@article {pmid31743877,
year = {2019},
author = {Shenghua, P and Ziqin, Z and Shuyu, T and Huixia, Z and Xianglu, R and Jiao, G},
title = {An integrated fecal microbiome and metabolome in the aged mice reveal anti-aging effects from the intestines and biochemical mechanism of FuFang zhenshu TiaoZhi(FTZ).},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {121},
number = {},
pages = {109421},
doi = {10.1016/j.biopha.2019.109421},
pmid = {31743877},
issn = {1950-6007},
abstract = {BACKGROUND/AIMS: Fufang Zhenzhu Tiao Zhi (FTZ) capsule is a Chinese herbal preparation under the guidance of professor Guo Jiao's new theory of "Tiaogan Qishu Huazhuo" for disorders of glucose and lipid metabolism for more than twenty yares, which has been demonstrated to exhibit potential anti-aging effects such as regulation of glucose and lipid metabolisms and antiinflammatory and antioxidative effects. This study attempts to reveal the anti-intestinal aging effect and possible mechanism of FTZ.

METHODS: The mice were divided into three groups: the control group, model group and treatment group. The treatment group was given 1.0 g/kg body weight of FTZ extract administered by oral gavage once a day for 12 consecutive weeks. Age-related alterations such as HE staining of intestinal tissue morphology, mRNA levels of intestinal telomerase and inflammatory cytokines were observed Fecal samples were used for ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF/MS) and 16S rRNA gene sequencing analyses to reveal age-related metabolic perturbations and gut flora disorders to demonstrate the effects of FTZ.

RESULTS: Emerged pathological morphology of intestinal tissues, upregulated relative expression level of gut inflammatory factors and decreased relative expression level of telomerase mRNA in aging mice illustrated characteristic senescent phenotypes in model group. FTZ treatment significantly lowered intestinal inflammation levels, enhanced telomerase activity, partially reversed the fecal metabolites abnormalities and restored the disorders of intestinal flora. Multiple potential metabolites were associated with linoleic acid, glycerophospholipid, α-linolenic acid, biosynthesis of unsaturated fatty acids and glycerolipid metabolisms. Several decreased beneficial butyrate-producing bacteria like S24-7, possible Alkaliphilus belonging to the Clostridia class and increased harmful bacteria such as potentially toxic metabolite hydrogen sulfide-producer Bilophila and Desulfovibrio, inflammation-mediator Mucispirillum were determined in present aging mice. These age-related poor alterations could be partially attenuated by FTZ treatment.

CONCLUSION: The pathologic changes of intestinal senescence and the decrease of telomerase mRNA in elderly mice was observed. FTZ may sever as a novel delaying intestinal aging strategy via three pathways for anti-inflammatory, improving gut metabolites and gut flora. This study not only provided biological basis for the theory of treating different diseases with the same treatment in TCM, but also provided objective evidence for incorporating aging into the system of"glucose-lipid metabolism disease".},
}

@article {pmid31743706,
year = {2019},
author = {Yumeng, X and Fukunaga, M and Kuda, T and Goto, M and Chiaraluce, G and Hoshiba, H and Takahashi, H and Kimura, B},
title = {Detection and isolation of protein susceptible indigenous bacteria affected by dietary milk-casein, albumen and soy-protein in the caecum of ICR mice.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ijbiomac.2019.09.159},
pmid = {31743706},
issn = {1879-0003},
abstract = {In this study, we fed ICR mice with a high-sucrose diet containing 20% w/w of milk-casein (MC), egg-white (EW), or soy-protein (SP) for 14 days in order to detect the presence of protein-susceptible gut indigenous bacteria (P-SIB). The caecal microbiome was examined by 16S rDNA amplicon sequencing using a next-generation MiSeq system. Principal coordinate analysis of the operational taxonomic units (OTUs) revealed that the microbiomes differed among the three groups. Typical SIB found in the MC-fed group were Bacteroides acidifaciens-, Bacteroides sartorii-, Eisenbergiella sp., and Lachnospiraceae sp.-like; in the EW-fed group were Lactobacillus murinus and Enterococcus faecium/avium-like; and in the SP-fed group were Muribaculaceae sp.-like bacteria. We also found that a few Lachnospiraceae sp.- and Clostridium disporicum-like bacteria were suppressed in the EW-fed mice. Out of the P-SIB detected, B. acidifaciens, L. murinus, E. faecium, and E. avium could be isolated and identified using BL agar and 16S rDNA BLAST search, respectively.},
}

@article {pmid31743445,
year = {2019},
author = {Sfriso, R and Egert, M and Gempeler, M and Voegeli, R and Campiche, R},
title = {Revealing the secret life of skin With the microbiome you never walk alone.},
journal = {International journal of cosmetic science},
volume = {},
number = {},
pages = {},
doi = {10.1111/ics.12594},
pmid = {31743445},
issn = {1468-2494},
abstract = {The human skin microbiome has recently become a focus for both the dermatological and cosmetic fields. Understanding the skin microbiota, i.e. the collection of vital microorganisms living on our skin, and how to maintain its delicate balance is an essential step to gain insight into the mechanisms responsible for healthy skin and its appearance. Imbalances in the skin microbiota composition (dysbiosis) are associated with several skin conditions, either pathological such as eczema, acne, allergies or dandruff or non-pathological such as sensitive skin, irritated skin or dry skin. Therefore, the development of approaches which preserve or restore the natural, individual balance of the microbiota represents a novel target not only for dermatologists but also for skin care applications. This review gives an overview on the current knowledge on the skin microbiome, the currently available sampling and analysis techniques as well as a description of current approaches undertaken in the skin care segment to help restoring and balancing the structure and functionality of the skin microbiota.},
}

@article {pmid31742590,
year = {2019},
author = {Parata, L and Nielsen, S and Xing, X and Thomas, T and Egan, S and Vergés, A},
title = {Age, gut location and diet impact the gut microbiome of a tropical herbivorous surgeonfish.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz179},
pmid = {31742590},
issn = {1574-6941},
abstract = {Herbivorous fishes play important ecological roles in coral reefs by consuming algae that can otherwise outcompete corals, but we know little about the gut microbiota that facilitates this process. This study focussed on the gut microbiota of an ecologically important coral reef fish, the convict surgeonfish Acanthurus triostegus. We sought to understand how the microbiome of this species varies along its gastrointestinal tract and how it varies between juvenile and adult fish. Further, we examined if the bacteria associated with the diet consumed by juveniles contributes to the gut microbiota. 16S rRNA gene amplicon sequencing showed that bacterial communities associated with the midgut and hindgut regions were distinct between adults and juveniles, however, no significant differences were seen for gut wall samples. The microbiota associated with the epilithic algal food source was similar to that of the juvenile midgut and gut wall but differed from the microbiome of the hindgut. A core bacterial community including members of taxa Epulopiscium and Brevinemataceae was observed across all gastrointestinal and diet samples, suggesting that these bacterial symbionts can be acquired by juvenile convict surgeonfish horizontally via their diet and then are retained into adulthood.},
}

@article {pmid31742491,
year = {2019},
author = {Beversdorf, DQ and Stevens, HE and Margolis, KG and de Water, JV},
title = {Prenatal stress and maternal immune dysregulation in autism spectrum disorders- potential points for intervention.},
journal = {Current pharmaceutical design},
volume = {},
number = {},
pages = {},
doi = {10.2174/1381612825666191119093335},
pmid = {31742491},
issn = {1873-4286},
abstract = {BACKGROUND: Genetics are a major etiological contributor to autism spectrum disorder (ASD). Environmental factors, however, also appear to contribute. ASD pathophysiology due to gene x environment is also beginning to be explored. One reason to focus on environmental factors is that they may allow opportunities for intervention or prevention.

METHODS AND RESULTS: Herein, we review two such factors that have been associated with a significant proportion of ASD risk, prenatal stress exposure and maternal immune dysregulation. Maternal stress susceptibility appears to interact with prenatal stress exposure to affect offspring neurodevelopment. We also explore how maternal stress may interact with the microbiome in the neurodevelopmental setting. Additionally, understanding of the impact of maternal immune dysfunction on ASD has recently been advanced by recognition of specific fetal brain proteins targeted by maternal autoantibodies, and identification of unique mid-gestational maternal immune profiles. This might also be interrelated with maternal stress exposure. Animal models have been developed to explore pathophysiology targeting each of these factors.

CONCLUSIONS: We are beginning to understand the behavioral, pharmacopathological, and epigenetic effects related to these interactions, and we are beginning to explore potential mitigating factors. Continued growth in understanding of these mechanisms may ultimately allow for the identification of multiple potential targets for prevention or intervention for this subset of environmental-associated ASD cases.},
}

@article {pmid31742291,
year = {2019},
author = {Chen, P and Hei, M and Kong, L and Liu, Y and Yang, Y and Mu, H and Zhang, X and Zhao, S and Duan, J},
title = {One water-soluble polysaccharide from Ginkgo biloba leaves with antidepressant activities via modulation of the gut microbiome.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo01178a},
pmid = {31742291},
issn = {2042-650X},
abstract = {Depression, a mental illness characterized by persistent feeling of sadness and loss of interest, has been a serious health problem worldwide. Manipulation of the microbiota by probiotics and prebiotics represents a novel emerging strategy for the treatment of various psychiatric disorders such as major depressive disorders. Here, we show that one water-soluble polysaccharide from Ginkgo biloba leaves (GPS) reduced stress-induced depression and reversed gut dysbiosis. Similar to the antidepressant paroxetine, GPS significantly reduced the immobility times in the tail suspension test (TST) and forced swimming test (FST) and anxiety-like behavior in the open field test (OFT). Consistent with the improvement of depression-like behavior above, GPS mice had elevated serotonin and dopamine levels in multiple brain regions including the hippocampus, cerebral cortex and olfactory bulb, relative to unpredictable chronic mild stress (UCMS) treatment mice. GPS treatment could alleviate the stress-induced reduction in the density of serotonin-positive and dopamine-positive cells. Fecal microbiome transplant (FMT) combined with antibiotic treatment showed that the anti-depressant activity of GPS had a causal relationship with intestinal microbes. By performing a pyrosequencing-based analysis of bacterial 16S rRNA (V3 + V4 region) in fecal of the mice, the results showed that GPS reversed depression-associated gut dysbiosis and increased the richness of Lactobacillus species which has been proven to be a path to relieve depression. Our results demonstrated that the polysaccharide from Ginkgo biloba leaves might be a promising pharmacotherapeutic candidate for treating depression.},
}

@article {pmid31741802,
year = {2019},
author = {Rice, MM and Maher, RL and Vega Thurber, R and Burkepile, DE},
title = {Different nitrogen sources speed recovery from corallivory and uniquely alter the microbiome of a reef-building coral.},
journal = {PeerJ},
volume = {7},
number = {},
pages = {e8056},
doi = {10.7717/peerj.8056},
pmid = {31741802},
issn = {2167-8359},
abstract = {Corals are in decline worldwide due to local anthropogenic stressors, such as nutrient loading, and global stressors, such as ocean warming. Anthropogenic nutrient loading, which is often rich in nitrate, inhibits coral growth and worsens corals' response to warming while natural sources of nitrogen, such as ammonium from fish excretion, promotes coral growth. Although the effects of nutrient loading and ocean warming have been well-studied, it remains unclear how these factors may interact with biotic processes, such as corallivory, to alter coral health and the coral microbiome. This study examined how nitrate vs. ammonium enrichment altered the effects of increased seawater temperature and simulated parrotfish corallivory on the health of Pocillopora meandrina and its microbial community. We tested the effects of nitrogen source on the response to corallivory under contrasting temperatures (control: 26 °C, warming: 29 °C) in a factorial mesocosm experiment in Moorea, French Polynesia. Corals were able to maintain growth rates despite simultaneous stressors. Seawater warming suppressed wound healing rates by nearly 66%. However, both ammonium and nitrate enrichment counteracted the effect of higher temperatures on would healing rates. Elevated seawater temperature and ammonium enrichment independently increased Symbiodiniaceae densities relative to controls, yet there was no effect of nitrate enrichment on algal symbiont densities. Microbiome variability increased with the addition of nitrate or ammonium. Moreover, microbial indicator analysis showed that Desulfovibrionaceae Operational taxonomic units (OTUs) are indicators of exclusively temperature stress while Rhodobacteraceae and Saprospiraceae OTUs were indicators of high temperature, wounding, and nitrogen enrichment. Overall, our results suggest that nitrogen source may not alter the response of the coral host to simultaneous stressors, but that the associated microbial community may be distinct depending on the source of enrichment.},
}

@article {pmid31741256,
year = {2019},
author = {Hashimoto, T and Kyono, K},
title = {Does dysbiotic endometrium affect blastocyst implantation in IVF patients?.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10815-019-01630-7},
pmid = {31741256},
issn = {1573-7330},
abstract = {PURPOSE: To analyze the pregnancy outcomes of IVF patients presenting eubiotic or dysbiotic endometrium at the time of embryo transfer and to analyze what bacterial profiles are suitable for embryo implantation.

METHODS: Ninety-nine IVF patients under 40 years old undergoing vitrified-warmed blastocyst transfer in HRT cycle had concurrent endometrial microbiome analysis. Samples from the endometrium were taken from the participants at the time of mock transfer; the bacterial profiles at genus level and percentage of lactobacilli in the endometrium of the patients were analyzed.

