methods use standard momentum methods to calculate parameters of gradient at each iteration, which may lead to erroneous gradient search directions so that the target loss function fails to achieve a better local minimum. In this article, we use a Nesterov momentum method to learn the target loss function and correct each gradient update by looking back at the previous gradient in the candidate search direction. By using indirect second-order information, the algorithm obtains faster convergence than the original algorithm. To further evaluate our approach from a comparative perspective, we conducted experiments on several datasets including social network data, phenotype similarity data, and microbiomic data.<br><br>CONCLUSIONS: The experimental results show that the proposed method achieves better results than several versions of mm-tSNE based on three evaluation indicators including the neighborhood preservation ratio (NPR), error rate and time complexity.},
}
@article {pmid30577530,
year = {2018},
author = {Yang, AJ and Marito, S and Yang, JJ and Keshari, S and Chew, CH and Chen, CC and Huang, CM},
title = {A Microtube Array Membrane (MTAM) Encapsulated Live Fermenting Staphylococcus epidermidis as a Skin Probiotic Patch against Cutibacterium acnes.},
journal = {International journal of molecular sciences},
volume = {20},
number = {1},
pages = {},
doi = {10.3390/ijms20010014},
pmid = {30577530},
issn = {1422-0067},
support = {106-2320-B-008, 105-2314-B-008-001, 101-2221-E-038-009-, 107-2314-B-008 -001, 107-2622-B-008-002-CC1 and 106/107-2622-B-008-001-CC1//Ministry of Science and Technology, Taiwan/ ; NHRI-EX106-10607SI//NHRI/ ; },
abstract = {Antibiotics without selectivity for acne treatment may destroy the beneficial microbes in the human microbiome that helps to fight Cutibacterium acnes (C. acnes), a bacterium associated with inflammatory acne vulgaris. Probiotic treatment by direct application of live Staphylococcus epidermidis (S. epidermidis) onto the open acne lesions may run the risk of bloodstream infections. Here, we fabricated the polysulfone microtube array membranes (PSF MTAM) to encapsulate probiotic S.epidermidis. We demonstrate that the application of the encapsulation of S.epidermidis in PSF MTAM enhanced the glycerol fermentation activities of S. epidermidis. To mimic the granulomatous type of acne inflammatory acne vulgaris, the ears of mice were injected intradermally with C.acnes to induce the secretion of macrophage inflammatory protein-2 (MIP-2), a murine counterpart of human interleukin (IL)-8. The C. acnes-injected mouse ears were covered with a PST MTAM encapsulated with or without S.epidermidis in the presence of glycerol. The application of S.epidermidis-encapsulated PST MTAM plus glycerol onto the C.acnes-injected mouse ears considerably reduced the growth of C. acnes and the production of MIP-2. Furthermore, no S. epidermidis leaked from PSF MTAM into mouse skin. The S. epidermidis-encapsulated PST MTAM functions as a probiotic acne patch.},
}
@article {pmid30577072,
year = {2018},
author = {Dzanibe, S and Jaspan, HB and Zulu, MZ and Kiravu, A and Gray, CM},
title = {Impact of maternal HIV exposure, feeding status, and microbiome on infant cellular immunity.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/JLB.MR0318-120R},
pmid = {30577072},
issn = {1938-3673},
abstract = {At least one-third of infants born in sub-Saharan Africa have been exposed to the effects of maternal HIV infection and antiretroviral treatment. Intrauterine HIV exposure is associated with increased rates of morbidity and mortality in children. Although the mechanisms responsible for poor infant health with HIV-1 exposure are likely to be multifactorial, we posit that the maternal environment during gestation and in the perinatal period results in altered infant immunity and is possibly the strongest contributing factor responsible for the disproportionally high infectious events among HIV-exposed infants who remain HIV uninfected. This review provides a synthesis of studies reporting the impact of intrauterine HIV exposure, feeding practices, and microbiota on immune ontogeny in the first year of life in HIV-exposed uninfected infants.},
}
@article {pmid30576690,
year = {2018},
author = {Hara, A and Iwasa, Y},
title = {Coupled dynamics of intestinal microbiome and immune system- a mathematical study.},
journal = {Journal of theoretical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtbi.2018.12.021},
pmid = {30576690},
issn = {1095-8541},
abstract = {An immune system sometimes causes an exaggerated response to harmless materials, such as pollens, eggs, and metals, which is known as an allergy. The regulatory T (Treg) cells suppress such allergic responses. Recently, it has been observed that intestinal microbiota have a close association with immune systems. For example, some strains of bacteria induce Treg cells by producing short-chain fatty acids, such as butyrate. Moreover, a sufficiently diverse T cell receptor repertoire of Treg cells is required to prevent inflammation of intestine driven by the commensal intestinal microbiome. In this study, we develop a simple mathematical model describing the dynamic interaction of T helper cells, Treg cells, and Treg-inducing intestinal microbes. The proposed model may have multiple stable equilibria, and the allergic response is intense at the dysbiotic equilibrium, in which the Treg-inducing microbes are scarce. First, we search for the condition by getting rid of the stable dysbiotic steady state. Further, we examine different methods to reduce the allergic response at the equilibrium (which may be dysbiotic or non-dysbiotic). Furthermore, we discuss the possible therapeutic interventions focusing on the intestinal microbiome to suppress the allergic immune responses.},
}
@article {pmid30576534,
year = {2018},
author = {Jacoby, RP and Kopriva, S},
title = {Metabolic niches in the rhizosphere microbiome: New tools and approaches to analyse metabolic mechanisms of plant-microbe nutrient exchange.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/ery438},
pmid = {30576534},
issn = {1460-2431},
abstract = {Plants nourish rhizospheric microbes via provision of carbon substrates, and microbiome composition is strongly influenced by metabolic phenomena such as niche differentiation, competitive exclusion, and cross-feeding. Despite intensive investigations of taxonomic breakdown in the root microbiome, there is relatively little biochemical knowledge of the metabolic niches occupied by microbial strains in the rhizosphere. Here, we summarise the new tools and approaches boosting our knowledge of the metabolic mechanisms that shape root microbiome composition. New studies have elucidated biochemical pathways that mediate root colonisation and pathogen suppression, and synthetic communities are emerging as a powerful tool to understand microbe-microbe interactions. Knowledge of root exudate composition is being advanced by new metabolomics methodologies, highlighting that specific exudate components can inhibit pathogen growth, and that certain metabolites can recruit mutualistic strains according to substrate uptake preferences. Microbial genomics is rapidly advancing, with large collections of isolated rhizosphere strains and mutant libraries giving new insights into the metabolic mechanisms of root colonisation. Exometabolomics is emerging as a powerful methodology to directly observe microbial uptake of root metabolites, and also for profiling microbial cross-feeding. Integrative studies using these resources should enable rapid advances, particularly when applied to standardised experimental setups and model synthetic communities.},
}
@article {pmid30576312,
year = {2018},
author = {Loke, MF and Chua, EG and Gan, HM and Thulasi, K and Wanyiri, JW and Thevambiga, I and Goh, KL and Wong, WF and Vadivelu, J},
title = {Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208584},
doi = {10.1371/journal.pone.0208584},
pmid = {30576312},
issn = {1932-6203},
abstract = {Colorectal cancer (CRC) is ranked the third most common cancer in human worldwide. However, the exact mechanisms of CRC are not well established. Furthermore, there may be differences between mechanisms of CRC in the Asian and in the Western populations. In the present study, we utilized a liquid chromatography-mass spectrometry (LC-MS) metabolomic approach supported by the 16S rRNA next-generation sequencing to investigate the functional and taxonomical differences between paired tumor and unaffected (normal) surgical biopsy tissues from 17 Malaysian patients. Metabolomic differences associated with steroid biosynthesis, terpenoid biosynthesis and bile metabolism could be attributed to microbiome differences between normal and tumor sites. The relative abundances of Anaerotruncus, Intestinimonas and Oscillibacter displayed significant relationships with both steroid biosynthesis and terpenoid and triterpenoid biosynthesis pathways. Metabolites involved in serotonergic synapse/ tryptophan metabolism (Serotonin and 5-Hydroxy-3-indoleacetic acid [5-HIAA]) were only detected in normal tissue samples. On the other hand, S-Adenosyl-L-homocysteine (SAH), a metabolite involves in methionine metabolism and methylation, was frequently increased in tumor relative to normal tissues. In conclusion, this study suggests that local microbiome dysbiosis may contribute to functional changes at the cancer sites. Results from the current study also contributed to the list of metabolites that are found to differ between normal and tumor sites in CRC and supported our quest for understanding the mechanisms of carcinogenesis.},
}
@article {pmid30576150,
year = {2018},
author = {Mu, C and Cai, Z and Bian, G and Du, Y and Ma, S and Su, Y and Liu, L and Volgmeir, J and Huang, R and Zhu, W},
title = {New insights into porcine milk N-glycome and the potential relation with offspring gut microbiome.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.8b00789},
pmid = {30576150},
issn = {1535-3907},
abstract = {N-glycans are an important source of milk oligosaccharides. In addition to free oligosaccharides found in milk, N-glycans can also be utilized by gut microbes. A potential for milk N-glycans to act as gut microbe regulators in suckling animals has attracted considerable attention; however, sow milk N-glycans and their potential effects upon the piglet's gut microbes in vivo remain unknown. In the present study, we profiled the milk N-glycans of Meishan and Yorkshire sows during lactation using UPLC and a mass spectrometry-based glycome method, and explored the correlations between milk N-glycans and offspring gut microbiota. Twenty-two N-glycan structures were identified in sow milk, among which 36% (8 out of 22) were fucosylated, 41% (9 out of 22) were sialylated, and 14% (3 out of 22) were high mannosylated. An N-glycan with a NeuGc structure was identified in sow milk for the first time. No compositional differences between the two breeds or between different lactation times were found in porcine milk N-linked oligosaccharides (PNOs); however, the abundances of different structures within this class did vary. The relative abundances of fucosylated PNO3 (GlcNAc4-Man3-Fuc) and sialylated PNO18 (GlcNAc4-Man3-Gal2-NeuAc) increased during lactation, and Meishan sows demonstrated a higher (P < 0.05) abundance of mannosylated PNO10 (GlcNAc2-Man6) and sialylated PNO17 (GlcNAc5-Man3-Gal-NeuAc) than Yorkshire sows. Apparent correlations between milk N-glycans and offspring gut microbial populations were found; for example, mannosylated PNO21 (GlcNAc2-Man9) was positively correlated with OTU706 (Lactobacillus amylovorus) and OTU1380 (Bacteroides uniformis). Overall, our results indicate that the sow milk N-glycome of Meishan and Yorkshire sows differs in N-glycome characteristics, and that this is correlated to abundances of certain piglet gut microbes. These findings provide a reference for future elucidation of the involvement of gut microbes in milk N-glycan metabolism, which is important to the health both of large domestic animals and humans.},
}
@article {pmid30576093,
year = {2018},
author = {Knoop, KA and Holtz, LR and Newberry, RD},
title = {Inherited nongenetic influences on the gut microbiome and immune system.},
journal = {Birth defects research},
volume = {110},
number = {20},
pages = {1494-1503},
doi = {10.1002/bdr2.1436},
pmid = {30576093},
issn = {2472-1727},
support = {AI112626//National Institute of Allergy and Infectious Diseases/ ; AI131342//National Institute of Allergy and Infectious Diseases/ ; AI136515//National Institute of Allergy and Infectious Diseases/ ; AI140755//National Institute of Allergy and Infectious Diseases/ ; DK097317//National Institute of Diabetes and Digestive and Kidney Diseases/ ; },
abstract = {The gut microbiome and the immune system codevelop around the time of birth, well after genetic information has been passed from the parents to the offspring. Each of these &quot;organ systems&quot; displays plasticity. The immune system can mount highly specific adaptive responses to newly encountered antigens, and the gut microbiota is affected by changes in the environment. Despite this plasticity, there is a growing appreciation that these organ systems, once established, are remarkably stable. In health, the immune system rapidly mounts responses to infections, and once cleared, resolves inflammatory responses to return to homeostasis. However, a skewed immune system, such as seen in allergy, does not easily return to homeostasis. Allergic responses are often seen to multiple antigens. Likewise, a dysbiotic gut microbiota is seen in multiple diseases. Attempts to reset the gut microbiota as a therapy for disease have met with varied success. Therefore, how these codeveloping &quot;organ systems&quot; become established is a central question relevant to our overall health. Recent observations suggest that maternal factors encountered both in utero and after birth can directly or indirectly impact the development of the offspring's gut microbiome and immune system. Here, we discuss how these nongenetic maternal influences can have long-term effects on the progeny's health.},
}
@article {pmid30575950,
year = {2018},
author = {Hartman, S and Sayler, K and Belsky, J},
title = {Prenatal stress enhances postnatal plasticity: The role of microbiota.},
journal = {Developmental psychobiology},
volume = {},
number = {},
pages = {},
doi = {10.1002/dev.21816},
pmid = {30575950},
issn = {1098-2302},
abstract = {Separate fields of inquiry indicate (a) that prenatal stress is associated with heightened behavioral and physiological reactivity and (b) that these postnatal phenotypes are themselves associated with increased susceptibility to both positive and negative environmental influences. Collectively, this work supports Pluess and Belsky's (Psychopathology, 2011, 23, 29) claim that prenatal stress fosters, promotes or &quot;programs&quot; postnatal developmental plasticity. Herein, we review animal and human evidence consistent with this hypothesis before advancing the novel idea that infant intestinal microbiota may be one candidate mechanism for instantiating developmental plasticity as a result of prenatal stress. We then review research indicating that prenatal stress predicts differences in infant intestinal microbiota; that infant intestinal microbiota is associated with behavioral and physiological reactivity phenotypes; and, thus, that prenatal stress may influence infant intestinal microbiota in a way that results in heightened physiological and behavioral reactivity and, thereby, postnatal developmental plasticity. Finally, we offer ideas for testing this claim and consider implications for intervention and use of probiotics during early infancy.},
}
@article {pmid30575793,
year = {2018},
author = {Koh, H},
title = {An adaptive microbiome α-diversity-based association analysis method.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {18026},
doi = {10.1038/s41598-018-36355-7},
pmid = {30575793},
issn = {2045-2322},
abstract = {To relate microbial diversity with various host traits of interest (e.g., phenotypes, clinical interventions, environmental factors) is a critical step for generic assessments about the disparity in human microbiota among different populations. The performance of the current item-by-item α-diversity-based association tests is sensitive to the choice of α-diversity metric and unpredictable due to the unknown nature of the true association. The approach of cherry-picking a test for the smallest p-value or the largest effect size among multiple item-by-item analyses is not even statistically valid due to the inherent multiplicity issue. Investigators have recently introduced microbial community-level association tests while blustering statistical power increase of their proposed methods. However, they are purely a test for significance which does not provide any estimation facilities on the effect direction and size of a microbial community; hence, they are not in practical use. Here, I introduce a novel microbial diversity association test, namely, adaptive microbiome α-diversity-based association analysis (aMiAD). aMiAD simultaneously tests the significance and estimates the effect score of the microbial diversity on a host trait, while robustly maintaining high statistical power and accurate estimation with no issues in validity.},
}
@article {pmid30575732,
year = {2018},
author = {Coryell, M and McAlpine, M and Pinkham, NV and McDermott, TR and Walk, ST},
title = {The gut microbiome is required for full protection against acute arsenic toxicity in mouse models.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {5424},
doi = {10.1038/s41467-018-07803-9},
pmid = {30575732},
issn = {2041-1723},
abstract = {Arsenic poisons an estimated 200 million people worldwide through contaminated food and drinking water. Confusingly, the gut microbiome has been suggested to both mitigate and exacerbate arsenic toxicity. Here, we show that the microbiome protects mice from arsenic-induced mortality. Both antibiotic-treated and germ-free mice excrete less arsenic in stool and accumulate more arsenic in organs compared to control mice. Mice lacking the primary arsenic detoxification enzyme (As3mt) are hypersensitive to arsenic after antibiotic treatment or when derived germ-free, compared to wild-type and/or conventional counterparts. Human microbiome (stool) transplants protect germ-free As3mt-KO mice from arsenic-induced mortality, but protection depends on microbiome stability and the presence of specific bacteria, including Faecalibacterium. Our results demonstrate that both a functional As3mt and specific microbiome members are required for protection against acute arsenic toxicity in mouse models. We anticipate that the gut microbiome will become an important explanatory factor of disease (arsenicosis) penetrance in humans, and a novel target for prevention and treatment strategies.},
}
@article {pmid30575647,
year = {2018},
author = {Ahmad, AF and Ward, NC and Dwivedi, G},
title = {The gut microbiome and heart failure.},
journal = {Current opinion in cardiology},
volume = {},
number = {},
pages = {},
doi = {10.1097/HCO.0000000000000598},
pmid = {30575647},
issn = {1531-7080},
abstract = {PURPOSE OF REVIEW: The human gut is populated by a complex community of microbiota that coexists with the host to maintain homeostasis. Accumulating evidence shows that changes in the composition and diversity of gut microbiota, known as dysbiosis, is associated with cardiovascular diseases, such as atherosclerosis, hypertension, and heart failure.<br><br>RECENT FINDINGS: Although recent advances in biochemical and molecular analyses have contributed to the detection, identification, and characterization of a variety of gut microbiota genomes and their associated metabolites, the exact mechanisms of action remain unclear. As the prevalence of cardiovascular disease continues to rise, investigating the gut microbiome as a potential strategy for clinical intervention is highly warranted.<br><br>SUMMARY: In this review, we discuss correlations between the gut microbiome and heart failure, as well as the effects of altering the microbiome as a potential therapeutic target in cardiovascular diseases including heart failure.},
}
@article {pmid30575298,
year = {2019},
author = {Timmis, K and Timmis, JK and Brüssow, H and Fernández, LÁ},
title = {Synthetic consortia of nanobody-coupled and formatted bacteria for prophylaxis and therapy interventions targeting microbiome dysbiosis-associated diseases and co-morbidities.},
journal = {Microbial biotechnology},
volume = {12},
number = {1},
pages = {58-65},
doi = {10.1111/1751-7915.13355},
pmid = {30575298},
issn = {1751-7915},
abstract = {Designed nanobody-linked synthetic consortia for microbiota dysbiosis therapies. A. Nanobodies (Nb) are selected for specific antigens on target bacteria destined for a synthetic therapy consortium that may consist of two (B) or multiple (C) members. For the treatment of dysbiosis co-morbidities requiring two functionally distinct consortia, these may be linked through a common member to generate a single bi-functional microbiota therapy (D).},
}
@article {pmid30575197,
year = {2018},
author = {Schmid, MW and Hahl, T and van Moorsel, SJ and Wagg, C and De Deyn, GB and Schmid, B},
title = {Feedbacks of plant identity and diversity on the diversity and community composition of rhizosphere microbiomes from a long-term biodiversity experiment.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.14987},
pmid = {30575197},
issn = {1365-294X},
abstract = {Soil microbes are known to be key drivers of a number of essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition in the rhizosphere is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this timeframe plants with a monoculture or mixture history changed in the bacterial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same field monocultures or mixtures (plant history in monoculture vs. mixture) in pots inoculated with microbes extracted from the field monoculture and mixture soils attached to the roots of the host plants (soil legacy). After five months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S-rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Bacterial community structure in the plant rhizosphere was primarily determined by soil legacy and by plant species identity, but not by plant history. In seven out of the eight plant species the number of individual OTUs with increased abundance was larger when inoculated with microbes from mixture soil. We conclude that plant species richness can affect belowground community composition and diversity, feeding back to the assemblage of rhizosphere bacterial communities in newly establishing plants via the legacy in soil. This article is protected by copyright. All rights reserved.},
}
@article {pmid30574860,
year = {2018},
author = {Griffiths, J and Jenkins, P and Vargova, M and Bowler, U and Juszczak, E and King, A and Linsell, L and Murray, D and Partlett, C and Patel, M and Berrington, J and Embleton, N and Dorling, J and Heath, PT and McGuire, W and Oddie, S},
title = {Enteral lactoferrin to prevent infection for very preterm infants: the ELFIN RCT.},
journal = {Health technology assessment (Winchester, England)},
volume = {22},
number = {74},
pages = {1-60},
doi = {10.3310/hta22740},
pmid = {30574860},
issn = {2046-4924},
abstract = {BACKGROUND: Infections acquired in hospital are an important cause of morbidity and mortality in very preterm infants. Several small trials have suggested that supplementing the enteral diet of very preterm infants with lactoferrin, an antimicrobial protein processed from cow's milk, prevents infections and associated complications.<br><br>OBJECTIVE: To determine whether or not enteral supplementation with bovine lactoferrin (The Tatua Cooperative Dairy Company Ltd, Morrinsville, New Zealand) reduces the risk of late-onset infection (acquired > 72 hours after birth) and other morbidity and mortality in very preterm infants.<br><br>DESIGN: Randomised, placebo-controlled, parallel-group trial. Randomisation was via a web-based portal and used an algorithm that minimised for recruitment site, weeks of gestation, sex and single versus multiple births.<br><br>SETTING: UK neonatal units between May 2014 and September 2017.<br><br>PARTICIPANTS: Infants born at < 32 weeks' gestation and aged < 72 hours at trial enrolment.<br><br>INTERVENTIONS: Eligible infants were allocated individually (1 : 1 ratio) to receive enteral bovine lactoferrin (150 mg/kg/day; maximum 300 mg/day) or sucrose (British Sugar, Peterborough, UK) placebo (same dose) once daily from trial entry until a postmenstrual age of 34 weeks. Parents, caregivers and outcome assessors were unaware of group assignment.<br><br>OUTCOMES: Primary outcome - microbiologically confirmed or clinically suspected late-onset infection. Secondary outcomes - microbiologically confirmed infection; all-cause mortality; severe necrotising enterocolitis (NEC); retinopathy of prematurity (ROP); bronchopulmonary dysplasia (BPD); a composite of infection, NEC, ROP, BPD and mortality; days of receipt of antimicrobials until 34 weeks' postmenstrual age; length of stay in hospital; and length of stay in intensive care, high-dependency and special-care settings.<br><br>RESULTS: Of 2203 enrolled infants, primary outcome data were available for 2182 infants (99%). In the intervention group, 316 out of 1093 (28.9%) infants acquired a late-onset infection versus 334 out of 1089 (30.7%) infants in the control group [adjusted risk ratio (RR) 0.95, 95% confidence interval (CI) 0.86 to 1.04]. There were no significant differences in any secondary outcomes: microbiologically confirmed infection (RR 1.05, 99% CI 0.87 to 1.26), mortality (RR 1.05, 99% CI 0.66 to 1.68), NEC (RR 1.13, 99% CI 0.68 to 1.89), ROP (RR 0.89, 99% CI 0.62 to 1.28), BPD (RR 1.01, 99% CI 0.90 to 1.13), or a composite of infection, NEC, ROP, BPD and mortality (RR 1.01, 99% CI 0.94 to 1.08). There were no differences in the number of days of receipt of antimicrobials, length of stay in hospital, or length of stay in intensive care, high-dependency or special-care settings. There were 16 reports of serious adverse events for infants in the lactoferrin group and 10 for infants in the sucrose group.<br><br>CONCLUSIONS: Enteral supplementation with bovine lactoferrin does not reduce the incidence of infection, mortality or other morbidity in very preterm infants.<br><br>FUTURE WORK: Increase the precision of the estimates of effect on rarer secondary outcomes by combining the data in a meta-analysis with data from other trials. A mechanistic study is being conducted in a subgroup of trial participants to explore whether or not lactoferrin supplementation affects the intestinal microbiome and metabolite profile of very preterm infants.<br><br>TRIAL REGISTRATION: Current Controlled Trials ISRCTN88261002.<br><br>FUNDING: This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 22, No. 74. See the NIHR Journals Library website for further project information. This trial was also sponsored by the University of Oxford, Oxford, UK. The funder provided advice and support and monitored study progress but did not have a role in study design or data collection, analysis and interpretation.},
}
@article {pmid30574802,
year = {2018},
author = {Murphy, R and Morgan, XC and Wang, XY and Wickens, K and Purdie, G and Fitzharris, P and Otal, A and Lawley, B and Stanley, T and Barthow, C and Crane, J and Mitchell, EA and Tannock, GW},
title = {Eczema-protective probiotic alters infant gut microbiome functional capacity but not composition: sub-sample analysis from a RCT.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-13},
doi = {10.3920/BM2017.0191},
pmid = {30574802},
issn = {1876-2891},
abstract = {Probiotic Lactobacillus rhamnosus HN001 given in early life has been shown to reduce infant eczema risk, but its effect on gut microbiota development has not been quantitatively and functionally examined. The aim of this study was to investigate the impact of early life probiotic exposure on the composition and functional capacity of infant gut microbiota from birth to 2 years considering the effects of age, delivery mode, antibiotics, pets and eczema. We performed shotgun metagenomic sequencing analysis of 650 infant faecal samples, collected at birth, 3, 12, and 24 months, as part of a randomised, controlled, 3-arm trial assessing the effect of L. rhamnosus HN001, Bifidobacterium animalis subsp. lactis HN019 supplementation on eczema development in 474 infants. There was a 50% reduced eczema risk in the HN001 probiotic group compared to placebo. Both mothers (from 35 weeks gestation until 6 months post-partum if breastfeeding) and infants (from birth to 2 years) received either a placebo or one of two probiotics, L. rhamnosus HN001 (6×109 cfu), or B. animalis subsp. lactis HN019 (9×109 cfu). L. rhamnosus HN001 probiotic supplementation was associated with increased overall glycerol-3 phosphate transport capacity and enrichment of L. rhamnosus. There were no other significant changes in infant gut microbiota composition or diversity. Increased capacity to transport glycerol-3-phosphate was positively correlated with relative abundance of L. rhamnosus. Children who developed eczema had gut microbiota with increased capacity for glycosaminoglycan degradation and flagellum assembly but had no significant differences in microbiota composition or diversity. Early life HN001 probiotic use is associated with both increased L. rhamnosus and increased infant gut microbiota functional capacity to transport glycerol-3 phosphate. The mechanistic relationship of such functional alteration in gut microbiota with reduced eczema risk and long-term health merits further investigation.},
}
@article {pmid30574559,
year = {2018},
author = {Leigh, BA and Bordenstein, SR and Brooks, AW and Mikaelyan, A and Bordenstein, SR},
title = {Finer-Scale Phylosymbiosis: Insights from Insect Viromes.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00131-18},
pmid = {30574559},
issn = {2379-5077},
abstract = {Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness (e.g., beta diversity relationships) of host-associated microbial communities parallels the phylogeny of the host species. Representing the most abundant biological entities on the planet and common members of the animal-associated microbiome, viruses can be influential members of host-associated microbial communities that may recapitulate, reinforce, or ablate phylosymbiosis. Here we sequence the metagenomes of purified viral communities from three different parasitic wasp Nasonia species, one cytonuclear introgression line of Nasonia, and the flour moth outgroup Ephestia kuehniella. Results demonstrate complete phylosymbiosis between the viral metagenome and insect phylogeny. Across all Nasonia contigs, 69% of the genes in the viral metagenomes are either new to the databases or uncharacterized, yet over 99% of the contigs have at least one gene with similarity to a known sequence. The core Nasonia virome spans 21% of the total contigs, and the majority of that core is likely derived from induced prophages residing in the genomes of common Nasonia-associated bacterial genera: Proteus, Providencia, and Morganella. We also assemble the first complete viral particle genomes from Nasonia-associated gut bacteria. Taken together, results reveal the first complete evidence for phylosymbiosis in viral metagenomes, new genome sequences of viral particles from Nasonia-associated gut bacteria, and a large set of novel or uncharacterized genes in the Nasonia virome. This work suggests that phylosymbiosis at the host-microbiome level will likely extend to the host-virome level in other systems as well. IMPORTANCE Viruses are the most abundant biological entity on the planet and interact with microbial communities with which they associate. The virome of animals is often dominated by bacterial viruses, known as bacteriophages or phages, which can (re)structure bacterial communities potentially vital to the animal host. Beta diversity relationships of animal-associated bacterial communities in laboratory and wild populations frequently parallel animal phylogenetic relationships, a pattern termed phylosymbiosis. However, little is known about whether viral communities also exhibit this eco-evolutionary pattern. Metagenomics of purified viruses from recently diverged species of Nasonia parasitoid wasps reared in the lab indicates for the first time that the community relationships of the virome can also exhibit complete phylosymbiosis. Therefore, viruses, particularly bacteriophages here, may also be influenced by animal evolutionary changes either directly or indirectly through the tripartite interactions among hosts, bacteria, and phage communities. Moreover, we report several new bacteriophage genomes from the common gut bacteria in Nasonia.},
}
@article {pmid30574558,
year = {2018},
author = {Fahimipour, AK and Ben Mamaar, S and McFarland, AG and Blaustein, RA and Chen, J and Glawe, AJ and Kline, J and Green, JL and Halden, RU and Van Den Wymelenberg, K and Huttenhower, C and Hartmann, EM},
title = {Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00200-18},
pmid = {30574558},
issn = {2379-5077},
abstract = {Humans purposefully and inadvertently introduce antimicrobial chemicals into buildings, resulting in widespread compounds, including triclosan, triclocarban, and parabens, in indoor dust. Meanwhile, drug-resistant infections continue to increase, raising concerns that buildings function as reservoirs of, or even select for, resistant microorganisms. Support for these hypotheses is limited largely since data describing relationships between antimicrobials and indoor microbial communities are scant. We combined liquid chromatography-isotope dilution tandem mass spectrometry with metagenomic shotgun sequencing of dust collected from athletic facilities to characterize relationships between indoor antimicrobial chemicals and microbial communities. Elevated levels of triclosan and triclocarban, but not parabens, were associated with distinct indoor microbiomes. Dust of high triclosan content contained increased Gram-positive species with diverse drug resistance capabilities, whose pangenomes were enriched for genes encoding osmotic stress responses, efflux pump regulation, lipid metabolism, and material transport across cell membranes; such triclosan-associated functional shifts have been documented in laboratory cultures but not yet from buildings. Antibiotic-resistant bacterial isolates were cultured from all but one facility, and resistance often increased in buildings with very high triclosan levels, suggesting links between human encounters with viable drug-resistant bacteria and local biocide conditions. This characterization uncovers complex relationships between antimicrobials and indoor microbiomes: some chemicals elicit effects, whereas others may not, and no single functional or resistance factor explained chemical-microbe associations. These results suggest that anthropogenic chemicals impact microbial systems in or around buildings and their occupants, highlighting an emergent need to identify the most important indoor, outdoor, and host-associated sources of antimicrobial chemical-resistome interactions. IMPORTANCE The ubiquitous use of antimicrobial chemicals may have undesired consequences, particularly on microbes in buildings. This study shows that the taxonomy and function of microbes in indoor dust are strongly associated with antimicrobial chemicals-more so than any other feature of the buildings. Moreover, we identified links between antimicrobial chemical concentrations in dust and culturable bacteria that are cross-resistant to three clinically relevant antibiotics. These findings suggest that humans may be influencing the microbial species and genes that are found indoors through the addition and removal of particular antimicrobial chemicals.},
}
@article {pmid30574320,
year = {2018},
author = {Rau, M and Rehman, A and Dittrich, M and Groen, AK and Hermanns, HM and Seyfried, F and Beyersdorf, N and Dandekar, T and Rosenstiel, P and Geier, A},
title = {Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease.},
journal = {United European gastroenterology journal},
volume = {6},
number = {10},
pages = {1496-1507},
doi = {10.1177/2050640618804444},
pmid = {30574320},
issn = {2050-6406},
abstract = {Background: Intestinal microbiota and their metabolites (e.g. short-chain fatty acids (SCFAs)) may influence nonalcoholic fatty liver disease (NAFLD).<br><br>Objective: The objective of this article is to analyze gut bacterial diversity together with fecal SCFA concentrations and immunophenotyping of peripheral blood in histology-proven NAFLD patients.<br><br>Methods: Thirty-two NAFLD patients (14 nonalcoholic fatty liver (NAFL), 18 nonalcoholic steatohepatitis (NASH)) and 27 healthy controls (HCs)) were included in this study. Bacterial communities in feces were profiled by 16S ribosomal RNA gene sequencing of the V3-V4 region. Fecal SCFA levels were analyzed by high-performance liquid chromatography. Fluorescence-activated cell sorting analysis was performed of peripheral blood mononuclear cells.<br><br>Results: NASH patients were characterized by higher abundance of Fusobacteria and Fusobacteriaceae compared to NAFL and HCs. Conforming to our finding that NAFLD patients had higher fecal acetate and propionate levels, taxonomical differences of fecal bacteria were dominated by SCFA-producing bacteria. Higher fecal propionate and acetate levels were associated with lower resting regulatory T-cells (rTregs) (CD4+CD45RA+CD25++) as well as higher Th17/rTreg ratio in peripheral blood as immunological characteristics of NASH patients.<br><br>Conclusions: NASH patients are characterized by a different gut microbiome composition with higher fecal SCFA levels and higher abundance of SCFA-producing bacteria in NAFLD. These changes are associated with immunological features of disease progression. Our data suggest an important role of the intestinal microbiome and immunomodulatory bacterial metabolites in human NAFLD.},
}
@article {pmid30573380,
year = {2018},
author = {Altomare, A and Putignani, L and Del Chierico, F and Cocca, S and Angeletti, S and Ciccozzi, M and Tripiciano, C and Dalla Piccola, B and Cicala, M and Guarino, MPL},
title = {Gut mucosal-associated microbiota better discloses Inflammatory Bowel Disease differential patterns than faecal microbiota.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2018.11.021},
pmid = {30573380},
issn = {1878-3562},
abstract = {BACKGROUND: Growing evidence supports the potential role of intestinal microbiota in the pathophysiology of Inflammatory Bowel Diseases (IBD) even if the literature does not reveal uniform alterations. The aim of the study was to evaluate the mucosal (MM) and faecal microbiota (FM) composition in a cohort of IBD patients compared to healthy controls (CTRLs).<br><br>METHODS: Faecal and mucosal samples were collected from 14 IBD patients and 11 CTRLs. The V1-V3 region of 16S rRNA locus was amplified on a 454-Junior Genome Sequencer. Reads were grouped into operational taxonomic units (OTUs) at a sequence similarity level of 97% for taxonomic assignment, and aligned for OTUs matching against Greengenes database.<br><br>RESULTS: Irrespective of disease localization and activity, in the MM of IBD patients a statistically significant increase of Proteobacteria (especially Enterobacteriaceae, Acidaminococcus, Veillonella dispar) and decrease of Firmicutes (especially Roseburia and Faecalibacterium prausnitzii) and Actinobacteria was found compared to CTRLs. In the colon district some specific bacterial biomarkers were identified: Enterobacteriaceae for IBD stools, Bacteroides for IBD biopsies, Mogibacteriaceae, Ruminococcaceae and Prevotella for CTRL stools, Ruminococcaceae for CTRL biopsies.<br><br>CONCLUSIONS: The profiles of FM were more similar to CTRLs, suggesting that microbiota adhering to the gut mucosa better discriminates patients from controls, with the identification of some interesting biomarkers.},
}
@article {pmid30572962,
year = {2018},
author = {Du Preez, S and Corbitt, M and Cabanas, H and Eaton, N and Staines, D and Marshall-Gradisnik, S},
title = {A systematic review of enteric dysbiosis in chronic fatigue syndrome/myalgic encephalomyelitis.},
journal = {Systematic reviews},
volume = {7},
number = {1},
pages = {241},
doi = {10.1186/s13643-018-0909-0},
pmid = {30572962},
issn = {2046-4053},
abstract = {BACKGROUND: Chronic fatigue syndrome or myalgic encephalomyelitis (CFS/ME) is an illness characterised by profound and pervasive fatigue in addition to a heterogeneous constellation of symptoms. The aetiology of this condition remains unknown; however, it has been previously suggested that enteric dysbiosis is implicated in the pathogenesis of CFS/ME. This review examines the evidence currently available for the presence of abnormal microbial ecology in CFS/ME in comparison to healthy controls, with one exception being probiotic-supplemented CFS/ME patients, and whether the composition of the microbiome plays a role in symptom causation.<br><br>METHODS: EMBASE, Medline (via EBSCOhost), Pubmed and Scopus were systematically searched from 1994 to March 2018. All studies that investigated the gut microbiome composition of CFS/ME patients were initially included prior to the application of specific exclusion criteria. The association between these findings and patient-centred outcomes (fatigue, quality of life, gastrointestinal symptoms, psychological wellbeing) are also reported.<br><br>RESULTS: Seven studies that met the inclusion criteria were included in the review. The microbiome composition of CFS/ME patients was compared with healthy controls, with the exception of one study that compared to probiotic-supplemented CFS/ME patients. Differences were reported in each study; however, only three were considered statistically significant, and the findings across all studies were inconsistent. The quality of the studies included in this review scored between poor (< 54%), fair (54-72%) and good (94-100%) using the Downs and Black checklist.<br><br>CONCLUSIONS: There is currently insufficient evidence for enteric dysbiosis playing a significant role in the pathomechanism of CFS/ME. Recommendations for future research in this field include the use of consistent criteria for the diagnosis of CFS/ME, reduction of confounding variables by controlling factors that influence microbiome composition prior to sample collection and including more severe cases of CFS/ME.},
}
@article {pmid30572961,
year = {2018},
author = {Popovic, A and Bourdon, C and Wang, PW and Guttman, DS and Voskuijl, W and Grigg, ME and Bandsma, RHJ and Parkinson, J},
title = {Design and application of a novel two-amplicon approach for defining eukaryotic microbiota.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {228},
doi = {10.1186/s40168-018-0612-3},
pmid = {30572961},
issn = {2049-2618},
support = {DG-06664//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {BACKGROUND: Due to a lack of systematic diagnostics, our understanding of the diversity and role of eukaryotic microbiota in human health is limited. While studies have shown fungal communities to be significant modulators of human health, information on the prevalence of taxa such as protozoa and helminths has been limited to a small number of species for which targeted molecular diagnostics are available. To probe the diversity of eukaryotic microbes and their relationships with other members of the microbiota, we applied in silico and experimental approaches to design a novel two-amplicon surveillance tool, based on sequencing regions of ribosomal RNA genes and their internal transcribed spacers. We subsequently demonstrated the utility of our approach by characterizing the eukaryotic microbiota of 46 hospitalized Malawian children suffering from Severe Acute Malnutrition (SAM).<br><br>RESULTS: Through in silico analysis and validation on a diverse panel of eukaryotes, we identified 18S rRNA variable genetic regions 4 and 5 (18S V4 V5), together with a region encoding 28S rRNA variable genetic region 2 and the internal transcribed spacers (transITS), as optimal for the systematic classification of eukaryotes. Sequencing of these regions revealed protozoa in all stool samples from children with SAM and helminths in most, including several eukaryotes previously implicated in malnutrition and diarrheal disease. Clinical comparisons revealed no association between protozoan parasites and diarrhea or HIV reactivity. However, the presence of Blastocystis correlated with bacterial alpha diversity and increased abundance of specific taxa, including Sporobacter, Cellulosibacter, Oscillibacter, and Roseburia.<br><br>CONCLUSION: We suggest this novel two-amplicon based strategy will prove an effective tool to deliver new insights into the role of eukaryotic microbiota in health and disease.},
}
@article {pmid30572705,
year = {2018},
author = {Zhu, X and Xiang, S and Feng, X and Wang, H and Tian, S and Xu, Y and Shi, L and Yang, L and Li, M and Shen, Y and Chen, J and Chen, Y and Han, J},
title = {Impact of Cyanocobalamin and Methylcobalamin on Inflammatory Bowel Disease and the Intestinal Microbiota Composition.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.8b05730},
pmid = {30572705},
issn = {1520-5118},
abstract = {Patients with inflammatory bowel disease (IBD) are usually advised to supplement various types of vitamin B12, since vitamin B12 is generally absorbed in colon. Thus, in the current study, the influence of cyanocobalamin (CNCBL) or methylcobalamin (MECBL) ingestion on IBD symptoms will be investigated. Then, whether and how the application of various cobalamins would modify the taxonomic and functional composition of the gut microbiome in mice will be examined carefully. Dextran sulfate sodium-induced IBD mice were treated with MECBL or CNCBL; disease activity index (DAI) scores and intestinal inflammatory condition of mice were evaluated. Faecal samples were collected; microbiota composition was determined with a 16s rRNA analysis, functional profiles were predicted by PICRUSt and short-chain fatty acids were measured. The consequence of higher relative abundances of Enterobacteriaceae and isomeric short chain fatty acids by cobalamins treatment revealed that a high concentration of CNCBL, but not MECBL, supplementation obviously aggravated IBD. A microbial ecosystem rich in Escherichia/Shigella and low in Lactobacillus, Blautia, and Clostridium XVIII was observed in IBD mice after a high concentration of CNCBL supplementation. In cobalamin-dependent enzymes, CNCBL was more efficient in adenosyl-cobalamin system than MECBL, vice versa in MECBL system. The distinct effects of various cobalamins were associated with the distribution and efficiency of vitamin B12-dependent riboswitches. CNCBL had a strong inhibitory effect on all riboswitches, especially on btuB and pocR riboswitches from Enterobacteriaceae. CNCBL aggravated IBD via enhancing the proportion of Enterobacteriaceae organisms through riboswitch and enzyme systems. The present study provides a critical reference for offering a suitable amount and type of cobalamin during a symbiotic condition.},
}
@article {pmid30572622,
year = {2018},
author = {Sánchez-Ponce, Y and Varela-Fascinetto, G and Romo-Vázquez, JC and López-Martínez, B and Sánchez-Huerta, JL and Parra-Ortega, I and Fuentes-Pananá, EM and Morales-Sánchez, A},
title = {Simultaneous Detection of Beta and Gamma Human Herpesviruses by Multiplex qPCR Reveals Simple Infection and Coinfection Episodes Increasing Risk for Graft Rejection in Solid Organ Transplantation.},
journal = {Viruses},
volume = {10},
number = {12},
pages = {},
doi = {10.3390/v10120730},
pmid = {30572622},
issn = {1999-4915},
support = {261307//Consejo Nacional de Ciencia y Tecnología/ ; HIM-2016-021//Fondo de Apoyo a la Investigación Hospital Infantil de México Federico Gómez/ ; },
abstract = {Herpesviruses are common components of the human microbiome that become clinically relevant when a competent immunosurveillance is compromised, such as in transplantation. Members of the beta and gamma subfamilies are associated with a wide diversity of pathologies, including end-organ disease and cancer. In this study, we developed a multiplex qPCR technique with high specificity, sensitivity, efficiency and predictability that allowed the simultaneous detection and quantification of beta and gamma human herpesviruses. The technique was tested in a cohort of 34 kidney- or liver-transplanted pediatric patients followed up for up to 12 months post-transplant. Viral load was determined in 495 leukocyte-plasma paired samples collected bi-weekly or monthly. Human herpesvirus (HHV) 7 was the herpesvirus most frequently found in positive samples (39%), followed by Epstein-Barr virus (EBV) (20%). Also, EBV and HHV7 were present in the majority of coinfection episodes (62%). The share of positive samples exclusively detected either in leukocytes or plasma was 85%, suggesting that these herpesviruses tended to take a latent or lytic path in an exclusive manner. Infection by human cytomegalovirus (HCMV) and HHV6, as well as coinfection by EBV/HHV7 and EBV/HHV6/HHV7, were associated with graft rejection (RR = 40.33 (p = 0.0013), 5.60 (p = 0.03), 5.60 (p = 0.03) and 17.64 (p = 0.0003), respectively). The routine monitoring of beta and gamma herpesviruses should be mandatory in transplant centers to implement preventive strategies.},
}
@article {pmid30568826,
year = {2016},
author = {Andrei, M and Gologan, S and Stoicescu, A and Ionescu, M and Nicolaie, T and Diculescu, M},
title = {Small Intestinal Bacterial Overgrowth Syndrome Prevalence in Romanian Patients with Inflammatory Bowel Disease.},
journal = {Current health sciences journal},
volume = {42},
number = {2},
pages = {151-156},
doi = {10.12865/CHSJ.42.02.06},
pmid = {30568826},
issn = {2067-0656},
abstract = {BACKGROUND: small intestinal bacterial overgrowth (SIBO) is an entity commonly associated with digestive disease. Recently, its association with inflammatory bowel diseases (IBD) made the object of an increasing number of investigations. Sometimes symptoms of excessive bacterial populations may overlap or mimic flares of inflammatory disease.<br><br>METHOD: patients with IBD (CD - Crohn disease and UC - ulcerative colitis) in remission underwent screening for the presence of SIBO using the hydrogen breath test.<br><br>RESULTS: of the 75 patients tested, the breath test was positive for SIBO in 25.3% (30.77% of patients with CD and 19.4% of patients with UC). The risk factors associated with the presence of this syndrome were identified as: pancolonic impairment in UC, perianal and ileo-colonic involvement in CD, postoperative absence of the ileocecal valve. Patients in remission with bacterial overgrowth tend to present more frequently: a higher daily average of stools, a lower BMI (body mass index) and much more frequent complaints of persistent flatulence.<br><br>CONCLUSIONS: patients with Crohn's disease suffer from small intestinal bacterial overgrowth syndrome more frequently than those with ulcerative colitis. The hydrogen breath test may be used, along with other laboratory methods, to distinguish between an inflammatory bowel disease and an overlap of small intestinal bacterial overgrowth.},
}
@article {pmid30558446,
year = {2018},
author = {Muhammad, JN and Fernandez, JR and Clay, OJ and Saag, MS and Overton, ET and Willig, AL},
title = {Associations of food insecurity and psychosocial measures with diet quality in adults aging with HIV.},
journal = {AIDS care},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/09540121.2018.1554239},
pmid = {30558446},
issn = {1360-0451},
abstract = {People aging with HIV face social stressors which may negatively affect their overall nutrition. Here, we assess relationships between self-reported measures of depression, perceived stress, social support, and food insecurity with diet quality in older adults with HIV. A retrospective analysis of self-reported data from parent study at The University of Alabama at Birmingham 1917 HIV Clinic was performed. The study sample consisted of sixty people living with HIV (PLWH) with controlled HIV infection (<50 copies/mL), aged 50 years or older who participated in a cross-sectional microbiome study. Dietary intake was measured using the NHANES 12-month Food Frequency Questionnaire (FFQ) and three Automated Self-Administered (ASA) 24-hr diet recalls to calculate diet quality scores using the Mediterranean Diet Score (MDS); alternative Healthy Eating Index (aHEI); and the Recommended Food Score (RFS) indices. Food insecurity was measured with the Food Security Questionnaire (FSQ). Participants completed the following psychosocial scales: (1) depression - Patient Health Questionnaire-8 (PHQ8); (2) perceived stress - Perceived Stress Scale (PSS-10); (3) social support - Multidimensional Scale of Perceived Social Support (MSPSS). Linear regression models were used to investigate relationships among variables controlling for gender and income. The cohort was characterized as follows: Mean age 56 ± 4.6 years, 80% African-American, and 32% women. Mean body mass index (BMI) was 28.4 ± 7.2 with 55% reporting food insecurity. Most participants reported having post-secondary education (53%), although 77% reported annual incomes <$20,000. Food insecurity was independently associated with measures of poor dietary intake: aHEI (β = -0.08, p = .02) and MDS (β = -0.23, p < 0.01) and with low dietary intake of fibre (β = -0.27, p = .04), vitamin E (β = -0.35, p = .01), folate (β = -0.31, p = .02), magnesium (β = -0.34, p = .01) and copper (β = -0.36, p = .01). These data indicate food insecurity is associated with poor diet quality among PLWH. Clinical interventions are needed to improve food access for PLWH of low SES.},
}
@article {pmid30572101,
year = {2018},
author = {Wang, S and Li, N and Zou, H and Wu, M},
title = {Gut microbiome-based secondary metabolite biosynthetic gene clusters detection in Parkinson's disease.},
journal = {Neuroscience letters},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neulet.2018.12.021},
pmid = {30572101},
issn = {1872-7972},
abstract = {The microbiota of individuals with Parkinson's disease (PD) has been the focus of research in recent years. However, the mechanisms underlying the interactions between the gut microbiome and the brain, as well as its role in PD pathogenesis, remain to be elucidated. In this study, we used a systematic approach to predict putative biosynthetic gene clusters (BGCs) from the raw metagenomic data of the gut microbiome, and identified 43 BGCs that were significantly enriched in the PD patients. Fourteen of these clusters originated from microbes that were not increased in the patients, and the most significantly enriched one encoded a putative efflux protein and a radical SAM protein, indicating a potential role in PD. Based on a random forest classifier, these BGCs can be used to correctly discriminate between PD patients and healthy controls, with a cross-validated AUC of 0.91 from the 31 early stage PD patients and 28 healthy controls. Our study provides an alternative method to analyze the microbiota of PD patients, and further increase our understanding of this disease.},
}
@article {pmid30571768,
year = {2018},
author = {Ajayi, TA and Cantrell, S and Spann, A and Garman, KS},
title = {Barrett's esophagus and esophageal cancer: Links to microbes and the microbiome.},
journal = {PLoS pathogens},
volume = {14},
number = {12},
pages = {e1007384},
doi = {10.1371/journal.ppat.1007384},
pmid = {30571768},
issn = {1553-7374},
}
@article {pmid30571698,
year = {2018},
author = {Mahnic, A and Rupnik, M},
title = {Different host factors are associated with patterns in bacterial and fungal gut microbiota in Slovenian healthy cohort.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0209209},
doi = {10.1371/journal.pone.0209209},
pmid = {30571698},
issn = {1932-6203},
abstract = {Gut microbiota in a healthy population is shaped by various geographic, demographic and lifestyle factors. Although the majority of research remains focused on the bacterial community, recent efforts to include the remaining microbial members like viruses, archaea and especially fungi revealed various functions they perform in the gut. Using the amplicon sequencing approach we analysed bacterial and fungal gut communities in a Slovenian cohort of 186 healthy volunteers. In the bacterial microbiome we detected 253 different genera. A core microbiome analysis revealed high consistency with previous studies, most prominently showing that genera Faecalibacterium, Bacteroides and Roseburia regularly comprise the core community. We detected a total of 195 fungal genera, but the majority of these showed low prevalence and are likely transient foodborne contaminations. The fungal community showed a low diversity per sample and a large interindividual variability. The most abundant fungi were Saccharomyces cerevisiae and Candida albicans. These, along with representatives from genera Penicillium and Debaryomyces, cover 82% of obtained reads. We report three significant questionnaire-based host covariates associated with microbiota composition. Bacterial community was associated with age and gender. More specifically, bacterial diversity was increased with age and was higher in the female population compared to male. The analysis of fungal community showed that more time dedicated to physical activity resulted in a higher fungal diversity and lower abundance of S. cerevisiae. This is likely dependent on different diets, which were reported by participants according to the respective rates of physical activity.},
}
@article {pmid30571464,
year = {2018},
author = {Jama, H and Kaye, DM and Marques, FZ},
title = {Population-Based Gut Microbiome Associations With Hypertension.},
journal = {Circulation research},
volume = {123},
number = {11},
pages = {1185-1187},
doi = {10.1161/CIRCRESAHA.118.313792},
pmid = {30571464},
issn = {1524-4571},
}
@article {pmid30571463,
year = {2018},
author = {Steves, CJ and Jackson, MA},
title = {Response to: Population-Based Gut Microbiome Associations With Hypertension.},
journal = {Circulation research},
volume = {123},
number = {11},
pages = {1188-1189},
doi = {10.1161/CIRCRESAHA.118.313913},
pmid = {30571463},
issn = {1524-4571},
}
@article {pmid30571343,
year = {2018},
author = {Yoshida, N and Emoto, T and Yamashita, T and Watanabe, H and Hayashi, T and Tabata, T and Hoshi, N and Hatano, N and Ozawa, G and Sasaki, N and Mizoguchi, T and Amin, HZ and Hirota, Y and Ogawa, W and Yamada, T and Hirata, KI},
title = {Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis.},
journal = {Circulation},
volume = {138},
number = {22},
pages = {2486-2498},
doi = {10.1161/CIRCULATIONAHA.118.033714},
pmid = {30571343},
issn = {1524-4539},
abstract = {BACKGROUND: It is increasingly recognized that gut microbiota play a pivotal role in the development of atherosclerotic cardiovascular disease. Previously, we have reported that the abundance of genus Bacteroides is lower in patients with coronary artery disease (CAD) than in patients without CAD with coronary risk factors or in healthy volunteers. However, it remains unclear which and how specific gut bacteria contribute to the progression of atherosclerosis.<br><br>METHODS: We recruited patients with CAD patients and controls without CAD with coronary risk factors. We then compared gut microbial composition using 16S ribosomal RNA gene sequencing in fecal samples to detect species with differential abundance between 2 groups. Subsequently, we used atherosclerosis-prone mice to study the mechanisms underlying the relationship between such species and atherosclerosis.<br><br>RESULTS: Human fecal 16S ribosomal RNA gene sequencing revealed a significantly lower abundance of Bacteroides vulgatus and Bacteroides dorei in patients with CAD. This significant differential abundance was confirmed by quantitative polymerase chain reaction. Gavage with live B. vulgatus and B. dorei attenuated atherosclerotic lesion formation in atherosclerosis-prone mice, markedly ameliorating endotoxemia followed by decreasing gut microbial lipopolysaccharide production, effectively suppressing proinflammatory immune responses. Furthermore, fecal lipopolysaccharide levels in patients with CAD were significantly higher and negatively correlated with the abundance of B. vulgatus and B. dorei.<br><br>CONCLUSIONS: Our translational research findings identify a previously unknown link between specific gut bacteria and atherosclerosis. Treatment with live B. vulgatus and B. dorei may help prevent CAD.<br><br>CLINICAL TRIAL REGISTRATION: URL: https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000018051 . Unique identifier: UMIN000015703.},
}
@article {pmid30571146,
year = {2018},
author = {Saglani, S and Custovic, A},
title = {Childhood Asthma: Advances Using Machine Learning and Mechanistic Studies.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.201810-1956CI},
pmid = {30571146},
issn = {1535-4970},
abstract = {A paradigm shift brought by the recognition that childhood asthma is a heterogeneous condition comprising several endotypes underpinned by different pathophysiology, coupled with advances in understanding important causal mechanisms, offers a real opportunity for a step change to reduce the burden of the disease on individual children, families and society. Data-driven approaches have provided a framework for revealing hidden structure within large datasets. One way of bridging findings from data-driven analyses into clinical practice is to link &quot;phenotypes&quot; identified using such techniques with a specific pathology. Epidemiological studies have provided important clues about mechanistic avenues that should be pursued to identify interventions to prevent asthma development or alter its natural history. Findings from cohort studies followed by mechanistic studies in humans and in neonatal mouse models have suggested that environments such as traditional farming may provide protection by modulating innate immune responses, and that impaired innate immunity may increase asthma susceptibility. The key question of which component of these exposures can be translated into interventions requires confirmation. Increasing mechanistic evidence is demonstrating that shaping the airway microbiome in early life may modulate immune function to confer protection. If we are to make advances, we have to foster cross-disciplinary collaborations between data scientists who turn &quot;big data&quot; into useful information about the hidden structures within large dataset which may help disaggregate &quot;asthma&quot;, with medical professionals and basic scientists who provide critical clinical and mechanistic insights about the mechanisms underpinning the architecture of the heterogeneity, to deliver mechanism-based stratified treatments and prevention.},
}
@article {pmid30570692,
year = {2018},
author = {Olanrewaju, OS and Ayangbenro, AS and Glick, BR and Babalola, OO},
title = {Plant health: feedback effect of root exudates-rhizobiome interactions.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9556-6},
pmid = {30570692},
issn = {1432-0614},
support = {UID81192//National Research Foundation/ ; },
abstract = {The well-being of the microbial community that densely populates the rhizosphere is aided by a plant's root exudates. Maintaining a plant's health is a key factor in its continued existence. As minute as rhizospheric microbes are, their importance in plant growth cannot be overemphasized. They depend on plants for nutrients and other necessary requirements. The relationship between the rhizosphere-microbiome (rhizobiome) and plant hosts can be beneficial, non-effectual, or pathogenic depending on the microbes and the plant involved. This relationship, to a large extent, determines the fate of the host plant's survival. Modern molecular techniques have been used to unravel rhizobiome species' composition, but the interplay between the rhizobiome root exudates and other factors in the maintenance of a healthy plant have not as yet been thoroughly investigated. Many functional proteins are activated in plants upon contact with external factors. These proteins may elicit growth promoting or growth suppressing responses from the plants. To optimize the growth and productivity of host plants, rhizobiome microbial diversity and modulatory techniques need to be clearly understood for improved plant health.},
}
@article {pmid30569038,
year = {2018},
author = {Pereira, DIA and Mohammed, NI and Ofordile, O and Camara, F and Baldeh, B and Mendy, T and Sanyang, C and Jallow, AT and Hossain, I and Wason, J and Prentice, AM},
title = {A novel nano-iron supplement to safely combat iron deficiency and anaemia in young children: The IHAT-GUT double-blind, randomised, placebo-controlled trial protocol.},
journal = {Gates open research},
volume = {2},
number = {},
pages = {48},
doi = {10.12688/gatesopenres.12866.2},
pmid = {30569038},
issn = {2572-4754},
abstract = {Background: Iron deficiency and its associated anaemia (IDA) are the leading forms of micronutrient malnutrition worldwide. Here we describe the rationale and design of the first clinical trial evaluating the efficacy and safety of an innovative nano iron supplement, iron hydroxide adipate tartrate (IHAT), for the treatment of IDA in young children (IHAT-GUT trial). Oral iron is often ineffective due to poor absorption and/or gastrointestinal adverse effects. IHAT is novel since it is effectively absorbed whilst remaining nanoparticulate in the gut, therefore should enable supplementation with fewer symptoms. Methods: IHAT-GUT is a three-arm, double-blind, randomised, placebo-controlled phase II trial conducted in Gambian children 6-35 months of age. The intervention consists of a 12-week supplementation with either IHAT, ferrous sulphate (both at doses bioequivalent to 12.5 mg Fe/day) or placebo. The trial aims to include 705 children with IDA who will be randomly assigned (1:1:1) to each arm. The primary objectives are to test non-inferiority of IHAT in relation to ferrous sulphate at treating IDA, and to test superiority of IHAT in relation to ferrous sulphate and non-inferiority in relation to placebo in terms of diarrhoea incidence and prevalence. Secondary objectives are mechanistic assessments, to test whether IHAT reduces the burden of enteric pathogens, morbidity, and intestinal inflammation, and that it does not cause detrimental changes to the gut microbiome, particularly in relation to Lactobacillaceae, Bifidobacteriaceae and Enterobacteriaceae. Discussion: This trial will test the hypothesis that supplementation with IHAT eliminates iron deficiency and improves haemoglobin levels without inducing gastrointestinal adverse effects. If shown to be the case, this would open the possibility for further testing and use of IHAT as a novel iron source for micronutrient intervention strategies in resource-poor countries, with the ultimate aim to help reduce the IDA global burden. Registration: This trial is registered at clinicaltrials.gov (NCT02941081).},
}
@article {pmid30568641,
year = {2018},
author = {Mahnert, A and Haratani, M and Schmuck, M and Berg, G},
title = {Enriching Beneficial Microbial Diversity of Indoor Plants and Their Surrounding Built Environment With Biostimulants.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2985},
doi = {10.3389/fmicb.2018.02985},
pmid = {30568641},
issn = {1664-302X},
abstract = {Microbial diversity is suggested as the key for plant and human health. However, how microbial diversity can be enriched is largely unknown but of great interest for health issues. Biostimulants offer the way to directly augment our main living areas by the healthy microbiome of indoor plants. Here, we investigated shifts of the microbiome on leaves of spider plants (Chlorophytum comosum) and its surrounding abiotic surfaces in the built environment after irrigation with a vermicompost-based biostimulant for 12 weeks. The biostimulant could not only promote plant growth, but changed the composition of the microbiome and abundance of intact microbial cells on plant leaves and even stronger on abiotic surfaces in close vicinity under constant conditions of the microclimate. Biostimulant treatments stabilized microbial diversity and resulted in an increase of Bacteroidetes and a surprising transient emerge of new phyla, e.g., Verrucomicrobia, Acidobacteria, and Thaumarchaeota. The proportion of potentially beneficial microorganisms like Brevibacillus, Actinoallomurus, Paenibacillus, Sphaerisporangium increased relatively; microbial diversity was stabilized, and the built environment became more plant-like. Detected metabolites like indole-3-acetic acid in the biostimulant were potentially contributed by species of Pseudomonas. Overall, effects of the biostimulant on the composition of the microbiome could be predicted with an accuracy of 87%. This study shows the potential of biostimulants not only for the plant itself, but also for other living holobionts like humans in the surrounding environment.},
}
@article {pmid30568635,
year = {2018},
author = {Liu, J and Zhao, R and Zhang, J and Zhang, G and Yu, K and Li, X and Li, B},
title = {Occurrence and Fate of Ultramicrobacteria in a Full-Scale Drinking Water Treatment Plant.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2922},
doi = {10.3389/fmicb.2018.02922},
pmid = {30568635},
issn = {1664-302X},
abstract = {Ultramicrobacteria (UMB) are omnipresent and numerically dominate in freshwater, as microbes can present in drinking water systems, however, the UMB communities that occur and their removal behaviors remain poorly characterized in drinking water treatment plants (DWTPs). To gain insights into these issues, we profiled bacterial cell density, community structure and functions of UMB and their counterpart large bacteria (LB) using flow cytometry and filtration paired with 16S rRNA gene high-throughput sequencing in a full-scale DWTP. Contrary to the reduction of bacterial density and diversity, the proportion of UMB in the total bacteria community increased as the drinking water treatment process progressed, and biological activated carbon facilitated bacterial growth. Moreover, UMB were less diverse than LB, and their community structure and predicted functions were significantly different. In the DWTP, UMB indicator taxa were mainly affiliated with α/β/γ-Proteobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, and Dependentiae. In particular, the exclusive clustering of UMB at the phylum level, e.g., Parcubacteria, Elusimicrobia, and Saccharibacteria, confirmed the fact that the ultra-small size of UMB is a naturally and evolutionarily conserved trait. Additionally, the streamlined genome could be connected to UMB, such as candidate phyla radiation (CPR) bacteria, following a symbiotic or parasitic lifestyle, which then leads to the observed high connectedness, i.e., non-random intra-taxa co-occurrence patterns within UMB. Functional prediction analysis revealed that environmental information processing and DNA replication and repair likely contribute to the higher resistance of UMB to drinking water treatment processes in comparison to LB. Overall, the study provides valuable insights into the occurrence and fate of UMB regarding community structure, phylogenetic characteristics and potential functions in a full-scale DWTP, and it is a useful reference for beneficial manipulation of the drinking water microbiome.},
}
@article {pmid30568608,
year = {2018},
author = {Li, Y and Hao, Y and Fan, F and Zhang, B},
title = {The Role of Microbiome in Insomnia, Circadian Disturbance and Depression.},
journal = {Frontiers in psychiatry},
volume = {9},
number = {},
pages = {669},
doi = {10.3389/fpsyt.2018.00669},
pmid = {30568608},
issn = {1664-0640},
abstract = {Good sleep and mood are important for health and for keeping active. Numerous studies have suggested that the incidence of insomnia and depressive disorder are linked to biological rhythms, immune function, and nutrient metabolism, but the exact mechanism is not yet clear. There is considerable evidence showing that the gut microbiome not only affects the digestive, metabolic, and immune functions of the host but also regulates host sleep and mental states through the microbiome-gut-brain axis. Preliminary evidence indicates that microorganisms and circadian genes can interact with each other. The characteristics of the gastrointestinal microbiome and metabolism are related to the host's sleep and circadian rhythm. Moreover, emotion and physiological stress can also affect the composition of the gut microorganisms. The gut microbiome and inflammation may be linked to sleep loss, circadian misalignment, affective disorders, and metabolic disease. In this review article, we discuss various functions of the gut microbiome and how its activities interact with the circadian rhythms and emotions of the host. Exploring the effects of the gut microbiome on insomnia and depression will help further our understanding of the pathogenesis of mental disorders. It is therefore important to regulate and maintain a normal gastrointestinal micro-ecological environment in patients when treating mental disorders.},
}
@article {pmid30568571,
year = {2018},
author = {Lukiw, WJ and Cong, L and Jaber, V and Zhao, Y},
title = {Microbiome-Derived Lipopolysaccharide (LPS) Selectively Inhibits Neurofilament Light Chain (NF-L) Gene Expression in Human Neuronal-Glial (HNG) Cells in Primary Culture.},
journal = {Frontiers in neuroscience},
volume = {12},
number = {},
pages = {896},
doi = {10.3389/fnins.2018.00896},
pmid = {30568571},
issn = {1662-4548},
abstract = {The remarkable co-localization of highly pro-inflammatory lipopolysaccharide (LPS) with sporadic Alzheimer's disease (AD)-affected neuronal nuclei suggests that there may be some novel pathogenic contribution of this heat stable neurotoxin to neuronal activity and neuron-specific gene expression. In this communication we show for the first time: (i) the association and envelopment of sporadic AD neuronal nuclei with LPS in multiple AD neocortical tissue samples; and (ii) a selective repression in the output of neuron-specific neurofilament light (NF-L) chain messenger RNA (mRNA), perhaps as a consequence of this association. The down-regulation of NF-L mRNA and protein is a characteristic attribute of AD brain and accompanies neuronal atrophy and an associated loss of neuronal architecture with synaptic deficits. To study this phenomenon further, human neuronal-glial (HNG) cells in primary culture were incubated with LPS, and DNA arrays, Northern, Western, and ELISA analyses were used to quantify transcription patterns for the three member neuron-specific intermediate filament-gene family NF-H, NF-M, and NF-L. As in sporadic AD limbic-regions, down-regulated transcription products for the NF-L intermediate filament protein was significant. These results support our novel hypothesis: (i) that internally sourced, microbiome-derived neurotoxins such as LPS contribute to a progressive disruption in the read-out of neuron-specific genetic-information; (ii) that the presence of LPS-enveloped neuronal nuclei is associated with a down-regulation in NF-L expression, a key neuron-specific cytoskeletal component; and (iii) this may have a bearing on progressive neuronal atrophy, loss of synaptic-contact and disruption of neuronal architecture, all of which are characteristic pathological features of sporadic-AD brain. This is the first report that provides evidence for a neuron-specific effect of a human GI-tract microbiome-derived neurotoxin on decreased NF-L abundance in both sporadic AD temporal lobe neocortex in vivo and in LPS-stressed HNG cells in vitro.},
}
@article {pmid30567928,
year = {2018},
author = {Vich Vila, A and Imhann, F and Collij, V and Jankipersadsing, SA and Gurry, T and Mujagic, Z and Kurilshikov, A and Bonder, MJ and Jiang, X and Tigchelaar, EF and Dekens, J and Peters, V and Voskuil, MD and Visschedijk, MC and van Dullemen, HM and Keszthelyi, D and Swertz, MA and Franke, L and Alberts, R and Festen, EAM and Dijkstra, G and Masclee, AAM and Hofker, MH and Xavier, RJ and Alm, EJ and Fu, J and Wijmenga, C and Jonkers, DMAE and Zhernakova, A and Weersma, RK},
title = {Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.},
journal = {Science translational medicine},
volume = {10},
number = {472},
pages = {},
doi = {10.1126/scitranslmed.aap8914},
pmid = {30567928},
issn = {1946-6242},
abstract = {Changes in the gut microbiota have been associated with two of the most common gastrointestinal diseases, inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). Here, we performed a case-control analysis using shotgun metagenomic sequencing of stool samples from 1792 individuals with IBD and IBS compared with control individuals in the general population. Despite substantial overlap between the gut microbiome of patients with IBD and IBS compared with control individuals, we were able to use gut microbiota composition differences to distinguish patients with IBD from those with IBS. By combining species-level profiles and strain-level profiles with bacterial growth rates, metabolic functions, antibiotic resistance, and virulence factor analyses, we identified key bacterial species that may be involved in two common gastrointestinal diseases.},
}
@article {pmid30567565,
year = {2018},
author = {Pothuraju, R and Rachagani, S and Junker, WM and Chaudhary, S and Saraswathi, V and Kaur, S and Batra, SK},
title = {Pancreatic cancer associated with obesity and diabetes: an alternative approach for its targeting.},
journal = {Journal of experimental &amp; clinical cancer research : CR},
volume = {37},
number = {1},
pages = {319},
doi = {10.1186/s13046-018-0963-4},
pmid = {30567565},
issn = {1756-9966},
support = {RO1 CA210637, RO1CA206444, and RO1 CA183459, UO1 CA200466, P50 CA127297 and PO1 CA217798//National Institutes of Health/ ; },
abstract = {BACKGROUND: Pancreatic cancer (PC) is among foremost causes of cancer related deaths worldwide due to generic symptoms, lack of effective screening strategies and resistance to chemo- and radiotherapies. The risk factors associated with PC include several metabolic disorders such as obesity, insulin resistance and type 2 diabetes mellitus (T2DM). Studies have shown that obesity and T2DM are associated with PC pathogenesis; however, their role in PC initiation and development remains obscure.<br><br>MAIN BODY: Several biochemical and physiological factors associated with obesity and/or T2DM including adipokines, inflammatory mediators, and altered microbiome are involved in PC progression and metastasis albeit by different molecular mechanisms. Deep understanding of these factors and causal relationship between factors and altered signaling pathways will facilitate deconvolution of disease complexity as well as lead to development of novel therapies. In the present review, we focuses on the interplay between adipocytokines, gut microbiota, adrenomedullin, hyaluronan, vanin and matrix metalloproteinase affected by metabolic alteration and pancreatic tumor progression.<br><br>CONCLUSIONS: Metabolic diseases, such as obesity and T2DM, contribute PC development through altered metabolic pathways. Delineating key players in oncogenic development in pancreas due to metabolic disorder could be a beneficial strategy to combat cancers associated with metabolic diseases in particular, PC.},
}
@article {pmid30567168,
year = {2018},
author = {van der Reijden, M and Riethoff, LFV and van der Reijden, WA and Griffioen-Keijzer, A},
title = {Infection of lung cavitations in a young dog owner with Hodgkin's lymphoma caused by Pasteurella multocida, without a dog bite: confirmed zoonotic transmission by tagmentation microbiome analysis.},
journal = {BMJ case reports},
volume = {11},
number = {1},
pages = {},
doi = {10.1136/bcr-2018-226646},
pmid = {30567168},
issn = {1757-790X},
abstract = {Pasteurella multocida is a known pathogen in humans, mostly reported after animal bite incidents. Atraumatic infections have been described, especially in immunocompromised patients. A 20-year-old patient with a history of stage IV Hodgkin's lymphoma with cavitating pulmonary lesions presented with a bilateral pneumonia. Shortly after finishing antibiotic treatment, she quickly developed the same symptoms of pneumonia. Bronchoscopy showed a large cavity in the right upper lobe and P. multocida was isolated from all bronchial cultures. The transmission route of P. multocida via the patient's dog was confirmed by sampling the full genome of the dog's mouth, which matched the unique P. multocida sequences found in the patient. This case demonstrates the importance of accurately determining the aetiology of the patient's symptoms, and Pasteurella infection should be considered in all immunocompromised patients with domestic animal contact, even without a bite incident.},
}
@article {pmid30566939,
year = {2018},
author = {Esser, D and Lange, J and Marinos, G and Sieber, M and Best, L and Prasse, D and Bathia, J and Rühlemann, MC and Boersch, K and Jaspers, C and Sommer, F},
title = {Functions of the Microbiota for the Physiology of Animal Metaorganisms.},
journal = {Journal of innate immunity},
volume = {},
number = {},
pages = {1-12},
doi = {10.1159/000495115},
pmid = {30566939},
issn = {1662-8128},
abstract = {Animals are usually regarded as independent entities within their respective environments. However, within an organism, eukaryotes and prokaryotes interact dynamically to form the so-called metaorganism or holobiont, where each partner fulfils its versatile and crucial role. This review focuses on the interplay between microorganisms and multicellular eukaryotes in the context of host physiology, in particular aging and mucus-associated crosstalk. In addition to the interactions between bacteria and the host, we highlight the importance of viruses and nonmodel organisms. Moreover, we discuss current culturing and computational methodologies that allow a deeper understanding of underlying mechanisms controlling the physiology of metaorganisms.},
}
@article {pmid30565881,
year = {2018},
author = {Lei, S and Xu, X and Cheng, Z and Xiong, J and Ma, R and Zhang, L and Yang, X and Zhu, Y and Zhang, B and Tian, B},
title = {Analysis of the community composition and bacterial diversity of the rhizosphere microbiome across different plant taxa.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e762},
doi = {10.1002/mbo3.762},
pmid = {30565881},
issn = {2045-8827},
support = {31670125//National Natural Science Foundation of China/ ; 2013CB127500//National Basic Research Program of China (973)/ ; 2017J01625//Natural Science Foundation of Fujian Province/ ; },
abstract = {Rhizobacteria play an important role in bridging the soil and plant microbiomes and improving the health and growth of plants. In this study, the bacterial community structures and compositions of rhizosphere microbiomes associated with six plant species, representing two orders and three families of wild plants grown in the same field, were evaluated. The six plant species examined harbored a core and similar bacterial communities of the rhizosphere microbiome, which was dominated by members of Rhizobiales, Sphingomonadales, Burkholderiales, and Xanthomonadales of Proteobacteria, Subgroup 4 of Acidobacteria, and Sphingobacteriales of Bacteroidetes. Plant species had a significant effect on the microbial composition and Operational Taxonomic Unit (OTU) abundance of the rhizosphere microbiome. Statistical analysis indicated a significant differential OTU richness (Chao1, p < 0.05) and bacterial diversity (Shannon index, p < 0.0001) of the rhizosphere microbiome at the plant species, genus, or families levels. The paralleled samples from the same plant species in the PCoA and hierarchical cluster analysis demonstrated a clear tendency to group together, although the samples were not strictly separated according to their taxonomic divergence at the family or order level. The CAP analysis revealed a great proportion (44.85%) of the variations on bacterial communities could be attributed to the plant species. The results demonstrated that largely conserved and taxonomically narrow bacterial communities of the rhizosphere microbiome existed around the plant root. The bacterial communities and diversity of the rhizosphere microbiome were significantly related to the plant taxa, at least at the species levels.},
}
@article {pmid30565880,
year = {2018},
author = {Thorn, CE and Bergesch, C and Joyce, A and Sambrano, G and McDonnell, K and Brennan, F and Heyer, R and Benndorf, D and Abram, F},
title = {A robust, cost-effective method for DNA, RNA and protein co-extraction from soil, other complex microbiomes, and pure cultures.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.12979},
pmid = {30565880},
issn = {1755-0998},
abstract = {The soil microbiome is inherently complex with high biological diversity, and spatial heterogeneity typically occurring on the sub-millimetre scale. To study the microbial ecology of soils, and other microbiomes, biomolecules i.e. nucleic acids and proteins, must be efficiently and reliably co-recovered from the same biological samples. Commercial kits are currently available for the co-extraction of DNA, RNA and proteins but none has been developed for soil samples. We present a new protocol drawing on existing phenol-chloroform based methods for nucleic acids co-extraction but incorporating targeted precipitation of proteins from the phenol phase. The protocol is cost-effective and robust, and easily implemented using reagents commonly available in laboratories. The method is estimated to be eight times cheaper than using disparate commercial kits for the isolation of DNA and/or RNA, and proteins, from soil. The method is effective, providing good quality biomolecules from a diverse range of soil types, with clay contents varying from 9.5 to 35.1%, which we successfully used for downstream, high-throughput gene sequencing and metaproteomics. Additionally, we demonstrate that the protocol can also be easily implemented for biomolecule co-extraction from other complex microbiome samples, including cattle slurry and microbial communities recovered from anaerobic bioreactors, as well as from Gram-positive and Gram-negative pure cultures. This article is protected by copyright. All rights reserved.},
}
@article {pmid30565818,
year = {2018},
author = {Zhang, H and Yoshizawa, S and Sun, Y and Huang, Y and Chu, X and González, JM and Pinhassi, J and Luo, H},
title = {Repeated Evolutionary Transitions of Flavobacteria from Marine to Non-Marine Habitats.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14509},
pmid = {30565818},
issn = {1462-2920},
abstract = {The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na+ -dependent transporters, osmolyte transporters, and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K+ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K+ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na+ -translocating NADH:quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H+ -translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components. This article is protected by copyright. All rights reserved.},
}
@article {pmid30565684,
year = {2018},
author = {Wang, JC and Bergeron, M and Andersen, H and Tikhtman, R and Haslam, D and Hunter, T and Herr, AB and de Alarcon, A},
title = {Feasibility of shotgun metagenomics to assess microbial ecology of pediatric tracheostomy tubes.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.27356},
pmid = {30565684},
issn = {1531-4995},
abstract = {OBJECTIVE: Biofilm formation on medical devices such as tracheostomy tubes (TTs) is a serious problem. The clinical impact of biofilms on the airway is still unclear. Biofilms may play a role in granulation tissue development, recurrent airway infections, and failure of laryngotracheal reconstructions. The microbial ecology on TTs has yet to be elucidated. The purpose of this study was to determine the feasibility of shotgun metagenomics to assess the biodistribution of microorganisms on TTs.<br><br>METHODS: Four TTs were collected from pediatric patients (1.4-10.2 years) with (n = 2) and without (n = 2) granulation tissue formation. Duration of TT placement prior to retrieval from patients ranged from 5 to 365 days. DNA extraction was performed using the MO BIO UltraClean Microbial Isolation (Mo Bio Laboratories, Carlsbad, CA). Library generation using Nextera XT adapters (Illumina Inc., San Diego, CA) and metagenomic shotgun sequencing was performed using the Illumina NextSeq500 (Illumina Inc, San Diego, CA). Salinibacter ruber, a species not found in mammalian microbiome communities, was used as a DNA standard and represented 0.7% to 5.7% of the microbiome, ensuring good quality and abundance of sample DNA.<br><br>RESULTS: Metagenomic shotgun sequencing was successful for all patients. In TTs associated with granuloma, Fusobacterium nucleatum, Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae were predominant, most of which are considered pathogens. From TTs without granulomas, Neisseria mucosa, Neisseria sicca, Acinetobacter baumannii, and Haemophilus parainfluenzae were identified, primarily consistent with respiratory microbiome.<br><br>CONCLUSION: This study reveals that metagenomic shotgun sequencing of biofilms formed on pediatric TTs is feasible with an apparent difference in microbiome for patients with granulation tissue. Further studies are necessary to elucidate the pathogenesis of microbial ecology and its role in airway disease in patients with TTs.<br><br>LEVEL OF EVIDENCE: 2c. Laryngoscope, 2018.},
}
@article {pmid30565323,
year = {2018},
author = {Hård, AL and Nilsson, AK and Lund, AM and Hansen-Pupp, I and Smith, LEH and Hellström, A},
title = {Review shows that donor milk does not promote the growth and development of preterm infants as well as maternal milk.},
journal = {Acta paediatrica (Oslo, Norway : 1992)},
volume = {},
number = {},
pages = {},
doi = {10.1111/apa.14702},
pmid = {30565323},
issn = {1651-2227},
abstract = {AIM: This non-systematic review examined differences in the composition of raw maternal breast milk and pasteurised donor milk and possible health effects on preterm infants.<br><br>METHODS: We searched PubMed up to July 2018 for studies published in English that focused on four comparisons: raw maternal milk versus donor milk, human milk before and after Holder pasteurisation, milk from mothers who delivered preterm and at term and milk collected during early and late lactation. We also searched for possible effects of the milk components, as well as the effects of maternal and donor milk on preterm infants' health.<br><br>RESULTS: Raw maternal milk contained factors involved in antioxidant and anti-inflammatory defence, gut microbiome establishment and the maturation of immune defences, food tolerability and metabolism. Many of these factors were reduced or abolished in processed donor milk. Both maternal milk and donor milk have been associated with a reduced incidence of necrotising enterocolitis. High-dose feeding with maternal milk during the neonatal period reportedly reduced the risk of other morbidities and promoted growth and neurodevelopment.<br><br>CONCLUSION: Many of the components in raw maternal breast milk were lacking in pasteurised donor milk, which was inferior in promoting the growth and development of very preterm infants. This article is protected by copyright. All rights reserved.},
}
@article {pmid30565246,
year = {2019},
author = {Abdel-Motal, UM and Al-Shaibi, A and Elawad, M and Lo, B},
title = {Zero tolerance! A perspective on monogenic disorders with defective regulatory T cells and IBD-like disease.},
journal = {Immunological reviews},
volume = {287},
number = {1},
pages = {236-240},
doi = {10.1111/imr.12717},
pmid = {30565246},
issn = {1600-065X},
support = {//Sidra Medicine/ ; },
abstract = {Recently, several studies have investigated a number of rare monogenic autoimmune disorders, in which the causative genetic defects were identified and found to affect the development or function of regulatory T cells (Tregs). The studies of these disorders have facilitated a deeper understanding of the mechanisms involved in immune regulation and tolerance. Furthermore, these studies have highlighted the importance of Tregs in maintaining homeostasis at the mucosal interface between the host and microbiome. Here, we offer our perspective on these monogenic autoimmune disorders, highlighting their overlapping clinical features with inflammatory bowel disease.},
}
@article {pmid30565165,
year = {2018},
author = {Serena, G and Fasano, A},
title = {Use of Probiotics to Prevent Celiac Disease and IBD in Pediatrics.},
journal = {Advances in experimental medicine and biology},
volume = {},
number = {},
pages = {},
doi = {10.1007/5584_2018_317},
pmid = {30565165},
issn = {0065-2598},
abstract = {The incidence of chronic inflammatory diseases (CIDs) is increasing worldwide. Their dramatic rise associated with limited effective strategies to slow down these epidemics calls for a better understanding of their pathophysiology in order to decrease the burdens on childhood. Several cross-sectional studies have demonstrated the association between intestinal dysbiosis and active diseases. Although informative, these studies do not mechanistically link alterations of the microflora with disease pathogenesis and, therefore, with potential therapeutic targets. More prospective studies are needed to determine whether intestinal dysbiosis plays a causative role in the onset and development of CIDs. Furthermore, given the complexity of the microflora interaction with the host, it is necessary to design a systems-level model of interactions between the host and the development of disease by integrating microbiome, metagenomics, metatranscriptomics, and metabolomics with either clinical either environmental data.In this chapter we will discuss the current knowledge regarding the microbiome's contribution to celiac disease and inflammatory bowel disease with a particular focus on how probiotics may be used as potential preventive therapy for CIDs.},
}
@article {pmid30564562,
year = {2018},
author = {Proal, A and Marshall, T},
title = {Myalgic Encephalomyelitis/Chronic Fatigue Syndrome in the Era of the Human Microbiome: Persistent Pathogens Drive Chronic Symptoms by Interfering With Host Metabolism, Gene Expression, and Immunity.},
journal = {Frontiers in pediatrics},
volume = {6},
number = {},
pages = {373},
doi = {10.3389/fped.2018.00373},
pmid = {30564562},
issn = {2296-2360},
abstract = {The illness ME/CFS has been repeatedly tied to infectious agents such as Epstein Barr Virus. Expanding research on the human microbiome now allows ME/CFS-associated pathogens to be studied as interacting members of human microbiome communities. Humans harbor these vast ecosystems of bacteria, viruses and fungi in nearly all tissue and blood. Most well-studied inflammatory conditions are tied to dysbiosis or imbalance of the human microbiome. While gut microbiome dysbiosis has been identified in ME/CFS, microbes and viruses outside the gut can also contribute to the illness. Pathobionts, and their associated proteins/metabolites, often control human metabolism and gene expression in a manner that pushes the body toward a state of illness. Intracellular pathogens, including many associated with ME/CFS, drive microbiome dysbiosis by directly interfering with human transcription, translation, and DNA repair processes. Molecular mimicry between host and pathogen proteins/metabolites further complicates this interference. Other human pathogens disable mitochondria or dysregulate host nervous system signaling. Antibodies and/or clonal T cells identified in patients with ME/CFS are likely activated in response to these persistent microbiome pathogens. Different human pathogens have evolved similar survival mechanisms to disable the host immune response and host metabolic pathways. The metabolic dysfunction driven by these organisms can result in similar clusters of inflammatory symptoms. ME/CFS may be driven by this pathogen-induced dysfunction, with the nature of dysbiosis and symptom presentation varying based on a patient's unique infectious and environmental history. Under such conditions, patients would benefit from treatments that support the human immune system in an effort to reverse the infectious disease process.},
}
@article {pmid30564526,
year = {2018},
author = {Williams, LE and Kleinschmidt, CE and Mecca, S},
title = {Bacterial communities in the digester bed and liquid effluent of a microflush composting toilet system.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6077},
doi = {10.7717/peerj.6077},
pmid = {30564526},
issn = {2167-8359},
abstract = {Lack of access to clean water and sanitation is a major factor impacting public health in communities worldwide. To address this, the S-Lab at Providence College and the Global Sustainable Aid Project developed a microflush composting toilet system to isolate and treat human waste. Solid waste is composted within a filter-digester bed via an aerobic process involving microbes and invertebrates. Liquid waste may be sanitized by solar disinfection (SODIS) or slow sand filtration (SSF). Here, we used 16S rRNA amplicon sequencing of samples from a scaled-down test version of the system to better understand the bacterial component of the toilet system. Immediately after fecal matter was deposited in the test system, the bacterial community of the filter-digester bed at the site of deposition resembled that of the human gut at both the phylum and genus level, which was expected. Genus-level analysis of filter-digester bed samples collected over the next 30 days from the site of deposition showed reduced or undetectable levels of fecal-associated taxa, with the exception of Clostridium XI, which persisted at low abundance throughout the sampling period. Starting with the sample collected on day 4, the bacterial community of the filter-digester bed at the site of deposition was dominated by bacterial taxa commonly associated with environmental sources, reflecting a major shift in bacterial community composition. These data support the toilet system's capacity for processing solid human waste. We also analyzed how SODIS and SSF sanitization methods affected the bacterial community composition of liquid effluent collected on day 15 from the test system. Untreated and treated liquid effluent samples were dominated by Proteobacteria. At the genus level, the bacterial community of the untreated effluent included taxa commonly associated with environmental sources. In the SODIS-treated effluent, these genera increased in abundance, whereas in the SSF-treated effluent, they were greatly reduced or undetectable. By analyzing operational taxonomic units that were unclassified at the genus level, we observed that SSF appears to introduce new taxa into the treated effluent, likely from the biological film of microbes and small animals that constitutes the key element of SSF. These data will inform continued development of liquid waste handling strategies for the toilet system. Using the test system as an indicator of the performance of the full-scale version, we have shown the effectiveness of the microflush composting toilet system for containing and eliminating gut-associated bacteria, thereby improving sanitation and contributing to better public health in rural and peri-urban communities.},
}
@article {pmid30564204,
year = {2018},
author = {Vigneron, A and Cruaud, P and Mohit, V and Martineau, MJ and Culley, AI and Lovejoy, C and Vincent, WF},
title = {Multiple Strategies for Light-Harvesting, Photoprotection, and Carbon Flow in High Latitude Microbial Mats.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2881},
doi = {10.3389/fmicb.2018.02881},
pmid = {30564204},
issn = {1664-302X},
abstract = {Microbial mats are ubiquitous in polar freshwater ecosystems and sustain high concentrations of biomass despite the extreme seasonal variations in light and temperature. Here we aimed to resolve genomic adaptations for light-harvesting, bright-light protection, and carbon flow in mats that undergo seasonal freeze-up. To bracket a range of communities in shallow water habitats, we sampled cyanobacterial mats in the thawed littoral zone of two lakes situated at the northern and southern limits of the Canadian Arctic permafrost zone. We applied a multiphasic approach using pigment profiles from high performance liquid chromatography, Illumina MiSeq sequencing of the 16S and 18S rRNA genes, and metagenomic analysis. The mats shared a taxonomic and functional core microbiome, dominated by oxygenic cyanobacteria with light-harvesting and photoprotective pigments, bacteria with bacteriochlorophyll, and bacteria with light-driven Type I rhodopsins. Organisms able to use light for energy related processes represented up to 85% of the total microbial community, with 15-30% attributable to cyanobacteria and 55-70% attributable to other bacteria. The proportion of genes involved in anaplerotic CO2 fixation was greater than for genes associated with oxygenic photosynthesis. Diverse heterotrophic bacteria, eukaryotes (including metazoans and fungi) and viruses co-occurred in both communities. The results indicate a broad range of strategies for capturing sunlight and CO2, and for the subsequent flow of energy and carbon in these complex, light-driven microbial ecosystems.},
}
@article {pmid30564203,
year = {2018},
author = {Crenn, K and Duffieux, D and Jeanthon, C},
title = {Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2879},
doi = {10.3389/fmicb.2018.02879},
pmid = {30564203},
issn = {1664-302X},
abstract = {Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community-level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and collection cultures, regarded here as short- and long-term associations, respectively. Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning-sequencing of 16S rRNA genes obtained from whole-genome amplification products. The prevalence of epibiotic bacteria was higher in cultures and dependent of the host species. Culture approaches demonstrated that both diatoms carry distinct bacterial communities in short- and long-term associations. Bacterial epibonts, commonly associated with phytoplankton, were repeatedly isolated from cells of diatom collection cultures but were not recovered from environmental cells. Our results suggest that in controlled laboratory culture conditions bacterial-diatom and bacterial-bacterial interactions select for a simplified, but specific, epibiotic microbiota shaped and adapted for long-term associations.},
}
@article {pmid30564198,
year = {2018},
author = {Kreuch, D and Keating, DJ and Wu, T and Horowitz, M and Rayner, CK and Young, RL},
title = {Gut Mechanisms Linking Intestinal Sweet Sensing to Glycemic Control.},
journal = {Frontiers in endocrinology},
volume = {9},
number = {},
pages = {741},
doi = {10.3389/fendo.2018.00741},
pmid = {30564198},
issn = {1664-2392},
abstract = {Sensing nutrients within the gastrointestinal tract engages the enteroendocrine cell system to signal within the mucosa, to intrinsic and extrinsic nerve pathways, and the circulation. This signaling provides powerful feedback from the intestine to slow the rate of gastric emptying, limit postprandial glycemic excursions, and induce satiation. This review focuses on the intestinal sensing of sweet stimuli (including low-calorie sweeteners), which engage similar G-protein-coupled receptors (GPCRs) to the sweet taste receptors (STRs) of the tongue. It explores the enteroendocrine cell signals deployed upon STR activation that act within and outside the gastrointestinal tract, with a focus on the role of this distinctive pathway in regulating glucose transport function via absorptive enterocytes, and the associated impact on postprandial glycemic responses in animals and humans. The emerging role of diet, including low-calorie sweeteners, in modulating the composition of the gut microbiome and how this may impact glycemic responses of the host, is also discussed, as is recent evidence of a causal role of diet-induced dysbiosis in influencing the gut-brain axis to alter gastric emptying and insulin release. Full knowledge of intestinal STR signaling in humans, and its capacity to engage host and/or microbiome mechanisms that modify glycemic control, holds the potential for improved prevention and management of type 2 diabetes.},
}
@article {pmid30564113,
year = {2018},
author = {Verdi, S and Jackson, MA and Beaumont, M and Bowyer, RCE and Bell, JT and Spector, TD and Steves, CJ},
title = {An Investigation Into Physical Frailty as a Link Between the Gut Microbiome and Cognitive Health.},
journal = {Frontiers in aging neuroscience},
volume = {10},
number = {},
pages = {398},
doi = {10.3389/fnagi.2018.00398},
pmid = {30564113},
issn = {1663-4365},
abstract = {The preservation of cognitive abilities with aging is a priority both for individuals and nations given the aging populations of many countries. Recently the gut microbiome has been identified as a new territory to explore in relation to cognition. Experiments using rodents have identified a link between the gut microbiome and cognitive function, particularly that low microbial diversity leads to poor cognition function. Similar studies in humans could identify novel targets to encourage healthy cognition in an aging population. Here, we investigate the association of gut microbiota and cognitive function in a human cohort considering the influence of physical frailty. We analyzed 16S rRNA gene sequence data, derived from fecal samples obtained from 1,551 individuals over the age of 40. Cognitive data was collected using four cognitive tests: verbal fluency (n = 1,368), Deary-Liewald Reaction Time Test (DLRT; n = 873), Mini Mental State Examination (recall; n = 1,374) and Paired Associates Learning from the Cambridge Neuropsychological Test Automated Battery (CANTAB-PAL; n = 405). We use mixed effects models to identify associations with alpha diversity, operational taxonomic units (OTUs) and taxa and performed further analyses adjusting for physical frailty. We then repeated the analyses in a subset of individuals with dietary data, also excluding those using medications shown to influence gut microbiome composition. DLRT and verbal fluency were negatively associated with alpha diversity of the gut microbiota (False-Discovery Rate, FDR, p < 0.05). However, when considering frailty as a covariate, only associations between the DLRT and diversity measures remained. Repeating analyses excluding Proton pump inhibitor (PPI) and antibiotic users and accounting for diet, we similarly observe significant negative associations between the DLRT and alpha diversity measures and a further negative association between DLRT and the abundance of the order Burkholderiales that remains significant after adjusting for host frailty. This highlights the importance of considering concurrent differences in physical health in studies of cognitive performance and suggests that physical health has a relatively larger association with the gut microbiome. However, the frailty independent cognitive-gut microbiota associations that were observed might represent important targets for further research, with potential for use in diagnostic surveillance in cognitive aging and interventions to improve vitality.},
}
@article {pmid30562947,
year = {2018},
author = {Ishii, C and Nakanishi, Y and Murakami, S and Nozu, R and Ueno, M and Hioki, K and Aw, W and Hirayama, A and Soga, T and Ito, M and Tomita, M and Fukuda, S},
title = {A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet.},
journal = {International journal of molecular sciences},
volume = {19},
number = {12},
pages = {},
doi = {10.3390/ijms19124079},
pmid = {30562947},
issn = {1422-0067},
support = {15H01522//Japan Society for the Promotion of Science/ ; 16H04901//Japan Society for the Promotion of Science/ ; 17H05654//Japan Society for the Promotion of Science/ ; 18H04805//Japan Society for the Promotion of Science/ ; JPMJPR1537//Japan Science and Technology Agency/ ; },
abstract = {Intestinal microbiota and their metabolites are strongly associated with host physiology. Developments in DNA sequencing and mass spectrometry technologies have allowed us to obtain additional data that enhance our understanding of the interactions among microbiota, metabolites, and the host. However, the strategies used to analyze these datasets are not yet well developed. Here, we describe an original analytical strategy, metabologenomics, consisting of an integrated analysis of mass spectrometry-based metabolome data and high-throughput-sequencing-based microbiome data. Using this approach, we compared data obtained from C57BL/6J mice fed an American diet (AD), which contained higher amounts of fat and fiber, to those from mice fed control rodent diet. The feces of the AD mice contained higher amounts of butyrate and propionate, and higher relative abundances of Oscillospira and Ruminococcus. The amount of butyrate positively correlated with the abundance of these bacterial genera. Furthermore, integrated analysis of the metabolome data and the predicted metagenomic data from Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) indicated that the abundance of genes associated with butyrate metabolism positively correlated with butyrate amounts. Thus, our metabologenomic approach is expected to provide new insights and understanding of intestinal metabolic dynamics in complex microbial ecosystems.},
}
@article {pmid30562368,
year = {2018},
author = {Fuirst, M and Veit, RR and Hahn, M and Dheilly, N and Thorne, LH},
title = {Effects of urbanization on the foraging ecology and microbiota of the generalist seabird Larus argentatus.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0209200},
doi = {10.1371/journal.pone.0209200},
pmid = {30562368},
issn = {1932-6203},
abstract = {Larus gull species have proven adaptable to urbanization and due to their generalist feeding behaviors, they provide useful opportunities to study how urban environments impact foraging behavior and host-associated microbiota. We evaluated how urbanization influenced the foraging behavior and microbiome characteristics of breeding herring gulls (Larus argentatus) at three different colonies on the east coast of the United States. Study colonies represented high, medium and low degrees of urbanization, respectively. At all colonies, gulls frequently foraged at landfills and in other urban environments, but both the use of urban environments and gull foraging metrics differed with the degree of urbanization. Gulls at the more urban colonies used urban environments more frequently, showed higher rates of site fidelity and took shorter trips. Gulls at less urban colonies used a greater diversity of habitat types and foraged offshore. We observed high microbial diversity at all colonies, though microbial diversity was highest at the least urban colony where gulls used a wider variety of foraging habitats. This suggests that gulls may acquire a wider range of bacteria when visiting a higher variety of foraging sites. Our findings highlight the influence of urban habitats on gull movements and microbiome composition and diversity during the breeding season and represent the first application of amplicon sequence variants, an objective and repeatable method of bacterial classification, to study the microbiota of a seabird species.},
}
@article {pmid30562162,
year = {2018},
author = {Peng, W and Yi, P and Yang, J and Xu, P and Wang, Y and Zhang, Z and Huang, S and Wang, Z and Zhang, C},
title = {Association of gut microbiota composition and function with a senescence-accelerated mouse model of Alzheimer's Disease using 16S rRNA gene and metagenomic sequencing analysis.},
journal = {Aging},
volume = {},
number = {},
pages = {},
doi = {10.18632/aging.101693},
pmid = {30562162},
issn = {1945-4589},
abstract = {Although an intriguing potential association of the gut microbiome with Alzheimer's disease (AD) has attracted recent interest, few studies have directly assessed this relationship or underlying mechanism. Here, we compared the gut microbiota composition and functional differentiation of senescence-accelerated mouse prone 8 (SAMP8) mice with control senescence-accelerated mouse resistant 1 (SAMR1) mice using 16S rRNA gene and metagenomic sequencing analysis, respectively. Specifically, 16S sequencing results showed that the SAMP8 mice displayed a characteristic composition of the gut microbiome that clearly differed from that of the SAMR1 mice. Moreover, network analysis revealed that the gut microbiota of SAMP8 mice had decreased correlation density and clustering of operational taxonomic units. Metagenomic results revealed that the predominant Cluster of Orthologous Groups functional category related to these changes was the metabolism cluster in SAMP8 mice. The Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation further demonstrated enrichment of the relative abundance of some dominant metabolism-related KEGG pathways in the SAMP8 mice, consistent with the suggested pathogenic mechanisms of AD. In conclusion, this study suggests that perturbations of the gut microbiota composition and the functional metagenome may be associated with AD. Further studies are warranted to elucidate the potential new mechanism contributing to AD progression.},
}
@article {pmid30562060,
year = {2018},
author = {Arora, T and Rudenko, O and Egerod, KL and Husted, AS and Kovatcheva-Datchary, P and Akrami, R and Kristensen, M and Schwartz, TW and Bäckhed, F},
title = {Microbial fermentation of flaxseed fibers modulates the transcriptome of GPR41-expressing enteroendocrine cells and protects mice against diet-induced obesity.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00391.2018},
pmid = {30562060},
issn = {1522-1555},
abstract = {Dietary fibers, an integral part of the human diet, require the enzymatic activity of the gut microbiota for complete metabolism into short chain fatty acids (SCFAs). SCFAs are important modulators of host metabolism and physiology and act in part as signaling molecules by activating G-protein coupled receptors (GPR) such as GPR41. Flaxseed fibers improve metabolism in rodents and mice, but their fermentation profiles, effects on enteroendocrine cells and associated metabolic benefits are unknown. We fed GPR41-RFP mice, an enteroendocrine reporter mouse strain, chow, high fat diet (HFD) or HFD supplemented either with 10% non-fermentable fiber cellulose or fermentable flaxseed fibers for 12 weeks to assess changes in cecal gut microbiota, enteroendocrine cell transcriptome in ileum and colon, and physiological parameters. We observed that flaxseed fibers restructured the gut microbiota and promoted proliferation of the genera Bifidobacterium and Akkermansia compared with HFD. The shifts in cecal bacterial composition restored levels of the SCFAs butyrate similar to the chow diet, resulting in colonic, but not ileal, enteroendocrine cell transcriptional changes in genes related to cell cycle, mRNA and protein transport compared with HFD. Consistent with effects on enteroendocrine functions, flaxseed fibers also protected mice from diet-induced obesity, potentially by preventing reduction in energy expenditure induced by HFD. Our study shows that flaxseed fibers alter cecal microbial ecology, are fermented to SCFAs in cecum, and modulate enteroendocrine cell transcriptome in colon, which may contribute to their metabolically favorable phenotype.},