RESULTS: Thirty-one cases (31.3%) had dysbiotic endometrium. The background profiles, pregnancy rates per transfer (52.9% vs 54.8%), and miscarriage rates (11.1% vs 5.9%) were comparable between patients with eubiotic or dysbiotic endometrium. Major bacterial genera other than Lactobacillus detected in the dysbiotic endometrium were Atopobium, Gardnerella, and Streptococcus. Some patients achieved ongoing pregnancies with 0% Lactobacillus in the endometrium. The endometrial bacterial profiles of pregnant cases with dysbiotic endometrium were comparable with those of non-pregnant cases.

CONCLUSION: Analyzing microbiota at the species-level resolution may be necessary for identifying the true pathogenic bacteria of the endometrium and avoiding over-intervention against non-Lactobacillus microbiota. Further studies are necessary for analyzing the mechanism of how the pathogenic bacteria affect embryo implantation.},
}

@article {pmid31741078,
year = {2019},
author = {Kim, Y and Keogh, JB and Clifton, PM},
title = {Non-nutritive Sweeteners and Glycaemic Control.},
journal = {Current atherosclerosis reports},
volume = {21},
number = {12},
pages = {49},
doi = {10.1007/s11883-019-0814-6},
pmid = {31741078},
issn = {1534-6242},
abstract = {PURPOSE OF REVIEW: The consumption of foods and beverages containing non-nutritive sweeteners (NNS) has increased worldwide over the last three decades. Consumers' choice of NNS rather than sugar or other nutritive sweeteners may be attributable to their potential to reduce weight gain.

RECENT FINDINGS: It is not clear what the effects of NNS consumption are on glycaemic control and the incidence of type 2 diabetes. This review aims to examine this question in epidemiological, human intervention and animal studies. It is not clear that NNS consumption has an effect on the incidence of type 2 diabetes or on glycaemic control even though there is some evidence for the modification of the microbiome and for interaction with sweet taste receptors in the oral cavity and the intestines' modification of secretion of glucagon-like peptide-1 (GLP-1), peptide YY (PYY), ghrelin and glucose-dependent insulinotropic polypeptide (GIP), which may affect glycaemia following consumption of NNS. In conclusion, long-term studies of NNS consumption are required to draw a firm conclusion about the role of NNS consumption on glycaemic control.},
}

@article {pmid31740609,
year = {2019},
author = {Bostick, JW and Wang, Y and Shen, Z and Ge, Y and Brown, J and Chen, ZE and Mohamadzadeh, M and Fox, JG and Zhou, L},
title = {Dichotomous regulation of group 3 innate lymphoid cells by nongastric Helicobacter species.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1908128116},
pmid = {31740609},
issn = {1091-6490},
abstract = {Intestinal innate lymphoid cells (ILCs) contribute to the protective immunity and homeostasis of the gut, and the microbiota are critically involved in shaping ILC function. However, the role of the gut microbiota in regulating ILC development and maintenance still remains elusive. Here, we identified opposing effects on ILCs by two Helicobacter species, Helicobacter apodemus and Helicobacter typhlonius, isolated from immunocompromised mice. We demonstrated that the introduction of both Helicobacter species activated ILCs and induced gut inflammation; however, these Helicobacter species negatively regulated RORγt+ group 3 ILCs (ILC3s), especially T-bet+ ILC3s, and diminished their proliferative capacity. Thus, these findings underscore a previously unknown dichotomous regulation of ILC3s by Helicobacter species, and may serve as a model for further investigations to elucidate the host-microbe interactions that critically sustain the maintenance of intestinal ILC3s.},
}

@article {pmid31739805,
year = {2019},
author = {Auffret, MD and Dewhurst, RJ and Duthie, CA and Rooke, JA and Wallace, RJ and Freeman, TC and Stewart, R and Watson, M and Roehe, R},
title = {Correction to: The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.},
journal = {Microbiome},
volume = {7},
number = {1},
pages = {149},
doi = {10.1186/s40168-019-0764-9},
pmid = {31739805},
issn = {2049-2618},
abstract = {Following publication of the original article [1], the authors reported an error in the Additional file 1.},
}

@article {pmid31739712,
year = {2019},
author = {Zafman, KB and Bergh, EP and Cohen, N and Odom, E and Fox, NS},
title = {The effect of microbiome exposure at birth on pediatric outcomes using a twin cohort discordant for microbiome exposure at birth.},
journal = {The journal of maternal-fetal & 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 = {1-7},
doi = {10.1080/14767058.2019.1684469},
pmid = {31739712},
issn = {1476-4954},
abstract = {Objective: Microbiome exposure at birth has been associated with long-term pediatric outcomes. However, it is difficult to determine if differences in outcomes are truly due to microbiome exposure at birth or other exposures after birth and in early infancy. Using a twin cohort, we sought to determine the association between length of exposure to the maternal vaginal-fecal microbiome and long-term pediatric health outcomes by comparing outcomes between presenting and nonpresenting twins born to women who labored.Methods: We performed a mail-based survey study of women in a single maternal-fetal medicine practice who delivered twin pregnancies ≥24 weeks. The survey study was sent to women when twins were between 2 and 10 years old to assess the long-term health outcomes, including any medical diagnoses or problems with grown and development. For this study, we included all women who labored, and we compared health outcomes for the presenting versus nonpresenting twin with the primary outcome being the development of asthma/reactive airway disease and allergies. The length of exposure to the maternal vaginal-fecal microbiome was measured using the time from rupture of membranes (ROM) to delivery of each twin. Chi-square and Student's t-test were used.Results: Two hundred fifty-seven sets of twins were eligible for analyses. The presenting twin had a longer time of ROM than the nonpresenting twin (617 ± 2408 min versus 2 ± 5 minutes, p < .001). There were no significant differences between health outcomes for the presenting versus nonpresenting twin in the overall cohort, including the development of asthma/reactive airway disease (9.3 versus 10.1%, p = .77) or allergies (12.5 versus 7.8%, p = .08). There were no differences in any outcomes when comparing the presenting versus nonpresenting twin for those twins delivered vaginally or by cesarean delivery.Conclusion: In twins born to women who labored and either delivered vaginally or via cesarean section, delivery order was not associated with any significant increase in defined adverse pediatric outcomes, including the development of asthma or allergies. Using twins as a model for microbiome exposure may help to elucidate the role of the maternal vaginal-fecal microbiome on long-term pediatric health outcomes.},
}

@article {pmid31739506,
year = {2019},
author = {Lu, YT and Wang, SH and Liou, ML and Shen, TA and Lu, YC and Hsin, CH and Yang, SF and Chen, YY and Chang, TH},
title = {Microbiota Dysbiosis in Fungal Rhinosinusitis.},
journal = {Journal of clinical medicine},
volume = {8},
number = {11},
pages = {},
doi = {10.3390/jcm8111973},
pmid = {31739506},
issn = {2077-0383},
abstract = {Fungal rhinosinusitis is a unique phenotype of chronic rhinosinusitis with unique clinical and histological characteristics. The role of bacterial microbiota in various phenotypes chronic rhinosinusitis is not thoroughly understood. Therefore, we conducted 16s rRNA amplification sequencing to determine differences in bacterial communities between phenotypes (fungal vs. non- fungal) and anatomical sites (middle meatus vs. nasopharynx). Endoscope-guided swabs were used to collect samples from the middle meatus and nasopharynx of seven consecutive patients with fungal and 18 consecutive patients with non-fungal rhinosinusitis. DNA was extracted and investigated through 16S rRNA amplification. Among samples from the middle meatus, Shannon diversity was significantly lower in those from the fungal rhinosinusitis group (p = 0.029). However, no significant differences in diversity were noted between nasopharynx samples (p = 0.85). Fungal rhinosinusitis samples exhibited a distinct distribution of taxon relative abundance, which involved not only the absence of rhinosinusitis-associated commensal Corynebacterium and Fusobacterium in the middle meatus but also a significant increase in Haemophilus prevalence and abundance. This is the first study to compare bacterial communities in fungal and non-fungal rhinosinusitis samples. Our findings demonstrated that bacterial community dysbiosis was more apparent in fungal rhinosinusitis samples and was limited to the middle meatus.},
}

@article {pmid31739446,
year = {2019},
author = {Loverdos, K and Bellos, G and Kokolatou, L and Vasileiadis, I and Giamarellos, E and Pecchiari, M and Koulouris, N and Koutsoukou, A and Rovina, N},
title = {Lung Microbiome in Asthma: Current Perspectives.},
journal = {Journal of clinical medicine},
volume = {8},
number = {11},
pages = {},
doi = {10.3390/jcm8111967},
pmid = {31739446},
issn = {2077-0383},
abstract = {A growing body of evidence implicates the human microbiome as a potentially influential player actively engaged in shaping the pathogenetic processes underlying the endotypes and phenotypes of chronic respiratory diseases, particularly of the airways. In this article, we specifically review current evidence on the characteristics of lung microbiome, and specifically the bacteriome, the modes of interaction between lung microbiota and host immune system, the role of the "lung-gut axis", and the functional effects thereof on asthma pathogenesis. We also attempt to explore the possibilities of therapeutic manipulation of the microbiome, aiming at the establishment of asthma prevention strategies and the optimization of asthma treatment.},
}

@article {pmid31739261,
year = {2019},
author = {Dong, ZX and Li, HY and Chen, YF and Wang, F and Deng, XY and Lin, LB and Zhang, QL and Li, JL and Guo, J},
title = {Colonization of the gut microbiota of honey bee (Apis mellifera) workers at different developmental stages.},
journal = {Microbiological research},
volume = {231},
number = {},
pages = {126370},
doi = {10.1016/j.micres.2019.126370},
pmid = {31739261},
issn = {1618-0623},
abstract = {The role of the gut microbiome in animal health has become increasingly evident. Although the structure of the gut microbiome of A. mellifera is well known, little is known about the dynamic change across different developmental stages. In this study, we explored the dynamic changes of the gut microbiota of A. mellifera at different developmental stages covering the whole life cycle using high-throughput 16S rRNA gene sequencing. The results indicated that the core (shared) gut microbiota changes significantly among different developmental stages. The diversity of the bacterial community in workers among different ages was significantly different. In addition, by comparing the core gut microbiota among different-aged workers, we found that newly emerged workers had fewer core microbiota. Three genera, Gilliamella, Frischella, and Snodgrassella, were significantly colonized at 1 day poste mergence (dpe); Lactobacillus, Bifidobacterium, Commensalibacter were significantly colonized at 3 dpe and significantly reduced with Gilliamella. Lactobacillus kunkeei and Bartonella were significantly colonized at 12 dpe and were significantly decreased with Lactobacillus helsingborgensis. Commensalibacter and Bifidobacterium were significantly decreased at 25 dpe, and Bacteroides, Escherichia-Shigella, and Porphyromonadaceae were significantly decreased between 19 and 25 dpe. Our results reveal the succession of the gut microbiota of workers from birth to senescence, which provides a theoretical basis for further exploring the roles of gut microbiota during different developmental stages.},
}

@article {pmid31738994,
year = {2019},
author = {Mansbach, JM and Luna, PN and Shaw, CA and Hasegawa, K and Petrosino, JF and Piedra, PA and Sullivan, AF and Espinola, JA and Stewart, CJ and Camargo, CA},
title = {Increased Moraxella and Streptococcus following severe bronchiolitis is associated with recurrent wheezing.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2019.10.034},
pmid = {31738994},
issn = {1097-6825},
abstract = {BACKGROUND: The role of the airway microbiome in the development of recurrent wheezing and asthma remains uncertain, particularly in the high-risk group of infants hospitalized for bronchiolitis.

OBJECTIVE: Examine the relation of nasal microbiota at bronchiolitis hospitalization and 3 later points to the risk of recurrent wheezing by age 3 years.

METHODS: In 17 US centers, researchers collected clinical data and nasal swabs from infants hospitalized for bronchiolitis. Trained parents collected nasal swabs 3 weeks post-hospitalization and, when healthy, during summer and 1 year post-hospitalization. We applied 16S rRNA gene sequencing to all nasal swabs. We used joint modeling to examine the relation of longitudinal nasal microbiota abundances to risk of recurrent wheezing.

MEASUREMENTS AND MAIN RESULTS: Among 842 infants hospitalized for bronchiolitis, there was 88% follow-up at 3 years and 31% developed recurrent wheezing. The median age at enrollment was 3.2 months (IQR, 1.7-5.8 months). In joint modeling analyses adjusting for 16 covariates, including viral etiology, a 10% increase in relative abundance of Moraxella or Streptococcus 3 weeks after day 1 of hospitalization was associated with an increased risk of recurrent wheezing (HR 1.38; 95% highest density interval [HDI] 1.11-1.85; and HR 1.76; 95%HDI 1.13-3.19, respectively). Increased Streptococcus the summer after hospitalization was also associated with a higher risk of recurrent wheezing (HR 1.76; 95%HDI 1.15-3.27).