}
@article {pmid30561547,
year = {2019},
author = {Ghaemi, MS and DiGiulio, DB and Contrepois, K and Callahan, B and Ngo, TTM and Lee-McMullen, B and Lehallier, B and Robaczewska, A and Mcilwain, D and Rosenberg-Hasson, Y and Wong, RJ and Quaintance, C and Culos, A and Stanley, N and Tanada, A and Tsai, A and Gaudilliere, D and Ganio, E and Han, X and Ando, K and McNeil, L and Tingle, M and Wise, P and Maric, I and Sirota, M and Wyss-Coray, T and Winn, VD and Druzin, ML and Gibbs, R and Darmstadt, GL and Lewis, DB and Partovi Nia, V and Agard, B and Tibshirani, R and Nolan, G and Snyder, MP and Relman, DA and Quake, SR and Shaw, GM and Stevenson, DK and Angst, MS and Gaudilliere, B and Aghaeepour, N},
title = {Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {1},
pages = {95-103},
doi = {10.1093/bioinformatics/bty537},
pmid = {30561547},
issn = {1367-4811},
abstract = {Motivation: Multiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy. Modeling the chronology of these adaptations during full-term pregnancy provides the frameworks for future studies examining deviations implicated in pregnancy-related pathologies including preterm birth and preeclampsia.<br><br>Results: We performed a multiomics analysis of 51 samples from 17 pregnant women, delivering at term. The datasets included measurements from the immunome, transcriptome, microbiome, proteome and metabolome of samples obtained simultaneously from the same patients. Multivariate predictive modeling using the Elastic Net (EN) algorithm was used to measure the ability of each dataset to predict gestational age. Using stacked generalization, these datasets were combined into a single model. This model not only significantly increased predictive power by combining all datasets, but also revealed novel interactions between different biological modalities. Future work includes expansion of the cohort to preterm-enriched populations and in vivo analysis of immune-modulating interventions based on the mechanisms identified.<br><br>Datasets and scripts for reproduction of results are available through: https://nalab.stanford.edu/multiomics-pregnancy/.<br><br>Supplementary information: Supplementary data are available at Bioinformatics online.},
}
@article {pmid30561425,
year = {2018},
author = {Crafa, P and Russo, M and Miraglia, C and Barchi, A and Moccia, F and Nouvenne, A and Leandro, G and Meschi, T and De' Angelis, GL and Di Mario, F},
title = {From Sidney to OLGA: an overview of atrophic gastritis.},
journal = {Acta bio-medica : Atenei Parmensis},
volume = {89},
number = {8-S},
pages = {93-99},
pmid = {30561425},
issn = {0392-4203},
abstract = {Chronic gastritis is a long-lasting disease that can lead to a loss of appropriate gastric glands. Gastritis, as term, apply to an inflammation of the stomach, histologically proven, sometimes with structural mucosal changes. Worldwide Helicobacter pylori's infection play a pivotal role as the main etiological effector of chronic active gastritis. H. p. is a bacterium with a selective tropism for the gastric mucosa, able to survive in a hostile environment for colonization of organisms other than itself, able to develop strategies for survival and for avoidance of the defence mechanisms, causing inflammatory changes, that vary from asymptomatic mild gastritis to more severe injury such as peptic ulcer as well as premalignant lesions and malignant tumours. The pattern and distribution of gastritis strongly correlate with these sequelae and chronic atrophic gastritis with intestinal metaplasia is now assessed as a precancerous lesion with definite risk of evolution towards intraepithelial lesions of both low and high grade, as expected in the model of the Correa's cascade. In fact, the leading complication of chronic gastritis remains its close correlation with gastric cancer being biologically linked to H. pylori infection, nowadays known as a class I carcinogen. Gastric carcinogenesis is due to environmental factors, as well as to bacterial strain, host responses and gastric mucosal microbiome dysbiosis. Since, individual patients show different gastric cancer risk, it is mandatory to identify patients at risk of developing gastric cancer to offer a targeted search for lesions with a more rapid development of neoplasm liable, in an early phase, to a less destructive treatment. OLGA staging system is the most reliable and powerful system that allow the recognition of patient with a higher risk of developing gastric cancer.},
}
@article {pmid30561397,
year = {2018},
author = {Reddavide, R and Rotolo, O and Caruso, MG and Stasi, E and Notarnicola, M and Miraglia, C and Nouvenne, A and Meschi, T and De' Angelis, GL and Di Mario, F and Leandro, G},
title = {The role of diet in the prevention and treatment of Inflammatory Bowel Diseases.},
journal = {Acta bio-medica : Atenei Parmensis},
volume = {89},
number = {9-S},
pages = {60-75},
pmid = {30561397},
issn = {0392-4203},
abstract = {Inflammatory bowel diseases (IBD) - Crohn's disease (CD) and ulcerative colitis (UC) - are chronic conditions characterised by relapsing inflammation of the gastrointestinal tract. They represent an increasing public health concern and an aetiological enigma due to unknown causal factors. The current knowledge on the pathogenesis of IBD is that genetically susceptible individuals develop intolerance to a dysregulated gut microflora (dysbiosis) and chronic inflammation develops as a result of environmental triggers. Among the environmental factors associated with IBD, diet plays an important role in modulating the gut microbiome, and, consequently, it could have a therapeutic impact on the disease course. An overabundance of calories and some macronutrients typical of the Western dietetic pattern increase gut inflammation, whereas several micronutrients characteristic of the Mediterranean Diet have the potential to modulate gut inflammation, according to recent evidence. Immunonutrition has emerged as a new concept putting forward the role of vitamins such as vitamins A, C, E, and D, folic acid, beta carotene and trace elements such as zinc, selenium, manganese and iron. However, when assessed in clinical trials, specific micronutrients showed a limited benefit. Further research is required to evaluate the role of individual food compounds and complex nutritional interventions with the potential to decrease inflammation as a means of prevention and management of IBD. The current dietary recommendations for disease prevention and management are scarce and non evidence-based. This review summarizes the current knowledge on the complex interaction between diet, microbiome and immune-modulation in IBD, with particular focus to the role of the Mediterranean Diet as a tool for prevention and treatment of the disease.},
}
@article {pmid30561131,
year = {2018},
author = {Limketkai, BN and Hendler, S and Ting, PS and Parian, AM},
title = {Fecal Microbiota Transplantation for the Critically Ill Patient.},
journal = {Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/ncp.10228},
pmid = {30561131},
issn = {1941-2452},
abstract = {The gut microbiome has been implicated in a diversity of diseases, such as irritable bowel syndrome, inflammatory bowel disease, hepatic steatosis, metabolic syndrome, obesity, and anxiety. Current research also suggests the presence of a bidirectional relationship between the composition of the gut microbiome and critical illness. In the critical care setting, multiple factors (eg, use of antibiotics, aberrant nutrition, bloodstream infections, bowel ischemia, and abnormal bowel motility) strongly contribute to intestinal dysbiosis. Conversely, early studies have associated intestinal dysbiosis with worse clinical outcomes in the intensive care unit (ICU), such as infection, organ failure, and mortality. The possibility of intestinal dysbiosis influencing these clinical outcomes has prompted the question of whether microbiome manipulation strategies, such as fecal microbiota transplantation (FMT), may have a role in the management of critical illness. After a literature search of FMT used in the ICU for indications other than Clostridium difficile infections, we found 4 case reports that describe the use of FMT in 5 critically ill patients with systemic inflammatory responses and no clear source of infection. This review discusses the relationship between the gut microbiome and critical illness, early data on the use of FMT in critical care, and safety considerations of FMT in the critically ill and immunocompromised populations.},
}
@article {pmid30561098,
year = {2018},
author = {Summers, SC and Quimby, JM and Isaiah, A and Suchodolski, JS and Lunghofer, PJ and Gustafson, DL},
title = {The fecal microbiome and serum concentrations of indoxyl sulfate and p-cresol sulfate in cats with chronic kidney disease.},
journal = {Journal of veterinary internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/jvim.15389},
pmid = {30561098},
issn = {1939-1676},
support = {N/A//Buttons Fund For Feline Chronic Kidney Disease Research/ ; P30CA046934//University of Colorado Cancer Center Shared Resource Support Grant/ ; },
abstract = {BACKGROUND: Intestinal dysbiosis has been documented in humans with chronic kidney disease (CKD) and is thought to contribute to production of the uremic toxins indoxyl sulfate (IS) and p-cresol sulfate (pCS). Characteristics of the fecal microbiome in cats with CKD and correlation to serum concentrations of uremic toxins are unknown.<br><br>OBJECTIVES: To characterize the fecal microbiome and measure serum IS and pCS concentrations of cats with CKD in comparison to healthy older cats.<br><br>ANIMALS: Thirty client-owned cats with CKD (International Renal Interest Society stages 2-4) and 11 older (≥8 years) healthy control cats.<br><br>METHODS: Prospective, cross-sectional study. Fecal samples were analyzed by sequencing of 16S rRNA genes and Escherichia coli quantitative PCR (qPCR). Serum concentrations of IS and pCS measured using liquid chromatography tandem mass spectrometry.<br><br>RESULTS: Cats with CKD had significantly decreased fecal bacterial diversity and richness. Escherichia coli qPCR showed no significant difference in bacteria count between control and CKD cats. Cats with stage 2 (P = .01) and stages 3 and 4 (P = .0006) CKD had significantly higher serum IS concentrations compared to control cats. No significant difference found between stage 2 and stages 3 and 4 CKD. The pCS concentrations were not significantly different between CKD cats and control cats.<br><br>Decreased fecal microbiome diversity and richness is associated with CKD in cats. Indoxyl sulfate concentration is significantly increased with CKD, and cats with stage 2 CKD may suffer from a similar uremic toxin burden as do cats with later stage disease.},
}
@article {pmid30561093,
year = {2018},
author = {Cherkasov, SV and Popova, LY and Vivtanenko, TV and Demina, RR and Khlopko, YA and Balkin, AS and Plotnikov, AO},
title = {Oral microbiomes in children with asthma and dental caries.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.13020},
pmid = {30561093},
issn = {1601-0825},
abstract = {OBJECTIVE: Recently, a significant association between dental caries and the severity of bronchial asthma in children has been revealed. This finding indicates a possible relationship between the oral microbiome and the pathogenesis of asthma. The purpose of our study was to estimate differences in the dental plaque microbiota of asthmatic children with and without dental caries by 16S rDNA sequencing.<br><br>MATERIAL AND METHODS: Dental plaque samples were obtained with a spoon excavator from the occlusal surface of one deciduous tooth (the second mandibular left molar in caries-free children and the most affected tooth in caries-affected children). Total DNA was extracted from dental plaque. DNA libraries were analysed by 16S rRNA gene sequencing on the MiSeq (Illumina) platform.<br><br>RESULTS: There were no significant differences in the composition of bacterial communities from both caries-affected and caries-free children with asthma. The 'caries-enriched' genus was Veillonella (Veillonellaceae, Selenomonadales, Negativicutes). Relative abundance of Neisseria was significantly higher in caries-free children with asthma (p<0.05).<br><br>CONCLUSIONS: The most significant difference in compared bacterial communities was a higher relative abundance of Veillonella in caries-affected plaques that suggests its involvement in pathogenesis of caries. Potential respiratory pathogens are present in oral cavity of both caries-affected and caries-free asthmatic children. This article is protected by copyright. All rights reserved.},
}
@article {pmid30561033,
year = {2018},
author = {Ai, L and Ren, Y and Li, Y and Chen, H and Qian, Y and Lu, S and Xu, A and Ren, L and Zhao, S and Chen, Z and Chen, YX and Xu, J and Fang, JY},
title = {Synbindin deficiency inhibits colon carcinogenesis by attenuating Wnt cascade and balancing gut microbiome.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.32074},
pmid = {30561033},
issn = {1097-0215},
abstract = {The molecular mechanisms that control the development of colorectal cancer (CRC) remain poorly defined. Here we show Synbindin promoted CRC oncogenesis by activating Wnt signaling and altering gut microbiome. Synbindin upregulation in human CRCs was associated with poor patient prognosis. Intestine-specific disruption of Synbindin balanced the disturbed gut microbiota and protected mice against tumor formation in the colitis-associated cancer (CAC) model. The protective role was compromised after gut microbiota depletion. In host, increased goblet cells and mucin2 expression, together with increased intestinal epithelial cells (IECs) apoptosis and decreased epithelial proliferation were observed. Further transcriptomic sequencing identified Wnt signaling a major regulatory node downstream of Synbindin. Combined molecular and cellular characterizations revealed that Synbindin confers Dishevelled-3 (DVL3)-based signalosome assembly and acts as a modular scaffold for DVL3 and Axin2 complex, orchestrating the intensity of Wnt signaling. These findings identify a critical role of Synbindin in gut microbiome composition and Wnt signaling activation in colorectal carcinogenesis, and highlight Synbindin as an adaptor protein with multifaceted roles. This article is protected by copyright. All rights reserved.},
}
@article {pmid30560755,
year = {2018},
author = {Seddik, H and Xu, L and Wang, Y and Mao, SY},
title = {A rapid shift to high-grain diet results in dynamic changes in rumen epimural microbiome in sheep.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {1-9},
doi = {10.1017/S1751731118003269},
pmid = {30560755},
issn = {1751-732X},
abstract = {The rapid shift to high-grain (HG) diets in ruminants can affect the function of the rumen epithelium, but the dynamic changes in the composition of the epithelium-associated (epimural) bacterial community in sheep still needs further investigation. Twenty male lambs were randomly allocated to four groups (n = 5). Animals of the first group received hay diet and represented a control group (CON). Simultaneously, animals in the other three groups (HG groups) were rapidly shifted to an HG diet (60% concentrate)which continued for 7 (HG7), 14 (HG14) and 28 (HG28) days, correspondingly. Results showed that ruminal pH dramatically decreased due to the rapid shift to the HG diet (P <0.001), while, the concentrations of butyrate (P <0.001), lactate (P = 0.001), valerate (P = 0.008) and total volatile fatty acids (P = 0.001) increased. Diversity estimators showed a dramatic decrease after the shift without recovering as the HG feeding continued. The principal coordinates analysis showed that CON group clustered separately from all HG groups with the presence of significant difference only between HG7 and HG28 (P = 0.034). The non-parametric multivariate analysis (npmv R-package) deduced that the primary significant differences in phyla and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt)-predicted Kyoto Encyclopedia of Genes and Genomes (KEGGs) was attributed mainly to the diet composition (P <0.001, P = 0.001) compared to its application period (P = 0.140, 0.545) which showed a significant effect only on the genus (P = 0.001) and the operational taxonomic units (OTUs) level (P = 0.011). The Kruskal-Wallis test deduced that six phyla showed a significant effect due to the shift in diet composition. At the genus level, HG feeding altered the abundance of 12 taxa, four of which showed a significant variation due to the duration of the HG diet application. Similarly, we found that 21 OTUs showed significant variations due to the duration of the HG diet application. Furthermore, the genes abundance predicted by PICRUSt revealed that the HG feeding significantly affected seven metabolic pathways identified in the KEGG. Particularly, the abundance of gene families associated with carbohydrates metabolism were significantly higher in HG feeding groups (P = 0.027). Collectively, these results revealed that the rapid transition to an HG diet causes dramatic alterations in ruminal fermentation and the composition and function of ruminal epithelium-associated microbiome in sheep, while, the duration of the HG diet application causes drastic alterations to the abundance of some species.},
}
@article {pmid30560450,
year = {2018},
author = {Meng, T and Wang, Q and Abbasi, P and Ma, Y},
title = {Deciphering differences in the chemical and microbial characteristics of healthy and Fusarium wilt-infected watermelon rhizosphere soils.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9564-6},
pmid = {30560450},
issn = {1432-0614},
support = {41701304//National Natural Science Foundation of China/ ; 2016M601756//Postdoctoral Science Foundation of Jiangsu Province (CN)/ ; 1701018B//Jiangsu Planned Projects for Postdoctoral Research Funds/ ; 2015CB150500//National Program on Key Basic Research Project of China/ ; },
abstract = {Plant health is determined by the comprehensive effect of soil physicochemical and biological properties. In this study, we compared the chemical properties and microbiomes of the rhizosphere soils of healthy, Fusarium oxysporum-infected, and dead watermelon plants and attempted to assess their potential roles in plant health and Fusarium wilt expression. The rhizosphere soils were collected from watermelon plants grown in a greenhouse under the same field management practices, and various soil microbial and chemical characteristics were analyzed. The rhizosphere soil of healthy plants had the lowest abundance of F. oxysporum and pH and the highest contents of ammonium (NH4+) and nitrate (NO3-). The relative content of hemicellulose was decreased in the rhizosphere soil of F. oxysporum-infected plants. The differences in soil microbial compositions among the watermelons at the three health statuses were obvious, and their microbiomes changed gradually along with plant health status. The microbiome in the rhizosphere soil of healthy plants had the highest relative abundances of potential antagonists and the lowest relative abundances of potential pathogens. The specific microbial composition together with some chemical properties of the rhizosphere soil of healthy plants might be responsible for inhibiting Fusarium wilt expression.},
}
@article {pmid30560340,
year = {2018},
author = {Qing, Y and Xie, H and Su, C and Wang, Y and Yu, Q and Pang, Q and Cui, F},
title = {Gut Microbiome, Short-Chain Fatty Acids, and Mucosa Injury in Young Adults with Human Immunodeficiency Virus Infection.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-018-5428-2},
pmid = {30560340},
issn = {1573-2568},
support = {81101231//National Natural Science Foundation of China/ ; 2017YSKY0001//Basic Scientific Research Projects of Sichuan Provincial Scientific Research Institutes/ ; },
abstract = {BACKGROUND: HIV progression is characterized by immune activation and microbial translocation from the gut. Short-chain fatty acids (SCFAs) are essential for gut homeostasis. Decreased intestinal SCFAs play a role in rapid HIV progression.<br><br>AIMS: To compare the SCFA profile, intestinal microbiome, and intestinal mucosal injury between patients with HIV (but not AIDS) and healthy controls.<br><br>METHODS: This was a prospective study of 15 patients without AIDS and 10 controls conducted between July 2016 and January 2017 at the Institute of Dermatology and Venereology (Sichuan Academy of Medical Sciences). Stool specimens were collected to analyze the microbiome and SCFAs. Blood I-FABP and D-lactate (gut injury markers) were measured as well as T cells in HIV-positive patients. Intestinal mucosa was observed by colonoscopy.<br><br>RESULTS: Rikenellaceae, Microbacteriaceae, Roseburia, Lachnospiraceae, Alistipes, and Ruminococcaceae were decreased, while Moraxellaceae and Psychrobacter were increased in HIV-positive patients. Butyric acid (p = 0.04) and valeric acid (p = 0.03) were reduced in HIV-positive patients. Colonoscopy revealed no visible damage in all subjects. There were no differences in I-FABP and D-lactate between groups. Butyric and valeric acids mainly positively correlated with Rikenellaceae, Ruminococcaceae, Alistipes, Roseburia, and Lachnospiraceae. CD8+ cells were positively correlated with Proteobacteria. CD4+ cells, and CD4/CD8 were negatively correlated with acetic acid. CD8+ cells were positively correlated with valeric acid.<br><br>CONCLUSION: The differences in the distribution of intestinal flora between HIV-infected and healthy individuals, especially some SCFAs, suggest that there is already a predisposition to intestinal mucosa damage in HIV-infected individuals.},
}
@article {pmid30559716,
year = {2018},
author = {Bhagavata Srinivasan, SP and Raipuria, M and Bahari, H and Kaakoush, NO and Morris, MJ},
title = {Impacts of Diet and Exercise on Maternal Gut Microbiota Are Transferred to Offspring.},
journal = {Frontiers in endocrinology},
volume = {9},
number = {},
pages = {716},
doi = {10.3389/fendo.2018.00716},
pmid = {30559716},
issn = {1664-2392},
abstract = {Background: It is well established that maternal exercise during pregnancy improves metabolic outcomes associated with obesity in mothers and offspring, however, its effects on the gut microbiota of both mother and offspring, are unknown. Here, we investigated whether wheel running exercise prior to and during pregnancy and prolonged feeding of an obesogenic diet were associated with changes in the gut microbiomes of Sprague-Dawley rat dams and their offspring. Female rats were fed either chow or obesogenic diet, and half of each diet group were given access to a running wheel 10 days before mating until delivery, while others remained sedentary. 16S rRNA gene amplicon sequencing was used to assess gut microbial communities in dams and their male and female offspring around the time of weaning. Results: Statistical analyses at the operational taxonomic unit (OTU) level revealed that maternal obesogenic diet decreased gut microbial alpha diversity and altered abundances of bacterial taxa previously associated with obesity such as Bacteroides and Blautia in dams, and their offspring of both sexes. Distance based linear modeling revealed that the relative abundances of Bacteroides OTUs were associated with adiposity measures in both dams and offspring. We identified no marked effects of maternal exercise on the gut microbiota of obesogenic diet dams or their offspring. In contrast, maternal exercise decreased gut microbial alpha diversity and altered the abundance of 88 microbial taxa in offspring of control dams. Thirty of these taxa were altered in a similar direction in offspring of sedentary obesogenic vs. control diet dams. In particular, the relative abundances of Oscillibacter OTUs were decreased in offspring of both exercised control dams and sedentary obesogenic diet dams, and associated with blood glucose concentrations and adiposity measures. Analyses of predicted bacterial metabolic pathways inferred decreased indole alkaloid biosynthesis in offspring of both obesogenic diet and exercised control dams. Conclusions: Our data suggest that maternal exercise prior to and during pregnancy resulted in gut dysbiosis in offspring of control dams. Importantly, alterations in the maternal gut microbiota by obesogenic diet or obesity were transferred to their offspring.},
}
@article {pmid30559439,
year = {2018},
author = {Wang, X and Li, Y and Chen, W and Shi, H and Eren, AM and Morozov, A and He, C and Luo, GZ and Pan, T},
title = {Transcriptome-wide reprogramming of N6-methyladenosine modification by the mouse microbiome.},
journal = {Cell research},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41422-018-0127-2},
pmid = {30559439},
issn = {1748-7838},
support = {K01 DK111764//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; RM1 HG008935//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; },
}
@article {pmid30559407,
year = {2018},
author = {Vatanen, T and Plichta, DR and Somani, J and Münch, PC and Arthur, TD and Hall, AB and Rudolf, S and Oakeley, EJ and Ke, X and Young, RA and Haiser, HJ and Kolde, R and Yassour, M and Luopajärvi, K and Siljander, H and Virtanen, SM and Ilonen, J and Uibo, R and Tillmann, V and Mokurov, S and Dorshakova, N and Porter, JA and McHardy, AC and Lähdesmäki, H and Vlamakis, H and Huttenhower, C and Knip, M and Xavier, RJ},
title = {Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0321-5},
pmid = {30559407},
issn = {2058-5276},
abstract = {The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.},
}
@article {pmid30559406,
year = {2018},
author = {Kintses, B and Méhi, O and Ari, E and Számel, M and Györkei, Á and Jangir, PK and Nagy, I and Pál, F and Fekete, G and Tengölics, R and Nyerges, Á and Likó, I and Bálint, A and Molnár, T and Bálint, B and Vásárhelyi, BM and Bustamante, M and Papp, B and Pál, C},
title = {Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0313-5},
pmid = {30559406},
issn = {2058-5276},
abstract = {The human gut microbiota has adapted to the presence of antimicrobial peptides (AMPs), which are ancient components of immune defence. Despite its medical importance, it has remained unclear whether AMP resistance genes in the gut microbiome are available for genetic exchange between bacterial species. Here, we show that AMP resistance and antibiotic resistance genes differ in their mobilization patterns and functional compatibilities with new bacterial hosts. First, whereas AMP resistance genes are widespread in the gut microbiome, their rate of horizontal transfer is lower than that of antibiotic resistance genes. Second, gut microbiota culturing and functional metagenomics have revealed that AMP resistance genes originating from phylogenetically distant bacteria have only a limited potential to confer resistance in Escherichia coli, an intrinsically susceptible species. Taken together, functional compatibility with the new bacterial host emerges as a key factor limiting the genetic exchange of AMP resistance genes. Finally, our results suggest that AMPs induce highly specific changes in the composition of the human microbiota, with implications for disease risks.},
}
@article {pmid30559359,
year = {2018},
author = {Schwartz, MH and Wang, H and Pan, JN and Clark, WC and Cui, S and Eckwahl, MJ and Pan, DW and Parisien, M and Owens, SM and Cheng, BL and Martinez, K and Xu, J and Chang, EB and Pan, T and Eren, AM},
title = {Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis.},
journal = {Nature communications},
volume = {9},
number = {1},
pages = {5353},
doi = {10.1038/s41467-018-07675-z},
pmid = {30559359},
issn = {2041-1723},
abstract = {Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat- and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.},
}
@article {pmid30559350,
year = {2018},
author = {},
title = {How snuggling close affects bats' microbiome.},
journal = {Nature},
volume = {564},
number = {7736},
pages = {304},
doi = {10.1038/d41586-018-07706-1},
pmid = {30559350},
issn = {1476-4687},
}
@article {pmid30559213,
year = {2018},
author = {Tedijanto, C and Olesen, SW and Grad, YH and Lipsitch, M},
title = {Estimating the proportion of bystander selection for antibiotic resistance among potentially pathogenic bacterial flora.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1810840115},
pmid = {30559213},
issn = {1091-6490},
abstract = {Bystander selection-the selective pressure for resistance exerted by antibiotics on microbes that are not the target pathogen of treatment-is critical to understanding the total impact of broad-spectrum antibiotic use on pathogenic bacterial species that are often carried asymptomatically. However, to our knowledge, this effect has never been quantified. We quantify bystander selection for resistance for a range of clinically relevant antibiotic-species pairs as the proportion of all antibiotic exposures received by a species for conditions in which that species was not the causative pathogen (&quot;proportion of bystander exposures&quot;). Data sources include the 2010-2011 National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey, the Human Microbiome Project, and additional carriage and etiological data from existing literature. For outpatient prescribing in the United States, we find that this proportion over all included antibiotic classes is over 80% for eight of nine organisms of interest. Low proportions of bystander exposure are often associated with infrequent bacterial carriage or concentrated prescribing of a particular antibiotic for conditions caused by the species of interest. Applying our results, we roughly estimate that pneumococcal conjugate vaccination programs result in nearly the same proportional reduction in total antibiotic exposures of Streptococcus pneumoniae, Staphylococcus aureus, and Escherichia coli, despite the latter two organisms not being targeted by the vaccine. These results underscore the importance of considering antibiotic exposures of bystanders, in addition to the target pathogen, in measuring the impact of antibiotic resistance interventions.},
}
@article {pmid30559181,
year = {2018},
author = {Baker, SJ and Payne, DJ and Rappuoli, R and De Gregorio, E},
title = {Technologies to address antimicrobial resistance.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1717160115},
pmid = {30559181},
issn = {1091-6490},
abstract = {Bacterial infections have been traditionally controlled by antibiotics and vaccines, and these approaches have greatly improved health and longevity. However, multiple stakeholders are declaring that the lack of new interventions is putting our ability to prevent and treat bacterial infections at risk. Vaccine and antibiotic approaches still have the potential to address this threat. Innovative vaccine technologies, such as reverse vaccinology, novel adjuvants, and rationally designed bacterial outer membrane vesicles, together with progress in polysaccharide conjugation and antigen design, have the potential to boost the development of vaccines targeting several classes of multidrug-resistant bacteria. Furthermore, new approaches to deliver small-molecule antibacterials into bacteria, such as hijacking active uptake pathways and potentiator approaches, along with a focus on alternative modalities, such as targeting host factors, blocking bacterial virulence factors, monoclonal antibodies, and microbiome interventions, all have potential. Both vaccines and antibacterial approaches are needed to tackle the global challenge of antimicrobial resistance (AMR), and both areas have the underpinning science to address this need. However, a concerted research agenda and rethinking of the value society puts on interventions that save lives, by preventing or treating life-threatening bacterial infections, are needed to bring these ideas to fruition.},
}
@article {pmid30559176,
year = {2018},
author = {Relman, DA and Lipsitch, M},
title = {Microbiome as a tool and a target in the effort to address antimicrobial resistance.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1717163115},
pmid = {30559176},
issn = {1091-6490},
abstract = {Reciprocal, intimate relationships between the human microbiome and the host immune system are shaped by past microbial encounters and prepare the host for future ones. Antibiotics and other antimicrobials leave their mark on both the microbiome and host immunity. Antimicrobials alter the structure of the microbiota, expand the host-specific pool of antimicrobial-resistance genes and organisms, degrade the protective effects of the microbiota against invasion by pathogens, and may impair vaccine efficacy. Through these effects on the microbiome they may affect immune responses. Vaccines that exert protective or therapeutic effects against pathogens may reduce the use of antimicrobials, the development and spread of antimicrobial resistance, and the harmful impacts of these drugs on the microbiome. Other strategies involving manipulation of the microbiome to deplete antibiotic-resistant organisms or to enhance immune responses to vaccines may prove valuable in addressing antimicrobial resistance as well. This article describes the intersections of immunity, microbiome and antimicrobial exposure, and the use of vaccines and other alternative strategies for the control and management of antimicrobial resistance.},
}
@article {pmid30559036,
year = {2018},
author = {Freitas, RC and Marques, HIF and Silva, MACD and Cavalett, A and Odisi, EJ and Silva, BLD and Montemor, JE and Toyofuku, T and Kato, C and Fujikura, K and Kitazato, H and Lima, AOS},
title = {Evidence of selective pressure in whale fall microbiome proteins and its potential application to industry.},
journal = {Marine genomics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.margen.2018.11.004},
pmid = {30559036},
issn = {1876-7478},
abstract = {The present study addresses the microbiome of the first whale fall (YOKO 16) that has been described in the deep sea in the southern Atlantic Ocean (São Paulo Plateau; 4204 m depth), in terms of its metabolic uniqueness. Sets of ten thousand protein sequences from YOKO 16 and 29 public domain metagenomes (SRA and GenBank databases) that represent various marine, terrestrial and gut-associated microbial communities were analyzed. The determination of protein functionality, based on the KAAS server, indicated that the YOKO 16 microbiome has industrially-relevant proteins, such as proteases and lipases, that have low similarity (~50%) with previously-described enzymes. The amino acid usage in the YOKO 16 protein sequences (based on blastp and Clustal analysis) revealed a pattern of preference similar to that of extremophiles, with an increased usage of polar, charged and acidic amino acids and a decreased usage of nonpolar residues. We concluded that the targeted microbiome is of potential biotechnological use, which justifies the allocation of resources for the discovery of enzymes in deep-sea whale fall communities.},
}
@article {pmid30558682,
year = {2018},
author = {Sirová, D and Bárta, J and Šimek, K and Posch, T and Pech, J and Stone, J and Borovec, J and Adamec, L and Vrba, J},
title = {Hunters or farmers? Microbiome characteristics help elucidate the diet composition in an aquatic carnivorous plant.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {225},
doi = {10.1186/s40168-018-0600-7},
pmid = {30558682},
issn = {2049-2618},
support = {P504-17-10493S//Grantová Agentura České Republiky/ ; P504/11/0783//Grantová Agentura České Republiky/ ; RVO 67985939//Grantová Agentura České Republiky/ ; },
abstract = {BACKGROUND: Utricularia are rootless aquatic carnivorous plants which have recently attracted the attention of researchers due to the peculiarities of their miniaturized genomes. Here, we focus on a novel aspect of Utricularia ecophysiology-the interactions with and within the complex communities of microorganisms colonizing their traps and external surfaces.<br><br>RESULTS: Bacteria, fungi, algae, and protozoa inhabit the miniature ecosystem of the Utricularia trap lumen and are involved in the regeneration of nutrients from complex organic matter. By combining molecular methods, microscopy, and other approaches to assess the trap-associated microbial community structure, diversity, function, as well as the nutrient turn-over potential of bacterivory, we gained insight into the nutrient acquisition strategies of the Utricularia hosts.<br><br>CONCLUSIONS: We conclude that Utricularia traps can, in terms of their ecophysiological function, be compared to microbial cultivators or farms, which center around complex microbial consortia acting synergistically to convert complex organic matter, often of algal origin, into a source of utilizable nutrients for the plants.},
}
@article {pmid30558669,
year = {2018},
author = {Deshpande, NP and Riordan, SM and Castaño-Rodríguez, N and Wilkins, MR and Kaakoush, NO},
title = {Signatures within the esophageal microbiome are associated with host genetics, age, and disease.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {227},
doi = {10.1186/s40168-018-0611-4},
pmid = {30558669},
issn = {2049-2618},
support = {15/CDF/1-11//Cancer Institute NSW/ ; APP1111461//National Health and Medical Research Council/ ; },
abstract = {BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host. Here, the esophageal microbiomes of 106 prospectively recruited patients were assessed using 16S rRNA and 18S rRNA amplicon sequencing as well as shotgun sequencing, and associations with age, gender, proton pump inhibitor use, host genetics, and disease were tested.<br><br>RESULTS: The esophageal microbiome was found to cluster into functionally distinct community types (esotypes) defined by the relative abundances of Streptococcus and Prevotella. While age was found to be a significant factor driving microbiome composition, bacterial signatures and functions such as enrichment with Gram-negative oral-associated bacteria and microbial lactic acid production were associated with the early stages of the esophageal adenocarcinoma cascade. Non-bacterial microbes such as archaea, Candida spp., and bacteriophages were also identified in low abundance in the esophageal microbiome. Specific host SNPs in NOTCH2, STEAP2-AS1, and NREP were associated with the composition of the esophageal microbiome in our cohort.<br><br>CONCLUSIONS: This study provides the most comprehensive assessment of the esophageal microbiome to date and identifies novel signatures and host markers that can be investigated further in the context of esophageal adenocarcinoma development.},
}
@article {pmid30558668,
year = {2018},
author = {Davis, NM and Proctor, DM and Holmes, SP and Relman, DA and Callahan, BJ},
title = {Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {226},
doi = {10.1186/s40168-018-0605-2},
pmid = {30558668},
issn = {2049-2618},
support = {R01 DE023113//National Institute of Dental and Craniofacial Research/ ; R01 AI112401//National Institute of Allergy and Infectious Diseases/ ; },
abstract = {BACKGROUND: The accuracy of microbial community surveys based on marker-gene and metagenomic sequencing (MGS) suffers from the presence of contaminants-DNA sequences not truly present in the sample. Contaminants come from various sources, including reagents. Appropriate laboratory practices can reduce contamination, but do not eliminate it. Here we introduce decontam (https://github.com/benjjneb/decontam), an open-source R package that implements a statistical classification procedure that identifies contaminants in MGS data based on two widely reproduced patterns: contaminants appear at higher frequencies in low-concentration samples and are often found in negative controls.<br><br>RESULTS: Decontam classified amplicon sequence variants (ASVs) in a human oral dataset consistently with prior microscopic observations of the microbial taxa inhabiting that environment and previous reports of contaminant taxa. In metagenomics and marker-gene measurements of a dilution series, decontam substantially reduced technical variation arising from different sequencing protocols. The application of decontam to two recently published datasets corroborated and extended their conclusions that little evidence existed for an indigenous placenta microbiome and that some low-frequency taxa seemingly associated with preterm birth were contaminants.<br><br>CONCLUSIONS: Decontam improves the quality of metagenomic and marker-gene sequencing by identifying and removing contaminant DNA sequences. Decontam integrates easily with existing MGS workflows and allows researchers to generate more accurate profiles of microbial communities at little to no additional cost.},
}
@article {pmid30558657,
year = {2018},
author = {Cervantes-Echeverría, M and Equihua-Medina, E and Cornejo-Granados, F and Hernández-Reyna, A and Sánchez, F and López-Contreras, BE and Canizales-Quinteros, S and Ochoa-Leyva, A},
title = {Whole-genome of Mexican-crAssphage isolated from the human gut microbiome.},
journal = {BMC research notes},
volume = {11},
number = {1},
pages = {902},
doi = {10.1186/s13104-018-4010-5},
pmid = {30558657},
issn = {1756-0500},
support = {SALUD-2014-C01-234188//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {OBJECTIVES: crAssphage is a newly found phage described as the most abundant virus in the human gut microbiome. The majority of the crAssphage proteins are unknown in sequences databases, and its pathogenicity and epidemiology in humans are yet unclear. Hence, being one of the most abundant phages in the human gut microbiome more investigation at the genomic level is necessary to improve our understanding, especially in the Latin American population.<br><br>DATA DESCRIPTION: In this article, we provide the whole genome of a crAssphage isolated from the human gut microbiome of the Mexican population, which was named Mexican-crAssphage. The genome consists of 96,283 bp, G+C content of 29.24% and 87 coding sequences. Notably, we did not find any transfer RNA genes in the genome sequence. We also sequenced viral-like enriched particles from 28 fecal samples, and we detected the presence of the Mexican-crAssphage genome in 8 samples (28.5%). To our knowledge, our data is the first whole genome report of the crAssphage isolated from the Latin American Population and provides valuable information for the experimental characterization of the most abundant human gut bacteriophage. The whole genome shotgun project of the Mexican-crAssphage is available at DDBJ/ENA/GenBank under the GenBank MK069403.},
}
@article {pmid30558599,
year = {2018},
author = {Siwek, M and Slawinska, A and Stadnicka, K and Bogucka, J and Dunislawska, A and Bednarczyk, M},
title = {Prebiotics and synbiotics - in ovo delivery for improved lifespan condition in chicken.},
journal = {BMC veterinary research},
volume = {14},
number = {1},
pages = {402},
doi = {10.1186/s12917-018-1738-z},
pmid = {30558599},
issn = {1746-6148},
support = {UMO-2013/11/B/NZ9/00783//Narodowe Centrum Nauki/ ; #RBSI14WZCL//MIUR Rome Italy/ ; },
abstract = {Commercially produced chickens have become key food-producing animals in the global food system. The scale of production in industrial settings has changed management systems to a point now very far from traditional methods. During the perinatal period, newly hatched chicks undergo processing, vaccination and transportation, which introduces a gap in access to feed and water. This gap, referred to as the hatching window, dampens the potential for microflora inoculation and as such, prevents proper microbiome, gastrointestinal system and innate immunity development. As a consequence, the industrial production of chickens with a poor microbial profile leads to enteric microbial infestation and infectious disease outbreaks, which became even more prevalent after the withdrawal of antibiotic growth promoters on many world markets (e.g., the EU).This review presents the rationale, methodology and life-long effects of in ovo stimulation of chicken microflora. In ovo stimulation provides efficient embryonic microbiome colonization with commensal microflora during the perinatal period. A carefully selected bioactive formulation (prebiotics, probiotics alone or combined into synbiotics) is delivered into the air cell of the egg on day 12 of egg incubation. The prebiotic penetrates the outer and inner egg membranes and stimulates development on the innate microflora in the embryonic guts. Probiotics are available after the mechanical breakage of the shell membranes by the chick's beak at the beginning of hatching (day 19). The intestinal microflora after in ovo stimulation is potent enough for competitive exclusion and programs the lifespan condition. We present the effects of different combinations of prebiotic and probiotic delivered in ovo on day 12 of egg incubation on microflora, growth traits, feed efficiency, intestinal morphology, meat microstructure and quality, immune system development, physiological characteristics and the transcriptome of the broiler chickens.We discuss the differences between in ovo stimulation (day 12 of egg incubation) and in ovo feeding (days 17-18 of egg incubation) and speculate about possible future developments in this field. In summary, decades of research on in ovo stimulation and the lifelong effects support this method as efficient programming of lifespan conditions in commercially raised chickens.},
}
@article {pmid30558589,
year = {2018},
author = {Neumann, G and Wall, R and Rangel, I and Marques, TM and Repsilber, D},
title = {Qualitative modelling of the interplay of inflammatory status and butyrate in the human gut: a hypotheses about robust bi-stability.},
journal = {BMC systems biology},
volume = {12},
number = {1},
pages = {144},
doi = {10.1186/s12918-018-0667-6},
pmid = {30558589},
issn = {1752-0509},
support = {20110225//Swedish Knowledge Foundation (KK Stiftelse)/ ; },
abstract = {BACKGROUND: Gut microbiota interacts with the human gut in multiple ways. Microbiota composition is altered in inflamed gut conditions. Likewise, certain microbial fermentation products as well as the lipopolysaccharides of the outer membrane are examples of microbial products with opposing influences on gut epithelium inflammation status. This system of intricate interactions is known to play a core role in human gut inflammatory diseases. Here, we present and analyse a simplified model of bidirectional interaction between the microbiota and the host: in focus is butyrate as an example for a bacterial fermentation product with anti-inflammatory properties.<br><br>RESULTS: We build a dynamical model based on an existing model of inflammatory regulation in gut epithelial cells. Our model introduces both butyrate as a bacterial product which counteracts inflammation, as well as bacterial LPS as a pro-inflammatory bacterial product. Moreover, we propose an extension of this model that also includes a feedback interaction towards bacterial composition. The analysis of these dynamical models shows robust bi-stability driven by butyrate concentrations in the gut. The extended model hints towards a further possible enforcement of the observed bi-stability via alteration of gut bacterial composition. A theoretical perspective on the stability of the described switch-like character is discussed.<br><br>CONCLUSIONS: Interpreting the results of this qualitative model allows formulating hypotheses about the switch-like character of inflammatory regulation in the gut epithelium, involving bacterial products as constitutive parts of the system. We also speculate about possible explanations for observed bimodal distributions in bacterial compositions in the human gut. The switch-like behaviour of the system proved to be mostly independent of parameter choices. Further implications of the qualitative character of our modeling approach for the robustness of the proposed hypotheses are discussed, as well as the pronounced role of butyrate compared to other inflammatory regulators, especially LPS, NF- κB and cytokines.},
}
@article {pmid30557670,
year = {2018},
author = {Lobach, AR and Roberts, A and Rowland, IR},
title = {Assessing the in vivo data on low/no-calorie sweeteners and the gut microbiota.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fct.2018.12.005},
pmid = {30557670},
issn = {1873-6351},
abstract = {Low/no-calorie sweeteners (LNCS) are continually under the spotlight in terms of their safety and benefits; in 2014 a study was published linking LNCS to an enhanced risk of glucose intolerance through modulation of the gut microbiota. In response, an in-depth review of the literature was undertaken to evaluate the major contributors to potential changes in the gut microbiota and their corresponding sequelae, and to determine if consuming LNCS (e.g., acesulfame K, aspartame, cyclamate, neotame, saccharin, sucralose, steviol glycosides) contributes to changes in the microbiome based on the data reported in human and animal studies. A few rodent studies with saccharin have reported changes in the gut microbiome, but primarily at high doses that bear no relevance to human consumption. This and other studies suggesting an effect of LNCS on the gut microbiota were found to show no evidence of an actual adverse effect on human health. The sum of the data provides clear evidence that changes in the diet unrelated to LNCS consumption are likely the major determinants of change in gut microbiota numbers and phyla, confirming the viewpoint supported by all the major international food safety and health regulatory authorities that LNCS are safe at currently approved levels.},
}
@article {pmid30557659,
year = {2018},
author = {Myers, SA and Gobejishvili, L and Ohri, SS and Garrett Wilson, C and Andres, KR and Riegler, AS and Donde, H and Joshi-Barve, S and Barve, S and Whittemore, SR},
title = {Following spinal cord injury, PDE4B drives an acute, local inflammatory response and a chronic, systemic response exacerbated by gut dysbiosis and endotoxemia.},
journal = {Neurobiology of disease},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbd.2018.12.008},
pmid = {30557659},
issn = {1095-953X},
abstract = {Emerging evidence links changes in the gut microbiome and intestinal barrier function to alterations in CNS function. We examined the role of endotoxin-responsive, cAMP-specific, Pde4 subfamily b (Pde4b) enzyme in gut dysbiosis induced neuro-inflammation and white matter loss following spinal cord injury (SCI). Using a thoracic contusion model in C57Bl/6 wild type female mice, SCI led to significant shifts in the gut bacterial community including an increase in the phylum Proteobacteria, which consists of endotoxin-harboring, gram-negative bacteria. This was accompanied by increased systemic inflammatory marker, soluble CD14, along with markers of the endoplasmic reticulum stress response (ERSR) and inflammation in the SCI epicenter. Deletion of Pde4b reduced epicenter expression of markers for the ERSR and inflammation, at both acute and chronic time points post-SCI. Correspondingly, expression of oligodendrocyte mRNAs increased. Within the injury penumbra, inflammatory protein markers of activated astrocytes (GFAP), macrophage/microglia (CD11b, Iba1), and the proinflammatory mediator Cox2, were decreased in Pde4b-/- mice. The absence of Pde4b improved white matter sparing and recovery of hindlimb locomotion following injury. Importantly, SCI-induced gut dysbiosis, bacterial overgrowth and endotoxemia were also prevented in Pde4b-/- mice. Taken together, these findings indicate that PDE4B plays an important role in the development of acute and chronic inflammatory response and consequent recovery following SCI.},
}
@article {pmid30557653,
year = {2018},
author = {MacLaren, R and Radcliffe, RA and Van Matre, ET and Robertson, CE and Ir, D and Frank, DN},
title = {The Acute Influence of Acid Suppression with Esomeprazole on Gastrointestinal Microbiota and Brain Gene Expression Profiles in a Murine Model of Restraint Stress.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2018.11.048},
pmid = {30557653},
issn = {1873-7544},
abstract = {The central nervous system (CNS) and gastrointestinal tract (GIT) are linked through neuro-endocrine and humoral pathways. Critically ill patients suffer severe physical and emotional stress and frequently receive acid suppressants; however, stress and acid suppression may alter GIT microbiota. This study evaluated the effects of acid suppression on the GIT microbiota and genome-wide expression of brain-specific genes in a murine model of restraint stress. Twenty-four male C57BL/6J mice were randomly assigned to three days of restraint stress by hypothermic immobilization or control environment for three hours daily and either esomeprazole 2 mg/kg or saline by intraperitoneal injection daily. Bacterial communities associated with the stomach, ileum, cecum, and mid-colon were determined by broad-range 16S rRNA gene sequencing, while RNA-sequencing assessed mRNA expression in the hippocampus. Both stress (p<0.001) and esomeprazole (p=0.006) had significant, independent effects on the composition of stomach microbiota. Stress had no impact on the hippocampus but the addition of esomeprazole induced differential expression of 124 genes, many of which are involved in cognitive and behavior pathways. Gene expression was correlated with the abundances of multiple microbial families. Acute stress has region-specific effects on the distribution of GIT commensal bacteria which is heightened with acid suppression. Several key biological processes in the hippocampus that are needed for neurocognition are affected by dysbiosis caused by acid suppression during stress. Further studies should evaluate associations between microbiota, host gene expression, the abundance of CNS neurocognitive modulators, and their impact on cognition and behavior.},
}
@article {pmid30557528,
year = {2018},
author = {You, Y and Liang, D and Wei, R and Li, M and Li, Y and Wang, J and Wang, X and Zheng, X and Jia, W and Chen, T},
title = {Evaluation of metabolite-microbe correlation detection methods.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ab.2018.12.008},
pmid = {30557528},
issn = {1096-0309},
abstract = {Different correlation detection methods have been specifically designed for the microbiome data analysis considering the compositional data structure and different sequencing depths. Along with the speedy development of omics studies, there is an increasing interest in discovering the biological associations between microbes and host metabolites. This raises the need of finding proper statistical methods that facilitate the correlation analysis across different omics studies. Here, we comprehensively evaluated six different correlation methods, i.e., Pearson correlation, Spearman correlation, Sparse Correlations for Compositional data (SparCC), Correlation inference for Compositional data through Lasso (CCLasso), Mutual Information Coefficient (MIC), and Cosine similarity methods, for the correlations detection between microbes and metabolites. Three simulated and two real-world data sets (from public databases and our lab) were used to examine the performance of each method regarding its specificity, sensitivity, similarity, accuracy, and stability with different sparsity. Our results indicate that although each method had its own pros and cons in different scenarios, Spearman correlation and MIC outperform the others with their overall performances. A strategic guidance was also proposed for the correlation analysis between microbe and metabolite.},
}
@article {pmid30557447,
year = {2018},
author = {Megat Mohd Azlan, PI and Chin, SF and Low, TY and Hui-Min, N and Jamal, R},
title = {Analysing the Secretome of Gut Microbiota as the Next Strategy For Early Detection of Colorectal Cancer.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e1800176},
doi = {10.1002/pmic.201800176},
pmid = {30557447},
issn = {1615-9861},
abstract = {Dysbiosis of gut microbiome can contribute to inflammation, and subsequently initiation and progression of colorectal cancer (CRC). Throughout these stages, various proteins and metabolites are secreted to the external environment by microorganisms or the hosts themselves. Studying these proteins may help enhance our understanding of the host-microorganism relationship or they may even serve as useful biomarkers for CRC. However, secretomic studies of gut microbiome of CRC patients, until now, are scarcely performed. In this viewpoint article, we focus on the roles of gut microbiome in CRC, highlight the current findings on CRC secretome and address the emerging challenges and strategies to drive forward this area of research. This article is protected by copyright. All rights reserved.},
}
@article {pmid30556840,
year = {2018},
author = {Ribaldone, DG and Vernero, M and Pellicano, R},