CONCLUSIONS: Enrichment of Moraxella or Streptococcus after bronchiolitis hospitalization was associated with recurrent wheezing by age 3 years, possibly providing new avenues to ameliorate the long-term respiratory outcomes of infants with severe bronchiolitis.},
}

@article {pmid31738795,
year = {2019},
author = {Cheong, HC and Yap, PSX and Chong, CW and Cheok, YY and Lee, CYQ and Tan, GMY and Sulaiman, S and Hassan, J and Sabet, NS and Looi, CY and Gupta, R and Arulanandam, B and AbuBakar, S and Teh, CSJ and Chang, LY and Wong, WF},
title = {Diversity of endocervical microbiota associated with genital Chlamydia trachomatis infection and infertility among women visiting obstetrics and gynecology clinics in Malaysia.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224658},
doi = {10.1371/journal.pone.0224658},
pmid = {31738795},
issn = {1932-6203},
abstract = {The cervical microbiota constitutes an important protective barrier against the invasion of pathogenic microorganisms. A disruption of microbiota within the cervical milieu has been suggested to be a driving factor of sexually transmitted infections. These include Chlamydia trachomatis which frequently causes serious reproductive sequelae such as infertility in women. In this study, we profiled the cervical microbial composition of a population of 70 reproductive-age Malaysian women; among which 40 (57.1%) were diagnosed with genital C. trachomatis infection, and 30 (42.8%) without C. trachomatis infection. Our findings showed a distinct compositional difference between the cervical microbiota of C. trachomatis-infected subjects and subjects without C. trachomatis infection. Specifically, significant elevations of mostly strict and facultative anaerobes such as Streptococcus, Megasphaera, Prevotella, and Veillonella in the cervical microbiota of C. trachomatis-positive women were detected. The results from the current study highlights an interaction of C. trachomatis with the environmental microbiome in the endocervical region.},
}

@article {pmid31738775,
year = {2019},
author = {Byrd, DA and Chen, J and Vogtmann, E and Hullings, A and Song, SJ and Amir, A and Kibriya, MG and Ahsan, H and Chen, Y and Nelson, H and Knight, R and Shi, J and Chia, N and Sinha, R},
title = {Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0224757},
doi = {10.1371/journal.pone.0224757},
pmid = {31738775},
issn = {1932-6203},
abstract = {The gut microbiome likely plays a role in the etiology of multiple health conditions, especially those affecting the gastrointestinal tract. Little consensus exists as to the best, standard methods to collect fecal samples for future microbiome analysis. We evaluated three distinct populations (N = 132 participants) using 16S rRNA gene amplicon sequencing data to investigate the reproducibility, stability, and accuracy of microbial profiles in fecal samples collected and stored via fecal occult blood test (FOBT) or Flinders Technology Associates (FTA) cards, fecal immunochemical tests (FIT) tubes, 70% and 95% ethanol, RNAlater, or with no solution. For each collection method, based on relative abundance of select phyla and genera, two alpha diversity metrics, and four beta diversity metrics, we calculated intraclass correlation coefficients (ICCs) to estimate reproducibility and stability, and Spearman correlation coefficients (SCCs) to estimate accuracy of the fecal microbial profile. Comparing duplicate samples, reproducibility ICCs for all collection methods were excellent (ICCs ≥75%). After 4-7 days at ambient temperature, ICCs for microbial profile stability were excellent (≥75%) for most collection methods, except those collected via no-solution and 70% ethanol. SCCs comparing each collection method to immediately-frozen no-solution samples ranged from fair to excellent for most methods; however, accuracy of genus-level relative abundances differed by collection method. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT/FTA cards, FIT tubes, 95% ethanol, and RNAlater are excellent choices for fecal sample collection methods in future microbiome studies. Furthermore, establishing standard collection methods across studies is highly desirable.},
}

@article {pmid31738691,
year = {2019},
author = {Batzer, JC and Mueller, DS},
title = {Soybean Fungal Endophytes Alternaria and Diaporthe spp. are Differentially Impacted by Fungicide Application.},
journal = {Plant disease},
volume = {},
number = {},
pages = {PDIS05191001RE},
doi = {10.1094/PDIS-05-19-1001-RE},
pmid = {31738691},
issn = {0191-2917},
abstract = {In field trials in Iowa, we investigated the association of a fungicide applied at early pod set to the diversity and composition of foliar endophytic fungi in presenescent soybeans. The main purpose of our study was to determine whether fungicides affect the microbiome of soybean plants during the pod-fill reproductive stage. In a replicated experiment focused on the impact of a fungicide application including a quinone outside inhibitor (QoI) and a pyrazole-carboxamide spanning two growing seasons, healthy stems and leaves near the tops of soybean were sampled for endophytic fungi. The survey yielded 1,791 isolates belonging to 17 putative species, identified by morphology and sequence analysis of the ribosomal DNA internal transcribed spacer region. Taxa were grouped by genus into operational taxonomic units: Alternaria, Colletotrichum, and Diaporthe were the dominant genera isolated. Plant parts were analyzed separately using a multivariate community analysis of isolate counts per plant. The 14.3% fluxapyroxad and 28.6% pyraclostrobin fungicide spray significantly increased the proportion of Diaporthe isolates over no-spray controls, whereas the inverse occurred for foliar Alternaria isolates. In addition, seed harvested from fields with shorter-season varieties and sprayed with fungicide showed higher percentages of Diaporthe isolates than fields with no fungicide spray. In conclusion, soybean farmers may want to consider that the application of a QoI fungicide in the absence of disease pressure might adversely impact seed quality.},
}

@article {pmid31738402,
year = {2019},
author = {Seo, DO and Holtzman, DM},
title = {Gut microbiota: from the forgotten organ to a potential key player in the pathology of Alzheimer disease.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/gerona/glz262},
pmid = {31738402},
issn = {1758-535X},
abstract = {More than three hundred years ago, Antony van Leewenhoeck first described observing single-celled microorganisms, which he termed 'animalcules', examining his saliva under a microscope. Although the idea of the coexistence of microorganisms in our body is not new, we have only recently been able to investigate their ecological relationship to our body, with the development of high throughput molecular techniques. The diverse microorganism communities residing in our guts are established and maintained by complex interactions among microorganisms and their host. Notably, their alteration has been implicated in influencing various diseases including neurological diseases. Alzheimer disease (AD) is the most common cause of dementia characterized by a progressive decline in memory and thinking severe enough to interfere with daily life. Despite the great progress in linking genetic risk factors with AD pathogenesis, treatments targeted at AD pathology and its modifiers have not yet resulted in a disease modifying therapy. There is mounting evidence that the gut microbiota interacts with AD pathogenesis by disrupting neuroinflammation and metabolic homeostasis - the gut microbiota has gone from being the forgotten organ to a potential key player in the AD pathology.},
}

@article {pmid31737933,
year = {2019},
author = {Gerner, C and Costigliola, V and Golubnitschaja, O},
title = {MULTIOMIC patterns in body fluids: Technological challenge with a great potential to implement the advanced paradigm of 3P medicine.},
journal = {Mass spectrometry reviews},
volume = {},
number = {},
pages = {},
doi = {10.1002/mas.21612},
pmid = {31737933},
issn = {1098-2787},
abstract = {Liquid biopsy (LB) is defined as a sample of any of body fluids (blood, saliva, tear fluid, urine, sweat, amniotic, cerebrospinal and pleural fluids, cervicovaginal secretion, and wound efflux, amongst others), which can be ex vivo analysed to detect and quantity the target(s) of interest. LB represents diagnostic approach relevant for organ-specific changes and systemic health conditions including both manifested diseases and their prestages such as suboptimal health. Further, experts emphasise that DNA-based analysis alone does not provide sufficient information for optimal diagnostics and effective treatments. Consequently, of great scientific and clinical utility are molecular patterns detected by hybrid technologies such as metabolomic tools and molecular imaging. Future proposed strategies utilise multiomic pillars (generally genome, tanscriptome, proteome, metabolome, epigenome, radiome, and microbiome), system-biological approach, and multivariable algorithms for diagnostic, prognostic, and therapeutic purposes. Current article analyses pros and cons of the mass spectrometry-based technologies, provides eminent examples of a success story "from discovery to clinical application," and demonstrates a "road-map" for the technology-driven paradigm change from reactive to predictive, preventive and personalised medical services as the medicine of the future benefiting the patient and healthcare at large. © 2019 Wiley Periodicals, Inc. Mass Spec Rev.},
}

@article {pmid31737577,
year = {2019},
author = {Khan, S and Voordouw, MJ and Hill, JE},
title = {Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {374},
doi = {10.3389/fcimb.2019.00374},
pmid = {31737577},
issn = {2235-2988},
abstract = {Gardnerella spp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome. Gardnerella has four subgroups (A, B, C, and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated clinical signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the four Gardnerella subgroups were investigated in vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of the Gardnerella subgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3, or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of neutral interactions, most (69.3%) of the mixed communities exhibited competition. Competition reduced the growth rates of subgroups A, B, and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups. All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition among Gardnerella subgroups, which likely contributes to the observed distributions of Gardnerella spp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.},
}

@article {pmid31737576,
year = {2019},
author = {Vardhan, M and Flaminio, Z and Sapru, S and Tilley, CP and Fu, MR and Comfort, C and Li, X and Saxena, D},
title = {The Microbiome, Malignant Fungating Wounds, and Palliative Care.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {373},
doi = {10.3389/fcimb.2019.00373},
pmid = {31737576},
issn = {2235-2988},
abstract = {Malignant fungating wounds present in 5-14% of advanced cancer patients in the United States and are a result of cancerous cells infiltrating and proliferating in the skin. Presentation of malignant fungating wounds often occurs in the last 6 months of life and therefore become symbols of impending death for patients and their families. Due to the incurable and severe nature of these wounds, patients require palliative care until death to minimize pain and suffering. Symptoms associated with these chronic wounds include malodor, pain, bleeding, necrosis, large amounts of exudate, increased microbial growth, and more. Limited research using culture-based techniques has been conducted on malignant fungating wounds and therefore no optimal approach to treating these wounds has been established. Despite limited data, associations between the cutaneous microbiome of these wounds and severity of symptoms have been made. The presence of at least one strain of obligate anaerobic bacteria is linked with severe odor and exudate. A concentration of over 105/g bacteria is linked with increased pain and exudate. Bacterial metabolites such as DMTS and putrescine are linked with components of malignant fungating wound odor and degradation of periwound skin. The few but significant associations made between the malignant fungating wound microbiome and severity of symptoms indicate that further study on this topic using 16S rRNA gene sequencing may reveal potential therapeutic targets within the microbiome to significantly improve current methods of treatment used in the palliative care approach.},
}

@article {pmid31737352,
year = {2019},
author = {O'Farrell, HE and Shaw, JG and Goh, F and Bowman, RV and Fong, KM and Krause, L and Yang, IA},
title = {Potential clinical utility of multiple target quantitative polymerase chain reaction (qPCR) array to detect microbial pathogens in patients with chronic obstructive pulmonary disease (COPD).},
journal = {Journal of thoracic disease},
volume = {11},
number = {Suppl 17},
pages = {S2254-S2265},
doi = {10.21037/jtd.2019.10.39},
pmid = {31737352},
issn = {2072-1439},
abstract = {Background: Culture-independent methods such as quantitative polymerase chain reaction (qPCR) are more sensitive for detecting pathogens than conventional culture. This study aimed to test the clinical potential of a multiple target qPCR array in identifying sputum pathogens, compared to traditional culture.

Methods: Forty chronic obstructive pulmonary disease (COPD) patients provided spontaneous sputum and blood samples during an exacerbation event (n=25 patients) and in stable state (n=15 patients). Sputum was processed and analysed by microscopy, culture and sensitivity testing (MCS) to identify living microbial isolates, and multiple target qPCR (44 targets for bacterial and fungal pathogens and antibiotic resistance genes), and 16S rRNA gene sequencing.

Results: Six microbial isolates (5 bacterial, 1 fungal) were cultured from 20 exacerbation and 10 stable patient sputum samples. Four of these microbial isolates had their presence in patient sputum confirmed by qPCR. All bacterial targets detected by qPCR were further confirmed by 16S rRNA gene sequencing at a genus level. qPCR identified significantly more bacterial pathogens than culture (P<0.001). The most prevalent bacterial species identified by qPCR were Streptococcus pneumoniae (72% of patients), Pseudomonas aeruginosa (40%), Prevotella oris (32%) and Haemophilus influenzae (17%). Microbial species diversity and richness were not significantly different between samples obtained from exacerbating and clinically stable cases. 16S rRNA gene sequencing identified Pseudomonas 4408227 (P=0.022, FDR =0.043 AUC =0.72) as a significantly different bacterial OTU (operational taxonomic units) in exacerbation sputum samples compared to stable state samples.

Conclusions: Multiple target qPCR was more sensitive for detection of sputum pathogens in COPD patients than conventional culture. 16S rRNA gene sequencing confirmed the identity at a genus level of all bacterial targets detected by qPCR, as well as identifying bacterial OTUs that could potentially be used to distinguish between exacerbation and stable COPD disease states. Multiple target qPCR pathogen detection in the sputum of COPD patients warrants further investigation to determine how it may influence COPD clinical management.},
}

@article {pmid31737344,
year = {2019},
author = {Vaughan, A and Frazer, ZA and Hansbro, PM and Yang, IA},
title = {COPD and the gut-lung axis: the therapeutic potential of fibre.},
journal = {Journal of thoracic disease},
volume = {11},
number = {Suppl 17},
pages = {S2173-S2180},
doi = {10.21037/jtd.2019.10.40},
pmid = {31737344},
issn = {2072-1439},
abstract = {Current management strategies for chronic obstructive pulmonary disease (COPD) incorporate a step-wise, multidisciplinary approach to effectively manage patient symptoms and prevent disease progression. However, there has been limited advancement in therapies to address the underlying cause of COPD pathogenesis. Recent research has established the link between the lungs and the gut-the gut-lung axis -and the gut microbiome is a major component. The gut microbiome is likely perturbed in COPD, contributing to chronic inflammation. Diet is a readily modifiable factor and the diet of COPD patients is often deficient in nutrients such as fibre. The metabolism of dietary fibre by gut microbiomes produces anti-inflammatory short chain fatty acid (SCFAs), which could protect against inflammation in the lungs. By addressing the 'fibre gap' in the diet of COPD patients, this targeted dietary intervention may reduce inflammation, both systemically and in the airways, and value-add to the paradigm shift in respiratory medicine, from reactive to personalised and participatory medicine.},
}

@article {pmid31737343,
year = {2019},
author = {Parris, BA and O'Farrell, HE and Fong, KM and Yang, IA},
title = {Chronic obstructive pulmonary disease (COPD) and lung cancer: common pathways for pathogenesis.},
journal = {Journal of thoracic disease},
volume = {11},
number = {Suppl 17},
pages = {S2155-S2172},
doi = {10.21037/jtd.2019.10.54},
pmid = {31737343},
issn = {2072-1439},
abstract = {Chronic obstructive pulmonary disease (COPD) and lung cancer comprise the leading causes of lung disease-related mortality worldwide. Exposure to tobacco smoke is a mutual aetiology underlying the two diseases, accounting for almost 90% of cases. There is accumulating evidence supporting the role of immune dysfunction, the lung microbiome, extracellular vesicles and underlying genetic susceptibility in the development of COPD and lung cancer. Further, epigenetic factors, involving DNA methylation and microRNA expression, have been implicated in both diseases. Chronic inflammation is a key feature of COPD and could be a potential driver of lung cancer development. Using next generation technologies, further studies investigating the genomics, epigenetics and gene-environment interaction in key molecular pathways will continue to elucidate the pathogenic mechanisms underlying the development of COPD and lung cancer, and contribute to the development of novel diagnostic and prognostic tools for early intervention and personalised therapeutic strategies.},
}

@article {pmid31737072,
year = {2019},
author = {Grobbelaar, C and Ford, AM},
title = {The Role of MicroRNA in Paediatric Acute Lymphoblastic Leukaemia: Challenges for Diagnosis and Therapy.},
journal = {Journal of oncology},
volume = {2019},
number = {},
pages = {8941471},
doi = {10.1155/2019/8941471},
pmid = {31737072},
issn = {1687-8450},
abstract = {Acute lymphoblastic leukaemia (ALL) is the most common cancer of childhood. Although the overall survival of children with ALL is now more than 90%, leukaemia remains one of the leading causes of death from disease. In developed countries, the overall survival of patients with ALL has increased to more than 80%; however, those children cured from ALL still show a significant risk of short- and long-term complications as a consequence of their treatment. Accordingly, there is a need not only to develop new methods of diagnosis and prognosis but also to provide patients with less toxic therapies. MicroRNAs (miRNAs) are small ribonucleic acids (RNA), usually without coding potential, that regulate gene expression by directing their target messenger RNAs (mRNAs) for degradation or translational suppression. In paediatric ALL, several miRNAs have been observed to be overexpressed or underexpressed in patient cohorts compared to healthy individuals, while numerous studies have identified specific miRNAs that can be used as biomarkers to diagnose ALL, classify it into subgroups, and predict prognosis. Likewise, a variety of miRNAs identify as candidate targets for treatment, although there are numerous obstacles to overcome before their clinical use in patients. Here, we summarise the roles played by different miRNAs in childhood leukaemia, focussing primarily on their use as diagnostic tools and potential therapeutic targets, as well as a role in predicting treatment outcome. Finally, we discuss the potential roles of miRNA in immunotherapy and the novel contributions made by gut miRNAs to regulation of the host microbiome.},
}

@article {pmid31736922,
year = {2019},
author = {Gu, L and Deng, H and Ren, Z and Zhao, Y and Yu, S and Guo, Y and Dai, J and Chen, X and Li, K and Li, R and Wang, G},
title = {Dynamic Changes in the Microbiome and Mucosal Immune Microenvironment of the Lower Respiratory Tract by Influenza Virus Infection.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2491},
doi = {10.3389/fmicb.2019.02491},
pmid = {31736922},
issn = {1664-302X},
abstract = {Influenza is a major public health concern, and the high mortality rate is largely attributed to secondary bacterial infections. There are several mechanisms through which the virus increases host susceptibility to bacterial colonization, but the micro-environment in lower respiratory tract (LRT) of host, infected with influenza virus, is unclear. To this end, we analyzed the LRT microbiome, transcriptome of lung and metabolome of bronchoalveolar lavage fluid (BALF) in mice inoculated intra-nasally with H1N1 to simulate human influenza, and we observed significant changes in the composition of microbial community and species diversity in the acute (7 days post inoculation or dpi), convalescent (14 dpi) and the recovery (28 dpi) periods. The dominant bacterial class shifted from Alphaproteobacteria to Gammaproteobacteria and Actinobacteria in the infected mice, with a significant increase in the relative abundance of anaerobes and facultative anaerobes like Streptococcus and Staphylococcus. The dysbiosis in the LRT of infected mice was not normalized even in the recovery phase of the infection. In addition, the infected lung transcriptome showed significant differences in the expression levels of genes associated with bacterial infection and immune responses. Finally, the influenza virus infection also resulted in significant changes in the metabolome of the BALF. These alterations in the microbiome, transcriptome, and metabolome of infected lungs were not only appeared at the acute period, but also observed at the recovery period. Furthermore, the infection of influenza virus induced a long-term effect in LRT micro-environmental homeostasis, which may give a chance for the invasion of potential pathogens.},
}

@article {pmid31736900,
year = {2019},
author = {Zhao, C and Zhao, H and Zhang, S and Luo, J and Zhu, X and Wang, L and Zhao, P and Hua, H and Cui, J},
title = {The Developmental Stage Symbionts of the Pea Aphid-Feeding Chrysoperla sinica (Tjeder).},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2454},
doi = {10.3389/fmicb.2019.02454},
pmid = {31736900},
issn = {1664-302X},
abstract = {Chrysoperla sinica (Tjeder) is widely recognized as an important holometabolous natural enemy of various insect pests in different cropping systems and as a non-target surrogate in environmental risk assessment of Bt rice (i.e., genetically modified rice to express a toxin gene from Bacillus thuringiensis). Like other complex organisms, abundant microbes live inside C. sinica; however, to date, microbiome composition and diversity of the whole life cycle in C. sinica has not yet been well characterized. In the current study, we analyze the composition and biodiversity of microbiota across the whole life cycle of C. sinica by using high-throughput Illumina sequencing of the 16S ribosomal RNA gene. Collectively, Proteobacteria and Firmicutes dominated the microenvironment at all stages, but their relative abundances fluctuated by host developmental stage. Interestingly, eggs, neonates, and adults shared similar microbes, including an abundance of Rickettsia and Wolbachia. After larva feeding, Staphylococcus, Enterobacteriaceae, and Serratia were enriched in larvae and pupa, suggesting that food may serve as a major factor contributing to altered microbial community divergence at different developmental stages. Our findings demonstrated that C. sinica harbor a variety of bacteria, and that dynamic changes in community composition and relative abundances of members of its microbiome occur during different life cycle stages. Evaluating the role of these bacterial symbionts in this natural enemy may assist in developing environmental risk assessments and novel biological control strategies.},
}

@article {pmid31736899,
year = {2019},
author = {Ma, Q and Bücking, H and Gonzalez Hernandez, JL and Subramanian, S},
title = {Single-Cell RNA Sequencing of Plant-Associated Bacterial Communities.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2452},
doi = {10.3389/fmicb.2019.02452},
pmid = {31736899},
issn = {1664-302X},
abstract = {Plants in soil are not solitary, hence continually interact with and obtain benefits from a community of microbes ("microbiome"). The meta-functional output from the microbiome results from complex interactions among the different community members with distinct taxonomic identities and metabolic capacities. Particularly, the bacterial communities of the root surface are spatially organized structures composed of root-attached biofilms and planktonic cells arranged in complex layers. With the distinct but coordinated roles among the different member cells, bacterial communities resemble properties of a multicellular organism. High throughput sequencing technologies have allowed rapid and large-scale analysis of taxonomic composition and metabolic capacities of bacterial communities. However, these methods are generally unable to reconstruct the assembly of these communities, or how the gene expression patterns in individual cells/species are coordinated within these communities. Single-cell transcriptomes of community members can identify how gene expression patterns vary among members of the community, including differences among different cells of the same species. This information can be used to classify cells based on functional gene expression patterns, and predict the spatial organization of the community. Here we discuss strategies for the isolation of single bacterial cells, mRNA enrichment, library construction, and analysis and interpretation of the resulting single-cell RNA-Seq datasets. Unraveling regulatory and metabolic processes at the single cell level is expected to yield an unprecedented discovery of mechanisms involved in bacterial recruitment, attachment, assembly, organization of the community, or in the specific interactions among the different members of these communities.},
}

@article {pmid31736898,
year = {2019},
author = {De Seta, F and Campisciano, G and Zanotta, N and Ricci, G and Comar, M},
title = {The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2451},
doi = {10.3389/fmicb.2019.02451},
pmid = {31736898},
issn = {1664-302X},
abstract = {Regarding bacterial vaginosis (BV), the relevance of the vaginal microbiota to the women's health fulfills a key role, but knowledge gaps regarding aerobic vaginitis (AV) exist. This study aims to characterize vaginal microbiome and its relationship with the local immune mediators, providing an opportunity to define the link between vaginal commensal microorganisms and opportunistic pathogens in the relation of a given vaginal community state type (CST). A total of 90 vaginal samples from Caucasian asymptomatic women of reproductive age (18-40 years) attending the yearly examination and not reporting any vaginal complaints were retrospectively evaluated for microbiome assessment and immune factor dosage. The samples were tested by the Ion Torrent PGM and the Luminex Bio-Plex technologies for the analysis of microbiome and immune factors, respectively. In our study, the CST classification together with the local immune response profiling represented a good predictive indicator of the vaginal health, suggesting that the predominance of a specific Lactobacillus and its relative abundance are pivotal elements to maintain a physiologic status. A vaginal colonization from Bifidobacterium may absolve a protective role similar to that of Lactobacillus, corresponding to a newly identified CST, although studies are needed to better clarify its clinical significance. Moreover, within each CST, a different pattern of inflammation is activated and orchestrated both by the dominant Lactobacillus spp. and by specific non-Lactobacillus bacteria and can give insights into the pathogenic mechanisms. In conclusion, this study contributes to the characterization of vaginal dysbiosis, reshaping this concept by taking into consideration the CST profiling, local immune marker, and immune-microbial network.},
}

@article {pmid31736893,
year = {2019},
author = {Neu, L and Proctor, CR and Walser, JC and Hammes, F},
title = {Small-Scale Heterogeneity in Drinking Water Biofilms.},
journal = {Frontiers in microbiology},
volume = {10},
number = {},
pages = {2446},
doi = {10.3389/fmicb.2019.02446},
pmid = {31736893},
issn = {1664-302X},
abstract = {Biofilm heterogeneity has been characterized on various scales for both natural and engineered ecosystems. This heterogeneity has been attributed to spatial differences in environmental factors. Understanding their impact on localized biofilm heterogeneity in building plumbing systems is important for both management and representative sampling strategies. We assessed heterogeneity within the confined engineered ecosystem of a shower hose by high-resolution sampling (200 individual biofilm sections per hose) on varying scales (μm to m). We postulated that a biofilm grown on a single material under uniform conditions should be homogeneous in its structure, bacterial numbers, and community composition. A biofilm grown for 12 months under controlled laboratory conditions, showed homogeneity on large-scale. However, some small-scale heterogeneity was clearly observed. For example, biofilm thickness of cm-sections varied up to 4-fold, total cell concentrations (TCC) 3-fold, and relative abundance of dominant taxa up to 5-fold. A biofilm grown under real (i.e., uncontrolled) use conditions developed considerably more heterogeneity in all variables which was attributed to more discontinuity in environmental conditions. Interestingly, biofilm communities from both hoses showed comparably low diversity, with <400 taxa each, and only three taxa accounting for 57%, respectively, 73% of the community. This low diversity was attributed to a strong selective pressure, originating in migrating carbon from the flexible hoses as major carbon source. High-resolution sampling strategy enabled detailed analysis of spatial heterogeneity within an individual drinking water biofilm. This study gives insight into biofilm structure and community composition on cm-to m-scale and is useful for decision-making on sampling strategies in biofilm research and monitoring.},
}