title = {Is microbiome a target for the management of allergy associated diseases in children?.},
journal = {European review for medical and pharmacological sciences},
volume = {22},
number = {23},
pages = {8061-8062},
pmid = {30556840},
issn = {2284-0729},
}
@article {pmid30556775,
year = {2018},
author = {Burns, MB and Blekhman, R},
title = {Integrating tumor genomics into studies of the microbiome in colorectal cancer.},
journal = {Gut microbes},
volume = {},
number = {},
pages = {1-6},
doi = {10.1080/19490976.2018.1549421},
pmid = {30556775},
issn = {1949-0984},
abstract = {Although the gut microbiome has been linked to colorectal cancer (CRC) development, associations of microbial taxa with CRC status are often inconsistent across studies. We have recently shown that tumor genomics, a factor that is rarely incorporated in analyses of the CRC microbiome, has a strong effect on the composition of the microbiota. Here, we discuss these results in the wider context of studies characterizing interaction between host genetics and the microbiome, and describe the implications of our findings for understanding the role of the microbiome in CRC.},
}
@article {pmid30556145,
year = {2018},
author = {Khan, R and Bril, F and Cusi, K and Newsome, PN},
title = {Modulation of Insulin Resistance in NAFLD.},
journal = {Hepatology (Baltimore, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/hep.30429},
pmid = {30556145},
issn = {1527-3350},
abstract = {Non-alcoholic fatty liver disease (NAFLD) has an estimated prevalence of 25% in the general population, and cirrhosis secondary to Non-Alcoholic Steatohepatitis (NASH) is predicted to become the leading cause of liver transplantation and yet there is a lack of effective licensed treatments. There is a close relationship between insulin resistance and NAFLD, with the prevalence of NAFLD being five-fold higher in patients with diabetes compared to patients without. Insulin resistance is implicated both in the pathogenesis of NAFLD and in disease progression from steatosis to NASH. Thus modulation of insulin resistance represents a potential strategy for NAFLD treatment. This review highlights key proposed mechanisms linking insulin resistance and NAFLD, such as changes in rates of adipose tissue lipolysis and de novo lipogenesis, impaired mitochondrial fatty acid oxidation, changes in fat distribution, alterations in the gut microbiome, and alterations in levels of adipokines and cytokines. Further, it goes on to discuss the main pharmacological strategies used to treat insulin resistance in patients with NAFLD, and their efficacy based on recently published experimental and clinical data. These include (biguanides, glucagon-like peptide 1 receptor (GLP-1) agonists, Dipeptidyl peptidase 4 (DPP-4) inhibitors, Peroxisome Proliferator-Activated Receptor (PPAR- γ/ α/δ) agonists, Sodium Glucose Cotransporter (SGLT2) inhibitors and Farnesoid X receptor (FXR) agonists), with further novel treatments on the horizon. Ideally treatment would improve insulin resistance, reduce cardiovascular risk and produce demonstrable improvements in NASH histology - this is likely to be achieved with a combinatorial approach. This article is protected by copyright. All rights reserved.},
}
@article {pmid30555804,
year = {2018},
author = {Chen, Y and Guo, J and Shi, D and Fang, D and Chen, C and Li, L},
title = {Ascitic Bacterial Composition Is Associated With Clinical Outcomes in Cirrhotic Patients With Culture-Negative and Non-neutrocytic Ascites.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {420},
doi = {10.3389/fcimb.2018.00420},
pmid = {30555804},
issn = {2235-2988},
abstract = {Ascites bacterial burden is associated with poor clinical outcomes in patients with end-stage liver disease. However, the impact of ascitic microbial composition on clinical course was still not clear. In this study, the ascitic microbiota composition of 100 cirrhotic patients with culture-negative and non-neutrocytic ascites were researched with 16S rRNA pyrosequencing and enterotype-like cluster analysis. Results: By characterizing the ascitic microbial composition, two distinct microbial clusters were observed, Cluster 1 (86 patients) and Cluster 2 (14 patients). Cluster 1 showed lower microbial richness than Cluster 2. At the phylum level, Cluster 1 had greater abundance of Bacteroidetes and Firmicutes, but less abundance of Proteobacteria and Actinobacteria than Cluster 2. At the family level, family Bacteroidales S24-7 group, Prevotellaceae, Lachnospiraceae, Lactobacillaceae, Rikenellaceae, and Vibrionaceae were found over-represented in Cluster 1. And family Acetobacteraceae, Erysipelotrichaceae, Rickettsiaceae, and Streptococcaceae were found enriched in Cluster 2. The levels of plasma cytokine IL-17A, IL-7, and PDGF-BB were found significantly higher in Cluster 1 than in Cluster 2. There were four OTUs closely correlated with plasma cytokines, which were OTU 140 and OTU 271 (both from Bacteroidales S24-7 group), OTU 68 (Veillonellaceae), and OTU 53 (Helicobacteraceae). Patients from Cluster 1 showed significant higher short-term mortality than patients from Cluster 2. Conclusion: Our study demonstrated that the microbial composition of culture-negative and non-neutrocytic ascites in cirrhotic patients is associated with short-term clinical outcomes. The results here offer a rational for the identification of patients with high risk, and provide references for selective use of prophylactic methods.},
}
@article {pmid30555774,
year = {2018},
author = {Ebersole, JL and Dawson, DA and Emecen Huja, P and Pandruvada, S and Basu, A and Nguyen, L and Zhang, Y and Gonzalez, OA},
title = {Age and Periodontal Health - Immunological View.},
journal = {Current oral health reports},
volume = {5},
number = {4},
pages = {229-241},
doi = {10.1007/s40496-018-0202-2},
pmid = {30555774},
issn = {2196-3002},
abstract = {Purpose of the Review: Aging clearly impacts a wide array of systems, in particular the breadth of the immune system leading to immunosenescence, altered immunoactivation, and coincident inflammaging processes. The net result of these changes leads to increased susceptibility to infections, increased neoplastic occurrences, and elevated frequency of autoimmune diseases with aging. However, as the bacteria in the oral microbiome that contribute to the chronic infection of periodontitis is acquired earlier in life, the characteristics of the innate and adaptive immune systems to regulate these members of the autochthonous microbiota across the lifespan remains ill defined.<br><br>Recent Findings: Clear data demonstrate that both cells and molecules of the innate and adaptive immune response are adversely impacted by aging, including in the oral cavity, yielding a reasonable tenet that the increased periodontitis noted in aging populations is reflective of the age-associated immune dysregulation. Additionally, this facet of host-microbe interactions and disease needs to accommodate the population variation in disease onset and progression, which may also reflect an accumulation of environmental stressors and/or decreased protective nutrients that could function at the gene level (ie. epigenetic) or translational level for production and secretion of immune system molecules.<br><br>Summary: Finally, the majority of studies of aging and periodontitis have emphasized the increased prevalence/severity of disease with aging, all based upon chronological age. However, evolving areas of study focusing on &quot;biological aging&quot; to help account for population variation in disease expression, may suggest that chronic periodontitis represents a co-morbidity that contributes to &quot;gerovulnerability&quot; within the population.},
}
@article {pmid30555669,
year = {2018},
author = {Liu, F and Horton-Sparks, K and Hull, V and Li, RW and Martínez-Cerdeño, V},
title = {The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism.},
journal = {Molecular autism},
volume = {9},
number = {},
pages = {61},
doi = {10.1186/s13229-018-0251-3},
pmid = {30555669},
issn = {2040-2392},
abstract = {Background: Gut microbiota has the capacity to impact the regular function of the brain, which can in turn affect the composition of microbiota. Autism spectrum disorder (ASD) patients suffer from gastrointestinal problems and experience changes in gut microbiota; however, it is not yet clear whether the change in the microbiota associated with ASD is a cause or a consequence of the disease.<br><br>Methods: We have investigated the species richness and microbial composition in a valproic acid (VPA)-induced rat model autism. Fecal samples from the rectum were collected at necropsy, microbial total DNA was extracted, 16 rRNA genes sequenced using Illumina, and the global microbial co-occurrence network was constructed using a random matrix theory-based pipeline. Collected rat microbiome data were compared to available data derived from cases of autism.<br><br>Results: We found that VPA administration during pregnancy reduced fecal microbial richness, changed the gut microbial composition, and altered the metabolite potential of the fecal microbial community in a pattern similar to that seen in patients with ASD. However, the global network property and network composition as well as microbial co-occurrence patterns were largely preserved in the offspring of rats exposed to prenatal administration of VPA.<br><br>Conclusions: Our data on the microbiota of the VPA rat model of autism indicate that this model, in addition to behaviorally and anatomically mimicking the autistic brain as previously shown, also mimics the microbiome features of autism, making it one of the best-suited rodent models for the study of autism and ASD.},
}
@article {pmid30555521,
year = {2018},
author = {Jia, N and Lin, X and Ma, S and Ge, S and Mu, S and Yang, C and Shi, S and Gao, L and Xu, J and Bo, T and Zhao, J},
title = {Amelioration of hepatic steatosis is associated with modulation of gut microbiota and suppression of hepatic miR-34a in Gynostemma pentaphylla (Thunb.) Makino treated mice.},
journal = {Nutrition &amp; metabolism},
volume = {15},
number = {},
pages = {86},
doi = {10.1186/s12986-018-0323-6},
pmid = {30555521},
issn = {1743-7075},
abstract = {Background: Non-alcoholic fatty liver disease (NAFLD) is a chronic and progressive liver disease with an increased risk of morbidity and mortality. However, so far no specific pharmacotherapy has been approved. Gynostemma pentaphylla (Thunb.) Makino (GP) is a traditional Chinese medicine that is widely used against hyperlipemia as well as hyperglycemia. This study aims to evaluate the effect of GP on NAFLD and explore the possible mechanism.<br><br>Methods: High-fat-diet induced NAFLD mice model were orally administrated with GP at dose of 11.7 g/kg or equivalent volume of distilled water once a day for 16 weeks. Body weight, food intake and energy expenditure were assessed to evaluate the general condition of mice. The triglycerides, total cholesterol content in the liver and liver histopathology, serum lipid profile and serum insulin level, fecal microbiome, hepatic microRNAs and relative target genes were analyzed.<br><br>Results: Mice in GP treatment group displayed improved hepatic triglycerides content with lower lipid droplet in hepatocyte and NAFLD activity score. Besides, GP treatment altered the composition of gut microbiota and the relative abundance of some of the key components that are implicated in metabolic disorders, especially phylum Firmicutes (Eubacterium, Blautia, Clostridium and Lactobacillus). Several hepatic microRNAs were downregulated by GP treatment such as miR-130a, miR-34a, miR-29a, miR-199a, among which the expression miR-34a was altered by more than four-fold compared to that of HFD group (3:14). The correlation analysis showed that miR-34a was strongly related to the change of gut microbiota especially phylum Firmicutes (R = 0.796). Additionally, the target genes of miR-34a (HNF4α, PPARα and PPARα) were restored by GP both in mRNA and protein levels.<br><br>Conclusion: Our results suggested that GP modulated the gut microbiota and suppressed hepatic miR-34a, which was associated with the amelioration of hepatic steatosis.},
}
@article {pmid30555453,
year = {2018},
author = {Cernava, T and Vasfiu, Q and Erlacher, A and Aschenbrenner, IA and Francesconi, K and Grube, M and Berg, G},
title = {Adaptions of Lichen Microbiota Functioning Under Persistent Exposure to Arsenic Contamination.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2959},
doi = {10.3389/fmicb.2018.02959},
pmid = {30555453},
issn = {1664-302X},
abstract = {Host-associated microbiota play an important role in the health and persistence of more complex organisms. In this study, metagenomic analyses were used to reveal microbial community adaptations in three lichen samples as a response to different arsenic concentrations at the sampling sites. Elevated arsenic concentrations at a former mining site expanded the spectrum and number of relevant functions in the lichen-associated microorganisms. Apparent changes affected the abundance of numerous detoxification-related genes, they were substantially enhanced in arsenic-polluted samples. Complementary quantifications of the arsenite S-adenosylmethionine methyltransferase (arsM) gene showed that its abundance is not strictly responding to the environmental arsenic concentrations. The analyzed samples contained rather low numbers of the arsM gene with a maximum of 202 gene copies μl-1 in total community DNA extracts. In addition, bacterial isolates were screened for the presence of arsM. Positive isolates were exposed to different As(III) and As(V) concentrations and tolerated up to 30 mM inorganic arsenic in fluid media, while no substantial biotransformations were observed. Obtained data deepens our understanding related to adaptions of whole microbial communities to adverse environmental conditions. Moreover, this study provides the first evidence that the integrity of bacteria in the lichen holobiont is maintained by acquisition of specific resistances.},
}
@article {pmid30555441,
year = {2018},
author = {Nagpal, R and Wang, S and Solberg Woods, LC and Seshie, O and Chung, ST and Shively, CA and Register, TC and Craft, S and McClain, DA and Yadav, H},
title = {Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2897},
doi = {10.3389/fmicb.2018.02897},
pmid = {30555441},
issn = {1664-302X},
abstract = {Gut microbiome plays a fundamental role in several aspects of host health and diseases. There has been an exponential surge in the use of animal models that can mimic different phenotypes of the human intestinal ecosystem. However, data on host species-specific signatures of gut microbiome and its metabolites like short-chain fatty acids (SCFAs; i.e., acetate, propionate, and butyrate) and lactate in these models and their similarities/differences from humans remain limited, due to high variability in protocols and analyses. Here, we analyze the fecal microbiota composition and the fecal levels of SCFAs and lactate in three of the most-widely used animal models, i.e., mice, rats, and non-human primates (NHPs) and compare them with human subjects, using data generated on a single platform with same protocols. The data show several species-specific similarities and differences in the gut microbiota and fecal organic acids between these species groups. Based on β-diversity, the gut microbiota in humans seems to be closer to NHPs than to mice and rats; however, among rodents, mice microbiota appears to be closer to humans than rats. The phylum-level analyses demonstrate higher Firmicutes-Bacteroidetes ratio in humans and NHPs vs. mice and rats. Human microbiota is dominated by Bacteroides followed by Ruminococcaceae and Clostridiales. Mouse gut is predominated by members of the family S24-7 followed by those from the order Clostridiales, whereas rats and NHPs have higher abundance of Prevotella compared with mice and humans. Also, fecal levels of lactate are higher in mice and rats vs. NHPs and humans, while acetate is highest in human feces. These data of host species-specific gut microbiota signatures in some of the most widely used animal models in context to the human microbiota might reflect disparities in host factors, e.g., diets, genetic origin, gender and age, and hence call for prospective studies investigating the features of gut microbiome in such animal models by controlling for these host elements.},
}
@article {pmid30555437,
year = {2018},
author = {Bao, J and Zheng, H and Wang, Y and Zheng, X and He, L and Qi, W and Wang, T and Guo, B and Guo, G and Zhang, Z and Zhang, W and Li, J and McManus, DP},
title = {Echinococcus granulosus Infection Results in an Increase in Eisenbergiella and Parabacteroides Genera in the Gut of Mice.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2890},
doi = {10.3389/fmicb.2018.02890},
pmid = {30555437},
issn = {1664-302X},
abstract = {Cystic echinococcosis (CE) is a chronic infectious disease caused by Echinococcus granulosus. To confirm whether the infection impacts on the gut microbiota, we established a mouse model of E. granulosus infection in this study whereby BALB/c mice were infected with micro-cysts of E. granulosus. After 4 months of infection, fecal samples were collected for high-throughput sequencing of the hypervariable regions of the 16S rRNA gene. Sequence analysis revealed a total of 13,353 operational taxonomic units (OTUs) with only 40.6% of the OTUs having genera reference information and 101 of the OTUs were significantly increased in infected mice. Bioinformatics analysis showed that the common core microbiota were not significantly changed at family level. However, two genera (Eisenbergiella and Parabacteroides) were enriched in the infected mice (PAMOV A < 0.05) at genus level. Functional analysis indicated that seven pathways were altered in the E. granulosus Infection Group compared with the Uninfected Group. Spearman correlation analysis showed strong correlations of IgG, IgG1 and IgG2a with nine major genera. E. granulosus cyst infection may change the gut microbiota which may be associated with metabolic pathways.},
}
@article {pmid30555436,
year = {2018},
author = {Tsai, T and Sales, MA and Kim, H and Erf, GF and Vo, N and Carbonero, F and van der Merwe, M and Kegley, EB and Buddington, R and Wang, X and Maxwell, CV and Zhao, J},
title = {Isolated Rearing at Lactation Increases Gut Microbial Diversity and Post-weaning Performance in Pigs.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2889},
doi = {10.3389/fmicb.2018.02889},
pmid = {30555436},
issn = {1664-302X},
abstract = {Environment and diet are two major factors affecting the human gut microbiome. In this study, we used a pig model to determine the impact of these two factors during lactation on the gut microbiome, immune system, and growth performance. We assigned 80 4-day-old pigs from 20 sows to two rearing strategies at lactation: conventional rearing on sow's milk (SR) or isolated rearing on milk replacer supplemented with solid feed starting on day 10 (IR). At weaning (day 21), SR and IR piglets were co-mingled (10 pens of 4 piglets/pen) and fed the same corn-soybean meal-dried distiller grain with solubles- and antibiotic-free diets for eight feeding phase regimes. Fecal samples were collected on day 21, 62, and 78 for next-generation sequencing of the V4 hypervariable region of the bacterial 16S rRNA gene. Results indicate that IR significantly increased swine microbial diversity and changed the microbiome structure at day 21. Such changes diminished after the two piglet groups were co-mingled and fed the same diet. Post-weaning growth performance also improved in IR piglets. Toward the end of the nursery period (NP), IR piglets had greater average daily gain (0.49 vs. 0.41 kg/d; P < 0.01) and average daily feed intake (0.61 vs. 0.59 kg/d; P < 0.01) but lower feed efficiency (0.64 vs. 0.68; P = 0.05). Consequently, IR piglets were heavier by 2.9 kg (P < 0.01) at the end of NP, and by 4.1 kg (P = 0.08) at market age compared to SR piglets. Interestingly, pigs from the two groups had similar lean tissue percentage. Random forest analysis showed that members of Leuconostoc and Lactococcus best differentiated the IR and SR piglets at weaning (day 21), were negatively correlated with levels of Foxp3 regulatory T cell populations on day 20, and positively correlated with post-weaning growth performance. Our results suggest that rearing strategies may be managed so as to accelerate early-life establishment of the swine gut microbiome to enhance growth performance in piglets.},
}
@article {pmid30555435,
year = {2018},
author = {Fiedler, CJ and Schönher, C and Proksch, P and Kerschbaumer, DJ and Mayr, E and Zunabovic-Pichler, M and Domig, KJ and Perfler, R},
title = {Assessment of Microbial Community Dynamics in River Bank Filtrate Using High-Throughput Sequencing and Flow Cytometry.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2887},
doi = {10.3389/fmicb.2018.02887},
pmid = {30555435},
issn = {1664-302X},
abstract = {Surface-groundwater interactions play an important role in microbial community compositions of river bank filtrates. Surface water contaminations deriving from environmental influences are attenuated by biogeochemical processes in the hyporheic zone, which are essential for providing clean and high-quality drinking water in abstraction wells. Characterizing the flow regime of surface water into the groundwater body can provide substantial information on water quality, but complex hydraulic dynamics make predictions difficult. Thus, a bottom up approach using microbial community shifting patterns as an overall outcome of dynamic water characteristics could provide more detailed information on the influences that affect groundwater quality. The combination of high-throughput sequencing data together with flow cytometric measurements of total cell counts reveals absolute abundances among taxa, thus enhancing interpretation of bacterial dynamics. 16S rRNA high-throughput sequencing of 55 samples among six wells in a well field in Austria that is influenced by river bank filtrate within a time period of 3 months has revealed both, clear differences as well as strong similarity in microbiome compositions between wells and dates. A significant community shift from April to May occurred in four of six wells, suggesting that surface water flow regimes do affect these wells stronger than others. Triplicate sampling and subsequent sequencing of wells at different dates proved the method to be reproducible. Flow cytometric measurements of total cells indicate microbial shifts due to increased cell counts and emphasize the rise of allochthonous microorganisms. Typical freshwater bacterial lineages (Verrucomicrobia, Bacteroidetes, Actinobacteria, Cyanobacteria, Armatimonadetes) were identified as most increasing phyla during community shifts. The changes are most likely a result of increased water abstraction in the wells together with constant river water levels rather than rain events. The results provide important knowledge for future implementations of well utilization in dependency of the nearby Danube River water levels and can help drawing conclusions about the influence of surface water in the groundwater such that hygienically save and clean drinking water with a stable microbial community can be provided.},
}
@article {pmid30555434,
year = {2018},
author = {Yamamoto, K and Shiwa, Y and Ishige, T and Sakamoto, H and Tanaka, K and Uchino, M and Tanaka, N and Oguri, S and Saitoh, H and Tsushima, S},
title = {Bacterial Diversity Associated With the Rhizosphere and Endosphere of Two Halophytes: Glaux maritima and Salicornia europaea.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2878},
doi = {10.3389/fmicb.2018.02878},
pmid = {30555434},
issn = {1664-302X},
abstract = {Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants: Glaux maritima and Salicornia europaea. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the G. maritima samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for S. europaea, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in G. maritima and 126, 416, and 596 in S. europaea, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were Proteobacteria and Bacteroidetes. Actinobacteria was extremely abundant in the root endosphere from G. maritima. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes. Rhizobium, Actinoplanes, and Marinomonas were highly abundant in G. maritima, whereas Sulfurimonas and Coleofasciculus were highly abundant in S. europaea. A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between G. maritima and S. europaea. This is the first report to characterize the root microbiome of G. maritima, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between G. maritima and S. europaea.},
}
@article {pmid30554441,
year = {2018},
author = {Curtis, K and Stewart, CJ and Robinson, M and Molfese, DL and Gosnell, SN and Kosten, TR and Petrosino, JF and De La Garza, R and Salas, R},
title = {Insular Resting State Functional Connectivity is Associated with Gut Microbiota Diversity.},
journal = {The European journal of neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1111/ejn.14305},
pmid = {30554441},
issn = {1460-9568},
abstract = {The gut microbiota has recently gained attention as a possible modulator of brain activity. A number of reports suggest that the microbiota may be associated with neuropsychiatric conditions such as major depressive disorder, autism, and anxiety. The gut microbiota is thought to influence the brain via vagus nerve signaling, among other possible mechanisms. The insula processes and integrates these vagal signals. To determine if microbiota diversity and structure modulate brain activity, we collected fecal samples and examined insular function using resting state functional connectivity (RSFC). Thirty healthy participants (non-smokers, tobacco smokers, and electronic cigarette users, n=10 each) were studied. We found that the RSFC between the insula and several regions (frontal pole left, lateral occipital cortex right, lingual gyrus right, and cerebellum 4, 5 and vermis 9) were associated with bacterial microbiota diversity and structure. In addition, two specific bacteria genera, Prevotella and Bacteroides, were specifically different in tobacco smokers and also associated with insular connectivity. In conclusion, we show that insular connectivity is associated with microbiome diversity, structure, and at least two specific bateria genera. Furthemore, this association is potentially modulated by tobacco smoking, although the sample sizes for the different smoking groups were small and this result needs validation in a larger cohort. While replication is necessary, the microbiota is a readily accesible therapeutic target for modulating insular connectivity, which has previously been shown to be abnormal in anxiety and tobacco use disorders. This article is protected by copyright. All rights reserved.},
}
@article {pmid30554391,
year = {2018},
author = {Bianchi, F and Duque, ALRF and Saad, SMI and Sivieri, K},
title = {Gut microbiome approaches to treat obesity in humans.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9570-8},
pmid = {30554391},
issn = {1432-0614},
support = {(2013/50506-8; 2015/13965-0; 2015/08228-6)//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {The rising worldwide prevalence of obesity has become a major concern having many implications for the public health and the economy. It is well known that many factors such as lifestyle, increased intake of foods high in fat and sugar and a host's genetic profile can lead to obesity. Besides these factors, recent studies have pointed to the gut microbiota composition as being responsible for the development of obesity. Since then, many efforts have been made to understand the link between the gut microbiota composition and obesity, as well as the role of food ingredients, such as pro- and prebiotics, in the modulation of the gut microbiota. Studies involving the gut microbiota composition of obese individuals are however still controversial, making it difficult to treat obesity. In this sense, this mini-review deals with obesity and the relationship with gut microbiota, summarising the principal findings on gut microbiome approaches for treating obesity in humans.},
}
@article {pmid30554379,
year = {2018},
author = {Mrázek, J and Mekadim, C and Kučerová, P and Švejstil, R and Salmonová, H and Vlasáková, J and Tarasová, R and Čížková, J and Červinková, M},
title = {Melanoma-related changes in skin microbiome.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12223-018-00670-3},
pmid = {30554379},
issn = {1874-9356},
support = {CIGA 20162019//Fakultu Agrobiologie, Potravinových a Prírodních Zdroju, Ceská Zemedelská Univerzita v Praze/ ; CIGA 20162001//Fakultu Agrobiologie, Potravinových a Prírodních Zdroju, Ceská Zemedelská Univerzita v Praze/ ; CZ.02.1.01/0.0/0.0/15_003/0000460//Ministerstvo Školství, Mládeže a Telovýchovy/ ; LO1609//Ministerstvo Školství, Mládeže a Telovýchovy/ ; },
abstract = {Melanoma is the least common form of skin tumor, but it is potentially the most dangerous and responsible for the majority of skin cancer deaths. We suggest that the skin microbiome might be changed during the progression of melanoma. The aim of this study is to compare the composition of the skin microbiota between different locations (skin and melanoma) of a MeLiM (Melanoma-bearing Libechov Minipig) pig model (exophytic melanoma). Ninety samples were used for PCR-DGGE analysis with primers specifically targeting the V3 region of the 16S rRNA gene. The profiles were used for cluster analysis by UPGMA and principal coordinate analysis PCoA and also to calculate the diversity index (Simpson index of diversity). By comparing the obtained results, we found that both bacterial composition and diversity were significantly different between the skin and melanoma microbiomes. The abundances of Fusobacterium and Trueperella genera were significantly increased in melanoma samples, suggesting a strong relationship between melanoma development and skin microbiome changes.},
}
@article {pmid30554053,
year = {2018},
author = {Cerqueira, F and Matamoros, V and Bayona, J and Elsinga, G and Hornstra, LM and Piña, B},
title = {Distribution of antibiotic resistance genes in soils and crops. A field study in legume plants (Vicia faba L.) grown under different watering regimes.},
journal = {Environmental research},
volume = {170},
number = {},
pages = {16-25},
doi = {10.1016/j.envres.2018.12.007},
pmid = {30554053},
issn = {1096-0953},
abstract = {Social concern has raised during the last years due to the development of antibiotic resistance hotspots in different environmental compartments, including the edible parts of crops. To assess the influence of the water quality used for watering, we collected samples from soil, roots, leaves and beans from the legume plant Vicia faba (broad beans) in three agricultural peri-urban plots (Barcelona, NE Spain), irrigated with either groundwater, river water, or reclaimed water. Antibiotic resistance genes (ARGs) sul1, tetM, qnrS1, blaCTX-M-32,blaOXA-58, mecA, and blaTEM were quantified by real-time PCR, along with 16S rDNA and intl1 sequences, as proxies for bacterial abundance and integron prevalence, respectively. Microbiome composition of all samples were analyzed by high-throughput DNA sequencing. Results show a gradient of bacterial species diversity and of ARG prevalence from highly diverse soil samples to microbially-poor beans and leaves, in which Rhizobiales essentially displaced all other groups, and that presented very small loads of ARGs and integron sequences. The data suggest that the microbiome and the associated resistome were likely influenced by agricultural practices and water quality, and that future irrigation water legal standards should consider the specific Physiology of the different crop plants.},
}
@article {pmid30553904,
year = {2018},
author = {Xanthopoulos, A and Starling, RC and Kitai, T and Triposkiadis, F},
title = {Heart Failure and Liver Disease: Cardiohepatic Interactions.},
journal = {JACC. Heart failure},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jchf.2018.10.007},
pmid = {30553904},
issn = {2213-1787},
abstract = {Heart failure (HF) and liver disease often co-exist. This is because systemic disorders and diseases affect both organs (alcohol abuse, drugs, inflammation, autoimmunity, infections) and because of complex cardiohepatic interactions. The latter, which are the focus of this review, include the development of acute cardiogenic liver injury and congestive hepatopathy in HF as well as cardiac dysfunction and failure in the setting of liver cirrhosis, nonalcoholic fatty liver disease, and sequelae following liver transplantation. The emerging role of altered liver X receptor signaling in the pathogenesis of HF comorbidities as well as of the intestinal microbiome and its metabolites in HF and liver disease are fruitful areas for future research.},
}
@article {pmid30553752,
year = {2018},
author = {Whang, A and Nagpal, R and Yadav, H},
title = {Bi-directional drug-microbiome interactions of anti-diabetics.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ebiom.2018.11.046},
pmid = {30553752},
issn = {2352-3964},
abstract = {Type 2 diabetes (T2D) has become a global epidemic. Although several drugs are available to manage T2D, problems associated with person-to-person variability in drug efficacy and potential side-effects remain unresolved. Owing to the emerging role of the gut microbiome in obesity and T2D, the interaction between gut microbes and anti-diabetic drugs and its influence on drugs' functions remains of immediate research interest. On one hand, drugs can manipulate gut microbiome composition and metabolic capacity. Conversely, the metabolic activities of the microbiome and its metabolites can also influence drug metabolism and effects. Hence, understanding this bi-directional drug-microbiome interaction and how it influences the clinical outcomes of antidiabetic drugs can pave the way to develop next-generation strategies to ameliorate diabetes. This review presents evidences demonstrating the putative interactions between anti-diabetic drugs and the gut microbiome, and discusses the potential of microbiome modulators to manipulate drug-microbiome interactions and the drug metabolism.},
}
@article {pmid30552986,
year = {2018},
author = {Kozik, AJ and Huang, YJ},
title = {The Microbiome in Asthma: Role in pathogenesis, phenotype, and response to treatment.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2018.12.005},
pmid = {30552986},
issn = {1534-4436},
}
@article {pmid30552985,
year = {2018},
author = {Ciaccio, CE},
title = {Modulating the Microbiome: The Future of Allergy Therapeutics?.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2018.12.006},
pmid = {30552985},
issn = {1534-4436},
}
@article {pmid30552443,
year = {2018},
author = {Rothman, JA and Andrikopoulos, C and Cox-Foster, D and McFrederick, QS},
title = {Floral and Foliar Source Affect the Bee Nest Microbial Community.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1300-3},
pmid = {30552443},
issn = {1432-184X},
support = {NNX15AP99A//National Aeronautics and Space Administration/ ; 2018-67011-28123//National Institute of Food and Agriculture/ ; CA-R-ENT-5109-H//National Institute of Food and Agriculture/ ; },
abstract = {Managed pollinators such as the alfalfa leafcutting bee, Megachile rotundata, are essential to the production of a wide variety of agricultural crops. These pollinators encounter a diverse array of microbes when foraging for food and nest-building materials on various plants. To test the hypothesis that food and nest-building source affects the composition of the bee-nest microbiome, we exposed M. rotundata adults to treatments that varied both floral and foliar source in a 2 × 2 factorial design. We used 16S rRNA gene and internal transcribed spacer (ITS) sequencing to capture the bacterial and fungal diversity of the bee nests. We found that nest microbial communities were significantly different between treatments, indicating that bee nests become inoculated with environmentally derived microbes. We did not find evidence of interactions between the fungi and bacteria within our samples. Furthermore, both the bacterial and fungal communities were quite diverse and contained numerous exact sequence variants (ESVs) of known plant and bee pathogens that differed based on treatment. Our research indicates that bees deposit plant-associated microbes into their nests, including multiple plant pathogens such as smut fungi and bacteria that cause blight and wilt. The presence of plant pathogens in larval pollen provisions highlights the potential for bee nests to act as disease reservoirs across seasons. We therefore suggest that future research should investigate the ability of bees to transmit pathogens from nest to host plant.},
}
@article {pmid30552195,
year = {2018},
author = {Lin, Y and Gifford, S and Ducklow, H and Schofield, O and Cassar, N},
title = {Towards quantitative microbiome community profiling using internal standards.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.02634-18},
pmid = {30552195},
issn = {1098-5336},
abstract = {An inherent issue of high-throughput rRNA gene tag sequencing microbiome surveys is that they provide compositional data in relative abundances. This often leads to spurious correlations making the interpretation of relationships to biogeochemical rates challenging. To overcome this issue, we quantitatively estimated the abundance of microorganisms by spiking in known amounts of internal DNA standards. Using a 3-year sample set of diverse microbial communities from the Western Antarctica Peninsula, we demonstrated that the internal standard method yielded community profiles and taxa co-occurrence patterns substantially different from those derived using relative abundances. We found that the method provided results consistent with the traditional CHEMTAX analysis of pigments and total bacterial counts by flow cytometry. Using the internal standard method, we also showed that chloroplast 16S rRNA gene data in microbial surveys can be used to estimate abundances of certain eukaryotic phototrophs such as cryptophytes and diatoms. In Phaeocystis, scatter in the 16S/18S rRNA gene ratio may be explained by physiological adaptation to environmental conditions. We conclude that the internal standard method, when applied to rRNA gene microbial community profiling, is quantitative and that its application will substantially improve our understanding of microbial ecosystems.Importance High-throughput sequencing based marine microbiome profiling is rapidly expanding and changing how we study the oceans. Although powerful, the technique is not fully quantitative - it only provides taxon counts in relative abundances. In order to address this issue, we presented a method to quantitatively estimate microbial abundances per unit volume of seawater filtered by spiking in known amounts of internal DNA standards to each sample. We validated this method by comparing the calculated abundances to other independent estimates including chemical markers (pigments) and total bacterial cell counts by flow cytometry. The internal standard approach allows us to quantitatively estimate and compare marine microbial community profiles, with important implications for linking environmental microbiomes to quantitative processes such as metabolic and biogeochemical rates.},
}
@article {pmid30551760,
year = {2018},
author = {Wilson, AJ and Harrup, LE},
title = {Reproducibility and relevance in insect-arbovirus infection studies.},
journal = {Current opinion in insect science},
volume = {28},
number = {},
pages = {105-112},
doi = {10.1016/j.cois.2018.05.007},
pmid = {30551760},
issn = {2214-5753},
abstract = {Experimental infections of insects with arboviruses are performed to achieve a variety of objectives but principally to draw inferences about the potential role of field populations in transmission or to explore the molecular basis of vector-pathogen interactions. The design of such studies determines both their reproducibility and the extent to which their results can be extrapolated to natural environments, and is constrained by the resources available. We discuss recent findings regarding the effects of nutrition, the microbiome, co-infecting agents and feeding methods on the outcome of such experiments, and identify resource-efficient ways to increase their relevance and reproducibility, including the development of community standards for reporting such studies and better standards for cell line and colony authentication.},
}
@article {pmid30551580,
year = {2018},
author = {Ibarra-Juarez, LA and Desgarennes, D and Vázquez-Rosas-Landa, M and Villafan, E and Alonso-Sánchez, A and Ferrera-Rodríguez, O and Moya, A and Carrillo, D and Cruz, L and Carrión, G and López-Buenfil, A and García-Avila, C and Ibarra-Laclette, E and Lamelas, A},
title = {Impact of Rearing Conditions on the Ambrosia Beetle's Microbiome.},
journal = {Life (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/life8040063},
pmid = {30551580},
issn = {2075-1729},
abstract = {Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with Xyleborus affinis, Xyleborus bispinatus, and Xyleborus volvulus, evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions. Our results revealed that rearing conditions affected the fungal and bacterial microbiome structure and had a strong influence on bacterial metabolic capacities. We propose that the rearing conditions influence the ambrosia-associated fungal and bacterial communities. Furthermore, bacterial microbiome flexibility may help beetles adapt to different substrates.},
}
@article {pmid30551574,
year = {2018},
author = {Dias, DM and Kolba, N and Binyamin, D and Ziv, O and Regini Nutti, M and Martino, HSD and Glahn, RP and Koren, O and Tako, E},
title = {Iron Biofortified Carioca Bean (Phaseolus vulgaris L.)-Based Brazilian Diet Delivers More Absorbable Iron and Affects the Gut Microbiota In Vivo (Gallus gallus).},
journal = {Nutrients},
volume = {10},
number = {12},
pages = {},
doi = {10.3390/nu10121970},
pmid = {30551574},
issn = {2072-6643},
abstract = {Biofortification aims to improve the micronutrient concentration and bioavailability in staple food crops. Unlike other strategies utilized to alleviate Fe deficiency, studies of the gut microbiota in the context of Fe biofortification are scarce. In this study, we performed a 6-week feeding trial in Gallus gallus (n = 15), aimed to investigate the Fe status and the alterations in the gut microbiome following the administration of Fe-biofortified carioca bean based diet (BC) versus a Fe-standard carioca bean based diet (SC). The tested diets were designed based on the Brazilian food consumption survey. Two primary outcomes were observed: (1) a significant increase in total body Hb-Fe values in the group receiving the Fe-biofortified carioca bean based diet; and (2) changes in the gut microbiome composition and function were observed, specifically, significant changes in phylogenetic diversity between treatment groups, as there was increased abundance of bacteria linked to phenolic catabolism, and increased abundance of beneficial SCFA-producing bacteria in the BC group. The BC group also presented a higher intestinal villi height compared to the SC group. Our results demonstrate that the Fe-biofortified carioca bean variety was able to moderately improve Fe status and to positively affect the intestinal functionality and bacterial populations.},
}
@article {pmid30551387,
year = {2019},
author = {Liu, D and Lin, L and Lin, Y and Zhong, Y and Zhang, S and Liu, W and Zou, B and Liao, Q and Xie, Z},
title = {Zengye decoction induces alterations to metabolically active gut microbiota in aged constipated rats.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {109},
number = {},
pages = {1361-1371},
doi = {10.1016/j.biopha.2018.11.013},
pmid = {30551387},
issn = {1950-6007},
abstract = {Zengye decoction (ZYD), a traditional Chinese medicinal formula, has been used in the treatment of various chronic diseases, such as constipation and skin dryness syndrome. Clinically, the specific mechanisms and targets of ZYD for treating disease remain unclear. The present study was undertaken to investigate the effects of ZYD on the gut microbiota and host metabolites in aged constipated rats and the relationship between the intestinal microbiota and the host. Rats were divided randomly into three groups, the control group (n = 10), recovery group (n = 10) and ZYD group (n = 10). First, the aged constipation model was established for the ZYD group and recovery group. Then, rats in the ZYD group were treated with ZYD. Urinary and faecal samples of each animal were collected in microcentrifuge tubes. Next, 16s rRNA gene sequencing was employed to analyse the composition of the gut microbiome in faecal samples and afterwards the metabolic function of the altered gut microbiota was predicted. Additionally, 1H NMR profiling was used to detect the alterations of host metabolites in urine and faecal samples to verify the metabolic function results obtained from sequencing. As a result, ZYD reduced the level of harmful bacteria, such as Desulfovibrio, Ruminococcus, Prevotella and Dorea, and increased the abundance of Oxalobacter, Clostridium and Roseburia. The functional prediction of changes in the gut microbiota induced by ZYD revealed that ZYD promoted energy storage, regulated amino acid metabolism, inhibited methane metabolism, strengthened the physiological function of glutathione and reduced bacterial toxin. The 1H NMR profiles revealed that ZYD regulated the carbohydrates, short chain fatty acids, amino acids and amines in the aged constipated rats. In addition, most metabolic changes observed were related to the function of intestinal microbiota. These results suggest that ZYD can regulate the intestinal microbiota of constipated rats to normal levels and change the endogenous metabolites of the host through the intestinal microbiota to achieve therapeutic effects.},
}
@article {pmid30551119,
year = {2018},
author = {McClave, SA and Martindale, RG},
title = {Why do current strategies for optimal nutritional therapy neglect the microbiome?.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {60},
number = {},
pages = {100-105},
doi = {10.1016/j.nut.2018.09.024},
pmid = {30551119},
issn = {1873-1244},
abstract = {Strategies for providing optimal nutritional therapy have evolved over time, with the emphasis on specific directives (such as route, use of immunonutrition, high protein, organ-specific formulas, etc.), achieving variable degrees of success for improving outcomes in the intensive care unit. As the largest immune organ in the body comprising the largest interface between the host and the external environment, the gut can have an amplifying effect on a pattern of dysbiosis, immune dysregulation, and multiple organ failure seen in the critically ill patient. Conversely, maintenance of gut integrity can serve to restore a pattern of homeostasis, appropriate immune responses, symbiosis, and clinical recovery. Simply providing refined polymeric formulas as enteral nutrition may not take full advantage of the potential for optimal outcome that could be derived by giving therapy designed to directly stimulate gut defenses and support the intestinal microbiota. This article describes a series of strategies (such as use of intact whole food formulas, soluble fiber, fecal microbial transplantation, serum bovine immunoglobulin, or agents to promote commensal behavior) that should modulate the gut microbiome and shift the critically ill patient toward a pattern of health and recovery.},
}
@article {pmid30551046,
year = {2018},
author = {Soussan, R and Schimpf, C and Pilmis, B and Degroote, T and Tran, M and Bruel, C and Philippart, F and , },
title = {Ventilator-associated pneumonia: The central role of transcolonization.},
journal = {Journal of critical care},
volume = {50},
number = {},
pages = {155-161},
doi = {10.1016/j.jcrc.2018.12.005},
pmid = {30551046},
issn = {1557-8615},
abstract = {Ventilator-associated pneumonia remain frequent and serious diseases since they are associated with considerable crude mortality. Pathophysiology is centered on modifications of regional bacterial flora, especially tracheobronchial tree and oropharyngeal sphere. Bacterial migration from an anatomical area to another seems to be the main explanation of these alterations which are called &quot;transcolonization&quot;. The association of transcolonization and lack of tightness of the endotracheal tube cuff provides a direct pathway for bacteria from the upper to the subglottic airways, eventually leading to ventilator-associated pneumonia. Although modification of bacterial flora has been largely studied, the mechanism which underlays the ability of the implantation, growing and interactions with the local microbiome that leads to the observed transcolonization remains to be more clearly deciphered. The aim of our review is to emphasize the cornerstone importance of the &quot;transcolonization&quot; as a nosological entity playing a central role in ventilator-associated pneumonia.},
}
@article {pmid30550821,
year = {2018},
author = {Svolos, V and Hansen, R and Nichols, B and Quince, C and Ijaz, UZ and Papadopoulou, RT and Edwards, CA and Watson, D and Alghamdi, A and Brejnrod, A and Ansalone, C and Duncan, H and Gervais, L and Tayler, R and Salmond, J and Bolognini, D and Klopfleisch, R and Gaya, DR and Milling, S and Russell, RK and Gerasimidis, K},
title = {Treatment of Active Crohn's Disease With an Ordinary Food-based Diet That Replicates Exclusive Enteral Nutrition.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2018.12.002},
pmid = {30550821},
issn = {1528-0012},
abstract = {BACKGROUND &amp; AIMS: Exclusive enteral nutrition (EEN) is the only established dietary treatment for Crohn's disease (CD), but its acceptability is limited. There is a need for novel dietary treatments for CD.<br><br>METHODS: We evaluated the effects of an individualized, food-based diet (CD-TREAT), with similar composition to EEN, on the gut microbiome, inflammation and clinical response in a rat model, healthy adults, and children with relapsing CD. Twenty-five healthy adults randomly received EEN or CD-TREAT for 7 days, followed by a 14-day washout period, followed by the alternate diet. Fecal microbiome and metabolome were assessed before and after each diet. HLA-B7 and HLA-B27 transgenic rats with gut inflammation received EEN, CD-TREAT, or standard chow for 4 weeks. Fecal, luminal and tissue microbiome, fecal metabolites and gut inflammation were assessed. Five children received CD-TREAT with clinical activity and fecal calprotectin evaluated after 8-week treatment.<br><br>RESULTS: Among healthy adults, CD-TREAT was easier to comply with and more acceptable than EEN. CD-TREAT induced similar effects to EEN (EEN vs CD-TREAT) on fecal microbiome composition, metabolome, mean total sulfide (increase 133.0±80.5 vs 54.3±47.0 nmol/g), pH (increase 1.3±0.5 vs 0.9±0.6), the short-chain fatty acids (μmol/g) acetate (decrease 27.4±22.6 vs 21.6±20.4), propionate (decrease 5.7±7.8 vs 5.2±7.9), and butyrate (decrease 7.0±7.4 vs 10.2±8.5). In the rat model, CD-TREAT and EEN produced similar changes in bacterial load (decrease 0.3±0.3 log10 16S rRNA gene copies/g), short-chain fatty acids, microbiome, and ileitis severity (mean histopathology score reductions 1.25 for EEN (P=.015) and 1.0 for CD-TREAT (P=.044) vs chow). Among the children receiving CD-TREAT, 4 (80%) had a clinical response and 3 (60%) entered remission, with significant concurrent reductions in fecal calprotectin (mean decrease 918±555 mg/kg, (P=.002)).<br><br>CONCLUSION: CD-TREAT replicates EEN changes in the microbiome, reduces gut inflammation, is well-tolerated and is potentially effective in patients with active CD.},
}
@article {pmid30550810,
year = {2018},
author = {Nakatsuji, T and Gallo, RL},
title = {The role of the skin microbiome in atopic dermatitis.},
journal = {Annals of allergy, asthma &amp; immunology : official publication of the American College of Allergy, Asthma, &amp; Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2018.12.003},
pmid = {30550810},
issn = {1534-4436},
}
@article {pmid30550767,
year = {2018},
author = {Brusselaers, N and Shrestha, S and Van De Wijgert, J and Verstraelen, H},
title = {Vaginal dysbiosis, and the risk of human papillomavirus and cervical cancer: systematic review and meta-analysis.},
journal = {American journal of obstetrics and gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajog.2018.12.011},
pmid = {30550767},
issn = {1097-6868},
abstract = {OBJECTIVE: The vaginal microbiota proposedly influence the association between human papillomavirus and cervical cancer. Our aim was to assess if vaginal dysbiosis affects human papilloma virus acquistion, persistence, and progression to related cervical pre-malignancy.<br><br>DATA SORUCES: MEDLINE, Embase, CINAHL, Cochrane Library, and Web of Science (inception until June 2018). The study protocol was registered at PROSPERO (CRD42016035620).<br><br>STUDY ELIGIBILITY CRITERIA: This systematic review included all observational studies reporting on incident human papilloma virus, persistent human papilloma virus and/or related cervical disease, in women with or without vaginal dysbiosis prior to outcome assessment.<br><br>We used random effects models for meta-analyses and report pooled relative risks with 95% confidence intervals. The risk for incident and/or persistent human papilloma virus, or related cervical disease based on longitudinal results.<br><br>RESULTS: Out of 1,645 unique articles, 15 mainly prospective cohort studies were included, published between 2003 and 2017, including a total of 101,049 women. Vaginal dysbiosis was associated with an increased risk of incident human papilloma virus (overall relative risk=1.33, 1.18-1.50, I2=0%; among young women relative risk=1.43, 1.10-1.85, I2=0%), human papilloma virus persistence (overall relative risk=1.14, 1.01-1.28, I2=44.2%; for oncogenic types relative risk=1.18, 1.01-1.38, I2=0%), and high-grade lesions and cancer (relative risk=2.01, 1.40-3.01, I2=0%), but women with lesions/cancer were compared to those without regardless of their oncogenic human papilloma virus status. Overall, comparable results were found in the molecular vaginal microbiota studies.<br><br>CONCLUSIONS: This study supports a causal link between vaginal dysbiosis and cervical cancer along the oncogenic human papillomavirus acquisition, persistence, and cervicovaginal dysplasia development pathway.},
}
@article {pmid30550381,
year = {2018},
author = {Vanella, G and Archibugi, L and Stigliano, S and Capurso, G},
title = {Alcohol and gastrointestinal cancers.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOG.0000000000000502},
pmid = {30550381},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: Alcohol is a type I carcinogen and the WHO stated that it caused 5% of all deaths in 2016, of which 13% because of cancers. Among digestive tract cancers, this association is clear for esophageal, liver and colorectal cancer, and more debated for gastric and pancreatic cancer. The present review will revise recent evidence on epidemiologic association and mechanisms linking alcohol with the risk of esophageal, gastric, colorectal and pancreatic cancers.<br><br>RECENT FINDINGS: Moderate alcohol intake increases the risk of esophageal squamous cell carcinoma and colorectal cancer. Heavy alcohol intake is associated with an increased risk of gastric and pancreatic cancers. These risks also depend on genetic variants and the interaction with smoking is inconsistent. The carcinogenic mechanisms are multiple with a key role of acetaldehyde because of its ability to cause DNA damage, alter telomere length and induce ROS. Data on the role of the gut microbiome as possible mediator of alcohol-induced carcinogenesis are limited.<br><br>SUMMARY: There is sufficient evidence for the association between alcohol consumption and cancers of the esophagus, stomach, colon-rectum and pancreas. Public health policies to prevent these cancer types should include modification of alcohol intake habits, especially among individuals at increased risk.},
}
@article {pmid30548483,
year = {2018},
author = {Grev, J and Berg, M and Soll, R},
title = {Maternal probiotic supplementation for prevention of morbidity and mortality in preterm infants.},
journal = {The Cochrane database of systematic reviews},
volume = {12},
number = {},
pages = {CD012519},
doi = {10.1002/14651858.CD012519.pub2},
pmid = {30548483},
issn = {1469-493X},