@article {pmid31736368,
year = {2019},
author = {Brewer, MR and Maffei, D and Cerise, J and Ahn, S and DeVoti, J and Codipilly, C and Lee, A and Weinberger, B},
title = {Determinants of the lung microbiome in intubated premature infants at risk for bronchopulmonary dysplasia.},
journal = {The journal of maternal-fetal & 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 = {1-7},
doi = {10.1080/14767058.2019.1681961},
pmid = {31736368},
issn = {1476-4954},
abstract = {Background: Airway dysbiosis in premature infants may be associated with bronchopulmonary dysplasia (BPD). Early oropharyngeal colostrum (OPC) administration alters the oral microbiome, which may impact the lung microbiome. We aim to compare the oral and tracheal microbiota during the first week of life, and to determine whether early OPC administration affects microbial diversity or leukocyte inflammatory activity in the lung.Methods: Intubated premature infants (n = 42) were evaluated. The oral microbiome was characterized on day of life (DOL) 3, and the tracheal microbiome on DOL 3 and DOL 7, using 16S ribosomal DNA sequencing. Gene expression for inflammatory markers was quantified in airway leukocytes by real-time q-PCR.Results: The oral and tracheal microbiota were significantly different on DOL 3, but the tracheal microbiome on DOL 7 was more similar to the oral from DOL 3. Tracheal bacterial diversity decreased from DOL 3 to DOL 7. Longer time to first OPC administration tended to be associated with lower bacterial diversity in the airways.Conclusions: The tracheal microbiome in intubated premature infants in the first week is likely determined, in part, by the composition of the oral microbiome. Bacterial diversity in intubated babies decreases during the first week of life, a pattern that could be consistent with risk for BPD. Decreased bacterial diversity and increased inflammatory activity in the lung may also be associated with delayed administration of OPC.},
}

@article {pmid31736274,
year = {2019},
author = {Rosenbaum, JT and Karstens, L},
title = {Bugs, Drugs, and Shrugs.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.41166},
pmid = {31736274},
issn = {2326-5205},
abstract = {Experimental evidence "proves" that IL-17 plays a critical role in the pathogenesis of inflammatory bowel disease, but blocking IL-17 makes Crohn's disease worse.[1, 2] Only a subset of patients with melanoma benefit from checkpoint inhibitors[3] and only a subset of patients with any rheumatic disease benefit from a specific therapy. A scientist at the NIH using a rodent model can't replicate the experimental results of a scientist at Harvard. The intestinal microbiome might provide the explanation for each of these seemingly disparate conundrums.},
}

@article {pmid31736262,
year = {2019},
author = {Mazón-Suástegui, JM and Salas-Leiva, JS and Medina-Marrero, R and Medina-García, R and García-Bernal, M},
title = {Effect of Streptomyces probiotics on the gut microbiota of Litopenaeus vannamei challenged with Vibrio parahaemolyticus.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e967},
doi = {10.1002/mbo3.967},
pmid = {31736262},
issn = {2045-8827},
support = {258282//Sectoral Fund for Research and Education of Mexico/ ; },
abstract = {This study assessed the intestinal microbiota of juveniles of the White shrimp Litopenaus vannamei, whose feed was enriched with three probiotic formulations: Streptomyces sp. RL8 (RL8); a mix of Lactobacillus graminis and Streptomyces spp. RL8 and N7 (Lac-Strep); and a mix of Bacillus spp. and Streptomyces spp. RL8 and N7 (Bac-Strep). The analysis was performed by sequencing the V3 region of the 16S rRNA gene of treated animals and the control group before and after Vibrio parahaemolyticus challenge. After challenge, the highest Shannon diversity indexes corresponded to RL8 and Bac-Strep (3.94 ± 0.11 and 3.39 ± 0.3, respectively) and the lowest to the control group (2.58 ± 0.26). The most abundant phyla before and after challenge were Proteobacteria, Actinobacteria, and Bacteroidetes. The principal component analysis and Statistical Analysis of Metagenomic Profiles (STAMP) showed that the gut microbiota of the groups RL8 and Bac-Strep after challenge was different from the other experimental groups, which was characterized by a higher bacterial diversity, as well as a significant stimulation of the Bacteriovorax population and other antimicrobial producing genera that protected shrimp from infection.},
}

@article {pmid31735705,
year = {2019},
author = {Wen, CL and Sun, CJ and Yang, N},
title = {[The concepts and research progress: from heritability to microbiability].},
journal = {Yi chuan = Hereditas},
volume = {41},
number = {11},
pages = {1023-1040},
doi = {10.16288/j.yczz.19-130},
pmid = {31735705},
issn = {0253-9772},
abstract = {Heritability, one of the central quantitative genetic parameters, is critically important to measure the genetic variation of traits, especially in the studies of the response to selection in evolutionary biology and agriculture, and the prediction of disease risks in medicine. The statistical model and method for estimating heritability have been continually developed and improved, since the genetic variance components was first proposed by Fisher in 1918. Recently, the term "microbiability" (m 2), an analogous concept and estimated method to heritability, was introduced in gut microbiome research for evaluating the effect of entire microbiota on a host phenotype. In this review, we summarize the progress of statistical methods in the heritability estimation, as well as the current state of gut microbiome associations with the host genome, with a particular focus on the concept and estimated methods of microbiability. Our review will provide a reference for the future study of host phenotypic variation that can be inferred by the gut microbiota.},
}

@article {pmid31735286,
year = {2019},
author = {Vitiello, GA and Cohen, DJ and Miller, G},
title = {Harnessing the Microbiome for Pancreatic Cancer Immunotherapy.},
journal = {Trends in cancer},
volume = {5},
number = {11},
pages = {670-676},
doi = {10.1016/j.trecan.2019.10.005},
pmid = {31735286},
issn = {2405-8025},
abstract = {Late-stage pancreatic cancer harbors a fibrotic and immune-excluded tumor microenvironment that impedes immunotherapy success. A key to unlocking pancreatic cancer immunotherapy may be treating early-stage pancreatic cancer, when peripancreatic inflammation promoted by the microbiome potentiates oncogenic signaling and suppresses innate and adaptive immunity. Hence, understanding the role of microbiota in pancreatic cancer initiation, progression, and immunosuppression is crucial. We propose that not only are microbiota targets for immunomodulation in this disease, but also that microbiome profiling has a potential role in pancreatic cancer screening. Furthermore, combining microbiome profiling with liquid and tissue biopsy may validate the early pancreatic cancer treatment approach of microbiome modulation and immunotherapy.},
}

@article {pmid31735285,
year = {2019},
author = {Dong, J and Tai, JW and Lu, LF},
title = {miRNA-Microbiota Interaction in Gut Homeostasis and Colorectal Cancer.},
journal = {Trends in cancer},
volume = {5},
number = {11},
pages = {666-669},
doi = {10.1016/j.trecan.2019.08.003},
pmid = {31735285},
issn = {2405-8025},
abstract = {Gut homeostasis is maintained by dynamic host-microbiota interactions. Recently, miRNAs have emerged as key molecular regulators in the mediation of such interactions. Here, we discuss the role of a host miRNA-microbiome axis in gut homeostasis and colorectal cancer (CRC) and the involvement of diet and microbial metabolites in miRNA-mediated intestinal health.},
}

@article {pmid31735183,
year = {2019},
author = {Baron, R and Taye, M and Besseling-van der Vaart, I and Ujčič-Voortman, J and Szajewska, H and Seidell, JC and Verhoeff, A and , },
title = {The relationship of prenatal and infant antibiotic exposure with childhood overweight and obesity: a systematic review.},
journal = {Journal of developmental origins of health and disease},
volume = {},
number = {},
pages = {1-15},
doi = {10.1017/S2040174419000722},
pmid = {31735183},
issn = {2040-1752},
abstract = {This study aimed to assess the evidence regarding the relationship between early-life antibiotic exposure and childhood overweight/obesity by reviewing observational studies on prenatal antibiotic exposure and systematic reviews on infant antibiotic exposure. A search in Pubmed, Embase and Google Scholar covering the period 1st January till 1st December 2018 led to the identification of five studies on prenatal antibiotic exposure and four systematic reviews on infant antibiotic exposure. Positive trends between prenatal antibiotic exposure and overweight/obesity were reported in all studies; two studies reported a significant overall relationship and the other three reported significant relationships under certain conditions. Effect sizes ranged from odds ratio (OR): 1.04 (0.62-1.74) to relative risk (RR): 1.77 (1.25-2.51). Regarding infant antibiotics, one review concluded there was substantial evidence that infant antibiotic exposure increased the risk of childhood overweight/obesity [pooled effect sizes: RR: 1.21 (1.09-1.33) for overweight and RR: 1.18 (1.12-1.25) for obesity]. Two reviews concluded there was some evidence for a relationship [pooled effect sizes: OR: 1.05 (1.00-1.11) and OR: 1.11 (1.02-1.20)]. The fourth review concluded the studies were too heterogeneous for meta-analyses and the evidence regarding the relationship between infant antibiotic exposure and childhood overweight/obesity was inconclusive. More well-designed studies are needed that include data on intra-partum antibiotics and address important potential confounders (including maternal and childhood infections). This review points to some evidence of a relationship between early-life antibiotic exposure and childhood overweight/obesity; this is especially evident in certain children (i.e. exposed to multiple and broad-spectrum antibiotics, earlier postnatal exposure and male gender) and merits further research.},
}

@article {pmid31734603,
year = {2019},
author = {Liu, YX and Qin, Y and Bai, Y},
title = {Reductionist synthetic community approaches in root microbiome research.},
journal = {Current opinion in microbiology},
volume = {49},
number = {},
pages = {97-102},
doi = {10.1016/j.mib.2019.10.010},
pmid = {31734603},
issn = {1879-0364},
abstract = {Synthetic community (SynCom) approaches can provide functional and mechanistic insights into how plants regulate their microbiomes, and how the microbiome in turn influences plant growth and health. Microbial cultivation and reconstruction play pivotal roles in this process, which enables researchers to reproducibly investigate the interactions between plants and a major proportion of plant-associated microbes in controlled laboratory conditions. Here, we summarize the emergence, current achievements, and future opportunities for using SynCom experiments in plant microbiome research, with a focus on plant root-associated bacteria.},
}

@article {pmid31734483,
year = {2019},
author = {Khan, MS and Koizumi, N and Olds, JL},
title = {Biofixation of atmospheric nitrogen in the context of world staple crop production: Policy perspectives.},
journal = {The Science of the total environment},
volume = {701},
number = {},
pages = {134945},
doi = {10.1016/j.scitotenv.2019.134945},
pmid = {31734483},
issn = {1879-1026},
abstract = {The extensive use of nitrogen (N) fertilizers implicates a paradox: while fertilizers ensure the supply of a large amount of food, they cause negative environmental externalities, including reduced biodiversity, and eutrophic streams and lakes. Moreover, such fertilizers may also result in a major public health hazard: increased antibiotic resistance. This article discusses the critical implications of perturbations in N cycle caused by excessive use of fertilizers and resulting policy implications as they relate to ecosystem services. While there are solutions such as cover crops, these solutions are expensive and inconvenient for farmers. We advocate the use of biological fixation (BF) for staple crops-microbiome mediated natural supply of fixed N. This would involve engineering a microbiome that can be grown cheaply and at industrial scale. Fertilizers resulting from such innovation are termed as "biofertilizers" in this article. Following a qualitative cost-benefit analysis broken down by key stakeholders and a quick exploration of policy frameworks as they relate to the advancement of biofertilizers, we propose a practical pathway of where and how research investments should be directed to make such a solution feasible. We make five policy recommendations for decision-makers to facilitate a successful trajectory for this solution: (1) Future agricultural science should seek to understand how BF might be employed as a practical and efficient strategy. This effort would require that industry and the government partner to establish a pre-competitive research laboratory equipped with the latest state-of-the-art technologies that conduct metagenomic experiments to reveal signature microbiomes and form novel symbiotic connections. (2) To have a smooth ride in the market, ag-bio companies should: (i) create awareness among farmers; (ii) impart skills to farmers in testing and using biofertilizers, and (iii) conduct extensive field tests and more research in studying the scalability potential of such fertilizers. (3)The United States Department of Agriculture (USDA) and state governments should provide research and development (R&D) tax credits to biotech companies specifically geared towards R&D investments aimed at increasing the viability of BF and microbiome engineering. (4) To control agricultural pollution in the biosphere, federal governments should consider passing a Clean Agriculture Act (CAA), including a specific clause that regulate the use of chemical fertilizers. (5) Governments and the UN Food and Agriculture Organization (FAO) should coordinate Biological Advanced Research in Agriculture (BARA)-a global agricultural innovation initiative for investments and research in biological fixation and ethical, legal, and social implications of such innovation. While biological fixation will be central in BARA, we envision it to conduct research around other agricultural innovations as well, such as increasing photosynthetic efficiency.},
}

@article {pmid31734400,
year = {2019},
author = {Wasko, N and Nichols, F and Clark, RB},
title = {Multiple sclerosis, the microbiome, TLR2, and the hygiene hypothesis.},
journal = {Autoimmunity reviews},
volume = {},
number = {},
pages = {102430},
doi = {10.1016/j.autrev.2019.102430},
pmid = {31734400},
issn = {1873-0183},
abstract = {The pathophysiology of autoimmune diseases such as Multiple Sclerosis (MS) involves a complex interaction between genetic and environmental factors. Studies of monozygotic twins suggest a significant role for environmental factors in susceptibility to MS. Numerous studies, driven by the "Hygiene Hypothesis," have focused on the role of environmental factors in allergic and autoimmune diseases. The hygiene hypothesis postulates that individuals living in environments that are too "clean" lack the requisite exposure to "immune-tolerizing" microbial products, resulting in poorly regulated immune systems and increased immune-mediated diseases. Interestingly, few studies have linked MS with the hygiene hypothesis. Similarly, although numerous studies have examined the role of the microbiome in autoimmune diseases, there has been no consistent documentation of disease-specific alterations in the MS microbiome. In this review, we present evidence that integrating the hygiene hypothesis and the microbiome allows for the identification of novel pathophysiologic mechanisms in MS. Our central hypothesis is that the microbiome in MS represents a "defective environment" that fails to provide normal levels of "TLR2-tolerizing" bacterial products to the systemic immune system. Consistent with the hygiene hypothesis, we posit that this defective microbiome function results in abnormally regulated systemic innate immune TLR2 responses that play a critical role in both the inflammatory and defective remyelinative aspects of MS. We have completed proof of concept studies that support the inflammatory, remyelinating, and human immune response components of this paradigm. Our studies suggest that induction of TLR2 tolerance may represent a novel approach to treating MS, inhibiting autoimmune inflammation while simultaneously facilitating remyelination.},
}

@article {pmid31733968,
year = {2019},
author = {Przemieniecki, SW and Kosewska, A and Ciesielski, S and Kosewska, O},
title = {Changes in the gut microbiome and enzymatic profile of Tenebrio molitor larvae biodegrading cellulose, polyethylene and polystyrene waste.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {113265},
doi = {10.1016/j.envpol.2019.113265},
pmid = {31733968},
issn = {1873-6424},
abstract = {Recent studies have demonstrated the ability of mealworm (Tenebrio molitor) for plastic degradation. This study is focused on changes in microbiome structure depending on diets. Microbial community obtained from oat and cellulose diet formed similar group, two kinds of polyethylene formed another group, while polystyrene diet showed the highest dissimilarity. The highest relative abundance of bacteria colonizing gut was in PE-oxodegradable feeding, nevertheless all applied diets were higher in comparison to oat. Dominant phyla consisted of Proteobacteria, Bacteroides, Firmicutes and Actinobacteria, however after PS feeding frequency in Planctomycetes and Nitrospirae increased. The unique bacteria characteristic for cellulose diet belonged to Selenomonas, while Pantoea were characteristic for both polyethylene diets, Lactococcus and Elizabethkingia were unique for each plastic diet, and potential diazotropic bacteria were characteristic for polystyrene diet (Agrobacterium, Nitrosomonas, Nitrospira). Enzymatic similarity between oatmeal and cellulose diets, was shown. All three plastics diet resulted in different activity in both, digestive tract and bacteria. The enzymes with the highest activity were included phosphatases, esterases, leucine arylamidase, β-galactosidase, β-glucuronidase, α-glucosidase, β-glucosidase, chitinase, α-mannosidase and α-fucosidase. The activity of digestive tract was stronger than cultured gut bacteria. In addition to known polyethylene degradation methods, larvae may degrade polyethylene with esterase, cellulose and oatmeal waste activity is related with the activity of sugar-degrading enzymes, degradation of polystyrene with anaerobic processes and diazotrophs.},
}

@article {pmid31733964,
year = {2019},
author = {Chen, WY and Wu, JH and Chu, SC},
title = {Deciphering microbiomes in anaerobic reactors with superior trichloroethylene dechlorination performance at low pH conditions.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {113567},
doi = {10.1016/j.envpol.2019.113567},
pmid = {31733964},
issn = {1873-6424},
abstract = {Different pH conditions have been demonstrated to affect the activities of dechlorinating populations participating in the successive dechlorination of trichloroethylene to ethylene. However, the mechanism of the effect of pH conditions on the assembly of dechlorinating populations and their relations to the structure, function, and dynamics of the microbiome are unclear. In this study, we evaluated the effects of pH on microbiomes assembled in anaerobic trichloroethylene-dechlorinating reactors under neutral (pH 7.2), acidic (pH 6.2), and alkaline (pH 8.2) conditions. The results revealed that among the reactors, the acidic reactor had the highest efficiency for dechlorination without accumulation of dechlorinated metabolites, even at high loading rates. The results of high-throughput sequencing of the 16S rRNA gene indicated that the microbiomes in the 3 reactors underwent varied dynamic succession. The acidic reactor harbored a higher degree of complex microbes, dechlorinator diversity, and abundance of the Victoria subgroup of Dehalococcoides (1.2 ± 0.1 × 106 cell/mL), which were approximately 10-102-fold higher than those at neutral and alkaline conditions. The pH settings altered species-species connectivity and complexity of microbial interaction networks, with more commensal interactions in the dechlorinators of the acidic reactor. As predicted, abundances of several functional gene categories were in strong linearity with pH values, and the microbiome possessed significantly more abundant functions in the acidic reactor (P < 0.001), such as potentially stimulating hydrogen production, cobalamin synthesis, cobalt transport, transport and metabolism of amino acids and secondary metabolites, cell motility, and transcription. All results of microbiomic analyses consistently revealed the observed superior dechlorination process and suggested an association of the reductive dechlorination process with the pH-dependent microbiome. The results of this study provide a new insight into the trichloroethylene dechlorination with regards to pH, and they will be useful for improving bioremediation and management of trichloroethylene-contaminated sites.},
}

@article {pmid31733733,
year = {2019},
author = {Morales-Rodriguez, C and Sferrazza, I and Aleandri, M and Dalla Valle, M and Mazzetto, T and Speranza, S and Contarini, M and Vannini, A},
title = {Fungal community associated with adults of the chestnut gall wasp Dryocosmus kuriphilus after emergence from galls: Taxonomy and functional ecology.},
journal = {Fungal biology},
volume = {123},
number = {12},
pages = {905-912},
doi = {10.1016/j.funbio.2019.09.009},
pmid = {31733733},
issn = {1878-6146},
abstract = {The diversity of the fungal community associated with adults of Dryocosmus kuriphilus following emergence was examined using HTS analysis. Ascomycota dominated the fungal core-biome community. The functional guilds of the 90 taxa forming the core-biome were assessed, demonstrating three main groups: saprotrophs, plant pathogens and entomopathogens. Twenty-nine OTUs out of 90 were resolved to species level identifying 26 different fungal species. Among these species, many were cosmopolitan or previously recorded in Europe. Ten taxa were previously recorded on chestnut, including some recognized plant pathogens associated with foliage and green tissues such as Epicoccum nigrum, Gnomoniopsis castanea, Colletotrichum acutatum, Stromatoseptoria castaneicola, Ramularia endophylla. Beauveria bassiana; within the core microbiome, Fusarium larvarum represented the most abundant entomopathogenic species. Some of these species are known to impact directly or indirectly the vitality of the insects in the galls. The chestnut blight pathogen, Cryphonectria parasitica, was never found associated with D. kuriphilus. Based on the present study, an active role for D. kuriphilus as a vector of chestnut fungal endophyte/pathogens cannot be demonstrated but neither ruled out.},
}

@article {pmid31733672,
year = {2020},
author = {Lee, J and Banerjee, D},
title = {Metabolomics and the Microbiome as Biomarkers in Sepsis.},
journal = {Critical care clinics},
volume = {36},
number = {1},
pages = {105-113},
doi = {10.1016/j.ccc.2019.08.008},
pmid = {31733672},
issn = {1557-8232},
abstract = {Metabolomics is an emerging field of research interest in sepsis. Metabolomics provides new ways of exploring the diagnosis, mechanism, and prognosis of sepsis. Advancements in technologies have enabled significant improvements in identifying novel biomarkers associated with the disease progress of sepsis. The use of metabolomics in the critically ill may provide new approaches to enable precision medicine. Furthermore, the dynamic interactions of the host and its microbiome can lead to further progression of sepsis. Understanding these interactions and the changes in the host's genomics and the microbiome can provide novel preventive and therapeutic strategies against sepsis.},
}

@article {pmid31733109,
year = {2019},
author = {Jiang, HY and Zhang, X and Zhou, YY and Jiang, CM and Shi, YD},
title = {Infection, antibiotic exposure and risk of celiac disease: a systematic review and meta-analysis.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.14928},
pmid = {31733109},
issn = {1440-1746},
abstract = {BACKGROUND AND AIM: There is evidence of a relationship between infection (and the associated antibiotic exposure) and the risk of celiac disease (CD). This study performed a meta-analysis to investigate this relationship.

METHODS: To identify relevant studies, we conducted systematic searches of the PubMed, Embase, and Cochrane databases for articles published up to April 2019. Random-effects models were used to determine overall pooled estimates and 95% confidence intervals (CIs).

RESULTS: The meta-analysis included 19 observational studies (15 on infection and six on antibiotic exposure). Our results showed that any infection was associated with an increased risk of CD later in life (odds ratio [OR], 1.37; 95% CI: 1.2-1.56; P < .001). The I2 was 94% (high heterogeneity among studies). Subgroup analyses suggested that the risk of CD is not affected by the type of infectious agent, timing of exposure, and site of infection. Exposure to antibiotics was also associated with new-onset CD (OR, 1.2; 95% CI: 1.04-1.39; P <0.001).

CONCLUSION: Exposure to early infection or antibiotic appears to increase the odds of developing CD, suggesting that intestinal immune or microbiota dysbiosis may play a role in the pathogenesis of CD. These findings may influence clinical management and primary prevention of CD. However, non-causal explanations for these positive associations cannot be excluded.},
}

@article {pmid31733004,
year = {2019},
author = {Sun, Z and Wang, T and Aschalew, ND and Zhao, W and Chen, X and Zhang, XF and Zhen, YG and Qin, GX},
title = {Effects of yeast cultures with different fermentation times on the growth performance, caecal microbial community and metabolite profile of broilers.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.13241},
pmid = {31733004},
issn = {1439-0396},
support = {20160301003NY//Jilin Province Major Scientific & Technological Achievement Transformation Project/ ; },
abstract = {The objective of this study was to investigate the effects of yeast culture (YC) on the growth performance, caecal microbial community and metabolic profile of broilers. A total of 350 1-day-old healthy Arbor Acres broilers were randomly assigned to seven treatment groups. The first group received a basal diet without YC supplementation, whereas the remaining groups received a basal diet supplemented with either YC fermented for 12, 24, 36, 48 or 60 hr, or a commercial YC product (SZ2). MiSeq 16S rRNA high-throughput sequencing was used to investigate the bacterial community structure, and gas chromatography-mass spectrometry was used to identify the metabolites in the caeca of broilers. The broilers that received a diet supplemented with YC had a higher average daily gain and average daily feed intake than those received YC-free or SZ2-enriched diets. The feed conversion ratio (FCR) of YCs fermented for 24 hr resulted in the best feed efficiency, whereas the FCR of YC fermented for 60 hr resulted in poor feed efficiency (p < .05). In the caeca of broilers, the bacterial communities were well separated, as determined by principal component analysis, and the proportions of the eight genera were significantly different among the seven groups (p < .05). The genus Akkermansia was the most abundant when the diet supplemented with YC fermented for 24 hr (p < .05). Furthermore, the Firmicutes/Bacteroidetes ratio was positively correlated with the FCR in the caecum (r = .47, p < .005). Five differentially expressed metabolites (i.e., L-alanine, benzeneacetic acid, D-mannose, D-arabitol and cholesterol) were identified in the caeca of broilers that received diets supplemented with YCs fermented for 24 or 60 hr. In summary, the different fermentation times of the YCs can markedly improve the growth performance and FCR of broilers by altering the caecal microbial community, and the growth performance which is related to the changes in key metabolic pathways.},
}

@article {pmid31732935,
year = {2019},
author = {Bertolini, M and Dongari-Bagtzoglou, A},
title = {The Relationship of Candida albicans with the Oral Bacterial Microbiome in Health and Disease.},
journal = {Advances in experimental medicine and biology},
volume = {1197},
number = {},
pages = {69-78},
doi = {10.1007/978-3-030-28524-1_6},
pmid = {31732935},
issn = {0065-2598},
abstract = {Candida albicans is an opportunistic pathogen colonizing the oropharyngeal, esophageal, and gastrointestinal mucosa in most healthy humans. In immunocompromised hosts, this fungal organism can cause mucosal candidiasis in these sites. C. albicans also causes fungemia, a serious consequence of cancer cytotoxic chemotherapy, which is thought to develop from fungal translocation through compromised mucosal barriers. Changes in endogenous bacterial population size or composition as well as changes in the host environment can transform fungal commensals into opportunistic pathogens in the upper and lower GI tract. Pioneering studies from our group have shown that a ubiquitous oral commensal of the mitis streptococcal group (Streptococcus oralis) has a mutualistic relationship with C. albicans, with C. albicans enabling streptococcal biofilm growth at mucosal sites, and S. oralis facilitating invasion of the oral and esophageal mucosa by C. albicans. In these studies, we used a cortisone-induced immunosuppression mouse model. More recently, the development of a novel mouse chemotherapy model has allowed us to examine the interactions of C. albicans with the endogenous bacterial microbiota in the oral and small intestinal mucosa, two sites adversely affected by cytotoxic chemotherapy. In this model, oral inoculation with C. albicans causes severe dysbiosis in the mucosal bacterial composition in both sites. We also found that antibiotic treatment ameliorates invasion of the oral mucosa but aggravates dissemination through the intestinal mucosa. In this chapter, we discuss work from our laboratory and others examining the relationships of C. albicans with oral bacteria and their role in mucosal homeostasis or disease.},
}

@article {pmid31732930,
year = {2019},
author = {Belibasakis, GN and Hajishengallis, G},
title = {Advances in Oral Mucosal Immunity and the Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1197},
number = {},
pages = {1-9},
doi = {10.1007/978-3-030-28524-1_1},
pmid = {31732930},
issn = {0065-2598},
abstract = {The 1st International Conference on Oral Mucosal Immunity and the Microbiome (OMIM) took place at the Avra Imperial Hotel, Chania, Crete, Greece, between 26th and 30th September 2018, under the auspices of the Aegean Conferences. This was the first Aegean Conference of its kind in thematic oral research, and a unique blend of immunological and microbiological perspectives, which attracted leading scientists from around the world to discuss the latest advances in the field. The Conference was divided into eight sessions that spanned across 4 days and included the following topics: (a) mucosal barrier immunity; (b) host response and inflammation; (c) microbiome in homeostasis and dysbiosis; (d) fungal and viral pathogenesis; (e) oral microbiome and proteome; (f) microbial virulence and biofilms; (g) microbiome, cancer, and systemic disease; and (h) microbiota and inflammation. There was substantial thematic overlap among all sessions, which promoted constant involvement of the participating scientists. An important hallmark was the active debate between oral microbiologists and oral immunologists, who explored new ideas and potential research collaborations, a crucial aspect for bridging our understanding of oral diseases in the context of the whole body. Key findings are highlighted and thematically presented in the following sections.},
}

@article {pmid31732849,
year = {2019},
author = {Schütte, K and Malfertheiner, P and Schulz, C},
title = {What is the Relevance of Gastric Microbiota Beyond H. pylori?.},
journal = {Current treatment options in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s11938-019-00245-2},
pmid = {31732849},
issn = {1092-8472},
abstract = {PURPOSE: The role of Helicobacter pylori as key factor in gastric inflammation and the development of (pre-)cancerous lesions is undisputable. As an open system, the human upper gastrointestinal tract harbors a complex bacterial community which is highly impacted by the absence or presence of H. pylori. The interaction between other bacteria and H. pylori might impact on gastric carcinogenesis.