abstract = {BACKGROUND: Inflammation may contribute to preterm birth and to morbidity of preterm infants. Preterm infants are at risk for alterations in the normal protective microbiome. Oral probiotics administered directly to preterm infants have been shown to decrease the risk for severe necrotizing enterocolitis (NEC) as well as the risk of death, but there are safety concerns about administration of probiotics directly to preterm infants. Through decreasing maternal inflammation, probiotics may play a role in preventing preterm birth and/or decreasing the inflammatory milieu surrounding delivery of preterm infants, and may alter the microbiome of the preterm infant when given to mothers during pregnancy. Probiotics given to mothers after birth of preterm infants may effect infant bacterial colonization, which could potentially reduce the incidence of NEC.<br><br>OBJECTIVES: 1. To compare the efficacy of maternal probiotic administration versus placebo or no intervention in mothers during pregnancy for the prevention of preterm birth and the prevention of morbidity and mortality of infants born preterm.2. To compare the efficacy of maternal probiotic administration versus placebo, no intervention, or neonatal probiotic administration in mothers of preterm infants after birth on the prevention of mortality and preterm infant morbidities such as NEC.<br><br>SEARCH METHODS: We used the standard search strategy of Cochrane Neonatal to search the Cochrane Central Register of Controlled Trials (CENTRAL 2017, Issue 2), MEDLINE via PubMed (1966 to 21 March 2017), Embase (1980 to 21 March 2017), and CINAHL (1982 to 21 March 2017). We also searched clinical trials databases, conference proceedings, and the reference lists of retrieved articles for randomized controlled trials and quasi-randomized trials.<br><br>SELECTION CRITERIA: We included randomized controlled trials in the review if they administered oral probiotics to pregnant mothers at risk for preterm birth, or to mothers of preterm infants after birth. Quasi-randomized trials were eligible for inclusion, but none were identified. Studies enrolling pregnant women needed to administer probiotics at < 36 weeks' gestation until the trimester of birth. Probiotics considered were of the genera Lactobacillus, Bifidobacterium or Saccharomyces.<br><br>DATA COLLECTION AND ANALYSIS: We used the standard methods of the Cochrane Collaboration and Cochrane Neonatal to determine the methodologic quality of studies, and for data collection and analysis.<br><br>MAIN RESULTS: We included 12 eligible trials with a total of 1450 mothers and 1204 known infants. Eleven trials administered probiotics to mothers during pregnancy and one trial administered probiotics to mothers after birth of their preterm infants. No studies compared maternal probiotic administration directly with neonatal administration. Included prenatal trials were highly variable in the indication for the trial, the gestational age and duration of administration of probiotics, as well as the dose and formulation of the probiotics. The pregnant women included in these trials were overall at low risk for preterm birth. In a meta-analysis of trial data, oral probiotic administration to pregnant women did not reduce the incidence of preterm birth < 37 weeks (typical risk ratio (RR) 0.92, 95% confidence interval (CI) 0.32 to 2.67; 4 studies, 518 mothers and 506 infants), < 34 weeks (typical risk difference (RD) 0.00, 95% CI -0.02 to 0.02; 2 studies, 287 mothers and infants), the incidence of infant mortality (typical RD 0.00, 95% CI -0.02 to 0.02; 2 studies, 309 mothers and 298 infants), or the gestational age at birth (mean difference (MD) 0.15, 95% CI -0.33 to 0.63; 2 studies, 209 mothers with 207 infants).One trial studied administration of probiotics to mothers after preterm birth and included 49 mothers and 58 infants. There were no significant differences in the risk of any NEC (RR 0.44, 95% CI 0.13 to 1.46; 1 study, 58 infants), surgery for NEC (RR 0.15, 95% CI 0.01 to 2.58; 1 study, 58 infants), death (RR 0.66, 95% CI 0.06 to 6.88; 1 study, 58 infants), and death or NEC (RR 0.53, 95% CI 0.19 to 1.49; 1 study, 58 infants). There was an improvement in time to reach 50% enteral feeds in infants whose mothers received probiotics, but the estimate is imprecise (MD -9.60 days, 95% CI -19.04 to -0.16 days; 58 infants). No other improvement in any neonatal outcomes were reported. The estimates were imprecise and do not exclude the possibility of meaningful harms or benefits from maternal probiotic administration. There were no cases of culture-proven sepsis with the probiotic organism. The GRADE quality of evidence was judged to be low to very low due to inconsistency and imprecision.<br><br>AUTHORS' CONCLUSIONS: There is insufficient evidence to conclude whether there is appreciable benefit or harm to neonates of either oral supplementation of probiotics administered to pregnant women at low risk for preterm birth or oral supplementation of probiotics to mothers of preterm infants after birth. Oral supplementation of probiotics to mothers of preterm infants after birth may decrease time to 50% enteral feeds, however, this estimate is extremely imprecise. More research is needed for post-natal administration of probiotics to mothers of preterm infants, as well as to pregnant mothers at high risk for preterm birth.},
}
@article {pmid30548123,
year = {2018},
author = {Jiang, HY and Xu, LL and Zhang, X and Zhang, Z and Ruan, B},
title = {The Microbiome in Bipolar Depression: A Longitudinal Study of One Pair of Monozygotic Twins.},
journal = {Bipolar disorders},
volume = {},
number = {},
pages = {},
doi = {10.1111/bdi.12736},
pmid = {30548123},
issn = {1399-5618},
abstract = {The commensal gut microbiota is a dynamic entity that is influenced by a variety of factors. Previous study has reported considerable individual variability in the bacterial content between related and unrelated individuals, which makes it difficult to identify candidate microorganisms for specific diseases. However, findings from monozygotic (MZ) twins have revealed a high degree of similarity in the composition of gut microbiota between twins. This article is protected by copyright. All rights reserved.},
}
@article {pmid30547792,
year = {2018},
author = {Zhang, R and Chen, L and Cao, L and Li, KJ and Huang, Y and Luan, XQ and Li, G},
title = {Effects of smoking on the lower respiratory tract microbiome in mice.},
journal = {Respiratory research},
volume = {19},
number = {1},
pages = {253},
doi = {10.1186/s12931-018-0959-9},
pmid = {30547792},
issn = {1465-993X},
abstract = {BACKGROUND: Recent studies break with traditional opinion that the lower respiratory tract is sterile, and increasingly focus on the lung microbiome and disease. Smoking, as an important etiology of inflammatory lung disease, was considered as a factor influencing lung microbiome variations in our study, and we aimed to study the effect of smoking on inflammation and microbial diversity and community.<br><br>METHODS: Forty male mice were selected and randomly divided into a smoking and a non-smoking group. Mice in the smoking group were exposed to smoke smog for 2 h/day for 90 days. Blood and lung tissues were obtained after the experiment, and ELISA was used to measure interleukin-6 and C reactive protein concentrations. 16S rRNA gene quantification and sequencing technology were used to compare microbial diversity and community between the two groups. SAS 9.1 and R software were used to analyze the data.<br><br>RESULTS: Thirty-six mice survived, and the weight of the smoking group increased more slowly than that of the non-smoking group. Denser inflammation and congestion were observed in the lungs of the smoking mice compared with the non-smoking group Higher microbial diversity was observed in the smoking group, and Enterobacter, Acidimicrobiales_norank, and Caulobacteraceae_Unclassified genus were significantly more abundant in the non-smoking group (P < 0.001).<br><br>CONCLUSIONS: Smoking altered microbial diversities and communities in the lower respiratory tract of mice. Microbial variation should be considered in future studies focusing on smoking-induced inflammatory disease.},
}
@article {pmid30547751,
year = {2018},
author = {Yang, H and Yang, M and Fang, S and Huang, X and He, M and Ke, S and Gao, J and Wu, J and Zhou, Y and Fu, H and Chen, C and Huang, L},
title = {Evaluating the profound effect of gut microbiome on host appetite in pigs.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {215},
doi = {10.1186/s12866-018-1364-8},
pmid = {30547751},
issn = {1471-2180},
support = {31472071//National Natural Science Foundation of China/ ; 31702103//National Natural Science Foundation of China/ ; BX201700102//National Postdoctoral Program for Innovative Talents/ ; },
abstract = {BACKGROUND: There are growing evidences showing that gut microbiota should play an important role in host appetite and feeding behavior. However, what kind of microbe(s) and how they affect porcine appetite remain unknown.<br><br>RESULTS: In this study, 280 commercial Duroc pigs were raised in a testing station with the circadian feeding behavior records for a continuous period of 30-100 kg. We first analyzed the influences of host gender and genetics in porcine average daily feed intake (ADFI), but no significant effect was observed. We found that the Prevotella-predominant enterotype had a higher ADFI than the Treponema enterotype-like group. Furthermore, 12 out of the 18 OTUs positively associated with the ADFI were annotated to Prevotella, and Prevotella was the hub bacteria in the co-abundance network. These results suggested that Prevotella might be a keystone bacterial taxon for increasing host feed intake. However, some bacteria producing short-chain fatty acids (SCFAs) and lactic acid (e.g. Ruminococcaceae and Lactobacillus) showed negative associations with the ADFI. Predicted function capacity analysis showed that the genes for amino acid biosynthesis had significantly different enrichment between pigs with high and low ADFI.<br><br>CONCLUSIONS: The present study provided important information on the profound effect of gut microbiota on porcine appetite and feeding behavior. This will profit us to regulate porcine appetite through modulating the gut microbiome in the pig industry.},
}
@article {pmid30547746,
year = {2018},
author = {Fitzgerald, CB and Shkoporov, AN and Sutton, TDS and Chaplin, AV and Velayudhan, V and Ross, RP and Hill, C},
title = {Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa.},
journal = {BMC genomics},
volume = {19},
number = {1},
pages = {931},
doi = {10.1186/s12864-018-5313-6},
pmid = {30547746},
issn = {1471-2164},
support = {SFI/12/RC/2273//Science Foundation Ireland/Ireland ; SFI/14/SP APC/B3032//Science Foundation Ireland (IE)/ ; NA//Janssen Biotech (US)/ ; },
abstract = {BACKGROUND: Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.<br><br>RESULTS: In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms.<br><br>CONCLUSIONS: Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2-165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T).},
}
@article {pmid30547182,
year = {2018},
author = {Fischinger, S and Boudreau, CM and Butler, AL and Streeck, H and Alter, G},
title = {Sex differences in vaccine-induced humoral immunity.},
journal = {Seminars in immunopathology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00281-018-0726-5},
pmid = {30547182},
issn = {1863-2300},
abstract = {Vaccines are among the most impactful public health interventions, preventing millions of new infections and deaths annually worldwide. However, emerging data suggest that vaccines may not protect all populations equally. Specifically, studies analyzing variation in vaccine-induced immunity have pointed to the critical impact of genetics, the environment, nutrition, the microbiome, and sex in influencing vaccine responsiveness. The significant contribution of sex to modulating vaccine-induced immunity has gained attention over the last years. Specifically, females typically develop higher antibody responses and experience more adverse events following vaccination than males. This enhanced immune reactogenicity among females is thought to render females more resistant to infectious diseases, but conversely also contribute to higher incidence of autoimmunity among women. Dissection of mechanisms which underlie sex differences in vaccine-induced immunity has implicated hormonal, genetic, and microbiota differences across males and females. This review will highlight the importance of sex-dependent differences in vaccine-induced immunity and specifically will address the role of sex as a modulator of humoral immunity, key to long-term pathogen-specific protection.},
}
@article {pmid30546361,
year = {2018},
author = {Treangen, TJ and Wagner, J and Burns, MP and Villapol, S},
title = {Traumatic Brain Injury in Mice Induces Acute Bacterial Dysbiosis Within the Fecal Microbiome.},
journal = {Frontiers in immunology},
volume = {9},
number = {},
pages = {2757},
doi = {10.3389/fimmu.2018.02757},
pmid = {30546361},
issn = {1664-3224},
abstract = {The secondary injury cascade that is activated following traumatic brain injury (TBI) induces responses from multiple physiological systems, including the immune system. These responses are not limited to the area of brain injury; they can also alter peripheral organs such as the intestinal tract. Gut microbiota play a role in the regulation of immune cell populations and microglia activation, and microbiome dysbiosis is implicated in immune dysregulation and behavioral abnormalities. However, changes to the gut microbiome induced after acute TBI remains largely unexplored. In this study, we have investigated the impact of TBI on bacterial dysbiosis. To test the hypothesis that TBI results in changes in microbiome composition, we performed controlled cortical impact (CCI) or sham injury in male 9-weeks old C57BL/6J mice. Fresh stool pellets were collected at baseline and at 24 h post-CCI. 16S rRNA based microbiome analysis was performed to identify differential abundance in bacteria at the genus and species level. In all baseline vs. 24 h post-CCI samples, we evaluated species-level differential abundances via clustered and annotated operational taxonomic units (OTU). At a high-level view, we observed significant changes in two genera after TBI, Marvinbryantia, and Clostridiales. At the species-level, we found significant decreases in three species (Lactobacillus gasseri, Ruminococcus flavefaciens, and Eubacterium ventriosum), and significant increases in two additional species (Eubacterium sulci, and Marvinbryantia formatexigens). These results pinpoint critical changes in the genus-level and species-level microbiome composition in injured mice compared to baseline; highlighting a previously unreported acute dysbiosis in the microbiome after TBI.},
}
@article {pmid30546350,
year = {2018},
author = {Burrichter, A and Denger, K and Franchini, P and Huhn, T and Müller, N and Spiteller, D and Schleheck, D},
title = {Anaerobic Degradation of the Plant Sugar Sulfoquinovose Concomitant With H2S Production: Escherichia coli K-12 and Desulfovibrio sp. Strain DF1 as Co-culture Model.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2792},
doi = {10.3389/fmicb.2018.02792},
pmid = {30546350},
issn = {1664-302X},
abstract = {Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is produced by plants and other phototrophs and its biodegradation is a relevant component of the biogeochemical carbon and sulfur cycles. SQ is known to be degraded by aerobic bacterial consortia in two tiers via C3-organosulfonates as transient intermediates to CO2, water and sulfate. In this study, we present a first laboratory model for anaerobic degradation of SQ by bacterial consortia in two tiers to acetate and hydrogen sulfide (H2S). For the first tier, SQ-degrading Escherichia coli K-12 was used. It catalyzes the fermentation of SQ to 2,3-dihydroxypropane-1-sulfonate (DHPS), succinate, acetate and formate, thus, a novel type of mixed-acid fermentation. It employs the characterized SQ Embden-Meyerhof-Parnas pathway, as confirmed by mutational and proteomic analyses. For the second tier, a DHPS-degrading Desulfovibrio sp. isolate from anaerobic sewage sludge was used, strain DF1. It catalyzes another novel fermentation, of the DHPS to acetate and H2S. Its DHPS desulfonation pathway was identified by differential proteomics and demonstrated by heterologously produced enzymes: DHPS is oxidized via 3-sulfolactaldehyde to 3-sulfolactate (SL) by two NAD+-dependent dehydrogenases (DhpA, SlaB); the SL is cleaved by an SL sulfite-lyase known from aerobic bacteria (SuyAB) to pyruvate and sulfite. The pyruvate is oxidized to acetate, while the sulfite is used as electron acceptor in respiration and reduced to H2S. In conclusion, anaerobic sulfidogenic SQ degradation was demonstrated as a novel link in the biogeochemical sulfur cycle. SQ is also a constituent of the green-vegetable diet of herbivores and omnivores and H2S production in the intestinal microbiome has many recognized and potential contributions to human health and disease. Hence, it is important to examine bacterial SQ degradation also in the human intestinal microbiome, in relation to H2S production, dietary conditions and human health.},
}
@article {pmid30546102,
year = {2018},
author = {Ooi, CY and Syed, SA and Rossi, L and Garg, M and Needham, B and Avolio, J and Young, K and Surette, MG and Gonska, T},
title = {Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17834},
doi = {10.1038/s41598-018-36364-6},
pmid = {30546102},
issn = {2045-2322},
abstract = {Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Next to progressive airway disease, CF is also associated with intestinal inflammation and dysbiosis. Ivacaftor, a CFTR potentiator, has improved pulmonary and nutritional status but its effects on the intestinal microbiota and inflammation are unclear. Hence, we assessed the changes on the intestinal microbial communities (16S rRNA variable 3 gene region) and inflammatory markers (calprotectin and M2-pyruvate kinase [M2-PK]) in 16 CF individuals (8 children and 8 adults) before and after (median 6.1 months) ivacaftor. Stool calprotectin significantly decreased following ivacaftor (median [IQR]: 154.4 [102.1-284.2] vs. 87.5 [19.5-190.2] mg/kg, P = 0.03). There was a significant increase in Akkermansia with ivacaftor. Increased abundance of Akkermansia was associated with normal stool M2-PK concentrations, and decreased abundances of Enterobacteriaceae correlated with decreased stool calprotectin concentrations. In summary, changes in the gut microbiome and decrease in intestinal inflammation was associated with Ivacaftor treatment among individuals with CF carrying at least one gating CFTR mutation. Thus, CFTR-modifying therapy may adequately improve the aberrant pathophysiology and milieu of the CF gut to favor a more healthy microbiota, which in turn reduces intestinal inflammation.},
}
@article {pmid30545671,
year = {2018},
author = {Harris-Ricardo, J and Fang, L and Herrera-Herrera, A and Fortich-Mesa, N and Olier-Castillo, D and Cavanzo-Rojas, D and González-Quintero, R},
title = {Bacterial profile of the supragingival dental biofilm in children with deciduous and early mixed dentition using next generation sequencing (HOMINGS) technique.},
journal = {Enfermedades infecciosas y microbiologia clinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eimc.2018.10.019},
pmid = {30545671},
issn = {1578-1852},
abstract = {OBJECTIVE: Tdescribe the bacterial profile of the supragingival biofilm of children with temporary dentition (CTD) and early mixed dentition (CEMD), with the next-generation sequencing (HOMINGS) technique.<br><br>METHOD: A comparative descriptive study was carried out with 30 systemically healthy children aged between 5 and 7 years old from public schools in Cartagena-Colombia. All participants were caries-free applying the criteria of the International Caries Detection and Assessment System (ICDAS II) and had no caries experience according to the Decayed, Missing and Filled Teeth (DMFT) index. Supragingival biofilm samples were collected. Bacterial DNA was extracted and used for analysis using HOMINGS (Human Oral Microbe Identification using Next-Generation Sequencing) based on the sequencing of the V3-V4 region of the 16S rRNA gene using the Illumina MiSeq platform (V3-V4 primers).<br><br>RESULTS: A total of 360 species-specific and 65 genus-specific probes were identified. The bacterial genus most predominant in CTD were Streptococcus, Actinomyces, Veillonella and Fusobacterium (29.2% of all bacterial DNA present), while in CEMD the most predominant were Streptococcus, Leptotrichia, TM7 and Porphyromonas (24.5% of all bacterial DNA present). The bacterial species with the highest relative abundance in the oral biofilm microbiome from CTD were Streptococcus sanguinis, Rothia aeria, Gemella haemolysans, while in CEMD they were S. sanguinis, Leptotrichia spp. HOT-417 and Leptotrichia spp. HOT-498. The Shannon diversity index was 2.77 (SD=0.26) for CTD and 3.01 (SD=0.39) for CEMD (P=0.06).<br><br>CONCLUSIONS: The analysis of the bacterial profile of the supragingival dental biofilm in children with DMFT, by means of HOMINGS showed low microbiological diversity both in presence and in relative abundance in terms of genus as well as bacterial species.},
}
@article {pmid30545571,
year = {2018},
author = {Marlicz, W and Koulaouzidis, A},
title = {Celiac disease and small-bowel enteropathy - Seeing beyond the haze, the mist and the fog.},
journal = {Computers in biology and medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.compbiomed.2018.12.003},
pmid = {30545571},
issn = {1879-0534},
}
@article {pmid30545401,
year = {2018},
author = {Forbes, JD and Chen, CY and Knox, NC and Marrie, RA and El-Gabalawy, H and de Kievit, T and Alfa, M and Bernstein, CN and Van Domselaar, G},
title = {A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {221},
doi = {10.1186/s40168-018-0603-4},
pmid = {30545401},
issn = {2049-2618},
abstract = {BACKGROUND: Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at a higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology is common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of the gut microbiome in IMIDs. This study used 16S rRNA gene amplicon sequencing to compare the gut microbiota of patients with Crohn's disease (CD; N = 20), ulcerative colitis (UC; N = 19), multiple sclerosis (MS; N = 19), and rheumatoid arthritis (RA; N = 21) versus healthy controls (HC; N = 23). Biological replicates were collected from participants within a 2-month interval. This study aimed to identify common (or unique) taxonomic biomarkers of IMIDs using both differential abundance testing and a machine learning approach.<br><br>RESULTS: Significant microbial community differences between cohorts were observed (pseudo F = 4.56; p = 0.01). Richness and diversity were significantly different between cohorts (pFDR < 0.001) and were lowest in CD while highest in HC. Abundances of Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, and Streptococcus (pFDR < 0.001) were significantly higher in all disease cohorts relative to HC, whereas significantly lower abundances were observed for Gemmiger, Lachnospira, and Sporobacter (pFDR < 0.001). Several taxa were found to be differentially abundant in IMIDs versus HC including significantly higher abundances of Intestinibacter in CD, Bifidobacterium in UC, and unclassified Erysipelotrichaceae in MS and significantly lower abundances of Coprococcus in CD, Dialister in MS, and Roseburia in RA. A machine learning approach to classify disease versus HC was highest for CD (AUC = 0.93 and AUC = 0.95 for OTU and genus features, respectively) followed by MS, RA, and UC. Gemmiger and Faecalicoccus were identified as important features for classification of subjects to CD and HC. In general, features identified by differential abundance testing were consistent with machine learning feature importance.<br><br>CONCLUSIONS: This study identified several gut microbial taxa with differential abundance patterns common to IMIDs. We also found differentially abundant taxa between IMIDs. These taxa may serve as biomarkers for the detection and diagnosis of IMIDs and suggest there may be a common component to IMID etiology.},
}
@article {pmid30545218,
year = {2018},
author = {Liu, CW and Chi, L and Tu, P and Xue, J and Ru, H and Lu, K},
title = {Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.8b00666},
pmid = {30545218},
issn = {1535-3907},
abstract = {Quantitative metaproteomics is a relatively new research field by applying proteomics technique to study microbial proteins of microbiome, and holds the great potential to truly quantify the functional proteins actually expressed by microbes in the biological environment such as gastrointestinal tract. The significant association between arsenic exposure and gut microbiome perturbations has been reported; however, metaproteomics has not yet been applied to study arsenic induced proteome changes of microbiome. Most importantly, to our knowledge, isobaric-labeling based large-scale metaproteomics has not been reported using the advanced database search approaches such as MetaPro-IQ and matched metagenome database search strategies to provide high quantification accuracy and less missing quantification values. In the present study, a new experimental workflow coupled with isobaric labeling and MetaPro-IQ was demonstrated for metaproteomics study of arsenic induced gut microbiome perturbations. The advantages of this workflow were also discussed. For all 18 fecal samples analyzed, 7,611 protein groups were quantified without any missing values. The consistent results of expression profiles were observed between 16S rRNA gene sequencing and metaproteomics. This isobaric labeling based workflow demonstrated the significant improvement of quantitative metaproteomics for gut microbiome study.},
}
@article {pmid30544974,
year = {2018},
author = {Mohammed, H and Varoni, EM and Cochis, A and Cordaro, M and Gallenzi, P and Patini, R and Staderini, E and Lajolo, C and Rimondini, L and Rocchetti, V},
title = {Oral Dysbiosis in Pancreatic Cancer and Liver Cirrhosis: A Review of the Literature.},
journal = {Biomedicines},
volume = {6},
number = {4},
pages = {},
doi = {10.3390/biomedicines6040115},
pmid = {30544974},
issn = {2227-9059},
abstract = {The human body is naturally colonized by a huge number of different commensal microbial species, in a relatively stable equilibrium. When this microbial community undergoes dysbiosis at any part of the body, it interacts with the innate immune system and results in a poor health status, locally or systemically. Research studies show that bacteria are capable of significantly influencing specific cells of the immune system, resulting in many diseases, including a neoplastic response. Amongst the multiple different types of diseases, pancreatic cancer and liver cirrhosis were significantly considered in this paper, as they are major fatal diseases. Recently, these two diseases were shown to be associated with increased or decreased numbers of certain oral bacterial species. These findings open the way for a broader perception and more specific investigative studies, to better understand the possible future treatment and prevention. This review aims to describe the correlation between oral dysbiosis and both pancreatic cancer and liver cirrhotic diseases, as well as demonstrating the possible diagnostic and treatment modalities, relying on the oral microbiota, itself, as prospective, simple, applicable non-invasive approaches to patients, by focusing on the state of the art. PubMed was electronically searched, using the following key words: &quot;oral microbiota&quot; and &quot;pancreatic cancer&quot; (PC), &quot;liver cirrhosis&quot;, &quot;systemic involvement&quot;, and &quot;inflammatory mediators&quot;. Oral dysbiosis is a common problem related to poor oral or systemic health conditions. Oral pathogens can disseminate to distant body organs via the local, oral blood circulation, or pass through the gastrointestinal tract and enter into the systemic circulation. Once oral pathogens reach an organ, they modify the immune response and stimulate the release of the inflammatory mediators, this results in a disease. Recent studies have reported a correlation between oral dysbiosis and the increased risk of pancreatic and liver diseases and provided evidence of the presence of oral pathogens in diseased organs. The profound impact that microbial communities have on human health, provides a wide domain towards precisely investigating and clearly understanding the mechanism of many diseases, including cancer. Oral microbiota is an essential contributor to health status and imbalance in this community was correlated to oral and systemic diseases. The presence of elevated numbers of certain oral bacteria, particularly P. gingivalis, as well as elevated levels of blood serum antibodies, against this bacterial species, was associated with a higher risk of pancreatic cancer and liver cirrhosis incidence. Attempts are increasingly directed towards investigating the composition of oral microbiome as a simple diagnostic approach in multiple diseases, including pancreatic and liver pathosis. Moreover, treatment efforts are concerned in the recruitment of microbiota, for remedial purposes of the aforementioned and other different diseases. Further investigation is required to confirm and clarify the role of oral microbiota in enhancing pancreatic and liver diseases. Improving the treatment modalities requires an exertion of more effort, especially, concerning the microbiome engineering and oral microbiota transplantation.},
}
@article {pmid30544946,
year = {2018},
author = {Kelly, D and Yang, L and Pei, Z},
title = {Gut Microbiota, Fusobacteria, and Colorectal Cancer.},
journal = {Diseases (Basel, Switzerland)},
volume = {6},
number = {4},
pages = {},
doi = {10.3390/diseases6040109},
pmid = {30544946},
issn = {2079-9721},
support = {R21DE025352//National Institute of Dental and Craniofacial Research/ ; R01DK110014//National Institute of Diabetes and Digestive and Kidney Disease/ ; R01CA204113 and U01CA182370//National Cancer Institute of the National Institutes of Health/ ; },
abstract = {The gut microbiota has emerged as an environmental contributor to colorectal cancer (CRC) in both animal models and human studies. It is now generally accepted that bacteria are ubiquitous colonizers of all exposed human body surfaces, including the entire alimentary tract (5). Recently, the concept that a normal bacterial microbiota is essential for the development of inflammation-induced carcinoma has emerged from studies of well-known colonic bacterial microbiota. This review explores the evidence for a role of fusobacteria, an anaerobic gram-negative bacterium that has repeatedly been detected at colorectal tumor sites in higher abundance than surrounding histologically normal tissue. Mechanistic studies provide insight on the interplay between fusobacteria, other gut microbiota, barrier functions, and host responses. Studies have shown that fusobacteria activate host inflammatory responses designed to protect against pathogens that promote tumor growth. We discuss how future research identifying the pathophysiology underlying fusobacteria colon colonization during colorectal cancer may lead to new therapeutic targets for cancer. Furthermore, disease-protective strategies suppressing tumor development by targeting the local tumor environment via bacteria represent another exciting avenue for researchers and are highlighted in this review.},
}
@article {pmid30544936,
year = {2018},
author = {D'Argenio, V},
title = {The Prenatal Microbiome: A New Player for Human Health.},
journal = {High-throughput},
volume = {7},
number = {4},
pages = {},
doi = {10.3390/ht7040038},
pmid = {30544936},
issn = {2571-5135},
abstract = {The last few years have featured an increasing interest in the study of the human microbiome and its correlations with health status. Indeed, technological advances have allowed the study of microbial communities to reach a previously unthinkable sensitivity, showing the presence of microbes also in environments usually considered as sterile. In this scenario, microbial communities have been described in the amniotic fluid, the umbilical blood cord, and the placenta, denying a dogma of reproductive medicine that considers the uterus like a sterile womb. This prenatal microbiome may play a role not only in fetal development but also in the predisposition to diseases that may develop later in life, and also in adulthood. Thus, the aim of this review is to report the current knowledge regarding the prenatal microbiome composition, its association with pathological processes, and the future perspectives regarding its manipulation for healthy status promotion and maintenance.},
}
@article {pmid30544686,
year = {2018},
author = {Li, Y and Zhang, T and Chen, GY},
title = {Flavonoids and Colorectal Cancer Prevention.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {7},
number = {12},
pages = {},
doi = {10.3390/antiox7120187},
pmid = {30544686},
issn = {2076-3921},
support = {NIFA 2018-67017-27520//U.S. Department of Agriculture/ ; CA170922//U.S. Department of Defense/ ; },
abstract = {Colorectal cancer (CRC) is the third most common cancer, but despite advances in treatment, it remains the second most common cause of cancer-related mortality. Prevention may, therefore, be a key strategy in reducing colorectal cancer deaths. Given reports of an inverse association between fruit and vegetable consumption with colorectal cancer risk, there has been significant interest in understanding the metabolism and bioactivity of flavonoids, which are highly abundant in fruits and vegetables and account for their pigmentation. In this review, we discuss host and microbiota-mediated metabolism of flavonoids and the potential mechanisms by which flavonoids can exert protective effects against colon tumorigenesis, including regulation of signaling pathways involved in apoptosis, cellular proliferation, and inflammation and modulation of the gut microbiome.},
}
@article {pmid30544624,
year = {2018},
author = {Li, XW and Chen, HP and He, YY and Chen, WL and Chen, JW and Gao, L and Hu, HY and Wang, J},
title = {Effects of Rich-Polyphenols Extract of Dendrobium loddigesii on Anti-Diabetic, Anti-Inflammatory, Anti-Oxidant, and Gut Microbiota Modulation in db/db Mice.},
journal = {Molecules (Basel, Switzerland)},
volume = {23},
number = {12},
pages = {},
doi = {10.3390/molecules23123245},
pmid = {30544624},
issn = {1420-3049},
support = {2015A030313119//Department of Science and Technology of Guangdong Province/ ; 2014A020221006//Department of Science and Technology of Guangdong Province/ ; },
abstract = {Dendrobium is a traditional Chinese herb with anti-diabetic effects and has diverse bibenzyls as well as phenanthrenes. Little is known about Dendrobium polyphenols anti-diabetic activities, so, a rich-polyphenols extract of D. loddigesii (DJP) was used for treatment of diabetic db/db mice; the serum biochemical index and tissue appearance were evaluated. In order to gain an insight into the anti-diabetic mechanism, the oxidative stress index, tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6) and gut microbiota modulation were determined by ELISA, immunohistochemistry or high throughput sequencing 16S rRNA gene. The results revealed that DJP had the effects to decrease the blood glucose, body weight, low density lipoprotein cholesterol (LDL-C) levels and increase insulin (INS) level in the mice. DJP improved the mice fatty liver and diabetic nephropathy. DJP showed the anti-oxidative abilities to reduce the malondialdehyde (MDA) level and increase the contents of superoxide dismutase (SOD), catalase (CAT) as well as glutathione (GSH). DJP exerted the anti-inflammatory effects of decreasing expression of IL-6 and TNF-α. After treatment of DJP, the intestinal flora balance of the mice was ameliorated, increasing Bacteroidetes to Firmicutes ratios as well as the relative abundance of Prevotella/Akkermansia and reducing the relative abundance of S24-7/Rikenella/Escherichia coli. The function's prediction of gut microbiota indicated that the microbial compositions involved carbohydrate metabolism or lipid metabolism were changed. This study revealed for the first time that DJP improves the mice symptoms of diabetes and complications, which might be due to the effects that DJP induced the decrease of inflammation as well as oxidative stress and improvement of intestinal flora balance.},
}
@article {pmid30544486,
year = {2018},
author = {Skonieczna-Żydecka, K and Marlicz, W and Misera, A and Koulaouzidis, A and Łoniewski, I},
title = {Microbiome-The Missing Link in the Gut-Brain Axis: Focus on Its Role in Gastrointestinal and Mental Health.},
journal = {Journal of clinical medicine},
volume = {7},
number = {12},
pages = {},
doi = {10.3390/jcm7120521},
pmid = {30544486},
issn = {2077-0383},
abstract = {The central nervous system (CNS) and the human gastrointestinal (GI) tract communicate through the gut-brain axis (GBA). Such communication is bi-directional and involves neuronal, endocrine, and immunological mechanisms. There is mounting data that gut microbiota is the source of a number of neuroactive and immunocompetent substances, which shape the structure and function of brain regions involved in the control of emotions, cognition, and physical activity. Most GI diseases are associated with altered transmission within the GBA that are influenced by both genetic and environmental factors. Current treatment protocols for GI and non-GI disorders may positively or adversely affect the composition of intestinal microbiota with a diverse impact on therapeutic outcome(s). Alterations of gut microbiota have been associated with mood and depressive disorders. Moreover, mental health is frequently affected in GI and non-GI diseases. Deregulation of the GBA may constitute a grip point for the development of diagnostic tools and personalized microbiota-based therapy. For example, next generation sequencing (NGS) offers detailed analysis of microbiome footprints in patients with mental and GI disorders. Elucidating the role of stem cell⁻host microbiome cross talks in tissues in GBA disorders might lead to the development of next generation diagnostics and therapeutics. Psychobiotics are a new class of beneficial bacteria with documented efficacy for the treatment of GBA disorders. Novel therapies interfering with small molecules involved in adult stem cell trafficking are on the horizon.},
}
@article {pmid30544260,
year = {2018},
author = {King, JR and Varadé, J and Hammarström, L},
title = {Fucosyltransferase Gene Polymorphisms and Lewisb-Negative Status Are Frequent in Swedish Newborns, With Implications for Infectious Disease Susceptibility and Personalized Medicine.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpids/piy085},
pmid = {30544260},
issn = {2048-7207},
abstract = {Background: Single-nucleotide polymorphisms (SNPs) in the fucosyltransferase genes FUT2 and FUT3 have been associated with susceptibility to various infectious and inflammatory disorders. FUT variations influence the expression of human histo-blood group antigens (HBGAs) (H-type 1 and Lewis), which are highly expressed in the gut and play an important role in microbial attachment, metabolism, colonization, and shaping of the microbiome. In particular, FUT polymorphisms confer susceptibility to specific rotavirus and norovirus genotypes, which has important global health implications.<br><br>Methods: We designed a genotyping method using a nested polymerase chain reaction approach to determine the frequency of SNPs in FUT2 and FUT3, thereby inferring the prevalence of Lewisb-positive, Lewisb-negative, secretor, and nonsecretor phenotypes in 520 Swedish newborns.<br><br>Results: There was an increased frequency of homozygotes for the minor allele for 1 SNP in FUT2 and 4 SNPs in FUT3. Overall, 37.3% of newborns were found to have Lewis b negative phenotypes (Le (a+b-) or Le (a-b-). Using our new, sensitive genotyping method, we were able to genetically define the Le (a-b-) individuals based on their secretor status and found that the frequency of Lewis b negative newborns in our cohort was 28%.<br><br>Conclusions: Given the high frequency of fucosyltransferase polymorphisms observed in our newborn cohort and the implications for disease susceptibility, FUT genotyping might play a future role in personalized health care, including recommendations for disease screening, therapy, and vaccination.},
}
@article {pmid30544156,
year = {2018},
author = {Garcia-Grau, I and Simon, C and Moreno, I},
title = {Uterine microbiome-low biomass and high expectations.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioy257},
pmid = {30544156},
issn = {1529-7268},
abstract = {The existence of different bacterial communities throughout the female reproductive tract has challenged the traditional view of human fetal development as a sterile event. There is still no consensus on what physiological microbiota exists in the upper reproductive tract of the vast majority of women who are not in periods of infection or pregnancy, and the role of bacteria that colonize the upper reproductive tract in uterine diseases or pregnancy outcomes is not well established. Despite published studies and advances in uterine microbiome sequencing, some study aspects-such as study design, sampling method, DNA extraction, sequencing methods, downstream analysis, and assignment of taxa-have not yet been improved and standardized. It is time to further investigate the uterine microbiome to increase our understanding of the female reproductive tract and to develop more personalized reproductive therapies, highlighting the potential importance of using microbiological assessment in infertile patients.},
}
@article {pmid30543923,
year = {2018},
author = {Shoenfeld, Y and Ehrenfeld, M and Perry, O},
title = {The kaleidoscope of autoimmunity - From genes to microbiome.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clim.2018.12.003},
pmid = {30543923},
issn = {1521-7035},
}
@article {pmid30543775,
year = {2018},
author = {von Mutius, E},
title = {Intimate Crosstalk in Lower Airways at the Beginning of Life.},
journal = {Cell host &amp; microbe},
volume = {24},
number = {6},
pages = {758-759},
doi = {10.1016/j.chom.2018.11.014},
pmid = {30543775},
issn = {1934-6069},
abstract = {The early life formation of the immunological and microbial environment of the human lower airways remains unknown. In this issue of Cell Host &amp; Microbe, Pattaroni et al. (2018) shed light on this critical period, which is important for maturation or dysregulation of the microbiome and immune responses and disease development.},
}
@article {pmid30543547,
year = {2018},
author = {Lee, JT and Kim, CM and Ramakrishnan, V},
title = {Microbiome and disease in the upper airway.},
journal = {Current opinion in allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ACI.0000000000000495},
pmid = {30543547},
issn = {1473-6322},
abstract = {PURPOSE OF REVIEW: Microbiome refers to the genetic potential of resident microorganisms that inhabit a given niche. The exact role of the microbiome and its relation to chronic disease processes remains largely unknown, although various associations have been observed. We reviewed current literature investigating the microbiome of the upper airway by subsite (nasal cavity, sinus cavities, nasopharynx, and larynx) and its relation to chronic inflammatory disease processes.<br><br>RECENT FINDINGS: The disruption of indigenous microbiota at a specific subsite may lead to pathogen overgrowth and increased susceptibility to infection. This has previously been demonstrated in the gastrointestinal tract and lower airways. The role of the microbiome and its relation to pathogenesis of disease in the upper airway, however, is less clearly understood. The present review discusses the recent studies that appear to link dysbiosis to upper airway chronic inflammatory diseases.<br><br>SUMMARY: Despite mounting research, the role of microbiota in the upper airway remains poorly understood. Based on review of the current literature comparing healthy versus diseased patients with site-specific inflammatory conditions, a complex consortium of microbial communities inhabits the upper airway. Fluctuations in the baseline microbiome may contribute to disease pathogenesis, and improved understanding of the dynamics between shifting microbiota may be critical to guiding future medical therapy.},
}
@article {pmid30542789,
year = {2018},
author = {Raza, MH and Gul, K and Arshad, A and Riaz, N and Waheed, U and Rauf, A and Aldakheel, F and Alduraywish, S and Rehman, MU and Abdullah, M and Arshad, M},
title = {Microbiota in cancer development and treatment.},
journal = {Journal of cancer research and clinical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00432-018-2816-0},
pmid = {30542789},
issn = {1432-1335},
abstract = {PURPOSE: Human microbiota comprises of a variety of organisms ranging from bacterial species to viruses, fungi, and protozoa which are present on the epidermal and mucosal barriers of the body. It plays a key role in health and survival of the host by regulation of the systemic functions. Its apparent functions in modulation of the host immune system, inducing carcinogenesis and regulation of the response to the cancer therapy through a variety of mechanisms such as bacterial dysbiosis, production of genotoxins, pathobionts, and disruption of the host metabolism are increasingly becoming evident.<br><br>METHODS: Different electronic databases such as PubMed, Google Scholar, and Web of Science were searched for relevant literature which has been reviewed in this article.<br><br>RESULTS: Characterization of the microbiome particularly gut microbiota, understanding of the host-microbiota interactions, and its potential for therapeutic exploitation are necessary for the development of novel anticancer therapeutic strategies with better efficacy and lowered off-target side effects.<br><br>CONCLUSION: In this review, the role of microbiota is explained in carcinogenesis, mechanisms of microbiota-mediated carcinogenesis, and role of gut microbiota in modulation of cancer therapy.},
}
@article {pmid30542327,
year = {2018},
author = {Dai, D and Rhoads, WJ and Edwards, MA and Pruden, A},
title = {Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2695},
doi = {10.3389/fmicb.2018.02695},
pmid = {30542327},
issn = {1664-302X},
abstract = {Hot water premise plumbing has emerged as a critical nexus of energy, water, and public health. The composition of hot water microbiomes is of special interest given daily human exposure to resident flora, especially opportunistic pathogens (OPs), which rely on complex microbial ecological interactions for their proliferation. Here, we applied shotgun metagenomic sequencing to characterize taxonomic and functional shifts in microbiomes as a function of water heater temperature setting, stagnation in distal pipes, and associated shifts in water chemistry. A cross-section of samples from controlled, replicated, pilot-scale hot water plumbing rigs representing different temperature settings (39, 42, and 51°C), stagnation periods (8 h vs. 7 days), and time-points, were analyzed. Temperature setting exhibited an overarching impact on taxonomic and functional gene composition. Further, distinct taxa were selectively enriched by specific temperature settings (e.g., Legionella at 39°C vs. Deinococcus at 51°C), while relative abundances of genes encoding corresponding cellular functions were highly consistent with expectations based on the taxa driving these shifts. Stagnation in distal taps diminished taxonomic and functional differences induced by heating the cold influent water to hot water in recirculating line. In distal taps relative to recirculating hot water, reads annotated as being involved in metabolism and growth decreased, while annotations corresponding to stress response (e.g., virulence disease and defense, and specifically antibiotic resistance) increased. Reads corresponding to OPs were readily identified by metagenomic analysis, with L. pneumophila reads in particular correlating remarkably well with gene copy numbers measured by quantitative polymerase chain reaction. Positive correlations between L. pneumophila reads and those of known protozoan hosts were also identified. Elevated proportions of genes encoding metal resistance and hydrogen metabolism were noted, which was consistent with elevated corrosion-induced metal concentrations and hydrogen generation. This study provided new insights into real-world factors influencing taxonomic and functional compositions of hot water microbiomes. Here metagenomics is demonstrated as an effective tool for screening for potential presence, and even quantities, of pathogens, while also providing diagnostic capabilities for assessing functional responses of microbiomes to various operational conditions. These findings can aid in informing future monitoring and intentional control of hot water microbiomes.},
}
@article {pmid30541945,
year = {2018},
author = {Jayasudha, R and Chakravarthy, SK and Prashanthi, GS and Sharma, S and Garg, P and Murthy, SI and Shivaji, S},
title = {Alterations in gut bacterial and fungal microbiomes are associated with bacterial Keratitis, an inflammatory disease of the human eye.},
journal = {Journal of biosciences},
volume = {43},
number = {5},
pages = {835-856},
pmid = {30541945},
issn = {0973-7138},
abstract = {Dysbiosis, or imbalance in the gut microbiome, has been implicated in auto-immune, inflammatory, neurological diseases as well as in cancers. More recently it has also been shown to be associated with ocular diseases. In the present study, the association of gut microbiome dysbiosis with bacterial Keratitis, an inflammatory eye disease which significantly contributes to corneal blindness, was investigated. Bacterial and fungal gut microbiomes were analysed using fecal samples of healthy controls (HC, n = 21) and bacterial Keratitis patients (BK, n = 19). An increase in abundance of several antiinflammatory organisms including Dialister, Megasphaera, Faecalibacterium, Lachnospira, Ruminococcus and Mitsuokella and members of Firmicutes, Veillonellaceae, Ruminococcaceae and Lachnospiraceae was observed in HC compared to BK patients in the bacterial microbiome. In the fungal microbiome, a decrease in the abundance of Mortierella, Rhizopus, Kluyveromyces, Embellisia and Haematonectria and an increase in the abundance of pathogenic fungi Aspergillus and Malassezia were observed in BK patients compared to HC. In addition, heatmaps, PCoA plots and inferred functional profiles also indicated significant variations between the HC and BK microbiomes, which strongly suggest dysbiosis in the gut microbiome of BK patients. This is the first study demonstrating the association of gut microbiome with the pathophysiology of BK and thus supports the gut-eye axis hypothesis. Considering that Keratitis affects about 1 million people annually across the globe, the data could be the basis for developing alternate strategies for treatment like use of probiotics or fecal transplantation to restore the healthy microbiome as a treatment protocol for Keratitis.},
}
@article {pmid30541780,
year = {2018},
author = {Neumann, AP and Suen, G},
title = {The Phylogenomic Diversity of Herbivore-Associated Fibrobacter spp. Is Correlated to Lignocellulose-Degrading Potential.},
journal = {mSphere},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSphere.00593-18},
pmid = {30541780},
issn = {2379-5042},
abstract = {Members of the genus Fibrobacter are cellulose-degrading bacteria and common constituents of the gastrointestinal microbiota of herbivores. Although considerable phylogenetic diversity is observed among members of this group, few functional differences explaining the distinct ecological distributions of specific phylotypes have been described. In this study, we sequenced and performed a comparative analysis of whole genomes from 38 novel Fibrobacter strains against the type strains for the two formally described Fibrobacter species F. succinogenes strain S85 and F. intestinalis strain NR9. Significant differences in the number of genes encoding carbohydrate-active enzyme families involved in plant cell wall polysaccharide degradation were observed among Fibrobacter phylotypes. F. succinogenes genomes were consistently enriched in genes encoding carbohydrate-active enzymes compared to those of F. intestinalis strains. Moreover, genomes of F. succinogenes phylotypes that are dominant in the rumen had significantly more genes annotated to major families involved in hemicellulose degradation (e.g., CE6, GH10, and GH43) than did the genomes of F. succinogenes phylotypes typically observed in the lower gut of large hindgut-fermenting herbivores such as horses. Genes encoding a putative urease were also identified in 12 of the Fibrobacter genomes, which were primarily isolated from hindgut-fermenting hosts. Screening for growth on urea as the sole source of nitrogen provided strong evidence that the urease was active in these strains. These results represent the strongest evidence reported to date for specific functional differences contributing to the ecology of Fibrobacter spp. in the herbivore gut.IMPORTANCE The herbivore gut microbiome is incredibly diverse, and a functional understanding of this diversity is needed to more reliably manipulate this community for specific gain, such as increased production in ruminant livestock. Microbial degraders of plant cell wall polysaccharides in the herbivore gut, particularly Fibrobacter spp., are of fundamental importance to their hosts for digestion of a diet consisting primarily of recalcitrant plant fibers. Considerable phylogenetic diversity exists among members of the genus Fibrobacter, but much of this diversity remains cryptic. Here, we used comparative genomics, applied to a diverse collection of recently isolated Fibrobacter strains, to identify a robust association between carbohydrate-active enzyme gene content and the Fibrobacter phylogeny. Our results provide the strongest evidence reported to date for functional differences among Fibrobacter phylotypes associated with either the rumen or the hindgut and emphasize the general significance of carbohydrate-active enzymes in the evolution of fiber-degrading bacteria.},
}
@article {pmid30541450,
year = {2018},
author = {Whisner, CM and Maldonado, J and Dente, B and Krajmalnik-Brown, R and Bruening, M},
title = {Diet, physical activity and screen time but not body mass index are associated with the gut microbiome of a diverse cohort of college students living in university housing: a cross-sectional study.},
journal = {BMC microbiology},
volume = {18},
number = {1},
pages = {210},
doi = {10.1186/s12866-018-1362-x},
pmid = {30541450},
issn = {1471-2180},
support = {1DP5OD017910//National Institutes of Health/ ; },
abstract = {BACKGROUND: Modifiable lifestyle factors (e.g. dietary intake and physical activity) are important contributors to weight gain during college. The purpose of this study was to evaluate whether associations exist between body mass index, physical activity, screen time, dietary consumption (fat, protein, carbohydrates, and fiber), and gut microbial diversity during the first year of college. Racially/ethnically diverse college students (n = 82; 61.0% non-white) at a large Southwestern university completed self-reported physical activity and 24-h recall dietary assessments, height and weight measurements, and provided one fecal sample for gut microbiome analysis. Fecal microbial community composition was assessed with Illumina MiSeq next-generation sequencing of PCR amplified 16S rRNA genes. Post-hoc analyses compared microbial diversity by groups of high and low physical activity and fiber intake using QIIME and LEfSe bioinformatics software.<br><br>RESULTS: No statistically significant differences were observed between body mass index and gut microbiome abundance and diversity. Median daily consumption of dietary fiber was 11.2 (7.6, 14.9) g/d, while the median self-reported moderate-to-vigorous physical activity (MVPA) was 55.7 (27.9, 79.3) min/d and screen time 195.0 (195.0, 315.0) min/d. Microbial analysis by LEfSe identified Paraprevotellaceae, Lachnospiraceae, and Lachnospira as important phylotypes in college students reporting greater MVPA, while Enterobacteriaceae and Enterobacteriales were more enriched among students reporting less MVPA (p < 0.05). Barnesiellaceae, Alphaproteobacteria, and Ruminococcus were more abundant taxa among those consuming less than the median fiber intake (p < 0.05). Post-hoc analyses comparing weighted UniFrac distance metrics based on combined categories of high and low MVPA and fiber revealed that clustering distances between members of the high MVPA-low fiber group were significantly smaller when compared to distances between members of all other MVPA-fiber groups (p < 0.0001).<br><br>CONCLUSIONS: Habitual fiber consumption and MVPA behaviors help explain the differential abundance of specific microbial taxa and overall gut microbial diversity differences in first-year college students.},
}
@article {pmid30541282,
year = {2018},
author = {Whidbey, C and Sadler, NC and Nair, RN and Volk, RF and DeLeon, AJ and Bramer, LM and Fansler, SJ and Hansen, JR and Shukla, AK and Jansson, JK and Thrall, BD and Wright, AT},
title = {A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.8b09668},
pmid = {30541282},
issn = {1520-5126},
abstract = {Commensal microorganisms in the mammalian gut play important roles in host health and physiology, but a central challenge remains in achieving a de-tailed mechanistic understanding of specific microbial contributions to host biochemistry. New function-based approaches are needed that analyze gut microbial function at the molecular level by coupling detection and measurements of in situ bio-chemical activity with identification of the responsible microbes and enzymes. We have developed a platform employing β-glucuronidase selective activity-based probes to detect, isolate, and identify the microbial subpopulations in the gut responsible for this xenobiotic metabolism. We find that metabolic activity of gut microbiota can be plastic and that between individuals and during perturbation, phylogenetically disparate populations can provide β-glucuronidase activity. Our work links biochemical activity with molecular-scale resolution without relying on genomic inference.},
}
@article {pmid30525037,
year = {2018},
author = {Mirsepasi-Lauridsen, HC and Vrankx, K and Engberg, J and Friis-Møller, A and Brynskov, J and Nordgaard-Lassen, I and Petersen, AM and Krogfelt, KA},
title = {Disease-Specific Enteric Microbiome Dysbiosis in Inflammatory Bowel Disease.},
journal = {Frontiers in medicine},
volume = {5},
number = {},
pages = {304},
doi = {10.3389/fmed.2018.00304},
pmid = {30525037},
issn = {2296-858X},
abstract = {Inflammatory Bowel disease (IBD) is traditionally divided into Crohn's disease (CD) and ulcerative colitis (UC). UC is a relapsing non-transmural inflammatory disease that is restricted to the colon and is characterized by flare-ups of bloody diarrhea. CD is a chronic, segmental localized granulomatous disease that can affect any part of the entire gastrointestinal tract. Ileo-anal pouch is a procedure restoring functionality of the rectum after a colectomy. IBD is a multifactorial disease and flares of IBD are probably triggered by changes in the intestinal microbiota followed by an abnormal immune response. In this study, we aim to analyze the intestinal bacterial diversity in IBD patients during various stages of disease compared with healthy controls. Permission for human experiments and recruitment of participants was obtained from the Ethic Committee for Copenhagen County hospitals (Permission no. KA-03019, Permission no. KA-20060159). Stools from 26 healthy controls, 42 CD, 38 UC and 18 pouch patients were collected. Stool DNA extraction was performed using Qiagen, DNA mini stool kit Denmark. DGGE-PCR amplifying the V2-V3 region of 16S-rDNA gene of the bacteria was amplified by universal primers HDA1 and HDA2. Analysis of DGGE was performed blinded using BioNumerics version 7.5. After normalization, a DGGE gel band matching was performed. The similarities between profiles were calculated with a ranked Pearson correlation coefficient based on the band matching results using band intensities. Simpson's index of diversity and Pielou's species evenness were calculated. Based on the Shannon Diversity Index, UC patients had lower species diversity and bacterial evenness in comparison to healthy persons, p < 0.05. However, only CD and disease pouch patients had lower species diversity compared to those with inactive disease and healthy controls. Well-functioning pouch patients had decreased species evenness in comparison to diseased pouch patients and control group. During the active disease stage in CD and pouch, the patients have a low bacterial diversity in their gut when compared to the inactive stage. In UC patients, a generally low diversity was observed at all stages of the disease compared to healthy controls.},
}
@article {pmid30524961,
year = {2018},
author = {Carethers, JM},
title = {Clinical and Genetic Factors to Inform Reducing Colorectal Cancer Disparitites in African Americans.},
journal = {Frontiers in oncology},
volume = {8},
number = {},
pages = {531},
doi = {10.3389/fonc.2018.00531},
pmid = {30524961},
issn = {2234-943X},
abstract = {Colorectal cancer (CRC) is the third most prevalent and second deadliest cancer in the U.S. with 140,250 cases and 50,630 deaths for 2018. Prevention of CRC through screening is effective. Among categorized races in the U.S., African Americans (AAs) show the highest incidence and death rates per 100,000 when compared to Non-Hispanic Whites (NHWs), American Indian/Alaskan Natives, Hispanics, and Asian/Pacific Islanders, with an overall AA:NHW ratio of 1.13 for incidence and 1.32 for mortality (2010-2014, seer.cancer.gov). The disparity for CRC incidence and worsened mortality among AAs is likely multifactorial and includes environmental (e.g., diet and intestinal microbiome composition, prevalence of obesity, use of aspirin, alcohol, and tobacco use), societal (e.g., socioeconomic status, insurance and access to care, and screening uptake and behaviors), and genetic (e.g., somatic driver mutations, race-specific variants in genes, and inflammation and immunological factors). Some of these parameters have been investigated, and interventions that address specific parameters have proven to be effective in lowering the disparity. For instance, there is strong evidence raising screening utilization rates among AAs to that of NHWs reduces CRC incidence to that of NHWs. Reducing the age to commence CRC screening in AA patients may further address incidence disparity, due to the earlier age onset of CRC. Identified genetic and epigenetic changes such as reduced MLH1 hypermethylation frequency, presence of inflammation-associated microsatellite alterations, and unique driver gene mutations (FLCN and EPHA6) among AA CRCs will afford more precise approaches toward CRC care, including the use of 5-fluorouracil and anti-PD-1.},
}
@article {pmid30524957,
year = {2018},
author = {Yang, J and Mu, X and Wang, Y and Zhu, D and Zhang, J and Liang, C and Chen, B and Wang, J and Zhao, C and Zuo, Z and Heng, X and Zhang, C and Zhang, L},
title = {Dysbiosis of the Salivary Microbiome Is Associated With Non-smoking Female Lung Cancer and Correlated With Immunocytochemistry Markers.},
journal = {Frontiers in oncology},
volume = {8},
number = {},
pages = {520},
doi = {10.3389/fonc.2018.00520},
pmid = {30524957},
issn = {2234-943X},
abstract = {Background: Association between oral bacteria and increased risk of lung cancer have been reported in several previous studies, however, the potential association between salivary microbiome and lung cancer in non-smoking women have not been evaluated. There is also no report on the relationship between immunocytochemistry markers and salivary microbiota. Method: In this study, we assessed the salivary microbiome of 75 non-smoking female lung cancer patients and 172 matched healthy individuals using 16S rRNA gene amplicon sequencing. We also calculated the Spearman's rank correlation coefficient between salivary microbiota and three immunohistochemical markers (TTF-1, Napsin A and CK7). Result: We analyzed the salivary microbiota of 247 subjects and found that non-smoking female lung cancer patients exhibited oral microbial dysbiosis. There was significantly lower microbial diversity and richness in lung cancer patients when compared to the control group (Shannon index, P < 0.01; Ace index, P < 0.0001). Based on the analysis of similarities, the composition of the microbiota in lung cancer patients also differed from that of the control group (r = 0.454, P < 0.001, unweighted UniFrac; r = 0.113, P < 0.01, weighted UniFrac). The bacterial genera Sphingomonas (P < 0.05) and Blastomonas (P < 0.0001) were relatively higher in non-smoking female lung cancer patients, whereas Acinetobacter (P < 0.001) and Streptococcus (P < 0.01) were higher in controls. Based on Spearman's correlation analysis, a significantly positive correlation can be observed between CK7 and Enterobacteriaceae (r = 0.223, P < 0.05). At the same time, Napsin A was positively associated with genera Blastomonas (r = 0.251, P < 0.05). TTF-1 exhibited a significantly positive correlation with Enterobacteriaceae (r = 0.262, P < 0.05). Functional analysis from inferred metagenomes indicated that oral microbiome in non-smoking female lung cancer patients were related to cancer pathways, p53 signaling pathway, apoptosis and tuberculosis. Conclusions: The study identified distinct salivary microbiome profiles in non-smoking female lung cancer patients, revealed potential correlations between salivary microbiome and immunocytochemistry markers used in clinical diagnostics, and provided proof that salivary microbiota can be an informative source for discovering non-invasive lung cancer biomarkers.},
}
@article {pmid30524928,
year = {2018},
author = {Rijkschroeff, P and Loos, BG and Nicu, EA},
title = {Oral Polymorphonuclear Neutrophil Contributes to Oral Health.},
journal = {Current oral health reports},
volume = {5},
number = {4},
pages = {211-220},
doi = {10.1007/s40496-018-0199-6},
pmid = {30524928},
issn = {2196-3002},
abstract = {Purpose of Review: Oral health is maintained in a dynamic equilibrium between the host immunity and the oral microbiome. Oral polymorphonuclear neutrophils (oPMNs) are important innate immune cells in the oral cavity.<br><br>Recent Findings: The oPMNs play a co-controlling part in the maintenance of oral equilibrium. In human saliva, the oPMNs integrity is preserved, and their function remains unaffected. In general, oPMNs are in a higher state of baseline activation compared to peripheral PMNs. However, in periodontitis, the oPMNs' activation state can result in excessive release of damaging molecules in the extracellular environment.<br><br>Summary: The presence of oPMNs may unwittingly negatively impact the integrity of the oral tissues. While most of the oPMN functions occur intracellularly, release of their potent active mediators into the extracellular environment may jeopardize oral homeostasis and its integrity. The dual nature of oPMNs, both beneficial and detrimental, remains a challenging and understudied topic.},
}
@article {pmid30524418,
year = {2018},
author = {Banerjee, A and Pérez-López, E and Mossman, K},
title = {Commentary: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2863},
doi = {10.3389/fmicb.2018.02863},
pmid = {30524418},
issn = {1664-302X},
}
@article {pmid30524416,
year = {2018},
author = {Nho, SW and Abdelhamed, H and Paul, D and Park, S and Mauel, MJ and Karsi, A and Lawrence, ML},
title = {Taxonomic and Functional Metagenomic Profile of Sediment From a Commercial Catfish Pond in Mississippi.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2855},
doi = {10.3389/fmicb.2018.02855},
pmid = {30524416},
issn = {1664-302X},
abstract = {Metagenomic analyses of microbial communities from aquatic sediments are relatively few, and there are no reported metagenomic studies on sediment from inland ponds used for aquaculture. Catfish ponds in the southeastern U.S. are eutrophic systems. They are fertilized to enhance algae growth and encourage natural food production, and catfish are fed with commercial feed from spring to fall. As result, catfish pond sediment (CPS) contains a very dense, diverse microbial community that has significant effects on the physiochemical parameters of pond dynamics. Here we conducted an in-depth metagenomic analysis of the taxonomic and metabolic capabilities of a catfish pond sediment microbiome from a southeastern U.S. aquaculture farm in Mississippi using Illumina next-generation sequencing. A total of 3.3 Gbp of sequence was obtained, 25,491,518 of which encoded predicted protein features. The pond sediment was dominated by Proteobacteria sequences, followed by Bacteroidetes, Firmicutes, Chloroflexi, and Actinobacteria. Enzyme pathways for methane metabolism/methanogenesis, denitrification, and sulfate reduction appeared nearly complete in the pond sediment metagenome profile. In particular, a large number of Deltaproteobacteria sequences and genes encoding anaerobic functional enzymes were found. This is the first study to characterize a catfish pond sediment microbiome, and it is expected to be useful for characterizing specific changes in microbial flora in response to production practices. It will also provide insight into the taxonomic diversity and metabolic capabilities of microbial communities in aquaculture. Furthermore, comparison with other environments (i.e., river and marine sediments) will reveal habitat-specific characteristics and adaptations caused by differences in nutrients, vegetation, and environmental stresses.},
}
@article {pmid30523776,
year = {2018},
author = {König, S and May, K},
title = {Invited review: Phenotyping strategies and quantitative-genetic background of resistance, tolerance and resilience associated traits in dairy cattle.},
journal = {Animal : an international journal of animal bioscience},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S1751731118003208},
pmid = {30523776},
issn = {1751-732X},
abstract = {In dairy cattle, resistance, tolerance and resilience refer to the adaptation ability to a broad range of environmental conditions, implying stable performances (e.g. production level, fertility status) independent from disease or infection pressure. All three mechanisms resistance, tolerance and resilience contribute to overall robustness, implying the evaluation of phenotyping and breeding strategies for improved robustness in dairy cattle populations. Classically, breeding approaches on improved robustness rely on simple production traits, in combination with detailed environmental descriptors and enhanced statistical modelling to infer possible genotype by environment interactions. In this regard, innovative environmental descriptors were heat stress indicators, and statistical modelling focussed on random regression or reaction norm methodology. A robust animal has high breeding values over a broad spectra of environmental levels. During the last years, direct health traits were included into selection indices, implying advances in genetic evaluations for traits being linked to resistance or tolerance against infectious and non-infectious diseases. Up to now, genetic evaluation for health traits is primarily based on subjectively measured producer-recorded data, with disease trait heritabilities in a low-to-moderate range. Thus, it is imperative to identify objectively measurable phenotypes as suitable biomarkers. New technologies (e.g. mid-infrared spectrometry) offer possibilities to determine potential biomarkers via laboratory analyses. Novel biomarkers include measurable physiological traits (e.g. serum metabolites, hormone levels) as indicators for a current infection, or the host's reaction to environmental stressors. The rumen microbiome composition is proposed as a biomarker to detect interactions between host genotype and environmental effects. The understanding of host genetic variation in disease resistance and individual expression of robustness encourages analyses on the underlying immune response (IR) system. Recent advances have been made in order to infer the genetic background of IR traits and cows immunological competence in relation to functional and production traits. Thus, a last aspect of this review addresses the genetic background and current state of genetic control for resistance to economically relevant infectious and non-infectious dairy cattle diseases by considering immune-related factors.},
}
@article {pmid30523495,
year = {2018},
author = {Mumcu, G and Direskeneli, H},
title = {Triggering agents and microbiome as environmental factors on Behçet's syndrome.},
journal = {Internal and emergency medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11739-018-2000-1},
pmid = {30523495},
issn = {1970-9366},
abstract = {Environmental and other triggering factors are suggested to cause the onset and the clinical relapses of Behçet's syndrome (BS), a multi-systemic inflammatory disorder. In this review, environmental factors are discussed according to their interactions with etiopathogenesis, immune response and disease activity. Stress is a common self-triggering factor for most BS patients. Stimuli such as some foods can activate oral ulcers, and may be linked to the histamine content of the food. Oral/skin trauma and menstruation associated with hormonal factors aggravate, whereas allergy/atopy seem to alleviate the symptoms of BS. Infections are associated with BS, and microbial stimuli can activate inflammation in mucosal surfaces with increased Th1/Th17 responses. Fecal and oral microbiome patterns change in diversity and composition in BS. Better oral hygiene applications and anti-microbial interventions might be helpful to suppress oral ulcers in BS.},
}
@article {pmid30523482,
year = {2018},
author = {Kumari, R and Palaniyandi, S and Hildebrandt, GC},
title = {Microbiome: An Emerging New Frontier in Graft-Versus-Host Disease.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-018-5369-9},
pmid = {30523482},
issn = {1573-2568},
abstract = {Hematopoietic cell transplantation is an intensive therapy used to treat high-risk hematological malignant disorders and other life-threatening hematological and genetic diseases. Graft-versus-host disease (GVHD) presents a barrier to its wider application. A conditioning regimen and medications given to patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HCT) are capable of disturbing the homeostatic crosstalk between the microbiome and the host immune system and of leading to dysbiosis. Intestinal inflammation in the context of GVHD is associated with loss in microbial diversity that could serve as an independent predictor of mortality. Successful gastrointestinal decontamination using high doses of non-absorbable antibiotics likely affect allo-HCT outcomes leading to significantly less acute GVHD (aGVHD). Butyrate-producing Clostridia directly result in the increased presence of regulatory T cells in the gut, which are protective in GVHD development. Beyond the microbiome, Candida, a member of the mycobiome, colonization in the gut has been considered as a risk factor in pathophysiology of aGVHD and reduction in GVHD is observed with antifungal prophylaxis with fluconazole. Reduced number of goblet cells and Paneth cells have been shown to associate with GVHD and has a significant impact on the micro- and mycobiome density and their composition. Lower levels of 3-indoxyl sulfate at initial stages after allo-HCT are related with worse GVHD outcomes and increased mortality. Increased understanding of the vital role of the gut microbiome in GVHD can give directions to move the field towards the development of improved innovative approaches for preventing or treating GVHD following allo-HCT.},
}
@article {pmid30523432,
year = {2018},
author = {Uemura, M and Hayashi, F and Ishioka, K and Ihara, K and Yasuda, K and Okazaki, K and Omata, J and Suzutani, T and Hirakawa, Y and Chiang, C and Aoyama, A and Ohira, T},
title = {Obesity and mental health improvement following nutritional education focusing on gut microbiota composition in Japanese women: a randomised controlled trial.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-018-1873-0},
pmid = {30523432},
issn = {1436-6215},
abstract = {PURPOSE: Gut microbiota composition was supposedly related to obesity and psychological factors. We examined the effects of a nutritional education intervention focusing on gut microbiota composition on obesity and psychological factors among obese women.<br><br>METHODS: Forty-four obese Japanese women aged 40 or older were randomly assigned to either an intervention group (n = 22) or control group (n = 22). The intervention consisted of a 20-min dietary lecture and a 10-min counselling session by registered dieticians, every 2 weeks for eight consecutive weeks. Body weight, height, waist circumference, food frequency, and gut microbiota composition were measured, and self-rated health and psychological factors were scored before and after the intervention.<br><br>RESULTS: All participants completed the 8 week program. After the intervention, dietary fibre intake (p < 0.01), frequency of vegetable consumption (p = 0.020), and frequency of milk and milk product consumption (p < 0.01) increased significantly in the intervention group compared with the control group. Body weight and body mass index (BMI; p < 0.001), waist circumference (p < 0.01), and the depression scale score (p < 0.01) decreased significantly, while significant improvements were found in self-rated health (p = 0.045) and microbiome diversity (p < 0.01).<br><br>CONCLUSION: Nutritional education focusing on gut microbiota composition may improve obesity and psychological factors in obese women.},
}
@article {pmid30523325,
year = {2018},
author = {Guo, GL and Xie, W},
title = {Metformin action through the microbiome and bile acids.},
journal = {Nature medicine},
volume = {24},
number = {12},
pages = {1789-1790},
doi = {10.1038/s41591-018-0273-6},
pmid = {30523325},
issn = {1546-170X},
}
@article {pmid30523320,
year = {2018},
author = {Stower, H},
title = {Environmental shaping of the microbiome.},
journal = {Nature medicine},
volume = {24},
number = {12},
pages = {1782},
doi = {10.1038/s41591-018-0286-1},
pmid = {30523320},
issn = {1546-170X},
}
@article {pmid30523317,
year = {2018},
author = {Stower, H},
title = {The microbiome influence.},
journal = {Nature medicine},
volume = {24},
number = {12},
pages = {1782},
doi = {10.1038/s41591-018-0285-2},
pmid = {30523317},
issn = {1546-170X},
}
@article {pmid30523023,
year = {2018},
author = {Nagarajan, P and Asgari, MM and Green, AC and Guhan, SM and Arron, ST and Proby, CM and Rollison, DE and Harwood, CA and Toland, AE},
title = {Keratinocyte Carcinomas: Current concepts and future research priorities.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-18-1122},
pmid = {30523023},
issn = {1078-0432},
abstract = {Cutaneous squamous cell carcinoma (cSCC) and basal cell carcinoma (BCC) are keratinocyte carcinomas (KC), the most frequently diagnosed cancers in fair-skinned populations. Ultraviolet radiation (UVR) is the main driving carcinogen for these tumors but immunosuppression, pigmentary factors, and aging are also risk factors. Scientific discoveries have improved the understanding of the role of human papillomaviruses (HPV) in cSCC as well as the skin microbiome and a compromised immune system in the development of both cSCC and BCC. Genomic analyses have uncovered genetic risk variants, high-risk susceptibility genes, and somatic events that underlie common pathways important in KC tumorigenesis and tumor characteristics which have enabled development of prediction models for early identification of high-risk individuals. Advances in chemoprevention in high-risk individuals and progress in targeted and immune-based treatment approaches have the potential to decrease the morbidity and mortality associated with these tumors. As the incidence and prevalence of KC continue to increase, strategies for prevention, including effective sun protective behavior, educational interventions and reduction of tanning bed access and usage are essential. Gaps in our knowledge requiring additional research in order to reduce the high morbidity and costs associated with KC include better understanding of factors leading to more aggressive tumors, the roles of microbiome and HPV infection, prediction of response to therapies including immune checkpoint blockade, and how to tailor both prevention and treatment to individual risk factors and needs.},
}
@article {pmid30522530,
year = {2018},
author = {Edlund, A and Yang, Y and Yooseph, S and He, X and Shi, W and McLean, JS},
title = {Uncovering complex microbiome activities via metatranscriptomics during 24 hours of oral biofilm assembly and maturation.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {217},
doi = {10.1186/s40168-018-0591-4},
pmid = {30522530},
issn = {2049-2618},
support = {R00DE024543//National Institute of Dental and Craniofacial Research/ ; K99DE024543//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE023810//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE020102//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; 1R01DE026186//National Institute of Dental and Craniofacial Research/ ; R01GM095373//National Institute of General Medical Sciences/ ; },
abstract = {BACKGROUND: Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processes such as co-aggregation, competition for space and resources, and by bacterially produced reactive agents. Knowledge on the dynamics of assembly within complex communities is very limited and derives mainly from studies composed of a limited number of bacterial species. To fill current knowledge gaps, we applied parallel metagenomic and metatranscriptomic analyses during assembly and maturation of an in vitro oral biofilm. This model system has previously demonstrated remarkable reproducibility in taxonomic composition across replicate samples during maturation.<br><br>RESULTS: Time course analysis of the biofilm maturation was performed by parallel sampling every 2-3 h for 24 h for both DNA and RNA. Metagenomic analyses revealed that community taxonomy changed most dramatically between three and six hours of growth when pH dropped from 6.5 to 5.5. By applying comparative metatranscriptome analysis we could identify major shifts in overall community activities between six and nine hours of growth when pH dropped below 5.5, as 29,015 genes were significantly up- or down- expressed. Several of the differentially expressed genes showed unique activities for individual bacterial genomes and were associated with pyruvate and lactate metabolism, two-component signaling pathways, production of antibacterial molecules, iron sequestration, pH neutralization, protein hydrolysis, and surface attachment. Our analysis also revealed several mechanisms responsible for the niche expansion of the cariogenic pathogen Lactobacillus fermentum.<br><br>CONCLUSION: It is highly regarded that acidic conditions in dental plaque cause a net loss of enamel from teeth. Here, as pH drops below 5.5 pH to 4.7, we observe blooms of cariogenic lactobacilli, and a transition point of many bacterial gene expression activities within the community. To our knowledge, this represents the first study of the assembly and maturation of a complex oral bacterial biofilm community that addresses gene level functional responses over time.},
}
@article {pmid30522523,
year = {2018},
author = {Willis, JR and González-Torres, P and Pittis, AA and Bejarano, LA and Cozzuto, L and Andreu-Somavilla, N and Alloza-Trabado, M and Valentín, A and Ksiezopolska, E and Company, C and Onywera, H and Montfort, M and Hermoso, A and Iraola-Guzmán, S and Saus, E and Labeeuw, A and Carolis, C and Hecht, J and Ponomarenko, J and Gabaldón, T},
title = {Citizen science charts two major &quot;stomatotypes&quot; in the oral microbiome of adolescents and reveals links with habits and drinking water composition.},
journal = {Microbiome},
volume = {6},
number = {1},
pages = {218},
doi = {10.1186/s40168-018-0592-3},
pmid = {30522523},
issn = {2049-2618},
support = {BFU2015-67107//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; SEV-2012-02-08//Ministerio de Economía, Industria y Competitividad, Gobierno de España/ ; Saca la Lengua//&quot;la Caixa&quot; Foundation/ ; },
abstract = {BACKGROUND: The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the adolescent oral microbiome remains poorly studied. Here, we used a citizen science approach and 16S profiling to assess the oral microbiome of 1500 adolescents around Spain and its relationships with lifestyle, diet, hygiene, and socioeconomic and environmental parameters.<br><br>RESULTS: Our results provide a detailed snapshot of the adolescent oral microbiome and how it varies with lifestyle and other factors. In addition to hygiene and dietary habits, we found that the composition of tap water was related to important changes in the abundance of several bacterial genera. This points to an important role of drinking water in shaping the oral microbiota, which has been so far poorly explored. Overall, the microbiome samples of our study can be clustered into two broad compositional patterns (stomatotypes), driven mostly by Neisseria and Prevotella, respectively. These patterns show striking similarities with those found in unrelated populations.<br><br>CONCLUSIONS: We hypothesize that these stomatotypes represent two possible global optimal equilibria in the oral microbiome that reflect underlying constraints of the human oral niche. As such, they should be found across a variety of geographical regions, lifestyles, and ages.},
}
@article {pmid30522511,
year = {2018},
author = {An, Y and Li, Y and Wang, X and Chen, Z and Xu, H and Wu, L and Li, S and Wang, C and Luan, W and Wang, X and Liu, M and Tang, X and Yu, L},
title = {Cordycepin reduces weight through regulating gut microbiota in high-fat diet-induced obese rats.},
journal = {Lipids in health and disease},
volume = {17},
number = {1},
pages = {276},
doi = {10.1186/s12944-018-0910-6},
pmid = {30522511},
issn = {1476-511X},
support = {No.JCYJ2016031100720906//Technology and Innovation Commission of Shenzhen Municipality/ ; },
abstract = {BACKGROUND: An increasing number of studies have shown that obesity is the key etiological agent of cardiovascular diseases, nonalcoholic fatty liver disease, type 2 diabetes and several kinds of cancer and that gut microbiota change was one of the reasons suffering from obesity. At present, the gut microbiota has gained increased attention as a potential energy metabolism organ. Our recent study reported that cordycepin, a major bioactive component separated from Cordyceps militaris, prevented body weight gain in mice fed a high-fat diet directly acting to adipocytes, however, the effect of cordycepin regulating gut microbiota keeps unknown.<br><br>METHODS: In this research, we synthesized cordycepin (3-deoxyadenosine) by chemical methods and verified that cordycepin reduces body weight gain and fat accumulation around the epididymis and the kidneys of rats fed a high-fat diet. Furthermore, we used high-throughput sequencing on a MiSeq Illumina platform to test the species of intestinal bacteria in high-fat-diet-induced obese rats.<br><br>RESULTS: We found that cordycepin modifies the relative abundance of intestinal bacteria in high-fat-diet-induced obese rats. However, cordycepin did not alter the variety of bacteria in the intestine. Cordycepin treatment dramatically reversed the relative abundance of two dominant bacterial phyla (Bacteroidetes and Firmicutes) in the high-fat-diet-induced obese rats, resulting in abundance similar to that of the chow diet group.<br><br>CONCLUSION: Our study suggests that cordycepin can reduce body weight and microbiome done by cordycepin seems be a result among its mechanisms of obesity reduction.},
}
@article {pmid30522199,
year = {2018},
author = {Diao Wenqi, WQ and Xu Ming, M and He Bei, B},
title = {[The microbiome in chronic obstructive pulmonary disease].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {41},
number = {12},
pages = {982-985},
pmid = {30522199},
issn = {1001-0939},
}
@article {pmid30540709,
year = {2018},
author = {Chen, LA and Hourigan, SK and Grigoryan, Z and Gao, Z and Clemente, JC and Rideout, JR and Chirumamilla, S and Rabidazeh, S and Saeed, S and Elson, CO and Oliva-Hemker, M and Blaser, MJ and Sears, CL},
title = {Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPG.0000000000002210},
pmid = {30540709},
issn = {1536-4801},
abstract = {OBJECTIVES: The gut microbiome is believed to play a role in the susceptibility to and treatment of Clostridium difficile infections (CDIs). It is, however, unknown whether the gut microbiome is also affected by asymptomatic C difficile colonization. Our study aimed to evaluate the fecal microbiome of children based on C difficile colonization, and CDI risk factors, including antibiotic use and comorbid inflammatory bowel disease (IBD).<br><br>METHODS: Subjects with IBD and non-IBD controls were prospectively enrolled from pediatric clinics for a biobanking project (n = 113). A fecal sample was collected from each subject for research purposes only and was evaluated for asymptomatic toxigenic C difficile colonization. Fecal microbiome composition was determined by 16S rRNA sequencing.<br><br>RESULTS: We found reduced bacterial diversity and altered microbiome composition in subjects with C difficile colonization, concurrent antibiotic use, and/or concomitant IBD (all P < 0.05). Accounting for antibiotic use and IBD status, children colonized with C difficile had significant enrichment in taxa from the genera Ruminococcus, Eggerthella, and Clostridium. Children without C difficile had increased relative abundances of Faecalibacterium and Rikenellaceae. Imputed metagenomic functions of those colonized were enriched for genes in oxidative phosphorylation and beta-lactam resistance, whereas in the subjects without C difficile, several functions in translation and metabolism were over-represented.<br><br>CONCLUSIONS: In children, C difficile colonization, or factors that predispose to colonization such as antibiotic use and IBD status were associated with decreased gut bacterial diversity and altered microbiome composition. Averting such microbiome alterations may be a method to prevent or treat CDI.},
}
@article {pmid30540706,
year = {2018},
author = {Maltz, RM and Keirsey, J and Kim, SC and Mackos, AR and Gharaibeh, RZ and Moore, CC and Xu, J and Somogyi, A and Bailey, MT},
title = {Social Stress Affects Colonic Inflammation, the Gut Microbiome, and Short Chain Fatty Acid Levels and Receptors.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPG.0000000000002226},
pmid = {30540706},
issn = {1536-4801},
abstract = {OBJECTIVES: Gastrointestinal disorders, such as inflammatory bowel diseases (IBD) and functional gastrointestinal disorders (FGID), involve disrupted homeostatic interactions between the microbiota and the host. Both disorders are worsened during stress, and in laboratory mice, stress exposure has been shown to change the composition of the gut microbiome. Stress-induced changes to the microbiome exacerbate intestinal inflammation and alter intestinal motility in mice. However, it is not yet known whether microbiota-derived short chain fatty acids (butyrate, propionate, and acetate) and their receptors contribute to this effect.<br><br>METHODS: Mice were exposed to a social disruption (SDR) stress, or left undisturbed as a control. After the first stress exposure, mice were orally challenged with Citrobacter rodentium or with vehicle. The levels of SCFAs were measured using gas chromatography-mass spectrometry. SCFA receptors were measured via real time PCR. Microbial community composition was assessed using 16S rRNA gene sequencing.<br><br>RESULTS: Stress exposure reduced colonic SCFA levels. However, stress exposure and C. rodentium significantly increased SCFA levels and changed the expression of SCFA receptors. The levels of SCFAs did not correlate with the severity of colonic inflammation, but the colonic expression of the SCFA receptor GPR41 was positively associated with inflammatory cytokines and colonic histopathology scores. The relative abundances of several taxa of colonic bacteria were significantly changed by stress exposure, including SCFA producers.<br><br>CONCLUSIONS: Social stress can have a significant effect on infection-induced colonic inflammation, and stress-induced changes in microbial-produced metabolites and their receptors may be involved.},
}
@article {pmid30540704,
year = {2018},
author = {Davidovics, ZH and Michail, S and Nicholson, MR and Kociolek, LK and Pai, N and Hansen, R and Schwerd, T and Maspons, A and Shamir, R and Szajewska, H and Thapar, N and de Meij, T and Mosca, A and Vandenplas, Y and Kahn, SA and Kellermayer, R and , },
title = {Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection and Other Conditions in Children: A Joint Position Paper From the North American Society for Pediatric Gastroenterology, Hepatology, and Nutrition and the European Society for Pediatric Gastroenterology, Hepatology, and Nutrition.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPG.0000000000002205},
pmid = {30540704},
issn = {1536-4801},
abstract = {Fecal microbiota transplantation (FMT) is becoming part of the treatment algorithms against recurrent Clostridium difficile infection (rCDI) both in adult and pediatric gastroenterology practice. With our increasing recognition of the critical role the microbiome plays in human health and disease, FMT is also being considered as a potential therapy for other disorders, including inflammatory bowel disease (Crohn disease, ulcerative colitis), graft versus host disease, neuropsychiatric diseases, and metabolic syndrome. Controlled trials with FMT for rCDI have not been performed in children, and numerous clinical and regulatory considerations have to be considered when using this untraditional therapy. This report is intended to provide guidance for FMT in the treatment of rCDI in pediatric patients.},
}
@article {pmid30539975,
year = {2018},
author = {Wagner, NRF and Zaparolli, MR and Cruz, MRR and Schieferdecker, MEM and Campos, ACL},
title = {POSTOPERATIVE CHANGES IN INTESTINAL MICROBIOTA AND USE OF PROBIOTICS IN ROUX-EN-Y GASTRIC BYPASS AND SLEEVE VERTICAL GASTRECTOMY: AN INTEGRATIVE REVIEW.},
journal = {Arquivos brasileiros de cirurgia digestiva : ABCD = Brazilian archives of digestive surgery},
volume = {31},
number = {4},
pages = {e1400},
doi = {10.1590/0102-672020180001e1400},
pmid = {30539975},
issn = {2317-6326},
abstract = {INTRODUCTION: Studies suggest that weight loss induced by bariatric surgery and the remission of some comorbidities may be related to changes in the microbiota profile of individuals undergoing this procedure. In addition, there is evidence that manipulation of the intestinal microbiota may prove to be a therapeutic approach against obesity and metabolic diseases.<br><br>OBJECTIVE: To verify the changes that occur in the intestinal microbiota of patients undergoing bariatric surgery, and the impact of the usage of probiotics in this population.<br><br>METHODS: Articles published between 2007 and 2017 were searched in Medline, Lilacs and Pubmed with the headings: bariatric surgery, microbiota, microbiome and probiotics, in Portuguese, English and Spanish. Of the 166 articles found, only those studies in adults subjected to either Roux-en-Y gastric bypass or sleeve vertical gastrectomy published in original articles were enrolled. In the end, five studies on the change of intestinal microbiota composition, four on the indirect effects of those changes and three on the probiotics administration on this population were enrolled and characterized.<br><br>CONCLUSION: Bariatric surgery provides changes in intestinal microbiota, with a relative increase of the Bacteroidetes and Proteobacteria phyla and reduction of Firmicutes. This is possibly due to changes in the gastro-intestinal flux, coupled with a reduction in acidity, in addition to changes in eating habits. The usage of probiotics seems to reduce the gastro-intestinal symptoms in the post-surgery, favor the increase of vitamin B12 synthesis, as well as potentiate weight loss.},
}
@article {pmid30539656,
year = {2018},
author = {Yacoub, R and Nadkarni, GN and McSkimming, DI and Chaves, LD and Abyad, S and Bryniarski, MA and Honan, AM and Thomas, SA and Gowda, M and He, JC and Uribarri, J},
title = {Fecal microbiota analysis of polycystic kidney disease patients according to renal function: A pilot study.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {},
number = {},
pages = {1535370218818175},
doi = {10.1177/1535370218818175},
pmid = {30539656},
issn = {1535-3699},
abstract = {IMPACT STATEMENT: The heterogeneity of the renal disease, therapeutic interventions, and the original cause of the renal failure, all directly affect the microbiota. We delineate in this report the direct effect of decreased renal function on the bacterial composition following stringent criteria to eliminate the possibilities of other confounding factors and dissect the direct effects of the uremic milieu. We analyzed the microbiome following three different approaches to further evaluate the effects of mild, moderate and advanced renal insufficiency on the microbiome. We also present here a detailed functional analysis of the projected altered pathways secondary to changes in the microbiome composition.},
}
@article {pmid30539524,
year = {2018},
author = {Tripolt, NJ and Aberer, F and Url, J and Högenauer, C and Schreiber, F and Eherer, A and Sourij, C and Obermayer, AM and Stadlbauer, V and Svehlikova, E and Brunner, M and Kojzar, H and Pferschy, PN and Pieber, TR and Sourij, H},
title = {Impact of Duodeno-Jejunal Bypass Liner (EndoBarrierTM) Implantation on Insulin Sensitivity in Patients with Type 2 Diabetes Mellitus (T2DM): A Study Protocol for a Pilot Trial.},
journal = {Diabetes therapy : research, treatment and education of diabetes and related disorders},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13300-018-0540-z},
pmid = {30539524},
issn = {1869-6953},
support = {Joseph Skoda Award//Austrian Association for Internal Medicine/ ; },
abstract = {INTRODUCTION: A 60-cm endoscopically implantable duodenal-jejunal bypass liner (Endobarrier™, GI Dynamics, Lexington, MA, USA) has been introduced as a therapeutic option to support weight loss for a selected group of obese subjects with type 2 diabetes mellitus (T2DM). The sleeve prevents contact between chyme and the intestinal mucosa of the upper gastrointestinal tract. The primary aim of this study is to elucidate the changes in insulin sensitivity and beta-cell function after EndoBarrier™ implantation in obese patients with T2DM; changes in gut permeability and gut microbiome are also to be examined.<br><br>METHODS: This is an open, single-center, prospective trial in which ten obese subjects with T2DM and suboptimal glycemic control (glycosylated hemoglobin A1c (HbA1c) level > 48 mmol/mol) are investigated with regards to EndoBarrier™ implantation. The Endobarrier™ is implanted shortly after baseline and left in situ for a period of 36 weeks. Dual-energy X-ray absorptiometry measurement, assessment of beta-cell function and insulin sensitivity as measured by a Botnia clamp procedure, and a mixed-meal tolerance test are performed prior to implantation and at 4, 36, and 64 weeks after implantation. The composition of the gut microbiota is characterized from stool using 454 pyrosequencing of 16S rRNA genes. Gut permeability is assessed by a differential sugar absorption method.<br><br>PLANNED OUTCOME: This study will give mechanistic insights in particulr into changes of insulin sensitivity, beta-cell function or microbiome changes over time in subjects implanted with an EndobarrierTM device.<br><br>TRIAL REGISTRATION: NCT02769728, Registered 12 May 2016. Current Protocol Date/Version: 04 September 2017/Version 1.9.},
}
@article {pmid30539425,
year = {2018},
author = {Castillo, DE and Nanda, S and Keri, JE},
title = {Propionibacterium (Cutibacterium) acnes Bacteriophage Therapy in Acne: Current Evidence and Future Perspectives.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
doi = {10.1007/s13555-018-0275-9},
pmid = {30539425},
issn = {2193-8210},
abstract = {Acne vulgaris is the most common dermatological disorder worldwide. It is a multifactorial disease that involves increased sebum production, hyperkeratinization of the pilosebaceous unit, Propionibacterium acnes (Cutibacterium acnes) colonization, and inflammation. The human skin microbiome hosts a wide variety of microorganisms, including bacteria, viruses, and fungi. A delicate balance of these microorganisms is essential for the barrier function of the skin. Propionibacterium acnes represents nearly 90% of the human skin microbiome of healthy adults. Acne is a chronic recurrent disease that requires long-lasting treatment, which has led to the emergence of antibiotic resistance. New alternatives to traditional therapy are emerging, including antimicrobial peptides, natural engineered antibodies, and bacteriophages. Bacteriophages have been shown to play a role in human skin health and disease. There is evidence supporting phage therapy in many types of skin infections. P. acnes bacteriophages have been isolated and characterized. However, only a few in vitro studies have tested the ability of bacteriophages to kill P. acnes. Furthermore, there is no evidence on bacteriophage therapy in the treatment of acne in humans. In this review, we summarize the most recent evidence regarding P. acnes bacteriophages and the potential role of these bacteriophages in the treatment of acne. Further research on this field will provide the evidence to use phage therapy to decrease rates of antibiotic resistance and restore antibiotic susceptibility of P. acnes.},
}
@article {pmid30538693,
year = {2018},
author = {George, F and Daniel, C and Thomas, M and Singer, E and Guilbaud, A and Tessier, FJ and Revol-Junelles, AM and Borges, F and Foligné, B},
title = {Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2899},
doi = {10.3389/fmicb.2018.02899},
pmid = {30538693},
issn = {1664-302X},
abstract = {Lactic acid bacteria (LAB) are representative members of multiple ecosystems on earth, displaying dynamic interactions within animal and plant kingdoms in respect with other microbes. This highly heterogeneous phylogenetic group has coevolved with plants, invertebrates, and vertebrates, establishing either mutualism, symbiosis, commensalism, or even parasitism-like behavior with their hosts. Depending on their location and environment conditions, LAB can be dominant or sometimes in minority within ecosystems. Whatever their origins and relative abundance in specific anatomic sites, LAB exhibit multifaceted ecological and functional properties. While some resident LAB permanently inhabit distinct animal mucosal cavities, others are provided by food and may transiently occupy the gastrointestinal tract. It is admitted that the overall gut microbiome has a deep impact on health and diseases. Here, we examined the presence and the physiological role of LAB in the healthy human and several animal microbiome. Moreover, we also highlighted some dysbiotic states and related consequences for health, considering both the resident and the so-called &quot;transionts&quot; microorganisms. Whether LAB-related health effects act collectively or follow a strain-specificity dogma is also addressed. Besides the highly suggested contribution of LAB to interplay with immune, metabolic, and even brain-axis regulation, the possible involvement of LAB in xenobiotic detoxification processes and metal equilibrium is also tackled. Recent technological developments such as functional metagenomics, metabolomics, high-content screening and design in vitro and in vivo experimental models now open new horizons for LAB as markers applied for disease diagnosis, susceptibility, and follow-up. Moreover, identification of general and more specific molecular mechanisms based on antioxidant, antimicrobial, anti-inflammatory, and detoxifying properties of LAB currently extends their selection and promising use, either as probiotics, in traditional and functional foods, for dedicated treatments and mostly for maintenance of normobiosis and homeostasis.},
}
@article {pmid30538493,
year = {2018},
author = {Togasaki, K and Sukawa, Y and Kanai, T and Takaishi, H},
title = {Clinical efficacy of immune checkpoint inhibitors in the treatment of unresectable advanced or recurrent gastric cancer: an evidence-based review of therapies.},
journal = {OncoTargets and therapy},
volume = {11},
number = {},
pages = {8239-8250},
doi = {10.2147/OTT.S152514},
pmid = {30538493},
issn = {1178-6930},
abstract = {Standard treatment options for patients with advanced gastric cancer (GC) offer limited efficacy and are associated with some toxicity, which necessitates the development of more effective therapies for improving the treatment outcomes for this disease. Immunotherapy involving immune checkpoint inhibitors (ICIs) which inhibit the programmed death 1 (PD-1)/programmed death ligand 1 interaction has emerged as a new treatment option. Nivolumab, a human IgG4 monoclonal antibody inhibitor of PD-1, has demonstrated promising clinical activity and induced durable responses in patients with advanced GC. Nivolumab has recently been approved for treating patients with pretreated advanced GC in Japan. In the present review, we summarized current evidence of the clinical efficacy of ICIs in a variety of solid tumors and reported our experience in patients with GC who were treated with nivolumab and the interesting features that were observed in these cases. Certain ICI-specific clinical features such as pseudo- and hyper-progression of tumor and hyper-response to subsequent chemotherapy have been reported in several cancer types. Lastly, we discussed the present scenario regarding research on biomarkers for assessing the clinical benefits of ICI therapies.},
}
@article {pmid30538187,
year = {2018},
author = {Bevan, ER and McNally, A and Thomas, CM and Piddock, LJV and Hawkey, PM},
title = {Acquisition and Loss of CTX-M-Producing and Non-Producing Escherichia coli in the Fecal Microbiome of Travelers to South Asia.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.02408-18},
pmid = {30538187},
issn = {2150-7511},
abstract = {Over 80% of travelers from the United Kingdom to the Indian subcontinent acquire CTX-M-producing Escherichia coli (CTX-M-EC), but the mechanism of CTX-M-EC acquisition is poorly understood. We aimed to investigate the dynamics of CTX-M-EC acquisition in healthy travelers and how this relates to populations of non-CTX-M-EC in the fecal microbiome. This is a prospective observational study of healthy volunteers traveling from the United Kingdom to South Asia. Fecal samples were collected pre- and post-travel at several time points up to 12 months post-travel. A toothpicking experiment was used to determine the proportion of cephalosporin-sensitive E. coli in fecal samples containing CTX-M-EC. MLST and SNP type of pre-travel and post-travel E. coli were deduced by WGS. CTX-M-EC was acquired by 89% (16/18) of volunteers. Polyclonal acquisition of CTX-M-EC was seen in 8/15 volunteers (all had >3 STs across post-travel samples), suggesting multiple acquisition events. Indistinguishable CTX-M-EC clones (zero SNPs apart) are detectable in serial fecal samples up to 7 months after travel, indicating stable maintenance in the fecal microbiome on return to the United Kingdom in the absence of selective pressure. CTX-M-EC-containing samples were often co-colonized with novel, non-CTX-M strains after travel, indicating that acquisition of non-CTX-M-EC occurs alongside CTX-M-EC. The same pre-travel non-CTX-M strains (<10 SNPs apart) were found in post-travel fecal samples after CTX-M-EC had been lost, suggesting return of the fecal microbiome to the pre-travel state and long-term persistence of minority strains in travelers who acquire CTX-M-EC.IMPORTANCEEscherichia coli strains which produce CTX-M extended-spectrum beta-lactamases are endemic as colonizers of humans and in the environment in South Asia. This study demonstrates that acquisition of CTX-M-producing E. coli (CTX-M-EC) in travelers from the United Kingdom to South Asia is polyclonal, which is likely due to multiple acquisition events from contaminated food and drinking water during travel. CTX-M-EC frequently persists in the fecal microbiome for at least 1 year after acquisition, often alongside newly acquired non-CTX-M E. coli strains. In travelers who acquire CTX-M-EC, pre-travel non-CTX-M E. coli remains as a minority population in the gut until the CTX-M-EC strains are lost. The non-CTX-M strains are then reestablished as the predominant E. coli population. This study has shed light on the dynamics of CTX-M-EC acquisition, colonization, and loss after travel. Future work involving manipulation of nonvirulent resident E. coli could be used to prevent colonization with antibiotic-resistant E. coli.},
}
@article {pmid30538180,
year = {2018},
author = {Lang, JM and Pan, C and Cantor, RM and Tang, WHW and Garcia-Garcia, JC and Kurtz, I and Hazen, SL and Bergeron, N and Krauss, RM and Lusis, AJ},
title = {Impact of Individual Traits, Saturated Fat, and Protein Source on the Gut Microbiome.},
journal = {mBio},
volume = {9},
number = {6},
pages = {},
doi = {10.1128/mBio.01604-18},
pmid = {30538180},
issn = {2150-7511},
abstract = {Interindividual variation in the composition of the human gut microbiome was examined in relation to demographic and anthropometric traits, and to changes in dietary saturated fat intake and protein source. One hundred nine healthy men and women aged 21 to 65, with BMIs of 18 to 36, were randomized, after a two-week baseline diet, to high (15% total energy [E])- or low (7%E)-saturated-fat groups and randomly received three diets (four weeks each) in which the protein source (25%E) was mainly red meat (beef, pork) (12%E), white meat (chicken, turkey) (12%E), and nonmeat sources (nuts, beans, soy) (16%E). Taxonomic characterization using 16S ribosomal DNA was performed on fecal samples collected at each diet completion. Interindividual differences in age, body fat (%), height, ethnicity, sex, and alpha diversity (Shannon) were all significant factors, and most samples clustered by participant in the PCoA ordination. The dietary interventions did not significantly alter the overall microbiome community in ordination space, but there was an effect on taxon abundance levels. Saturated fat had a greater effect than protein source on taxon differential abundance, but protein source had a significant effect once the fat influence was removed. Higher alpha diversity predicted lower beta diversity between the experimental and baseline diets, indicating greater resistance to change in people with higher microbiome diversity. Our results suggest that interindividual differences outweighed the influence of these specific dietary changes on the microbiome and that moderate changes in saturated fat level and protein source correspond to modest changes in the microbiome.IMPORTANCE The microbiome has proven to influence health and disease, but how combinations of external factors affect the microbiome is relatively unknown. Diet can cause changes, but this is usually achieved by altering macronutrient ratios and has not focused on dietary protein source or saturated fat intake levels. In addition, each individual's unique microbiome profile can be an important factor during studies, and it has even been shown to affect therapeutic outcomes. We show here that the effects of individual differences outweighed the effect of experimental diets and that protein source is less influential than saturated fat level. This suggests that fat and protein composition, separate from macronutrient ratio and carbohydrate composition, is an important consideration in dietary studies.},
}
@article {pmid30534422,
year = {2015},
author = {Andrei, M and Nicolaie, T and Stoicescu, A and Teiușanu, A and Gologan, Ș and Diculescu, M},
title = {Intestinal Microbiome, Small Intestinal Bacterial Overgrowth and Inflammatory Bowel Diseases - What are the Connections?.},
journal = {Current health sciences journal},
volume = {41},
number = {3},
pages = {197-203},
doi = {10.12865/CHSJ.41.03.01},
pmid = {30534422},
issn = {2067-0656},
abstract = {IBD (inflammatory bowel diseases) represent chronic idiopathic inflammatory diseases, prone to relapse in the digestive tract; it is estimated that they result from the interaction of the intestinal microbiome with the intestinal immune system. The inflammatory microbiome exerts multiple beneficial roles. Perhaps the central element to developing IBD is dysbiosis; there is still an incompletely established association between intestinal microbiome changes in patients with IBD and SIBO (small intestinal bacterial overgrowth). Influencing the intestinal microbiome may play an adjuvant therapeutic role in the treatment of IBD. We present a synthesis of the connections between the entities mentioned above.},
}
@article {pmid30483601,
year = {2018},
author = {Jeffries, CL and Lawrence, GG and Golovko, G and Kristan, M and Orsborne, J and Spence, K and Hurn, E and Bandibabone, J and Tantely, LM and Raharimalala, FN and Keita, K and Camara, D and Barry, Y and Wat'senga, F and Manzambi, EZ and Afrane, YA and Mohammed, AR and Abeku, TA and Hedge, S and Khanipov, K and Pimenova, M and Fofanov, Y and Boyer, S and Irish, SR and Hughes, GL and Walker, T},
title = {Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa.},
journal = {Wellcome open research},
volume = {3},
number = {},
pages = {113},
doi = {10.12688/wellcomeopenres.14765.2},
pmid = {30483601},
issn = {2398-502X},
support = {//Wellcome Trust/United Kingdom ; },
abstract = {Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations in West Africa. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species across five malaria endemic countries to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species A, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species A. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species A but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.},
}
@article {pmid30537406,
year = {2018},
author = {Singer, E and Bonnette, J and Kenaley, S and Woyke, T and Juenger, TE},
title = {Plant compartment and genetic variation drive microbiome composition in switchgrass roots.},
journal = {Environmental microbiology reports},
volume = {},
number = {},
pages = {},
doi = {10.1111/1758-2229.12727},
pmid = {30537406},
issn = {1758-2229},