RECENT FINDINGS: Several studies demonstrated differences in the composition of the gastric bacterial community in different stages of gastritis and between samples from tumor and adjacent tissue. In addition, animal studies demonstrated an increased and accelerated development of precancerous lesions in mice colonized with intestinal flora and H. pylori compared with mice mono-infected with H. pylori.

CONCLUSION: Other bacteria beyond H. pylori enter the focus in research on gastric carcinogenesis. However, we are still far from a thorough understanding of the pathophysiology of host-microbiota interaction and its impact on the development of malignant and precancerous changes.},
}

@article {pmid31732723,
year = {2019},
author = {Altmäe, S and Franasiak, JM and Mändar, R},
title = {The seminal microbiome in health and disease.},
journal = {Nature reviews. Urology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41585-019-0250-y},
pmid = {31732723},
issn = {1759-4820},
abstract = {Owing to the fact that there are more microbial than human cells in our body and that humans contain more microbial than human genes, the microbiome has huge potential to influence human physiology, both in health and in disease. The use of next-generation sequencing technologies has helped to elucidate functional, quantitative and mechanistic aspects of the complex microorganism-host interactions that underlie human physiology and pathophysiology. The microbiome of semen is a field of increasing scientific interest, although this microbial niche is currently understudied compared with other areas of microbiome research. However, emerging evidence is beginning to indicate that the seminal microbiome has important implications for the reproductive health of men, the health of the couple and even the health of offspring, owing to transfer of microorganisms to the partner and offspring. As this field expands, further carefully designed and well-powered studies are required to unravel the true nature and role of the seminal microbiome.},
}

@article {pmid31732071,
year = {2019},
author = {Jeon, DY and Yum, SJ and Seo, DW and Kim, SM and Jeong, HG},
title = {Leaf-associated microbiota on perilla (Perilla frutescens var. frutescens) cultivated in South Korea to detect the potential risk of food poisoning.},
journal = {Food research international (Ottawa, Ont.)},
volume = {126},
number = {},
pages = {108664},
doi = {10.1016/j.foodres.2019.108664},
pmid = {31732071},
issn = {1873-7145},
abstract = {Perilla (Perilla frutescens) is a commonly consumed herb with various health benefits in Asia. However, the risks of food-borne illness owing to the presence of pathogens on perilla leaves have not been evaluated. In this study, we evaluated the microbiota of perilla leaves harvested in South Korea using Illumina MiSeq sequencing of the 16S rRNA gene. In total, 2,743,003 sequencing reads were obtained, and 92-437 operational taxonomic units were observed in all samples. Bacterial loads were quantified, and the diversity indices were compared. Differences in the microbiota among sampling times and regions were also investigated. Proteobacteria and Firmicutes were predominant phyla at both times. At the class level, the bacterial communities were composed primarily of Alphaproteobacteria, Bacilli, and Gammaproteobacteria. Diverse bacterial taxa, such as Bacillus, uncultured family Enterobacteriaceae, and Sphingomonas were detected, and the representative pathogenic species (i.e., Acinetobacter lwoffii, Klebsiella pneumoniae, and Staphylococcus aureus) were quantified by qRT-PCR. The results of the co-occurrence network analysis showed characteristics of bacterial taxa in the microbiome on perilla leaves and provided insights into the roles of correlations among diverse microbes, including potential pathogens. Based on these results, the potential risk of food-borne illness from consumption of perilla leaves may be higher in July than in April. In summary, the microbial compositions determined in this study can be used as a base data for food-safety management for prediction and prevention of future outbreaks.},
}

@article {pmid31731747,
year = {2019},
author = {Pekkala, S and Keskitalo, A and Kettunen, E and Lensu, S and Nykänen, N and Kuopio, T and Ritvos, O and Hentilä, J and Nissinen, TA and Hulmi, JJ},
title = {Blocking Activin Receptor Ligands Is Not Sufficient to Rescue Cancer-Associated Gut Microbiota-A Role for Gut Microbial Flagellin in Colorectal Cancer and Cachexia?.},
journal = {Cancers},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/cancers11111799},
pmid = {31731747},
issn = {2072-6694},
support = {308042//Academy of Finland/ ; 275922//Academy of Finland/ ; JJH//Cancer Society of Finland/ ; },
abstract = {Colorectal cancer (CRC) and cachexia are associated with the gut microbiota and microbial surface molecules. We characterized the CRC-associated microbiota and investigated whether cachexia affects the microbiota composition. Further, we examined the possible relationship between the microbial surface molecule flagellin and CRC. CRC cells (C26) were inoculated into mice. Activin receptor (ACVR) ligands were blocked, either before tumor formation or before and after, to increase muscle mass and prevent muscle loss. The effects of flagellin on C26-cells were studied in vitro. The occurrence of similar phenomena were studied in murine and human tumors. Cancer modulated the gut microbiota without consistent effects of blocking the ACVR ligands. However, continued treatment for muscle loss modified the association between microbiota and weight loss. Several abundant microbial taxa in cancer were flagellated. Exposure of C26-cells to flagellin increased IL6 and CCL2/MCP-1 mRNA and IL6 excretion. Murine C26 tumors expressed more IL6 and CCL2/MCP-1 mRNA than C26-cells, and human CRC tumors expressed more CCL2/MCP-1 than healthy colon sites. Additionally, flagellin decreased caspase-1 activity and the production of reactive oxygen species, and increased cytotoxicity in C26-cells. Conditioned media from flagellin-treated C26-cells deteriorated C2C12-myotubes and decreased their number. In conclusion, cancer increased flagellated microbes that may promote CRC survival and cachexia by inducing inflammatory proteins such as MCP-1. Cancer-associated gut microbiota could not be rescued by blocking ACVR ligands.},
}

@article {pmid31731228,
year = {2019},
author = {Getzke, F and Thiergart, T and Hacquard, S},
title = {Contribution of bacterial-fungal balance to plant and animal health.},
journal = {Current opinion in microbiology},
volume = {49},
number = {},
pages = {66-72},
doi = {10.1016/j.mib.2019.10.009},
pmid = {31731228},
issn = {1879-0364},
abstract = {Surfaces of plants and animals are colonized by complex multi-kingdom microbial communities that comprise prokaryotic (i.e. archaea, bacteria) and eukaryotic (i.e. fungi, protists) microbes. Composition and variation in these multi-kingdom microbial communities are influenced by host and environmental cues that drive microbial community differentiation between host niches. Recent evidence indicates that, beyond these major forces, interactions between microbiota members also contribute to the establishment, the stability, and the resilience of host-associated microbial communities. Particularly, the interplay between bacteria and fungi in host niches appears critical for community functionality and alteration of the balance between these microbes emerges as a potential cause of disease. Here, we discuss the extent to which interactions between these microbes drive variation in community composition across plant and animal niches and we provide examples illustrating that altering bacterial-fungal balance in the microbiome can lead to disease.},
}

@article {pmid31731227,
year = {2019},
author = {Mitter, B and Brader, G and Pfaffenbichler, N and Sessitsch, A},
title = {Next generation microbiome applications for crop production - limitations and the need of knowledge-based solutions.},
journal = {Current opinion in microbiology},
volume = {49},
number = {},
pages = {59-65},
doi = {10.1016/j.mib.2019.10.006},
pmid = {31731227},
issn = {1879-0364},
abstract = {Plants are associated with highly diverse microbiota, which are crucial partners for their host carrying out important functions. Essentially, they are involved in nutrient supply, pathogen antagonism and protection of their host against different types of stress. The potential of microbial inoculants has been demonstrated in numerous studies, primarily under greenhouse conditions. However, field application, for example, as biofertilizer or biocontrol agent, is still a challenge as the applied microorganisms often are not provided in sufficiently high cell numbers, are rapidly outcompeted and cannot establish or require specific conditions to mediate the desired effects. We still have limited understanding on the fate of inoculants and on holobiont interactions, that is, interactions between plants, micro-biota and macro-biota and the environment, under field conditions. A better understanding will provide the basis for establishing models predicting the behaviour of strains or consortia and will help identifying microbiome members being able to establish and to mediate desired effects under certain conditions. Such models may also inform about the best management practices modulating microbiota in a desired way. Also, smart delivery approaches of microbial inoculants as well as the selection or breeding of plant genotypes better able to interact with microbiota may represent promising avenues.},
}

@article {pmid31731215,
year = {2019},
author = {Meijer, LL and Zwart, ES and Brandt, BW and Mebius, R and Deng, D and Giovannetti, E and Zaura, E and Kazemier, G},
title = {Tumor microbiome: Pancreatic cancer and duodenal fluids contain multitudes, …but do they contradict themselves?.},
journal = {Critical reviews in oncology/hematology},
volume = {144},
number = {},
pages = {102824},
doi = {10.1016/j.critrevonc.2019.102824},
pmid = {31731215},
issn = {1879-0461},
}

@article {pmid31730997,
year = {2019},
author = {Şafak, B and Altunan, B and Topçu, B and Topkaya, AE},
title = {The gut microbiome in epilepsy.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {103853},
doi = {10.1016/j.micpath.2019.103853},
pmid = {31730997},
issn = {1096-1208},
abstract = {The close relationship between epilepsy and autoimmune diseases and the fact that the cause of epilepsy is idiopathic in 60% of cases suggest that intestinal microbiota may play a role in the etiology of epilepsy. In this study, we analyzed and compared the intestinal microbiota composition of patients with idiopathic focal epilepsy (n = 30) and healthy volunteer group (n = 10) by 16s ribosomal DNA sequencing. Proteobacteria phylum was found to be higher in patients with epilepsy (25.4%) than in healthy volunteers group (1.5%). The genera of Campylobacter, Delftia, Haemophilus, Lautropia, Neisseria among Proteobacteria phylum were found to be statistically significantly higher in patients with epilepsy than in healthy volunteers (p < 0.05). Fusobacteria phylum was detected in 10.6% of the patients with epilepsy but not in the healthy volunteer group. The genus of the Fusobacteria phylum was found as Leptotrichia and Fusobacterium. In our study, taxonomic drift and significant differences in the intestinal microbiota of patients with epilepsy according to healthy volunteer group showed that autoimmune mechanisms and inflammation may have a role in the etiology of epilepsy. Our data should be supported by other studies as to the role of the intestinal microbiome in the prevention and treatment of epilepsy.},
}

@article {pmid31730850,
year = {2019},
author = {Salazar, G and Paoli, L and Alberti, A and Huerta-Cepas, J and Ruscheweyh, HJ and Cuenca, M and Field, CM and Coelho, LP and Cruaud, C and Engelen, S and Gregory, AC and Labadie, K and Marec, C and Pelletier, E and Royo-Llonch, M and Roux, S and Sánchez, P and Uehara, H and Zayed, AA and Zeller, G and Carmichael, M and Dimier, C and Ferland, J and Kandels, S and Picheral, M and Pisarev, S and Poulain, J and , and Acinas, SG and Babin, M and Bork, P and Bowler, C and de Vargas, C and Guidi, L and Hingamp, P and Iudicone, D and Karp-Boss, L and Karsenti, E and Ogata, H and Pesant, S and Speich, S and Sullivan, MB and Wincker, P and Sunagawa, S},
title = {Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome.},
journal = {Cell},
volume = {179},
number = {5},
pages = {1068-1083.e21},
doi = {10.1016/j.cell.2019.10.014},
pmid = {31730850},
issn = {1097-4172},
abstract = {Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms. VIDEO ABSTRACT.},
}