abstract = {Switchgrass (Panicum virgatum) is a promising biofuel crop native to the United States with genotypes that are adapted to a wide range of distinct ecosystems. Various plants have been shown to undergo symbioses with plant growth promoting bacteria and fungi, however, plant-associated microbial communities of switchgrass have not been extensively studied to date. We present 16S ribosomal RNA gene and internal transcribed spacer (ITS) data of rhizosphere and root endosphere compartments of four switchgrass genotypes to test the hypothesis that host selection of its root microbiota prevails after transfer to non-native soil. We show that differences in bacterial, archaeal, and fungal community composition and diversity are strongly driven by plant compartment and switchgrass geno- and ecotypes. Plant-associated microbiota show an enrichment in Alphaproteobacteria and Actinobacteria as well as Sordariales and Pleosporales compared to the surrounding soil. Root associated compartments display low-complexity communities dominated and enriched in Actinobacteria, in particular Streptomyces, in the lowland genotypes, and in Alphaproteobacteria, specifically Sphingobium, in the upland genotypes. Our comprehensive root analysis serves as a snapshot into host-specific bacterial and fungal associations of switchgrass in the field and confirms that host-selected microbiomes persist after transfer to non-native soil. This article is protected by copyright. All rights reserved.},
}
@article {pmid30536648,
year = {2018},
author = {Taniguchi, H and Tanisawa, K and Sun, X and Kubo, T and Hoshino, Y and Hosokawa, M and Takeyama, H and Higuchi, M},
title = {Effects of short-term endurance exercise on gut microbiota in elderly men.},
journal = {Physiological reports},
volume = {6},
number = {23},
pages = {e13935},
doi = {10.14814/phy2.13935},
pmid = {30536648},
issn = {2051-817X},
support = {14J03810//Ministry of Education, Culture, Sports, Science, and Technology/ ; 2015-2019//Ministry of Education, Culture, Sports, Science, and Technology/ ; S1511017//Ministry of Education, Culture, Sports, Science, and Technology/ ; //Waseda University/ ; //&quot;Technologies for creating next-generation agriculture, forestry and fisheries&quot;/ ; //Strategic Research Foundation at Private Universities/ ; },
abstract = {Regular exercise reduces the risks for cardiovascular diseases. Although the gut microbiota has been associated with fitness level and cardiometabolic risk factors, the effects of exercise-induced gut microbiota changes in elderly individuals are unclear. This study evaluated whether endurance exercise modulates the gut microbiota in elderly subjects, and whether these changes are associated with host cardiometabolic phenotypes. In a randomized crossover trial, 33 elderly Japanese men participated in a 5-week endurance exercise program. 16S rRNA gene-based metagenomic analyses revealed that the effect of endurance exercise on gut microbiota diversity was not greater than interindividual differences, whereas changes in α-diversity indices during intervention were negatively correlated with changes in systolic and diastolic blood pressure, especially during exercise. Microbial composition analyses showed that the relative abundance of Clostridium difficile significantly decreased, whereas that of Oscillospira significantly increased during exercise as compared to the control period. The changes in these taxa were correlated with the changes in several cardiometabolic risk factors. The findings indicate that short-term endurance exercise has little effect on gut microbiota in elderly individuals, and that the changes in gut microbiota were associated with cardiometabolic risk factors, such as systolic and diastolic blood pressure, providing preliminary insight into the associations between the gut microbiota and cardiometabolic phenotypes.},
}
@article {pmid30536542,
year = {2018},
author = {Wang, H and Xu, J and Tang, W and Li, H and Xia, S and Zhao, J and Zhang, W and Yang, Y},
title = {Removal Efficacy of Opportunistic Pathogens and Bacterial Community Dynamics in Two Drinking Water Treatment Trains.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e1804436},
doi = {10.1002/smll.201804436},
pmid = {30536542},
issn = {1613-6829},
support = {51508397//National Natural Science Foundation of China/ ; 2017YFC0403403//National Key R&amp;D Program of China/ ; //fundamental Research Funds for the Central Universities/ ; },
abstract = {Drinking water treatment processes (DWTPs) impact pathogen colonization and microbial communities in finished water; however, their efficacies against opportunistic pathogens are not fully understood. In this study, the effects of treatment steps on the removal of Legionella spp., Legionella pneumophila, nontuberculous mycobacteria, Mycobacterium avium, and two amoeba hosts (Vermamoeba vermiformis, Acanthamoeba) are evaluated in two parallel trains of DWTPs equipped with different pretreatment units. Quantitative polymerase chain reaction analysis demonstrates significantly reduced numbers of total bacteria, Legionella, and mycobacteria during ozonation, followed by a rebound in granular activated carbon (GAC) filtration, whereas sand filtration exerts an overarching effect in removing microorganisms in both treatment trains. V. vermiformis is more prevalent in biofilm (34%) than water samples (7.7%), while Acanthamoeba is not found in the two trains of DWTPs. Illumina sequencing of bacterial 16S rRNA genes reveals significant community shifts at different treatment steps, as well as distinct bacterial community structures in water and biofilm samples in parallel units (e.g., ozonation, GAC, sand filtration) between the two trains (analysis of similarities (ANOSIM), p < 0.05), implying the potential influence of different pretreatment steps in shaping the downstream microbiome. Overall, the results provide insights to mitigation of opportunistic pathogens and engineer approaches for managing bacterial communities in DWTPs.},
}
@article {pmid30535916,
year = {2018},
author = {Albecker, MA and Belden, LK and McCoy, MW},
title = {Comparative Analysis of Anuran Amphibian Skin Microbiomes Across Inland and Coastal Wetlands.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-018-1295-9},
pmid = {30535916},
issn = {1432-184X},
support = {DEB 1136640//National Science Foundation/ ; Project No. 2014-R/14-HCE-3//North Carolina SeaGrant/ ; },
abstract = {Amphibians host a community of microbes on their skin that helps resist infectious disease via the dual influence of anti-pathogenic microbial species and emergent community dynamics. Many frogs rely on freshwater habitats, but salinization is rapidly increasing saltwater concentrations in wetlands around the globe, increasing the likelihood that frogs will come into contact with salt-contaminated habitats. Currently, we know little about how increased salt exposure will affect the symbiotic relationship between the skin microbes and frog hosts. To better understand how salt exposure in a natural context affects the frog skin microbiome, we use Hyla cinerea, a North American treefrog species that can inhabit brackish wetlands, to explore three questions. First, we determine the extent that microbial communities in the environment and on frog skin are similar across populations. Second, we assess the microbial species richness and relative abundance on frogs from habitats with different salinity levels to determine how salinity affects the microbiome. Third, we test whether the relative abundances of putatively pathogen-resistant bacterial species differ between frogs from inland and coastal environments. We found that the frog microbiome is more similar among frogs than to the microbial communities found in surface water and soil, but there is overlap between frog skin and the environmental samples. Skin microbial community richness did not differ among populations, but the relative abundances of microbes were different across populations and salinities. We found no differences in the relative abundances of the anti-fungal bacteria Janthinobacterium lividum, the genus Pseudomonas, and Serratia marcescens, suggesting that environmental exposure to saltwater has a limited influence on these putatively beneficial bacterial taxa.},
}
@article {pmid30535609,
year = {2018},
author = {Belizário, JE and Faintuch, J},
title = {Microbiome and Gut Dysbiosis.},
journal = {Experientia supplementum (2012)},
volume = {109},
number = {},
pages = {459-476},
doi = {10.1007/978-3-319-74932-7_13},
pmid = {30535609},
issn = {1664-431X},
abstract = {The gastrointestinal (GI) tract is the residence of trillions of microorganisms that include bacteria, archaea, fungi and viruses. The collective genomes of whole microbial communities (microbiota) integrate the gut microbiome. Up to 100 genera and 1000 distinct bacterial species were identified in digestive tube niches. Gut microbiomes exert permanent pivotal functions by promoting food digestion, xenobiotic metabolism and regulation of innate and adaptive immunological processes. Proteins, peptides and metabolites released locally and at distant sites trigger many cell signalling and pathways. This intense crosstalk maintains the host-microbial homeostasis. Diet, age, diet, stress and diseases cause increases or decreases in relative abundance and diversity bacterial specie of GI and other body sites. Studies in animal models and humans have shown that a persistent imbalance of gut's microbial community, named dysbiosis, relates to inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), diabetes, obesity, cancer, cardiovascular and central nervous system disorders. Notably specific bacterial communities are promising clinical target to treat inflammatory and infectious diseases. In this context, intestinal microbiota transplantation (IMT) is one optional treatment for IBD, in particular to patients with recurrent Clostridium difficile-induced pseudo-membrane colitis. Here we discuss on recent discoveries linking whole gut microbiome dysbiosis to metabolic and inflammatory diseases and potential prophylactic and therapeutic applications of faecal and phage therapy, probiotic and prebiotic diets.},
}
@article {pmid30535578,
year = {2018},
author = {Zhang, F and Zheng, W and Xue, Y and Yao, W},
title = {Suhuai suckling piglet hindgut microbiome-metabolome responses to different dietary copper levels.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9533-0},
pmid = {30535578},
issn = {1432-0614},
support = {JATS[2018]287//The earmarked fund for Jiangsu Agricultural Industry Technology System/ ; 31372321//National Natural Science Foundation of China/ ; },
abstract = {Unabsorbed copper accumulates in the hindgut of pigs that consume high levels of dietary copper, which enhances the coselection of antibiotic-resistant bacteria and is considered detrimental to the environment and to porcine health. In our study, a combination of 16S rRNA pyrosequencing and nontargeted metabolomics was used to investigate the microbiome-metabolome responses to dietary copper levels in the hindgut of suckling piglets. The results showed that the dietary copper level affected the abundance of several Clostridia genera and that the relative abundance of butyrate-producing bacteria, such as Coprococcus, Roseburia, and Acidaminococcus, was reduced in the 300 mg kg-1 (high) Cu group. Metabolomic analysis revealed that dietary copper levels affected protein and carbohydrate metabolites, protein biosynthesis, the urea cycle, galactose metabolism, gluconeogenesis, and amino acid metabolism (including the metabolism of arginine, proline, β-alanine, phenylalanine, tyrosine, and methionine). Furthermore, Pearson's correlation analysis showed that the abundance levels of Coprococcus (family Lachnospiraceae) and operational taxonomic unit (OTU) 18 (family Ruminococcaceae) were positively correlated with energy metabolism pathways (gluconeogenesis, glycolysis, and the pentose phosphate pathway). The abundance of Streptococcus was negatively correlated with amino acid metabolism pathways (protein biosynthesis, glycine, serine, threonine, methionine, phenylalanine, and tyrosine metabolism), and OTU583 and OTU1067 (family Rikenellaceae) were positively correlated with amino acid metabolism pathways. These results suggest that the copper levels consumed by LC (low-copper group) versus HC (high-copper group) animals alter the composition of the gut microbiota and modulate microbial metabolic pathways, which may further affect the health of suckling piglets.},
}
@article {pmid30535577,
year = {2018},
author = {Sawyer, A and Staley, C and Lamb, J and Sheaffer, C and Kaiser, T and Gutknecht, J and Sadowsky, MJ and Rosen, C},
title = {Cultivar and phosphorus effects on switchgrass yield and rhizosphere microbial diversity.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-018-9535-y},
pmid = {30535577},
issn = {1432-0614},
support = {2011-68005-30411//National Institute of Food and Agriculture/ ; N/A//Hueg-Harrison Fellowship/ ; },
abstract = {Switchgrass (Panicum virgatum L.) is a native perennial grass identified as a promising biofuel crop for production on marginal agricultural lands. As such, research into switchgrass fertility and the switchgrass rhizosphere microbiome has been ongoing in an effort to increase production sustainability. We examined the effects of cultivar and phosphorus (P) fertilization on biomass yield, P removal, and rhizosphere bacterial and fungal community structure in three switchgrass cultivars: Sunburst, Shawnee, and Liberty. The Liberty cv. is the first lowland-type bioenergy switchgrass adapted to USDA hardiness zones 4, 5, and 6. On a medium soil test P clay loam soil, biomass yield response to applied P was linear, increasing 135 kg ha-1 for every kilogram of P applied prior to establishment. Average post-frost biomass yield was 9.6 Mg ha-1 year-1 when unfertilized, and maximum biomass yield was 10.3 Mg ha-1 year-1 when fertilized at 58.6 kg ha-1 P, suggesting that P application on medium soil test P soils is beneficial for switchgrass establishment and early growth. Switchgrass cv. Shawnee was more productive than cvs. Liberty or Sunburst (11.3, 10.2, and 8.6 Mg ha-1 year-1, respectively). Both bacterial and fungal communities were significantly shaped by cultivar. These shifts, while inconsistent between year and cultivar, may reflect a selection of the microbial community from that present in soil to maximize total nutrient uptake, regardless of additional P amendments. Phosphorus fertilization did not affect microbial community structure. Results of this study suggest that the cultivar-associated selection of particular microbial taxa may have implications for increased productivity.},
}
@article {pmid30535155,
year = {2018},
author = {Van Der Pol, WJ and Kumar, R and Morrow, CD and Blanchard, EE and Taylor, CM and Martin, DH and Lefkowitz, EJ and Muzny, CA},
title = {In Silico and Experimental Evaluation of Primer Sets for Species-Level Resolution of the Vaginal Microbiota Using 16S Ribosomal RNA Gene Sequencing.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiy508},
pmid = {30535155},
issn = {1537-6613},
abstract = {Background: Identification of bacteria in human vaginal specimens is commonly performed using 16S ribosomal RNA (rRNA) gene sequences. However, studies utilize different 16S primer sets, sequence databases, and parameters for sample and database clustering. Our goal was to assess the ability of these methods to detect common species of vaginal bacteria.<br><br>Methods: We performed an in silico analysis of 16S rRNA gene primer sets, targeting different hypervariable regions. Using vaginal samples from women with bacterial vaginosis, we sequenced 16S genes using the V1-V3, V3-V4, and V4 primer sets. For analysis, we used an extended Greengenes database including 16S gene sequences from vaginal bacteria not already present. We compared results with those obtained using the SILVA 16S database. Using multiple database and sample clustering parameters, each primer set's ability to detect common vaginal bacteria at the species level was determined. We also compared these methods to the use of DADA2 for denoising and clustering of sequence reads.<br><br>Results: V4 sequence reads clustered at 99% identity and using the 99% clustered, extended Greengenes database provided optimal species-level identification of vaginal bacteria.<br><br>Conclusions: This study is a first step toward standardizing methods for 16S rRNA gene sequencing and bioinformatics analysis of vaginal microbiome data.},
}
@article {pmid30534630,
year = {2018},
author = {Lindheim, L and Manti, M and Fornes, R and Bashir, M and Czarnewski, P and Diaz, OE and Seifert, M and Engstrand, L and Villablanca, EJ and Obermayer-Pietsch, B and Stener-Victorin, E},
title = {Reproductive and Behavior Dysfunction Induced by Maternal Androgen Exposure and Obesity Is Likely Not Gut Microbiome-Mediated.},
journal = {Journal of the Endocrine Society},
volume = {2},
number = {12},
pages = {1363-1380},
doi = {10.1210/js.2018-00266},
pmid = {30534630},
issn = {2472-1972},
abstract = {Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic disorder of unclear etiology in women and is characterized by androgen excess, insulin resistance, and mood disorders. The gut microbiome is known to influence conditions closely related with PCOS, and several recent studies have observed changes in the stool microbiome of women with PCOS. The mechanism by which the gut microbiome interacts with PCOS is still unknown. We used a mouse model to investigate if diet-induced maternal obesity and maternal DHT exposure, mimicking the lean and obese PCOS women, cause lasting changes in the gut microbiome of offspring. Fecal microbiome profiles were assessed using Illumina paired-end sequencing of 16S rRNA gene V4 amplicons. We found sex-specific effects of maternal and offspring diet, and maternal DHT exposure on fecal bacterial richness and taxonomic composition. Female offspring exposed to maternal obesity and DHT displayed reproductive dysfunction and anxietylike behavior. Fecal microbiota transplantation from DHT and diet-induced obesity exposed female offspring to wild-type mice did not transfer reproductive dysfunction and did not cause the expected increase in anxietylike behavior in recipients. Maternal obesity and androgen exposure affect the gut microbiome of offspring, but the disrupted estrous cycles and anxietylike behavior are likely not microbiome-mediated.},
}
@article {pmid30534614,
year = {2018},
author = {Rampelli, S and Guenther, K and Turroni, S and Wolters, M and Veidebaum, T and Kourides, Y and Molnár, D and Lissner, L and Benitez-Paez, A and Sanz, Y and Fraterman, A and Michels, N and Brigidi, P and Candela, M and Ahrens, W},
title = {Pre-obese children's dysbiotic gut microbiome and unhealthy diets may predict the development of obesity.},
journal = {Communications biology},
volume = {1},
number = {},
pages = {222},
doi = {10.1038/s42003-018-0221-5},
pmid = {30534614},
issn = {2399-3642},
abstract = {It is widely accepted that the intestinal microbiome is connected to obesity, as key mediator of the diet impact on the host metabolic and immunological status. To investigate whether the individual gut microbiome has a potential in predicting the onset and progression of diseases, here we characterized the faecal microbiota of 70 children in a two-time point prospective study, within a four-year window. All children had normal weight at the beginning of this study, but 36 of them gained excessive weight at the subsequent check-up. Microbiome data were analysed together with the hosts' diet information, physical activity, and inflammatory parameters. We find that the gut microbiota structures were stratified into a discrete number of groups, characterized by different biodiversity that correlates with inflammatory markers and dietary habits, regardless of age, gender, and body weight. Collectively, our data underscore the importance of the microbiome-host-diet configuration as a possible predictor of obesity.},
}
@article {pmid30534599,
year = {2018},
author = {Escapa, IF and Chen, T and Huang, Y and Gajare, P and Dewhirst, FE and Lemon, KP},
title = {New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract.},
journal = {mSystems},
volume = {3},
number = {6},
pages = {},
doi = {10.1128/mSystems.00187-18},
pmid = {30534599},
issn = {2379-5077},
abstract = {The expanded Human Oral Microbiome Database (eHOMD) is a comprehensive microbiome database for sites along the human aerodigestive tract that revealed new insights into the nostril microbiome. The eHOMD provides well-curated 16S rRNA gene reference sequences linked to available genomes and enables assignment of species-level taxonomy to most next-generation sequences derived from diverse aerodigestive tract sites, including the nasal passages, sinuses, throat, esophagus, and mouth. Using minimum entropy decomposition coupled with the RDP Classifier and our eHOMD V1-V3 training set, we reanalyzed 16S rRNA V1-V3 sequences from the nostrils of 210 Human Microbiome Project participants at the species level, revealing four key insights. First, we discovered that Lawsonella clevelandensis, a recently named bacterium, and Neisseriaceae [G-1] HMT-174, a previously unrecognized bacterium, are common in adult nostrils. Second, just 19 species accounted for 90% of the total sequences from all participants. Third, 1 of these 19 species belonged to a currently uncultivated genus. Fourth, for 94% of the participants, 2 to 10 species constituted 90% of their sequences, indicating that the nostril microbiome may be represented by limited consortia. These insights highlight the strengths of the nostril microbiome as a model system for studying interspecies interactions and microbiome function. Also, in this cohort, three common nasal species (Dolosigranulum pigrum and two Corynebacterium species) showed positive differential abundance when the pathobiont Staphylococcus aureus was absent, generating hypotheses regarding colonization resistance. By facilitating species-level taxonomic assignment to microbes from the human aerodigestive tract, the eHOMD is a vital resource enhancing clinical relevance of microbiome studies. IMPORTANCE The eHOMD (http://www.ehomd.org) is a valuable resource for researchers, from basic to clinical, who study the microbiomes and the individual microbes in body sites in the human aerodigestive tract, which includes the nasal passages, sinuses, throat, esophagus, and mouth, and the lower respiratory tract, in health and disease. The eHOMD is an actively curated, web-based, open-access resource. eHOMD provides the following: (i) species-level taxonomy based on grouping 16S rRNA gene sequences at 98.5% identity, (ii) a systematic naming scheme for unnamed and/or uncultivated microbial taxa, (iii) reference genomes to facilitate metagenomic, metatranscriptomic, and proteomic studies and (iv) convenient cross-links to other databases (e.g., PubMed and Entrez). By facilitating the assignment of species names to sequences, the eHOMD is a vital resource for enhancing the clinical relevance of 16S rRNA gene-based microbiome studies, as well as metagenomic studies.},
}
@article {pmid30533450,
year = {2018},
author = {Deakin, G and Tilston, EL and Bennett, J and Passey, T and Harrison, N and Fernández-Fernández, F and Xu, X},
title = {Soil microbiome data of two apple orchards in the UK.},
journal = {Data in brief},
volume = {21},
number = {},
pages = {2042-2050},
doi = {10.1016/j.dib.2018.11.067},
pmid = {30533450},
issn = {2352-3409},
abstract = {The microbial communities in two apple orchards were characterised using amplicon-based metabarcoding. Samples were taken from tree station locations along a linear transect and from adjacent grass aisles, at both orchards. Comparison was made between the communities occurring at tree station locations and the grass aisles, and between orchards. Further discussion of these datasets is given in https://doi.org/10.1016/j.apsoil.2018.05.015 (Deakin et al., 2018).},
}
@article {pmid30533398,
year = {2018},
author = {Brock, DA and Haselkorn, TS and Garcia, JR and Bashir, U and Douglas, TE and Galloway, J and Brodie, F and Queller, DC and Strassmann, JE},
title = {Diversity of Free-Living Environmental Bacteria and Their Interactions With a Bactivorous Amoeba.},
journal = {Frontiers in cellular and infection microbiology},
volume = {8},
number = {},
pages = {411},
doi = {10.3389/fcimb.2018.00411},
pmid = {30533398},
issn = {2235-2988},
abstract = {A small subset of bacteria in soil interact directly with eukaryotes. Which ones do so can reveal what is important to a eukaryote and how eukaryote defenses might be breached. Soil amoebae are simple eukaryotic organisms and as such could be particularly good for understanding how eukaryote microbiomes originate and are maintained. One such amoeba, Dictyostelium discoideum, has both permanent and temporary associations with bacteria. Here we focus on culturable bacterial associates in order to interrogate their relationship with D. discoideum. To do this, we isolated over 250 D. discoideum fruiting body samples from soil and deer feces at Mountain Lake Biological Station. In one-third of the wild D. discoideum we tested, one to six bacterial species were found per fruiting body sorus (spore mass) for a total of 174 bacterial isolates. The remaining two-thirds of D. discoideum fruiting body samples did not contain culturable bacteria, as is thought to be the norm. A majority (71.4%) of the unique bacterial haplotypes are in Proteobacteria. The rest are in either Actinobacteria, Bacteriodetes, or Firmicutes. The highest bacterial diversity was found in D. discoideum fruiting bodies originating from deer feces (27 OTUs), greater than either of those originating in shallow (11 OTUs) or in deep soil (4 OTUs). Rarefaction curves and the Chao1 estimator for species richness indicated the diversity in any substrate was not fully sampled, but for soil it came close. A majority of the D. discoideum-associated bacteria were edible by D. discoideum and supported its growth (75.2% for feces and 81.8% for soil habitats). However, we found several bacteria genera were able to evade phagocytosis and persist in D. discoideum cells through one or more social cycles. This study focuses not on the entire D. discoideum microbiome, but on the culturable subset of bacteria that have important eukaryote interactions as prey, symbionts, or pathogens. These eukaryote and bacteria interactions may provide fertile ground for investigations of bacteria using amoebas to gain an initial foothold in eukaryotes and of the origins of symbiosis and simple microbiomes.},
}
@article {pmid30533302,
year = {2018},
author = {Li, X and Zhu, Y and Ringø, E and Wang, X and Gong, J and Yang, D},
title = {Intestinal microbiome and its potential functions in bighead carp (Aristichthys nobilis) under different feeding strategies.},
journal = {PeerJ},
volume = {6},
number = {},
pages = {e6000},
doi = {10.7717/peerj.6000},
pmid = {30533302},
issn = {2167-8359},
abstract = {Bighead carps (Aristichthys nobilis) were divided into four groups with different feeding strategies: group A, nature live food only (fertiliser only, 200 g urea + 160 g ethylamine phosphate + 250 g Huangjintai bio-fertiliser); group B, nature live food + 1/2 formulated feed; group C, nature live food + formulated feed; and group D, formulated feed only. The intestinal microbiomes of the different groups were compared through the Illumina MiSeq sequencing of the bacterial 16S rRNA gene. The specific growth rate (SGR), survival and blood biochemical factors of the fish were also investigated. Results showed that feeding treatment influenced the intestinal communities in the fish. In specific, more bacterial phyla dominated in groups A and B (phyla Bacteroidetes, Fusobacteria, Firmicutes and Proteobacteria in group A, phyla Proteobacteria and Fusobacteria in group B) than in groups C and D (phylum Proteobacteria). The diversity was also lower in groups C and D than in groups A and B. Unweighted pair-group method analysis revealed a clear difference in intestinal microbiota among the different feeding treatments. No difference in survival rate was found among the treatment groups, but the SGR was significantly higher (P < 0.01) in groups B, C and D than in group A. Functional analysis showed that the intestinal bacteria correlated with fish glucose metabolism in group A but with lipid metabolic activity in groups B, C and D. In summary, the intestinal microbiomes and their potential functions vary in bighead carp under different feeding treatments. This study provides new insights into the gut microbiomes of filter-feeding and formulated diet-fed fish.},
}
@article {pmid30533025,
year = {2018},
author = {Tinker, KA and Ottesen, EA},
title = {The hindgut microbiota of praying mantids is highly variable and includes both prey-associated and host-specific microbes.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208917},
doi = {10.1371/journal.pone.0208917},
pmid = {30533025},
issn = {1932-6203},
abstract = {Praying mantids are predators that consume a wide variety of insects. While the gut microbiome of carnivorous mammals is distinct from that of omnivores and herbivores, the role of the gut microbiome among predatory insects is relatively understudied. Praying mantids are the closest known relatives to termites and cockroaches, which are known for their diverse gut microbiota. However, little is known about the mantid gut microbiota or their importance to host health. In this work, we report the results of a 16S rRNA gene-based study of gut microbiome composition in adults and late-instar larvae of three mantid species. We found that the praying mantis gut microbiome exhibits substantial variation in bacterial diversity and community composition. The hindgut of praying mantids were often dominated by microbes that are present in low abundance or not found in the guts of their insect prey. Future studies will explore the role of these microbes in the digestion of the dietary substrates and/or the degradation of toxins produced by their insect prey.},
}
@article {pmid30532742,
year = {2018},
author = {Ma, JE and Jiang, HY and Li, LM and Zhang, XJ and Li, GY and Li, HM and Jin, XJ and Chen, JP},
title = {The Fecal Metagenomics of Malayan Pangolins Identifies an Extensive Adaptation to Myrmecophagy.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2793},
doi = {10.3389/fmicb.2018.02793},
pmid = {30532742},
issn = {1664-302X},
abstract = {The characteristics of flora in the intestine of an animal, including the number and abundance of different microbial species and their functions, are closely related to the diets of the animal and affect the physical condition of the host. The Malayan pangolin (Manis javanica) is an endangered species that specializes in myrmecophagy. Analyzing the microbiome in the intestine of the pangolin is imperative to protect this species. By sequencing the metagenomes of the feces of four pangolins, we constructed a non-redundant catalog of 211,868 genes representing 1,811 metagenomic species. Taxonomic annotation revealed that Bacteroidetes (49.9%), Proteobacteria (32.2%), and Firmicutes (12.6%) are the three main phyla. The annotation of gene functions identified 5,044 genes from 88 different glycoside hydrolase (GH) families in the Carbohydrate-Active enZYmes database and 114 gene modules related to chitin-degrading enzymes, corresponding to the catalytic domains of GH18 family enzymes, containing chitinase genes of classes III and V in the dataset. Fourteen gene modules corresponded to the catalytic domains of GH19 family enzymes, containing chitinase genes of classes I, II, and IV. These genes were found in 37 species belonging to four phyla: Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria. Moreover, when the metabolic pathways of these genes were summarized, 41,711 genes were associated with 147 unique KEGG metabolic pathways, and these genes were assigned to two Gene Ontology terms: metabolic process and catalytic activity. We also found several species that likely play roles in the digestion of cellulose and may be able to degrade chitin, including Enterobacter cloacae, Lactococcus lactis, Chitinimonas koreensis, and Chitinophaga pinensis. In addition, we identified some intestinal microflora and genes related to diseases in pangolins. Twenty-seven species were identified by STAMP analysis as differentially abundant in healthy and diseased animals: 20 species, including Cellulosilyticum lentocellum and Lactobacillus reuteri, were more abundant in healthy pangolins, while seven species, including Odoribacter splanchnicus, Marinilabilia salmonicolor, Xanthomonas citri, Xanthomonas vasicola, Oxalobacter formigenes, Prolixibacter bellariivorans, and Clostridium bolteae, were more abundant in diseased pangolins. These results will support the efforts to conserve pangolins.},
}
@article {pmid30532687,
year = {2018},
author = {Lucas, G},
title = {Gut thinking: the gut microbiome and mental health beyond the head.},
journal = {Microbial ecology in health and disease},
volume = {29},
number = {2},
pages = {1548250},
doi = {10.1080/16512235.2018.1548250},
pmid = {30532687},
issn = {0891-060X},
abstract = {Background: In recent decades, dominant models of mental illness have become increasingly focused on the head, with mental disorders being figured as brain disorders. However, research into the active role that the microbiome-gut-brain axis plays in affecting mood and behaviour may lead to the conclusion that mental health is more than an internalised problem of individual brains. Objective: This article explores the implications of shifting understandings about mental health that have come about through research into links between the gut microbiome and mental health problems such as depression and anxiety. It aims to analyse the different ways that the lines between mind and body and mental and physical health are re-shaped by this research, which is starting to inform clinical and public understanding. Design: As mental health has become a pressing issue of political and public concern it has become increasingly constructed in socio-cultural and personal terms beyond clinical spaces, requiring a conceptual response that exceeds biomedical inquiry. This article argues that an interdisciplinary critical medical humanities approach is well positioned to analyse the impact of microbiome-gut-brain research on conceptions of mind. Results: The entanglement of mind and matter evinced by microbiome-gut-brain axis research potentially provides a different way to conceptualise the physical and social concomitants of mental distress. Conclusion: Mental health is not narrowly located in the head but is assimilated by the physical body and intermingled with the natural world, requiring different methods of research to unfold the meanings and implications of gut thinking for conceptions of human selfhood.},
}
@article {pmid30532651,
year = {2018},
author = {Haruta, S and Yamamoto, K},
title = {Model Microbial Consortia as Tools for Understanding Complex Microbial Communities.},
journal = {Current genomics},
volume = {19},
number = {8},
pages = {723-733},
doi = {10.2174/1389202919666180911131206},
pmid = {30532651},
issn = {1389-2029},
abstract = {A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.},
}
@article {pmid30532650,
year = {2018},
author = {Ang, KS and Lakshmanan, M and Lee, NR and Lee, DY},
title = {Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications.},
journal = {Current genomics},
volume = {19},
number = {8},
pages = {712-722},
doi = {10.2174/1389202919666180911144055},
pmid = {30532650},
issn = {1389-2029},
abstract = {In nature, microbes do not exist in isolation but co-exist in a variety of ecological and biological environments and on various host organisms. Due to their close proximity, these microbes interact among themselves, and also with the hosts in both positive and negative manners. Moreover, these interactions may modulate dynamically upon external stimulus as well as internal community changes. This demands systematic techniques such as mathematical modeling to understand the intrinsic community behavior. Here, we reviewed various approaches for metabolic modeling of microbial communities. If detailed species-specific information is available, segregated models of individual organisms can be constructed and connected via metabolite exchanges; otherwise, the community may be represented as a lumped network of metabolic reactions. The constructed models can then be simulated to help fill knowledge gaps, and generate testable hypotheses for designing new experiments. More importantly, such community models have been developed to study microbial interactions in various niches such as host microbiome, biogeochemical and bioremediation, waste water treatment and synthetic consortia. As such, the metabolic modeling efforts have allowed us to gain new insights into the natural and synthetic microbial communities, and design interventions to achieve specific goals. Finally, potential directions for future development in metabolic modeling of microbial communities were also discussed.},
}
@article {pmid30532649,
year = {2018},
author = {Lim, MY and Cho, Y and Rho, M},
title = {Diverse Distribution of Resistomes in the Human and Environmental Microbiomes.},
journal = {Current genomics},
volume = {19},
number = {8},
pages = {701-711},
doi = {10.2174/1389202919666180911130845},
pmid = {30532649},
issn = {1389-2029},
abstract = {The routine therapeutic use of antibiotics has caused resistance genes to be disseminated across microbial populations. In particular, bacterial strains having antibiotic resistance genes are frequently observed in the human microbiome. Moreover, multidrug-resistant pathogens are now widely spread, threatening public health. Such genes are transferred and spread among bacteria even in different environments. Advances in high throughput sequencing technology and computational algorithms have accelerated investigation into antibiotic resistance genes of bacteria. Such studies have revealed that the antibiotic resistance genes are located close to the mobility-associated genes, which promotes their dissemination. An increasing level of information on genomic sequences of resistome should expedite research on drug-resistance in our body and environment, thereby contributing to the development of public health policy. In this review, the high prevalence of antibiotic resistance genes and their exchange in the human and environmental microbiome is discussed with respect to the genomic contents. The relationships among diverse resistomes, related bacterial species, and the antibiotics are reviewed. In addition, recent advances in bioinformatics approaches to investigate such relationships are discussed.},
}
@article {pmid30532085,
year = {2018},
author = {Chen, B and Yu, T and Xie, S and Du, K and Liang, X and Lan, Y and Sun, C and Lu, X and Shao, Y},
title = {Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome.},
journal = {Scientific data},
volume = {5},
number = {},
pages = {180285},
doi = {10.1038/sdata.2018.285},
pmid = {30532085},
issn = {2052-4463},
abstract = {Lepidoptera (butterflies and moths) is a major insect order including important pollinators and agricultural pests, however their microbiomes are little studied. Here, using next-generation sequencing (NGS)-based shotgun metagenomics, we characterize both the biodiversity and functional potential of gut microbiota of a lepidopteran model insect, the silkworm Bombyx mori. Two metagenomes, including the standard inbred strain Dazao (P50) and an improved hybrid strain Qiufeng × Baiyu (QB) widely used in commercial silk production, were generated, containing 45,505,084 and 69,127,002 raw reads, respectively. Taxonomic analysis revealed that a total of 663 bacterial species were identified in P50 silkworms, while 322 unique species in QB silkworms. Notably, Enterobacter, Acinetobacter and Enterococcus were dominated in both strains. The further functional annotation was performed by both BlastP and MG-RAST against various databases including Nr, COG, KEGG, CAZy and SignalP, which revealed >5 × 106 protein-coding genes. These datasets not only provide first insights into all bacterial genes in silkworm guts, but also help to generate hypotheses for subsequently testing functional traits of gut microbiota in an important insect group.},
}
@article {pmid30532043,
year = {2018},
author = {Kolodny, O and Weinberg, M and Reshef, L and Harten, L and Hefetz, A and Gophna, U and Feldman, MW and Yovel, Y},
title = {Coordinated change at the colony level in fruit bat fur microbiomes through time.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-018-0731-z},
pmid = {30532043},
issn = {2397-334X},
abstract = {The host-associated microbiome affects individual health and behaviour, and may be influenced by local environmental conditions. However, little is known about microbiomes' temporal dynamics in free-living species compared with their dynamics in humans and model organisms, especially in body sites other than the gut. Here, we investigate longitudinal changes in the fur microbiome of captive and free-living Egyptian fruit bats. We find that, in contrast to patterns described in humans and other mammals, the prominent dynamics is of change over time at the level of the colony as a whole. On average, a pair of fur microbiome samples from different individuals in the same colony collected on the same date are more similar to one another than a pair of samples from the same individual collected at different time points. This pattern suggests that the whole colony may be the appropriate biological unit for understanding some of the roles of the host microbiome in social bats' ecology and evolution. This pattern of synchronized colony changes over time is also reflected in the profile of volatile compounds in the bats' fur, but differs from the more individualized pattern found in the bats' gut microbiome.},
}
@article {pmid30531976,
year = {2018},
author = {Franzosa, EA and Sirota-Madi, A and Avila-Pacheco, J and Fornelos, N and Haiser, HJ and Reinker, S and Vatanen, T and Hall, AB and Mallick, H and McIver, LJ and Sauk, JS and Wilson, RG and Stevens, BW and Scott, JM and Pierce, K and Deik, AA and Bullock, K and Imhann, F and Porter, JA and Zhernakova, A and Fu, J and Weersma, RK and Wijmenga, C and Clish, CB and Vlamakis, H and Huttenhower, C and Xavier, RJ},
title = {Gut microbiome structure and metabolic activity in inflammatory bowel disease.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-018-0306-4},
pmid = {30531976},
issn = {2058-5276},
abstract = {The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has been associated with dramatic changes in the gut microbiota, changes in the gut metabolome-the molecular interface between host and microbiota-are less well understood. To address this gap, we performed untargeted metabolomic and shotgun metagenomic profiling of cross-sectional stool samples from discovery (n = 155) and validation (n = 65) cohorts of CD, UC and non-IBD control patients. Metabolomic and metagenomic profiles were broadly correlated with faecal calprotectin levels (a measure of gut inflammation). Across >8,000 measured metabolite features, we identified chemicals and chemical classes that were differentially abundant in IBD, including enrichments for sphingolipids and bile acids, and depletions for triacylglycerols and tetrapyrroles. While > 50% of differentially abundant metabolite features were uncharacterized, many could be assigned putative roles through metabolomic 'guilt by association' (covariation with known metabolites). Differentially abundant species and functions from the metagenomic profiles reflected adaptation to oxidative stress in the IBD gut, and were individually consistent with previous findings. Integrating these data, however, we identified 122 robust associations between differentially abundant species and well-characterized differentially abundant metabolites, indicating possible mechanistic relationships that are perturbed in IBD. Finally, we found that metabolome- and metagenome-based classifiers of IBD status were highly accurate and, like the vast majority of individual trends, generalized well to the independent validation cohort. Our findings thus provide an improved understanding of perturbations of the microbiome-metabolome interface in IBD, including identification of many potential diagnostic and therapeutic targets.},
}
@article {pmid30531816,
year = {2018},
author = {Borren, NZ and van der Woude, CJ and Ananthakrishnan, AN},
title = {Fatigue in IBD: epidemiology, pathophysiology and management.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41575-018-0091-9},
pmid = {30531816},
issn = {1759-5053},
abstract = {Fatigue is an important clinical problem in patients with IBD, affecting nearly 50% of patients in clinical remission and > 80% of those with active disease. The resulting decrease in quality of life and impaired work productivity and functioning contribute markedly to the societal costs of fatigue. However, despite the burden and effects of fatigue, little is known about its aetiology and pathophysiology, which impairs our ability to effectively treat this symptom. Here, we review the theories behind the development of fatigue in IBD and the role of contributing factors, including nutritional deficiency, inflammation and altered metabolism. We also explore the potential role of the gut microbiome in mediating fatigue and other psychological symptoms through the gut-brain axis. We discuss the efficacy of nutrient repletion and various psychological and pharmacological interventions on relieving fatigue in patients with IBD and expand the discussion to non-IBD-related fatigue when evidence exists. Finally, we present a therapeutic strategy for the management of fatigue in IBD and call for further mechanistic and clinical research into this poorly studied symptom.},
}
@article {pmid30530257,
year = {2018},
author = {Ho, L and Zhao, D and Ono, K and Ruan, K and Mogno, I and Tsuji, M and Carry, E and Brathwaite, J and Sims, S and Frolinger, T and Westfall, S and Mazzola, P and Wu, Q and Hao, K and Lloyd, TE and Simon, JE and Faith, J and Pasinetti, GM},
title = {Heterogeneity in gut microbiota drive polyphenol metabolism that influences α-synuclein misfolding and toxicity.},
journal = {The Journal of nutritional biochemistry},
volume = {64},
number = {},
pages = {170-181},
doi = {10.1016/j.jnutbio.2018.10.019},
pmid = {30530257},
issn = {1873-4847},
abstract = {The intestinal microbiota actively converts dietary flavanols into phenolic acids, some of which are bioavailable in vivo and may promote resilience to select neurological disorders by interfering with key pathologic mechanisms. Since every person harbors a unique set of gut bacteria, we investigated the influence of the gut microbiota's interpersonal heterogeneity on the production and bioavailability of flavonoid metabolites that may interfere with the misfolding of alpha (α)-synuclein, a process that plays a central role in Parkinson's disease and other α-synucleinopathies. We generated two experimental groups of humanized gnotobiotic mice with compositionally diverse gut bacteria and orally treated the mice with a flavanol-rich preparation (FRP). The two gnotobiotic mouse groups exhibited distinct differences in the generation and bioavailability of FRP-derived microbial phenolic acid metabolites that have bioactivity towards interfering with α-synuclein misfolding or inflammation. We also demonstrated that these bioactive phenolic acids are effective in modulating the development and progression of motor dysfunction in a Drosophila model of α-synucleinopathy. Lastly, through in vitro bacterial fermentation studies, we identified select bacteria that are capable of supporting the generation of these bioavailable and bioactive phenolic acids. Outcomes from our studies provide a better understanding of how interpersonal heterogeneity in the gut microbiota differentially modulates the efficacy of dietary flavanols to protect against select pathologic mechanisms. Collectively, our findings provide the basis for future developments of probiotic, prebiotic, or synbiotic approaches for modulating the onset and/or progression of α-synucleinopathies and other neurological disorders involving protein misfolding and/or inflammation.},
}
@article {pmid30530242,
year = {2018},
author = {Sirén, K and Mak, SST and Fischer, U and Hansen, LH and Gilbert, MTP},
title = {Multi-omics and potential applications in wine production.},
journal = {Current opinion in biotechnology},
volume = {56},
number = {},
pages = {172-178},
doi = {10.1016/j.copbio.2018.11.014},
pmid = {30530242},
issn = {1879-0429},
abstract = {The wine microbiome - that is the microbial communities associated with the fermentation of must, is one of the most important factors in transforming grapes to wine, including flavour and aroma. Recent developments in high throughput sequencing and other 'omics methodologies are rapidly changing the level and complexity of information that we are able to extract from the wine microbiome. This will significantly enhance not only our understanding of which microbes are present at the various stages of the grapevine growth and winemaking process, but also improve our understanding of the complex interactions between microbes, the substrate and environment, ultimately shaping wine production. In this perspective we describe the role and future potential of such techniques in wine production, and highlight the potential challenges that will be simultaneously faced.},
}
@article {pmid30530088,
year = {2018},
author = {Ben, Y and Fu, C and Hu, M and Liu, L and Wong, MH and Zheng, C},
title = {Human health risk assessment of antibiotic resistance associated with antibiotic residues in the environment: A review.},
journal = {Environmental research},
volume = {169},
number = {},
pages = {483-493},
doi = {10.1016/j.envres.2018.11.040},
pmid = {30530088},
issn = {1096-0953},
abstract = {The extensive use of antibiotics leading to the rapid spread of antibiotic resistance poses high health risks to humans, but to date there is still lack of a quantitative model to properly assess the risks. Concerns over the health risk of antibiotic residues in the environment are mainly (1) the potential hazard of ingested antibiotic residues in the environment altering the human microbiome and promoting emergence and selection for bacteria resistance inhabiting the human body, and (2) the potential hazard of creating a selection pressure on environmental microbiome and leading to reservoirs of antibiotic resistance in the environment. We provide a holistic view of health risk assessment of antibiotic resistance associated with antibiotic residues in the environment in contrast with that of the antibiotic resistant bacteria and discuss the main knowledge gaps and the future research that should be prioritized to achieve the quantitative risk assessment. We examined and summarized the available data and information on the four core elements of antibiotic resistance associated with antibiotic residues in the environment: hazard identification, exposure assessment, dose-response assessment, and risk characterization. The data required to characterize the risks of antibiotic residues in the environment is severely limited. The main future research needs have been identified to enable better assessments of antibiotic resistance associated with antibiotic residues in the environment: (1) establishment of a standardized monitoring guide of antibiotic residues and antibiotic resistance in the environment, (2) derivation of the relationship between antibiotic levels and pathogenic antibiotic-resistance development in different settings, and (3) establishment of the dose-response relationship between pathogenic antibiotic resistant bacteria and various infection diseases. After identification of key risk determinant parameters, we propose a conceptual framework of human health risk assessments of antibiotic residues in the environment. CAPSULE: A holistic view of human health risk assessment of antibiotic residues in the environment was provided.},
}
@article {pmid30529583,
year = {2018},
author = {Paramsothy, S and Nielsen, S and Kamm, MA and Deshpande, NP and Faith, JJ and Clemente, JC and Paramsothy, R and Walsh, AJ and van den Bogaerde, J and Samuel, D and Leong, RWL and Connor, S and Ng, W and Lin, E and Borody, TJ and Wilkins, MR and Colombel, JF and Mitchell, HM and Kaakoush, NO},
title = {Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2018.12.001},
pmid = {30529583},
issn = {1528-0012},
abstract = {BACKGROUND &amp; AIMS: Fecal microbiota transplantation (FMT) can induce remission in patients with ulcerative colitis (UC). In a randomized, controlled trial of FMT in patients with active UC, we aimed to identify bacterial taxonomic and functional factors associated with response to therapy.<br><br>METHODS: We performed a double-blind trial of 81 patients with active UC randomly assigned to groups that received an initial colonoscopic infusion and then intensive multi-donor FMT or placebo enemas, 5 days/week for 8 weeks. Patients in the FMT group received blended homogenized stool from 3-7 unrelated donors. Patients in the placebo group were eligible to receive open-label FMT, after the double-blind study period. We collected 314 fecal samples from the patients at screening, every 4 weeks during treatment, and 8 weeks after the blinded or open-label FMT therapy. We also collected 160 colonoscopic large bowel biopsies from the patients at study entry, at completion of 8 weeks of blinded therapy, and at the end of open-label FMT if applicable. We analyzed the 105 fecal samples from the 14 individual donors (n=55), which were combined into 21 multi-donor batches (n=50). Bacteria in colonic and fecal samples were analyzed by both 16S rRNA gene and transcript amplicon sequencing; 285 fecal samples were analyzed by shotgun metagenomics and 60 fecal samples were analyzed for metabolome features.<br><br>RESULTS: FMT increased microbial diversity and altered composition, based on analyses of colon and fecal samples collected before vs after FMT. Diversity was greater in fecal and colon samples collected before and after FMT treatment from patients who achieved remission compared to patients who did not. Patients in remission after FMT had enrichment of Eubacterium hallii and Roseburia inulivorans, compared to patients who did not achieve remission after FMT, and had increased levels of short-chain fatty acid biosynthesis and secondary bile acids. Patients who did not achieve remission had enrichment of Fusobacterium gonidiaformans, Sutterella wadsworthensis, and Escherichia and increased levels of heme and lipopolysaccharide biosynthesis. Bacteroides in donor stool were associated with remission in patients receiving FMT, and Streptococcus in donor stool associated with no response to FMT.<br><br>CONCLUSIONS: In an analysis of fecal and colonic mucosa samples from patients receiving FMT for active UC and stool samples from donors, we associated specific bacteria and metabolic pathways with induction of remission. These findings may be of value in the design of microbe-based therapies for UC. ClinicalTrials.gov no: NCT01896635.},
}
@article {pmid30529293,
year = {2018},
author = {Xie, K and Guo, L and Bai, Y and Liu, W and Yan, J and Bucher, M},
title = {Microbiomics and Plant Health: An Interdisciplinary and International Workshop on the Plant Microbiome.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2018.11.004},
pmid = {30529293},
issn = {1752-9867},
}
@article {pmid30529208,
year = {2018},
author = {Ariaeenejad, S and Hosseini, E and Maleki, M and Kavousi, K and Moosavi-Movahedi, AA and Salekdeh, GH},
title = {Identification and characterization of a novel thermostable xylanase from camel rumen metagenome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2018.12.041},
pmid = {30529208},
issn = {1879-0003},
abstract = {Metagenomics has emerged to isolate novel enzymes from the uncultured microbiota in the environment. In this study, the metagenomic data obtained from camel rumen was considered as the potential source of microbial xylanase enzymes with proper activity in extreme conditions. The metagenomic data were assembled and contigs were used for in-silico identification of candidate thermostable enzyme. A novel thermostable xylanase enzyme, named PersiXyn1, with 1146 bp full-length gene which encodes a 381 amino acid protein was identified. Using the DNA template extracted from camel rumen metagenomic samples, the candidate enzyme genes were cloned and expressed in proper E. coli strains. The phylogenetic analysis showed the evolutionary position of PersiXyn1 among the known thermostable xylanases. The results of the CD analysis and determining the secondary structure of the enzyme, confirmed the presence of a high percentage of β-sheets as an important characteristic of thermophilic xylanases. The PersiXyn1 was active at a broad range of pH (6-11) and temperature (25-90 °C). The optimum pH and temperature were 8 and 40 °C respectively, and the enzyme maintained 80% of its maximum activity in the pH 8 and temperature 40 °C for 1 h. The Scanning electron microscope (SEM) micrograph of enzyme treated pulp clearly showed that the effective use of enzymes in fiber separation may reduce the cost of carton paper production. The novelty of this enzyme lies in the fact that it is highly active and stable in a broad range of pH and temperature. This study highlights the potential importance of camel microbiome for discovering novel thermostable enzymes with applications in agriculture and industries.},
}
@article {pmid30529024,
year = {2018},
author = {Abraham, D and Feher, J and Scuderi, GL and Szabo, D and Dobolyi, A and Cservenak, M and Juhasz, J and Ligeti, B and Pongor, S and Gomez-Cabrera, MC and Vina, J and Higuchi, M and Suzuki, K and Boldogh, I and Radak, Z},
title = {Exercise and probiotics attenuate the development of Alzheimer's disease in transgenic mice: Role of microbiome.},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.exger.2018.12.005},
pmid = {30529024},
issn = {1873-6815},
abstract = {It has been suggested that exercise training and probiotic supplementation could decelerate the progress of functional and biochemical deterioration in APP/PS1 transgenic mice (APP/PS1TG). APP/PS1TG mice were subjected to exercise training and probiotic treatments and functional, biochemical and microbiome markers were analyzed. Under these conditions the mice significantly outperformed controls on The Morris Maze Test, and the number of beta-amyloid plaques decreased in the hippocampus. B. thetaiotaomicron levels correlated highly with the results of the Morris Maze Test (p < 0.05), and this group of bacteria was significantly elevated in the microbiome of the APP/PS1TG mice compared to the wild type. L. johnsonii levels positively correlated with the beta amyloid content and area. Data revealed that exercise and probiotic treatment can decrease the progress of Alzheimer's Disease and the beneficial effects could be partly mediated by alteration of the microbiome.},
}
@article {pmid30529020,
year = {2018},
author = {Robertson, RC and Manges, AR and Finlay, BB and Prendergast, AJ},
title = {The Human Microbiome and Child Growth - First 1000 Days and Beyond.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2018.09.008},
pmid = {30529020},
issn = {1878-4380},
abstract = {The assembly of microbial communities within the gastrointestinal tract during early life plays a critical role in immune, endocrine, metabolic, and other host developmental pathways. Environmental insults during this period, such as food insecurity and infections, can disrupt this optimal microbial succession, which may contribute to lifelong and intergenerational deficits in growth and development. Here, we review the human microbiome in the first 1000 days - referring to the period from conception to 2 years of age - and using a developmental model, we examine the role of early microbial succession in growth and development. We propose that an 'undernourished' microbiome is intergenerational, thereby perpetuating growth impairments into successive generations. We also identify and discuss the intertwining host-microbe-environment interactions occurring prenatally and during early infancy, which may impair the trajectories of healthy growth and development, and explore their potential as novel microbial targets for intervention.},
}
@article {pmid30528912,
year = {2018},
author = {Liddle, L and Burleigh, MC and Monaghan, C and Muggeridge, DJ and Sculthorpe, N and Pedlar, CR and Butcher, J and Henriquez, FL and Easton, C},
title = {Variability in nitrate-reducing oral bacteria and nitric oxide metabolites in biological fluids following dietary nitrate administration: An assessment of the critical difference.},
journal = {Nitric oxide : biology and chemistry},
volume = {83},
number = {},
pages = {1-10},
doi = {10.1016/j.niox.2018.12.003},
pmid = {30528912},
issn = {1089-8611},
abstract = {There is conflicting evidence on whether dietary nitrate supplementation can improve exercise performance. This may arise from the complex nature of nitric oxide (NO) metabolism which causes substantial inter-individual variability, within-person biological variation (CVB), and analytical imprecision (CVA) in experimental endpoints. However, no study has quantified the CVA and CVB of NO metabolites or the factors that influence their production. These data are important to calculate the critical difference (CD), defined as the smallest difference between sequential measurements required to signify a true change. The main aim of the study was to evaluate the CVB, CVA, and CD for markers of NO availability (nitrate and nitrite) in plasma and saliva before and after the ingestion of nitrate-rich beetroot juice (BR). We also assessed the CVB of nitrate-reducing bacteria from the dorsal surface of the tongue. It was hypothesised that there would be substantial CVB in markers of NO availability and the abundance of nitrate-reducing bacteria. Ten healthy male participants (age 25 ± 5 years) completed three identical trials at least 6 days apart. Blood and saliva were collected before and after (2, 2.5 and 3 h) ingestion of 140 ml of BR (∼12.4 mmol nitrate) and analysed for [nitrate] and [nitrite]. The tongue was scraped and the abundance of nitrate-reducing bacterial species were analysed using 16S rRNA next generation sequencing. There was substantial CVB for baseline concentrations of plasma (nitrate 11.9%, nitrite 9.0%) and salivary (nitrate 15.3%, nitrite 32.5%) NO markers. Following BR ingestion, the CVB for nitrate (plasma 3.8%, saliva 12.0%) and salivary nitrite (24.5%) were lower than baseline, but higher for plasma nitrite (18.6%). The CD thresholds that need to be exceeded to ensure a meaningful change from baseline are 25, 19, 37, and 87% for plasma nitrate, plasma nitrite, salivary nitrate, and salivary nitrite, respectively. The CVB for selected nitrate-reducing bacteria detected were: Prevotella melaninogenica (37%), Veillonella dispar (35%), Haemophilus parainfluenzae (79%), Neisseria subflava (70%), Veillonella parvula (43%), Rothia mucilaginosa (60%), and Rothia dentocariosa (132%). There is profound CVB in the abundance of nitrate-reducing bacteria on the tongue and the concentration of NO markers in human saliva and plasma. Where these parameters are of interest following experimental intervention, the CD values presented in this study will allow researchers to interpret the meaningfulness of the magnitude of the change from baseline.},
}
@article {pmid30528614,
year = {2018},
author = {Lee, J and Kim, JY and Yi, MH and Hwang, Y and Lee, IY and Nam, SH and Yong, D and Yong, TS},
title = {Comparative microbiome analysis of Dermatophagoides farinae, Dermatophagoides pteronyssinus, and Tyrophagus putrescentiae.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2018.10.062},
pmid = {30528614},
issn = {1097-6825},
abstract = {Three species of house dust mites, Dermatophagoides farinae, Dermatophagoides pteronyssinus, and Tyrophagus putrescentiae, showed distinct microbiomes, which may affect the induction of allergic diseases.},
}
@article {pmid30527803,
year = {2018},
author = {Kapp, JM and Sumner, W},
title = {Kombucha: a systematic review of the empirical evidence of human health benefit.},
journal = {Annals of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.annepidem.2018.11.001},
pmid = {30527803},
issn = {1873-2585},
abstract = {PURPOSE: Kombucha tea, a fermented beverage, has recently become popular in the United States as part of the functional food movement. This popularity is likely driven by its touted health benefits, coupled with the recent scientific movement investigating the role of the microbiome on human health. The purpose of this systematic review is to describe the literature related to empirical health benefits of kombucha as identified from human subjects research.<br><br>METHODS: In July 2018, we searched the term &quot;kombucha&quot; for all document types in the following databases across all available years: PubMed, Scopus, and Ovid. To identify federal research grants related to kombucha, we searched the National Institutes of Health Research Portfolio Online Reporting Tools. Finally, to identify ongoing human subjects research, we searched clinicaltrials.gov and clinicaltrialsregister.eu. We reviewed a total of 310 articles.<br><br>RESULTS: We found one study reporting the results of empirical research on kombucha in human subjects. We found no results for kombucha in Research Portfolio Online Reporting Tools, clinicaltrials.gov, or clinicaltrialsregister.eu.<br><br>CONCLUSIONS: The nonhuman subjects literature claims numerous health benefits of kombucha; it is critical that these assertions are tested in human clinical trials. Research opportunities are discussed.},
}
@article {pmid30527429,
year = {2018},
author = {López-Medina, C and Moltó, A},
title = {Update on the epidemiology, risk factors, and disease outcomes of axial spondyloarthritis.},
journal = {Best practice &amp; research. Clinical rheumatology},
volume = {32},
number = {2},
pages = {241-253},
doi = {10.1016/j.berh.2018.10.006},
pmid = {30527429},
issn = {1532-1770},
abstract = {Axial spondyloarthritis (axSpA) is the prototype of a class of a rheumatic chronic inflammatory disease named spondyloarthritis (SpA). The prevalence of axSpA ranges between 0.1% and 1.4% globally, hence showing geographic differences that can be explained mostly by the prevalence of the HLA-B27 antigen. However, not many studies have evaluated the incidence of this disease. Inflammation may be initiated in the enthesis as a consequence of the action of IL-23, which can activate resident T cells. The elevated expression of IL-23 has been explained by three hypotheses: the presence of HLA-B27, variations in the gut microbiome and the biomechanical stress at the enthesis. However, the role of IL-23 in this whole context is still unclear. In axSpA, the presence of syndesmophytes at baseline, systemic inflammation, and smoking may promote the spinal radiographic damage in these patients. The most frequent comorbidity in these patients is osteoporosis, which is directly associated with ankylosis and inflammation.},
}
@article {pmid30526748,
year = {2018},
author = {Mandell, BF},
title = {A new reason to reconsider that antibiotic prescription: The microbiome.},
journal = {Cleveland Clinic journal of medicine},
volume = {85},
number = {12},
pages = {906-907},
doi = {10.3949/ccjm.85b.12018},
pmid = {30526748},
issn = {1939-2869},
}
@article {pmid30526664,
year = {2018},
author = {Koedooder, R and Singer, M and Schoenmakers, S and Savelkoul, PHM and Morré, SA and de Jonge, JD and Poort, L and Cuypers, WSS and Budding, AE and Laven, JSE and , },
title = {The ReceptIVFity cohort study protocol to validate the urogenital microbiome as predictor for IVF or IVF/ICSI outcome.},
journal = {Reproductive health},
volume = {15},
number = {1},
pages = {202},
doi = {10.1186/s12978-018-0653-x},
pmid = {30526664},
issn = {1742-4755},
support = {8884//Eurostars (Valbiome)/ ; },
abstract = {BACKGROUND: During the last decade, research has shown that besides the known predictive factors, such as duration of subfertility, a women's age, the body mass index, also the microbiome might affect fertility. Micro-organisms together with their genetic information and the milieu in which they interact are called the microbiome. Studies have shown that the presence of certain microbiota during assisted reproductive technology (ART) has a positive impact on the outcome. However, the potential role of using the microbiome as a predictor for outcome of ART has not yet been investigated.<br><br>METHODS: In a prospective study, 300 women of reproductive age and with an indication for in-vitro Fertilization (IVF) with or without Intra Cytoplasmic Sperm Injection (ICSI) treatment will be included. Prior to the IVF or IVF-ICSI treatment, these women provided a midstream urine sample and a vaginal swab. The composition of the urinary and vaginal microbiome will be analysed with both Next Generation Sequencing and the IS-pro technique. The endpoints of the study are pregnancy achieved after fresh embryo transfer (ET) and within the subsequent year after inclusion. External validation of the findings will take place in an additional cohort of 50 women with an IVF or IVF-ICSI indication.<br><br>DISCUSSION: In the proposed study, the predictive accuracy of the composition of the urinary and vaginal microbiome for IVF or IVF-ICSI outcome will be only validated for fresh ET. Follow-up has to show whether the predictive accuracy will be similar during the consecutive frozen ET's as part of the IVF or IVF-ICSI treatment or for subsequent stimulated or natural cycles. In addition, external validation will take place in another cohort and hospital. Predictive knowledge of the microbiome profile may enable couples to make a more substantiated decision on whether to continue treatment or not. Hence, the unnecessary physical and emotional burden of a failed IVF or IVF-ICSI treatment can be avoided.<br><br>TRIAL REGISTRATION: ISRCTN ISRCTN83157250 . Registered 17 August 2018. Retrospectively registered.},
}
@article {pmid30526610,
year = {2018},
author = {Lamarche, D and Johnstone, J and Zytaruk, N and Clarke, F and Hand, L and Loukov, D and Szamosi, JC and Rossi, L and Schenck, LP and Verschoor, CP and McDonald, E and Meade, MO and Marshall, JC and Bowdish, DME and Karachi, T and Heels-Ansdell, D and Cook, DJ and Surette, MG and , and , and , },
title = {Microbial dysbiosis and mortality during mechanical ventilation: a prospective observational study.},
journal = {Respiratory research},
volume = {19},
number = {1},
pages = {245},
doi = {10.1186/s12931-018-0950-5},
pmid = {30526610},
issn = {1465-993X},
abstract = {BACKGROUND: Host-associated microbial communities have important roles in tissue homeostasis and overall health. Severe perturbations can occur within these microbial communities during critical illness due to underlying diseases and clinical interventions, potentially influencing patient outcomes. We sought to profile the microbial composition of critically ill mechanically ventilated patients, and to determine whether microbial diversity is associated with illness severity and mortality.<br><br>METHODS: We conducted a prospective, observational study of mechanically ventilated critically ill patients with a high incidence of pneumonia in 2 intensive care units (ICUs) in Hamilton, Canada, nested within a randomized trial for the prevention of healthcare-associated infections. The microbial profiles of specimens from 3 anatomical sites (respiratory, and upper and lower gastrointestinal tracts) were characterized using 16S ribosomal RNA gene sequencing.<br><br>RESULTS: We collected 65 specimens from 34 ICU patients enrolled in the trial (29 endotracheal aspirates, 26 gastric aspirates and 10 stool specimens). Specimens were collected at a median time of 3 days (lower respiratory tract and gastric aspirates; interquartile range [IQR] 2-4) and 6 days (stool; IQR 4.25-6.75) following ICU admission. We observed a loss of biogeographical distinction between the lower respiratory tract and gastrointestinal tract microbiota during critical illness. Moreover, microbial diversity in the respiratory tract was inversely correlated with APACHE II score (r = - 0.46, p = 0.013) and was associated with hospital mortality (Median Shannon index: Discharged alive; 1.964 vs. Deceased; 1.348, p = 0.045).<br><br>CONCLUSIONS: The composition of the host-associated microbial communities is severely perturbed during critical illness. Reduced microbial diversity reflects high illness severity and is associated with mortality. Microbial diversity may be a biomarker of prognostic value in mechanically ventilated patients.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov ID NCT01782755 . Registered February 4 2013.},
}
@article {pmid30526463,
year = {2018},
author = {Matarazzo, I and Toniato, E and Robuffo, I},
title = {Psychobiome feeding mind: poliphenolics in depression and anxiety.},
journal = {Current topics in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/1568026619666181210151348},
pmid = {30526463},
issn = {1873-4294},
abstract = {Recently gut bacterial populations seem to be involved in many functions and in the pathogenesis of several medical conditions. Traditionally the intestinal microbiome has been recognized to play an important role in metabolizing food compounds in simpler chemical structures for the absorption of different nutrients, and in maintenance control on gastrointestinal pathogens species. Bacterial populations are implicated in a complicated network of interactions within the immune system, epithelial cells, local endocrine system, that affects the peripheral and the central nervous system, via blood circulation. Microbiome influencing and talking to mind via immune, endocrine and metabolite signalling, is able to exert some clinical effects in different mental disease. It releases endocrine substances, through several pathways such as modulation of neuroinflammation and production of several neurotrasmitters precursors. It is recently called psychobiome. It is known that phenolic compounds are able to influence microbiome proliferation and to exert several roles, expecially regarding neuroinflammation in depressive and anxious behaviour. The clinical effects are reported in literature. The aim of this study is to highlights the interaction between polyphenols and microbiota- gut-brain axis.},
}
@article {pmid30525950,
year = {2018},
author = {Hibberd, AA and Yde, CC and Ziegler, ML and Honoré, AH and Saarinen, MT and Lahtinen, S and Stahl, B and Jensen, HM and Stenman, LK},
title = {Probiotic or synbiotic alters the gut microbiota and metabolism in a randomised controlled trial of weight management in overweight adults.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-16},
doi = {10.3920/BM2018.0028},
pmid = {30525950},
issn = {1876-2891},
abstract = {The gut microbiota contributes to host energy metabolism, and altered gut microbiota has been associated with obesity-related metabolic disorders. We previously reported that a probiotic alone or together with a prebiotic controls body fat mass in healthy overweight or obese individuals in a randomised, double-blind, placebo controlled clinical study (ClinicalTrials.gov NCT01978691). We now aimed to investigate whether changes in the gut microbiota may be associated with the observed clinical benefits. Faecal and plasma samples were obtained from a protocol compliant subset (n=134) of participants from a larger clinical study where participants were randomised (1:1:1:1) into four groups: (1) placebo, 12 g/d microcrystalline cellulose; (2) Litesse® Ultra™ polydextrose (LU), 12 g/day; (3) Bifidobacterium animalis subsp. lactis 420™ (B420), 1010 cfu/d in 12 g microcrystalline cellulose; (4) LU+B420, 1010 cfu/d of B420 in 12 g/d LU for 6 months of intervention. The faecal microbiota composition and metabolites were assessed as exploratory outcomes at baseline, 2, 4, 6 months, and +1 month post-intervention and correlated to obesity-related clinical outcomes. Lactobacillus and Akkermansia were more abundant with B420 at the end of the intervention. LU+B420 increased Akkermansia, Christensenellaceae and Methanobrevibacter, while Paraprevotella was reduced. Christensenellaceae was consistently increased in the LU and LU+B420 groups across the intervention time points, and correlated negatively to waist-hip ratio and energy intake at baseline, and waist-area body fat mass after 6 months treatment with LU+B420. Functional metagenome predictions indicated alterations in pathways related to cellular processes and metabolism. Plasma bile acids glycocholic acid, glycoursodeoxycholic acid, and taurohyodeoxycholic acid and tauroursodeoxycholic acid were reduced in LU+B420 compared to Placebo. Consumption of B420 and its combination with LU resulted in alterations of the gut microbiota and its metabolism, and may support improved gut barrier function and obesity-related markers.},
}
@article {pmid30525949,
year = {2018},
author = {Wing, AC and Kremenchutzky, M},
title = {Multiple sclerosis and faecal microbiome transplantation: are you going to eat that?.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-6},
doi = {10.3920/BM2018.0029},
pmid = {30525949},
issn = {1876-2891},
abstract = {Gut microbiome interaction goes beyond commensal function as vitamin production or support nutrients digestion. It also interplays with the host immune system and may be related to the development of immune-mediated diseases. Multiple sclerosis patients have dysbiosis compared to healthy individuals. But how this relates to disease development and severity is still uncertain. Dietary change including probiotic mixtures or ketogenic regimen has proven to change microbiome in multiple sclerosis (MS) subjects to one similar to healthy controls. However, proof of clinical benefits is lacking. We dissert on current knowledge about immune system and gut bacteria interactions. We discuss faecal microbial transplantation as a potential intervention to ameliorate gut dysbiosis in MS as well as the caveats of a clinical trial design.},
}
@article {pmid30525664,
year = {2018},
author = {Park, SR and Jung, T and Thuy-Boun, PS and Wang, AY and Yates, JR and Wolan, DW},
title = {ComPIL 2.0: An Updated Comprehensive Metaproteomics Database.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.8b00722},
pmid = {30525664},
issn = {1535-3907},
abstract = {We designed a metaproteomic analysis method (ComPIL) to accommodate the ever-increasing number of sequences against which experimental shotgun proteomics spectra could be accurately and rapidly queried. Our objective was to create these large databases for the analysis of complex meta-samples with unknown composition, including those derived from human, animal, and environmental microbiomes. The amount of high-throughput sequencing data has substantially increased since our original database was assembled in 2014. Here, we present a rebuild of the ComPIL libraries comprised of updated publicly disseminated sequence data as well as a modified version of the search engine ProLuCID-ComPIL optimized for querying experimental spectra. ComPIL 2.0 consists of 225 million protein records and roughly 9.5 billion unique tryptic peptide sequences and is 2.3 times the size of our original version. We searched a dataset collected on a healthy human gut microbiome proteomic sample and compared the results to demonstrate that ComPIL 2.0 showed a substantial increase in the number of unique identified peptides and proteins compared to the first ComPIL version. The high confidence of protein identification and accuracy demonstrated by the use of ComPIL 2.0 may encourage the method's application for large-scale proteomic annotation of complex protein systems.},
}
@article {pmid30522820,
year = {2018},
author = {Sgritta, M and Dooling, SW and Buffington, SA and Momin, EN and Francis, MB and Britton, RA and Costa-Mattioli, M},
title = {Mechanisms Underlying Microbial-Mediated Changes in Social Behavior in Mouse Models of Autism Spectrum Disorder.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuron.2018.11.018},
pmid = {30522820},
issn = {1097-4199},
abstract = {Currently, there are no medications that effectively treat the core symptoms of Autism Spectrum Disorder (ASD). We recently found that the bacterial species Lactobacillus (L.) reuteri reverses social deficits in maternal high-fat-diet offspring. However, whether the effect of L. reuteri on social behavior is generalizable to other ASD models and its mechanism(s) of action remains unknown. Here, we found that treatment with L. reuteri selectively rescues social deficits in genetic, environmental, and idiopathic ASD models. Interestingly, the effects of L. reuteri on social behavior are not mediated by restoring the composition of the host's gut microbiome, which is altered in all of these ASD models. Instead, L. reuteri acts in a vagus nerve-dependent manner and rescues social interaction-induced synaptic plasticity in the ventral tegmental area of ASD mice, but not in oxytocin receptor-deficient mice. Collectively, treatment with L. reuteri emerges as promising non-invasive microbial-based avenue to combat ASD-related social dysfunction.},
}
@article {pmid30521984,
year = {2018},
author = {Lee, FJ and Williams, KB and Levin, M and Wolfe, BE},
title = {The Bacterial Metabolite Indole Inhibits Regeneration of the Planarian Flatworm Dugesia japonica.},
journal = {iScience},
volume = {10},
number = {},
pages = {135-148},
doi = {10.1016/j.isci.2018.11.021},
pmid = {30521984},
issn = {2589-0042},
abstract = {Planarian flatworms have been used for over a century as models for regeneration. Planarians live in aquatic environments with constant exposure to microbes, but the mechanisms by which bacteria may mediate planarian regeneration are largely unknown. We characterized the microbiome of laboratory populations of the planarian Dugesia japonica and determined how individual bacteria impact D. japonica regeneration. Eight to ten taxa in the phyla Bacteroidetes and Proteobacteria consistently occur across planarian colonies housed in different research laboratories. Individual members of the D. japonica microbiome can delay regeneration including the development of eye spots and blastema formation. The microbial metabolite indole is produced in significant quantities by two bacteria that are consistently found in the D. japonica microbiome and contributes to delays in regeneration. Collectively, these results provide a baseline understanding of the bacteria associated with the planarian D. japonica and demonstrate how metabolite production by host-associated microbes can affect regeneration.},
}
@article {pmid30521932,
year = {2018},
author = {On Wah, DT and Kavaliers, M and Bishnoi, I and Ossenkopp, KP},
title = {Lipopolysaccharide (LPS) induced sickness in early adolescence alters the behavioral effects of the short-chain fatty acid, propionic acid, in late adolescence and adulthood: Examining anxiety and startle reactivity.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbr.2018.12.003},
pmid = {30521932},
issn = {1872-7549},
abstract = {Early life immune challenges are risk factors for neurodevelopmental disorders. In adolescence, they elicit behavioral symptoms that resemble clinical disorders. Stressors during this time may alter signaling from the gut microbiome, which increases the risk for psychiatric disorders. It was hypothesized that adolescent immune challenges may interact with a gut bacterial product, the short-chain fatty acid, propionic acid (PPA), to potentiate symptoms of anxiety and sensory abnormality. The present study investigated the effects of repeated lipopolysaccharide (LPS) exposure during early adolescence, on the behavioral effects of PPA in late adolescence and adulthood. Male adolescent rats were injected with LPS (0.2 mg/kg i.p.) or the vehicle on postnatal days (P) 28, P30, P32, and P34. They were later administered either PPA (500 mg/kg i.p.) or the vehicle during late adolescence on P40 and P43, and were subsequently tested on the light-dark anxiety test and acoustic startle response, respectively. In adulthood, the rats were again injected with PPA or the vehicle and tested on the light-dark and acoustic startle tasks on P74 and P77. The results of this study showed that LPS and PPA both decreased locomotor activity. PPA reduced vertical activity, percent prepulse inhibition, and acoustic startle response magnitude. LPS increased anxiogenic behaviors and induced a delayed increase in acoustic startle response magnitude in adulthood. Although no LPS and PPA interactions were found, the results of this study suggest that early adolescent immune activation can induce long-term behavioral changes that resemble the complex phenotypes of clinical disorders.},
}
@article {pmid30521852,
year = {2018},
author = {Cao, ZH and Green-Johnson, JM and Buckley, ND and Lin, QY},
title = {Bioactivity of soy-based fermented foods: A review.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.biotechadv.2018.12.001},
pmid = {30521852},
issn = {1873-1899},
abstract = {For centuries, fermented soy foods have been dietary staples in Asia and, now, in response to consumer demand, they are available throughout the world. Fermentation bestows unique flavors, boosts nutritional values and increases or adds new functional properties. In this review, we describe the functional properties and underlying action mechanisms of soy-based fermented foods such as Natto, fermented soy milk, Tempeh and soy sauce. When possible, the contribution of specific bioactive components is highlighted. While numerous studies with in vitro and animal models have hinted at the functionality of fermented soy foods, ascribing health benefits requires well-designed, often complex human studies with analysis of diet, lifestyle, family and medical history combined with long-term follow-ups for each subject. In addition, the contribution of the microbiome to the bioactivities of fermented soy foods, possibly mediated through direct action or bioactive metabolites, needs to be studied. Potential synergy or other interactions among the microorganisms carrying out the fermentation and the host's microbial community may also contribute to food functionality, but the details still require elucidation. Finally, safety evaluation of fermented soy foods has been limited, but is essential in order to provide guidelines for consumption and confirm lack of toxicity.},
}
@article {pmid30521647,
year = {2018},
author = {Jeżewska-Frąckowiak, J and Seroczyńska, K and Banaszczyk, J and Woźniak, D and Żylicz-Stachula, A and Skowron, PM},
title = {The promises and risks of probiotic Bacillus species.},
journal = {Acta biochimica Polonica},
volume = {},
number = {},
pages = {},
doi = {10.18388/abp.2018_2652},
pmid = {30521647},
issn = {1734-154X},
abstract = {Supplementing the human microbiome with probiotic microorganisms is a proposed solution for civilization syndromes such as dysbiosis and gastrointestinal tract (GIT) disorders. Bimodal probiotic strains of the Bacillus genus constitute the microbiota of the human environment, and are typically found in soil, water, a number of non-dairy fermented foods, as well as in human and animal GIT. Probiotic Bacillus sp. are Gram positive rods, with the ability of sporulation to survive environmental stress and preparation conditions. In vitro models of the human stomach and human studies with probiotic Bacillus reveal the mechanisms of its life cycle and sporulation. The Bacillus sp. probiotic biofilm introduces biochemical effects such as antimicrobial and enzymatic activity, thus contributing to protection from GIT and other infections. Despite the beneficial activity of Bacillus strains belonging to the safety group 1, a number of strains can pose a substantial health risk, carrying genes for various toxins or antibiotic resistance. Commercially available Bacillus probiotic preparations include strains from the subtilis and other closely related phylogenetic clades. Those intended for oral administration in humans, often encapsulated with appropriate supporting materials, still tend to be mislabeled or poorly characterized. Bacillus sp. MALDI-TOF analysis, combined with sequencing of characteristic 16S rRNA or enzyme coding genes, may provide accurate identification. A promising future application of the probiotic Bacillus sp. might be the microflora biocontrol in the human body and the closest human environment. Environmental probiotic Bacillus species display the potential to support human microflora, however controversies regarding the safety of certain strains is a key factor in their still limited application.},
}
@article {pmid30521592,
year = {2018},
author = {Indest, KJ and Everman, SJ and Lindsay, JH and Jung, CM and Smith, JC and Newell, SB},
title = {Effects of acute exposures of 2,4,6-trinitrotoluene and inorganic lead on the fecal microbiome of the green anole (Anolis carolinensis).},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208281},
doi = {10.1371/journal.pone.0208281},
pmid = {30521592},
issn = {1932-6203},
abstract = {Microbiome studies focused on ecologically relevant vertebrate models like reptiles have been limited. Because of their relatively small home range, fast maturation, and high fecundity, lizards are an excellent reptilian terrestrial indicator species. For this study we used the green anole, Anolis carolinensis, to assess the impact of military relevant contaminants on fecal microbiome composition. Fourteen day sub-acute exposures were conducted via oral gavage with 2,4,6-Trinitrotoluene (TNT) and inorganic lead at doses of 60 mg/kg and 20 mg/kg of body weight, respectively. Body weights and food consumption were monitored and fecal samples were collected for high-throughput 16S rRNA gene amplicon sequencing and analytical chemistry at days 0 and 15. At the end of the study, liver and gut were harvested for body burden data. Chemical analysis confirmed accumulation of TNT, TNT transformation products, and lead in liver tissue and fecal samples. Bacterial community analysis of fecal material revealed significant differences between day 0 and day 15 of TNT exposed anoles with an operational taxonomic unit (OTU) within the genus Erwinia representing 32% of the microbial community in TNT exposed anoles. Predictable changes in gut microbiome composition could offer an easily assayed, noninvasive biomarker for specific chemical exposure providing enhanced scientific support to risk assessments on military installations.},
}
@article {pmid30521585,
year = {2018},
author = {Wun, K and Theriault, BR and Pierre, JF and Chen, EB and Leone, VA and Harris, KG and Xiong, L and Jiang, Q and Spedale, M and Eskandari, OM and Chang, EB and Ho, KJ},
title = {Microbiota control acute arterial inflammation and neointimal hyperplasia development after arterial injury.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208426},
doi = {10.1371/journal.pone.0208426},
pmid = {30521585},
issn = {1932-6203},
abstract = {BACKGROUND: The microbiome has a functional role in a number of inflammatory processes and disease states. While neointimal hyperplasia development has been linked to inflammation, a direct role of the microbiota in neointimal hyperplasia has not yet been established. Germ-free (GF) mice are an invaluable model for studying causative links between commensal organisms and the host. We hypothesized that GF mice would exhibit altered neointimal hyperplasia following carotid ligation compared to conventionally raised (CONV-R) mice.<br><br>METHODS: Twenty-week-old male C57BL/6 GF mice underwent left carotid ligation under sterile conditions. Maintenance of sterility was assessed by cultivation and 16S rRNA qPCR of stool. Neointimal hyperplasia was assessed by morphometric and histologic analysis of arterial sections after 28 days. Local arterial cell proliferation and inflammation was assessed by immunofluorescence for Ki67 and inflammatory cell markers at five days. Systemic inflammation was assessed by multiplex immunoassays of serum. CONV-R mice treated in the same manner served as the control cohort. GF and CONV-R mice were compared using standard statistical methods.<br><br>RESULTS: All GF mice remained sterile during the entire study period. Twenty-eight days after carotid ligation, CONV-R mice had significantly more neointimal hyperplasia development compared to GF mice, as assessed by intima area, media area, intima+media area, and intima area/(intima+media) area. The collagen content of the neointimal lesions appeared qualitatively similar on Masson's trichrome staining. There was significantly reduced Ki67 immunoreactivity in the media and adventitia of GF carotid arteries 5 days after ligation. GF mice also had increased arterial infiltration of anti-inflammatory M2 macrophages compared to CONV-R mouse arteries and a reduced proportion of mature neutrophils. GF mice had significantly reduced serum IFN-γ-inducible protein (IP)-10 and MIP-2 5 days after carotid ligation, suggesting a reduced systemic inflammatory response.<br><br>CONCLUSIONS: GF mice have attenuated neointimal hyperplasia development compared to CONV-R mice, which is likely related to altered kinetics of wound healing and acute inflammation. Recognizing the role of commensals in the regulation of arterial remodeling will provide a deeper understanding of the pathophysiology of restenosis and support strategies to treat or reduce restenosis risk by manipulating microbiota.},
}
@article {pmid30521561,
year = {2018},
author = {Ponnusamy, L and Willcox, AC and Roe, RM and Davidson, SA and Linsuwanon, P and Schuster, AL and Richards, AL and Meshnick, SR and Apperson, CS},
title = {Bacterial microbiome of the chigger mite Leptotrombidium imphalum varies by life stage and infection with the scrub typhus pathogen Orientia tsutsugamushi.},
journal = {PloS one},
volume = {13},
number = {12},
pages = {e0208327},
doi = {10.1371/journal.pone.0208327},
pmid = {30521561},
issn = {1932-6203},
abstract = {Scrub typhus is a mites-borne rickettsiosis caused by the obligate intracellular Gram-negative bacterium Orientia tsutsugamushi. The disease is potentially life threatening and is prevalent in tropical Asia, islands of the western Pacific Ocean and northern Australia where an estimated one million cases occur annually. Orientia tsutsugamushi is transmitted by the bite of larval mites in the genus Leptotrombidium. In the present study, the composition of the microbiome in larvae, deutonymphs and adult males and females from laboratory colonies of L. imphalum that were infected as well as uninfected with O. tsutsugamushi were investigated by high-throughput sequencing of the bacterial 16S rRNA gene. Notably, the bacterial microbiomes of infected adult females were dominated by sequences of O. tsutsugamushi and an unidentified species of Amoebophilaceae, which together comprised 98.2% of bacterial sequences. To improve the taxonomic resolution of the Amoebophilaceae OTU a nearly full length sequence of the 16S rRNA gene was amplified, cloned, and Sanger sequenced. Infected female mites had 89 to 92% nucleotide identity with the Amoebophilaceae family, indicating that the bacterium was likely to be a species of a novel genus. The species composition of bacterial communities varied between mite life stages regardless of their infection status. Uninfected adults exhibited greater species diversity than adults infected with O. tsutsugamushi. In the infected colony, the rate of filial infection with Orientia was less than 100%. Larval and male mites that were PCR-negative for Orientia contained low numbers of sequences of Amoebophilaceae (0.01 and 0.06%, respectively) in their taxonomic profiles, suggesting that a mutualistic relationship exists between the novel species of Amoebophilaceae and O. tsutsugamushi. Our study findings provide the basis for further research to determine the influence of the novel Amoebophilaceae species on the bacterial microbiome and on vector susceptibility to and transovarial transmission of O. tsutsugamushi.},
}
@article {pmid30521380,
year = {2018},
author = {Calatayud, M and Dezutter, O and Hernandez-Sanabria, E and Hidalgo-Martinez, S and Meysman, FJR and Van de Wiele, T},
title = {Development of a host-microbiome model of the small intestine.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {},
number = {},
pages = {fj201801414R},
doi = {10.1096/fj.201801414R},
pmid = {30521380},
issn = {1530-6860},
abstract = {The intestinal epithelium plays an essential role in the balance between tolerant and protective immune responses to infectious agents. In vitro models do not typically consider the innate immune response and gut microbiome in detail, so these models do not fully mimic the physiologic aspects of the small intestine. We developed and characterized a long-term in vitro model containing enterocyte, goblet, and immune-like cells exposed to a synthetic microbial community representative of commensal inhabitants of the small intestine. This model showed differential responses toward a synthetic microbial community of commensal bacterial inhabitants of the small intestine in the absence or presence of LPS from Escherichia coli O111:B4. Simultaneous exposure to LPS and microbiota induced impaired epithelial barrier function; increased production of IL-8, IL-6, TNF-α, and C-X-C motif chemokine ligand 16; and augmented differentiation and adhesion of macrophage-like cells and the overexpression of dual oxidase 2 and TLR-2 and -4 mRNA. In addition, the model demonstrated the ability to assess the adhesion of specific bacterial strains from the synthetic microbial community-more specifically, Veillonella parvula-to the simulated epithelium. This novel in vitro model may assist in overcoming sampling and retrieval difficulties when studying host-microbiome interactions in the small intestine.-Calatayud, M., Dezutter, O., Hernandez-Sanabria, E., Hidalgo-Martinez, S., Meysman, F. J. R., Van de Wiele, T. Development of a host-microbiome model of the small intestine.},
}
@article {pmid30521034,
year = {2018},
author = {Moitinho-Silva, L and Nielsen, S and Amir, A and Gonzalez, A and Ackermann, GL and Cerrano, C and Astudillo-Garcia, C and Easson, C and Sipkema, D and Liu, F and Steinert, G and Kotoulas, G and McCormack, GP and Feng, G and Bell, JJ and Vicente, J and Björk, JR and Montoya, JM and Olson, JB and Reveillaud, J and Steindler, L and Pineda, MC and Marra, MV and Ilan, M and Taylor, MW and Polymenakou, P and Erwin, PM and Schupp, PJ and Simister, RL and Knight, R and Thacker, RW and Costa, R and Hill, RT and Lopez-Legentil, S and Dailianis, T and Ravasi, T and Hentschel, U and Li, Z and Webster, NS and Thomas, T},
title = {Erratum to: The sponge microbiome project.},
journal = {GigaScience},
volume = {7},
number = {12},
pages = {},
doi = {10.1093/gigascience/giy145},
pmid = {30521034},
issn = {2047-217X},
}
@article {pmid30520095,
year = {2018},
author = {Hernández-Rodríguez, D and Vásquez-Aguilar, AA and Serio-Silva, JC and Rebollar, EA and Azaola-Espinosa, A},
title = {Molecular detection of Bifidobacterium spp. in faeces of black howler monkeys (Alouatta pigra).},
journal = {Journal of medical primatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jmp.12395},
pmid = {30520095},
issn = {1600-0684},
support = {//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {BACKGROUND: Bifidobacterium genus are considered to be beneficial bacteria for their hosts; however, knowledge about the specific species that are part of the gut microbiome of howler monkeys is scarce. Polymerase chain reaction (PCR) is a useful technique for the identification of non-cultivable or difficult to grow bacterial species. With the goal of detecting species of the genus Bifidobacterium in black howler monkeys, we used PCR on DNA derived from faecal samples.<br><br>METHODS: We collected and extracted DNA from 40 faecal samples. Using specific primers, we performed PCR and nested PCR to detect members of the Bifidobacterium genus and a subset of species: Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum and Bifidobacterium animalis subsp. animalis.<br><br>RESULTS: 97.5% (39/40) of the samples were positive for Bifidobacterium spp. We found B longum in 100% of the analysed samples.<br><br>CONCLUSIONS: This is the first report of B longum in black howler monkey faeces.},
}
@article {pmid30519986,
year = {2018},
author = {Javan, GT and Finley, SJ and Tuomisto, S and Hall, A and Benbow, ME and Mills, D},
title = {An interdisciplinary review of the thanatomicrobiome in human decomposition.},
journal = {Forensic science, medicine, and pathology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12024-018-0061-0},
pmid = {30519986},
issn = {1556-2891},
support = {1401075//National Science Foundation/ ; 2017-MU-MU-0042//National Institute of Justice/ ; },
abstract = {Death does not occur instantaneously and organs do not decompose at the same rate or in the same way. Nulligravid human uteri and prostate glands are the last internal organs to deteriorate during decomposition; however, the reason for this very important observation is still enigmatic. Recent studies have elucidated that the composition and abundance of microbes in the human thanatomicrobiome (microbiome of death) varies by organ and changes as a function of time and temperature. The ileocecal area has the largest absolute postmortem burden that spreads to the liver and spleen and continues to the heart and brain depending on the cause of death. To truly understand the mechanisms of microbial assembly during decomposition, a thorough examination of different strategies utilized by the trillions of microbes that colonize decaying tissues is needed from a multi-organ and multidisciplinary approach. In this review, we highlight interdisciplinary research and provide an overview of human decomposition investigations of thanatomicrobiomic changes in internal organs.},
}
@article {pmid30519847,
year = {2018},
author = {Allegretti, JR and Fischer, M and Sagi, SV and Bohm, ME and Fadda, HM and Ranmal, SR and Budree, S and Basit, AW and Glettig, DL and de la Serna, EL and Gentile, A and Gerardin, Y and Timberlake, S and Sadovsky, R and Smith, M and Kassam, Z},
title = {Fecal Microbiota Transplantation Capsules with Targeted Colonic Versus Gastric Delivery in Recurrent Clostridium difficile Infection: A Comparative Cohort Analysis of High and Lose Dose.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10620-018-5396-6},
pmid = {30519847},
issn = {1573-2568},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridium. difficile infection (rCDI). FMT capsules have emerged, and it is unknown if delivery location and dose impact efficacy.<br><br>METHODS: We compared two cohorts of patients receiving two capsule formulations: gastric release (FMTgr) and targeted colonic release (FMTcr) at two different sites. Cohort A received FMTgr at (1) high dose: 60 capsules and low dose: 30 capsules. Patients in Cohort B received FMTcr at (1) high dose: 30 capsules (2) low dose: 10 capsules. Clinical cure rates and adverse events were monitored through week 8. Paired t-tests were used to compare diversity pre- and post-FMT.<br><br>RESULTS: 51 rCDI patients were enrolled. Cohort A contained n = 20 and Cohort B contained n = 31. Overall cure at week 8 for FMTgr was 75% (15/20) compared to 80.6% for FMTcr, (25/31), p = 0.63. Both formulations were safe with no serious adverse events. FMTcr was superior at increasing gut microbial diversity.<br><br>DISCUSSION: To our knowledge, this is the first study to compare targeted delivery of FMT capsules. While both capsules were safe and efficacious, microbial engraftment patterns were superior in FMTcr.},
}
@article {pmid30519775,
year = {2018},
author = {Slobodin, G and Rosner, I and Kessel, A},
title = {Dendritic cells in the pathogenesis of ankylosing spondylitis and axial spondyloarthritis.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10067-018-4388-4},
pmid = {30519775},
issn = {1434-9949},
abstract = {The interaction of dendritic cells (DCs) with the human microbiome, with distorted handling of the microbiota or its products via the direct effect of HLA B27, probably represents the initial element in the chain of events leading to the development of clinical axial spondyloarthritis. The mechanism of disease extension onto the skeleton and other tissues involved, such as uvea, may also involve migratory DCs. Finally, the role of DCs in the initiation of the inflammatory tissue response with activation of the IL-17 axis has been demonstrated. Further, some initial data suggests the possible connection of DCs with disease-related new bone formation.},
}
@article {pmid30519552,
year = {2018},
author = {Tye-Din, JA and Galipeau, HJ and Agardh, D},
title = {Celiac Disease: A Review of Current Concepts in Pathogenesis, Prevention, and Novel Therapies.},
journal = {Frontiers in pediatrics},
volume = {6},
number = {},
pages = {350},
doi = {10.3389/fped.2018.00350},
pmid = {30519552},
issn = {2296-2360},
abstract = {Our understanding of celiac disease and how it develops has evolved significantly over the last half century. Although traditionally viewed as a pediatric illness characterized by malabsorption, it is now better seen as an immune illness with systemic manifestations affecting all ages. Population studies reveal this global disease is common and, in many countries, increasing in prevalence. These studies underscore the importance of specific HLA susceptibility genes and gluten consumption in disease development and suggest that other genetic and environmental factors could also play a role. The emerging data on viral and bacterial microbe-host interactions and their alterations in celiac disease provides a plausible mechanism linking environmental risk and disease development. Although the inflammatory lesion of celiac disease is complex, the strong HLA association highlights a central role for pathogenic T cells responding to select gluten peptides that have now been defined for the most common genetic form of celiac disease. What remains less understood is how loss of tolerance to gluten occurs. New insights into celiac disease are now providing opportunities to intervene in its development, course, diagnosis, and treatment.},
}
@article {pmid30519501,
year = {2018},
author = {Cavuoto, KM and Banerjee, S and Miller, D and Galor, A},
title = {Composition and Comparison of the Ocular Surface Microbiome in Infants and Older Children.},
journal = {Translational vision science &amp; technology},
volume = {7},
number = {6},
pages = {16},
doi = {10.1167/tvst.7.6.16},
pmid = {30519501},
issn = {2164-2591},
abstract = {Purpose: Unlike other microbiomes of the body, the composition of the ocular surface microbiome (OSM) in children has yet to be thoroughly explored. Our goal was to evaluate the OSM in young infants and compare its composition to older children using both culture dependent and independent methodologies to assess for differences with age.<br><br>Methods: Prospective, observational, cross-sectional study of children <18 years of age at a university-based institution. The mucosal surfaces of both eyes, nose and throat were swabbed with a forensic-quality swab. Half of the swab was plated for culture and the other half underwent 16S sequencing. Culture results and microbiome diversity were analyzed.<br><br>Results: Fifty patients (mean age 37 months, range 1-168 months) were enrolled. Forty-seven eyes of 30 patients had positive cultures; four eyes grew >1 species. Culture positive patients were older (43 vs. 29 months, P = 0.19). Additionally, older children had greater diversity than children under 6 months of age by 16S sequencing (P = 0.05). Staphylococcus species were predominant by culture (35/52 isolates) and by 16S sequencing. The OSM was fairly similar to the nose microbiome, whereas the throat microbiome differed significantly and had a higher abundance of Streptococcaceae (P = 0.001).<br><br>Conclusions: The OSM is predominantly composed of Staphylococcus species in children, as demonstrated by both culture dependent and culture independent methods. Older children were more likely to have growth on culture and have more a complex bacterial milieu with 16S sequencing.<br><br>Translational Relevance: 16S sequencing provides more robust information regarding the composition of the microbiomes than culture dependent methods.},
}
@article {pmid30519226,
year = {2018},
author = {Storey, S and Ashaari, MM and Clipson, N and Doyle, E and de Menezes, AB},
title = {Opportunistic Bacteria Dominate the Soil Microbiome Response to Phenanthrene in a Microcosm-Based Study.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2815},
doi = {10.3389/fmicb.2018.02815},
pmid = {30519226},
issn = {1664-302X},
abstract = {Bioremediation offers a sustainable approach for removal of polycyclic aromatic hydrocarbons (PAHs) from the environment; however, information regarding the microbial communities involved remains limited. In this study, microbial community dynamics and the abundance of the key gene (PAH-RHDα) encoding a ring hydroxylating dioxygenase involved in PAH degradation were examined during degradation of phenanthrene in a podzolic soil from the site of a former timber treatment facility. The 10,000-fold greater abundance of this gene associated with Gram-positive bacteria found in phenanthrene-amended soil compared to unamended soil indicated the likely role of Gram-positive bacteria in PAH degradation. In contrast, the abundance of the Gram-negative PAHs-RHDα gene was very low throughout the experiment. While phenanthrene induced increases in the abundance of a small number of OTUs from the Actinomycetales and Sphingomonadale, most of the remainder of the community remained stable. A single unclassified OTU from the Micrococcaceae family increased ~20-fold in relative abundance, reaching 32% of the total sequences in amended microcosms on day 7 of the experiment. The relative abundance of this same OTU increased 4.5-fold in unamended soils, and a similar pattern was observed for the second most abundant PAH-responsive OTU, classified into the Sphingomonas genus. Furthermore, the relative abundance of both of these OTUs decreased substantially between days 7 and 17 in the phenanthrene-amended and control microcosms. This suggests that their opportunistic phenotype, in addition to likely PAH-degrading ability, was determinant in the vigorous growth of dominant PAH-responsive OTUs following phenanthrene amendment. This study provides new information on the temporal response of soil microbial communities to the presence and degradation of a significant environmental pollutant, and as such has the potential to inform the design of PAH bioremediation protocols.},
}
@article {pmid30519225,
year = {2018},
author = {Ogai, K and Nagase, S and Mukai, K and Iuchi, T and Mori, Y and Matsue, M and Sugitani, K and Sugama, J and Okamoto, S},
title = {Corrigendum: A Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping.},
journal = {Frontiers in microbiology},
volume = {9},
number = {},
pages = {2812},
doi = {10.3389/fmicb.2018.02812},
pmid = {30519225},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2018.02362.].},
}
@article {pmid30519157,
year = {2018},
author = {Pretorius, L and Kell, DB and Pretorius, E},
title = {Iron Dysregulation and Dormant Microbes as Causative Agents for Impaired Blood Rheology and Pathological Clotting in Alzheimer's Type Dementia.},
journal = {Frontiers in neuroscience},
volume = {12},
number = {},
pages = {851},
doi = {10.3389/fnins.2018.00851},
pmid = {30519157},
issn = {1662-4548},
abstract = {Alzheimer's disease and other similar dementias are debilitating neurodegenerative disorders whose etiology and pathogenesis remain largely unknown, even after decades of research. With the anticipated increase in prevalence of Alzheimer's type dementias among the more susceptible aging population, the need for disease-modifying treatments is urgent. While various hypotheses have been put forward over the last few decades, we suggest that Alzheimer's type dementias are triggered by external environmental factors, co-expressing in individuals with specific genetic susceptibilities. These external stressors are defined in the Iron Dysregulation and Dormant Microbes (IDDM) hypothesis, previously put forward. This hypothesis is consistent with current literature in which serum ferritin levels of individuals diagnosed with Alzheimer's disease are significantly higher compared those of age- and gender-matched controls. While iron dysregulation contributes to oxidative stress, it also causes microbial reactivation and virulence of the so-called dormant blood (and tissue) microbiome. Dysbiosis (changes in the microbiome) or previous infections can contribute to the dormant blood microbiome (atopobiosis), and also directly promotes systemic inflammation via the amyloidogenic formation and shedding of potent inflammagens such as lipopolysaccharides. The simultaneous iron dysregulation and microbial aberrations affect the hematological system, promoting fibrin amylodiogenesis, and pathological clotting. Systemic inflammation and oxidative stress can contribute to blood brain barrier permeability and the ensuing neuro-inflammation, characteristic of Alzheimer's type dementias. While large inter-individual variability exists, especially concerning disease pathogenesis, the IDDM hypothesis acknowledges primary causative factors which can be targeted for early diagnosis and/or for prevention of disease progression.},
}
@article {pmid30518941,
year = {2018},
author = {Kaur, US and Shet, A and Rajnala, N and Gopalan, BP and Moar, P and D, H and Singh, BP and Chaturvedi, R and Tandon, R},
title = {High Abundance of genus Prevotella in the gut of perinatally HIV-infected children is associated with IP-10 levels despite therapy.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {17679},
doi = {10.1038/s41598-018-35877-4},
pmid = {30518941},
issn = {2045-2322},
support = {ECR/2015/000304//DST | Science and Engineering Research Board (SERB)/ ; },
abstract = {Perinatal HIV infection is characterized by faster HIV disease progression and higher initial rate of HIV replication compared to adults. While antiretroviral therapy (ART) has greatly reduced HIV replication to undetectable levels, there is persistent elevated inflammation associated with HIV disease progression. Alteration of gut microbiota is associated with increased inflammation in chronic adult HIV infection. Here, we aim to study the gut microbiome and its role in inflammation in treated and untreated HIV-infected children. Examination of fecal microbiota revealed that perinatally infected children living with HIV had significantly higher levels of genus Prevotella that persisted despite ART. These children also had higher levels of soluble CD14 (sCD14), a marker of microbial translocation, and IP-10 despite therapy. The Prevotella positively correlated with IP-10 levels in both treated and untreated HIV-infected children, while genus Prevotella and species Prevotella copri was inversely associated with CD4 count. Relative abundance of genus Prevotella and species Prevotella copri showed positive