@article {pmid31730800,
year = {2019},
author = {Lee, W and Um, J and Hwang, B and Chan Lee, Y and Chung, BC and Hong, J},
title = {Assessing the progression of gastric cancer via profiling of histamine, histidine, and bile acids in gastric juice using LC-MS/MS.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {105539},
doi = {10.1016/j.jsbmb.2019.105539},
pmid = {31730800},
issn = {1879-1220},
abstract = {Bile acid (BA) imbalance may be directly associated with gastric cancer and indirectly influence stomach carcinogenesis via overexpression of histidine decarboxylase (HDC), which converts histidine (His) into histamine (HIST). Moreover, the progression of gastric cancer, could change the gut microbiome, including bacteria spp. that produce secondary BAs. Gastric juice has various metabolites that could indicate gastric cancer-related stomach conditions. Therefore, profiling of HIST, His, and BAs in gastric juice is crucial for understanding the etiological mechanisms of gastric cancer. We used a profiling method to simultaneously determine targeted metabolites in gastric juice using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We successfully analyzed 70 human gastric juice samples from patients with chronic superficial gastritis (CSG, n = 20), intestinal metaplasia (IM, n = 12), and gastric cancer (n = 38). Furthermore, we investigated the relevance between BA metabolism and gastric cancer. There were statistical differences in the metabolism of cholic acid (CA) into deoxycholic acid (DCA) based on the progression of CSG into IM and gastric cancer. Hence, the progression of gastric cancer might be related to the alterations in gut microbiome composition. We provide insight into the etiological mechanisms of the progression of gastric cancer and biomarkers to diagnose and treat gastric cancer.},
}

@article {pmid31730472,
year = {2019},
author = {Mohsen, A and Park, J and Chen, YA and Kawashima, H and Mizuguchi, K},
title = {Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {581},
doi = {10.1186/s12859-019-3187-5},
pmid = {31730472},
issn = {1471-2105},
support = {15654110//Ministry of Health, Labour and Welfare/ ; 17ek0210078h0002//Japan Agency for Medical Research and Development/ ; },
abstract = {BACKGROUND: To increase the accuracy of microbiome data analysis, solving the technical limitations of the existing sequencing machines is required. Quality trimming is suggested to reduce the effect of the progressive decrease in sequencing quality with the increased length of the sequenced library. In this study, we examined the effect of the trimming thresholds (0-20 for QIIME1 and 0-30 for QIIME2) on the number of reads that remained after the quality control and chimera removal (the good reads). We also examined the distance of the analysis results to the gold standard using simulated samples.

RESULTS: Quality trimming increased the number of good reads and abundance measurement accuracy in Illumina paired-end reads of the V3-V4 hypervariable region.

CONCLUSIONS: Our results suggest that the pre-analysis trimming step should be included before the application of QIIME1 or QIIME2.},
}

@article {pmid31730262,
year = {2019},
author = {Ruiz-Ruiz, S and Sanchez-Carrillo, S and Ciordia, S and Mena, MC and Méndez-García, C and Rojo, D and Bargiela, R and Zubeldia-Varela, E and Martínez-Martínez, M and Barbas, C and Ferrer, M and Moya, A},
title = {Functional microbiome deficits associated with ageing: Chronological age threshold.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e13063},
doi = {10.1111/acel.13063},
pmid = {31730262},
issn = {1474-9726},
support = {SAF2015-65878-R//Ministry of Science, Innovation and Universities/ ; RTI2018-095166-B-I00//Ministry of Science, Innovation and Universities/ ; BIO2017-85522-R//Ministry of Science, Innovation and Universities/ ; //European Regional Development Fund/ ; //Agencia Estatal de Investigación/ ; PIE14/00045//Instituto de Salud Carlos III/ ; AC17/00022//Instituto de Salud Carlos III/ ; //Fundación Agencia Española contra el Cáncer/ ; //AECC/ ; Prometeo/2018/A/133//Generalitat Valenciana/ ; //ProteoRed/ ; PT17/0019//PRB3-ISCIII/ ; },
abstract = {Composition of the gut microbiota changes during ageing, but questions remain about whether age is also associated with deficits in microbiome function and whether these changes occur sharply or progressively. The ability to define these deficits in populations of different ages may help determine a chronological age threshold at which deficits occur and subsequently identify innovative dietary strategies for active and healthy ageing. Here, active gut microbiota and associated metabolic functions were evaluated using shotgun proteomics in three well-defined age groups consisting of 30 healthy volunteers, namely, ten infants, ten adults and ten elderly individuals. Samples from each volunteer at intervals of up to 6 months (n = 83 samples) were used for validation. Ageing gradually increases the diversity of gut bacteria that actively synthesize proteins, that is by 1.4-fold from infants to elderly individuals. An analysis of functional deficits consistently identifies a relationship between tryptophan and indole metabolism and ageing (p < 2.8e-8). Indeed, the synthesis of proteins involved in tryptophan and indole production and the faecal concentrations of these metabolites are directly correlated (r2 > .987) and progressively decrease with age (r2 > .948). An age threshold for a 50% decrease is observed ca. 11-31 years old, and a greater than 90% reduction is observed from the ages of 34-54 years. Based on recent investigations linking tryptophan with abundance of indole and other "healthy" longevity molecules and on the results from this small cohort study, dietary interventions aimed at manipulating tryptophan deficits since a relatively "young" age of 34 and, particularly, in the elderly are recommended.},
}

@article {pmid31730200,
year = {2019},
author = {Esposito, A and Borruso, L and Rattray, JE and Brusetti, L and Ahmed, E},
title = {Taxonomic and functional insights into rock varnish microbiome using shotgun metagenomics.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz180},
pmid = {31730200},
issn = {1574-6941},
abstract = {Rock varnish is a microbial habitat, characterized by thin (5-500 μm) and shiny coatings of iron (Fe) and manganese (Mn) oxides associated with clay minerals. This structure is well studied by geologists, and recently there have been reports about the taxonomical composition of its microbiome. In this study, we investigated the rock varnish microbiome using shotgun metagenomics together with analyses of elemental composition, lipid and small molecule biomarkers, and rock surface analyses to explore the biogeography of microbial communities and their functional features. We report taxa and encoded functions represented in metagenomes retrieved from varnish or non-varnish samples, additionally, 8 nearly-complete genomes have been reconstructed spanning four phyla (Acidobacteria, Actinobacteria, Chloroflexi and TM7). The functional and taxonomic analyses presented in this study provide new insights into the ecosystem dynamics and survival strategies of microbial communities inhabiting varnish and non-varnish rock surfaces.},
}

@article {pmid31730167,
year = {2019},
author = {Grond, K and Bell, KC and Demboski, JR and Santos, M and Sullivan, JM and Hird, SM},
title = {No evidence for phylosymbiosis in western chipmunk species.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz182},
pmid = {31730167},
issn = {1574-6941},
abstract = {Phylosymbiosis refers to a congruent pattern between the similarity of microbiomes of different species and the branching pattern of the host phylogeny. Phylosymbiosis has been detected in a variety of vertebrate and invertebrate hosts, but has only been assessed in geographically isolated populations. We tested for phylosymbiosis in eight (sub)species of western chipmunks with overlapping ranges and ecological niches; we used a nuclear (Acrosin) and a mitochondrial (CYTB) phylogenetic marker because there are many instances of mitochondrial introgression in chipmunks. We predicted that similarity among microbiomes increases with: 1) increasing host mitochondrial relatedness, 2) increasing host nuclear genome relatedness, and 3) decreasing geographic distance among hosts. We did not find statistical evidence supporting phylosymbiosis in western chipmunks. Furthermore, in contrast to studies of other mammalian microbiomes, similarity of chipmunk microbiomes is not predominantly determined by host species. Sampling site explained most variation in microbiome composition, indicating an important role of local environment in shaping microbiomes. Fecal microbiomes of chipmunks were dominated by Bacteroidetes (72.2%), followed by Firmicutes (24.5%), which is one of the highest abundances of Bacteroidetes detected in wild mammals. Future work will need to elucidate the effects of habitat, ecology and host genomics on chipmunk microbiomes.},
}

@article {pmid31730166,
year = {2019},
author = {Trexler, RV and Bell, TH},
title = {Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnz228},
pmid = {31730166},
issn = {1574-6968},
abstract = {Experimental separation of the biotic and abiotic components of soil will help in understanding the role of taxonomy and composition in soil microbiome function. The most common approach to soil microbiome transfer involves direct dilution of a non-sterile source soil into sterile recipient soils, introducing both microorganisms and soil compounds, leaving abiotic and biotic factors confounded. Here, we contrast microbiome transfer into sterile recipient soils through 1) direct soil transfer at two dilutions, and 2) a new approach, sustained contact between source and recipient soils. Sustained soil-to-soil contact retains separation between source and recipient soils, allows for multiple colonization events, and increases confidence that microorganisms observed in recipient soils are active and growing. Each approach produced distinct microbiomes in recipient soils after 1 and 6 weeks of incubation, indicating that transfer method impacts microbial composition. The extent to which recipient microbiomes resembled source microbiomes varied by soil type, although in general, direct soil transfer appeared to most closely approximate source microbiomes. However, irrespective of transfer method, most bacterial sequences in recipient soils were from organisms transferred through all methods. We discuss the merits of each method for controlled soil microbiome studies.},
}

@article {pmid31729622,
year = {2019},
author = {Horvath, A and Leber, B and Feldbacher, N and Tripolt, N and Rainer, F and Blesl, A and Trieb, M and Marsche, G and Sourij, H and Stadlbauer, V},
title = {Effects of a multispecies synbiotic on glucose metabolism, lipid marker, gut microbiome composition, gut permeability, and quality of life in diabesity: a randomized, double-blind, placebo-controlled pilot study.},
journal = {European journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00394-019-02135-w},
pmid = {31729622},
issn = {1436-6215},
support = {COMET K1 CBmed//Österreichische Forschungsförderungsgesellschaft/ ; },
abstract = {PURPOSE: Diabesity, the combination of obesity and type 2 diabetes, is an ever-growing global health burden. Diabesity-associated dysbiosis of the intestinal microbiome has gained attention as a potential driver of disease and, therefore, a possible therapeutic target by means of pro- or prebiotic supplementation. This study tested the effects of a multispecies synbiotic (i.e. a combination of probiotics and prebiotics) on glucose metabolism, gut microbiota, gut permeability, neutrophil function and quality of life in treatment-experienced diabesity patients.

METHODS: A randomized, double-blind, placebo-controlled pilot study with 26 diabesity patients was conducted in which patients received a daily dose of a multispecies probiotic and a prebiotic (or a placebo) for 6 months.

RESULTS: There were no changes in glucose metabolism or mixed meal tolerance test responses throughout the study. The analysis of secondary outcomes revealed beneficial effects on hip circumference [- 1 (95% CI - 4; 3) vs +3 (- 1; 8) cm, synbiotics vs. placebo, respectively, p = 0.04], serum zonulin [- 0.04 (- 0.2; 0.1) vs +0.3 (- 0.05; 0.6) ng/ml, p = 0.004)] and the physical role item of the SF36 quality of life assessment [+ 5.4 (- 1.7; 12.5) vs - 5.0 (- 10.1; 0.2) points, p = 0.02] after 3 months of intervention, and lipoprotein (a) [- 2.1 (- 5.7; 1.6) vs +3.4 (- 0.9; 7.9) mg/dl, p = 0.02] after 6 months. There were no significant differences in alpha or beta diversity of the microbiome between groups or time points.

CONCLUSIONS: Glucose metabolism as the primary outcome was unchanged during the intervention with a multispecies synbiotic in patients with diabesity. Nevertheless, synbiotics improved some symptoms and biomarkers of type 2 diabetes and aspects of quality of life suggesting a potential role as adjuvant tool in the management of diabesity.},
}

@article {pmid31729564,
year = {2019},
author = {Eribo, OA and du Plessis, N and Ozturk, M and Guler, R and Walzl, G and Chegou, NN},
title = {The gut microbiome in tuberculosis susceptibility and treatment response: guilty or not guilty?.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-019-03370-4},
pmid = {31729564},
issn = {1420-9071},
abstract = {Although tuberculosis (TB) is a curable disease, it remains the foremost cause of death from a single pathogen. Globally, approximately 1.6 million people died of TB in 2017. Many predisposing factors related to host immunity, genetics and the environment have been linked to TB. However, recent evidence suggests a relationship between dysbiosis in the gut microbiome and TB disease development. The underlying mechanism(s) whereby dysbiosis in the gut microbiota may impact the different stages in TB disease progression, are, however, not fully explained. In the wake of recently emerging literature, the gut microbiome could represent a potential modifiable host factor to improve TB immunity and treatment response. Herein, we summarize early data detailing (1) possible association between gut microbiome dysbiosis and TB (2) the potential for the use of microbiota biosignatures to discriminate active TB disease from healthy individuals (3) the adverse effect of protracted anti-TB antibiotics treatment on gut microbiota balance, and possible link to increased susceptibility to Mycobacterium tuberculosis re-infection or TB recrudescence following successful cure. We also discuss immune pathways whereby the gut microbiome could impact TB disease and serve as target for clinical manipulation.},
}

@article {pmid31729407,
year = {2019},
author = {Laheij, AMGA and Raber-Durlacher, JE and Koppelmans, RGA and Huysmans, MDNJM and Potting, C and van Leeuwen, SJM and Hazenberg, MD and Brennan, MT and von Bültzingslöwen, I and Johansson, JE and de Soet, JJ and Haverman, TM and Buijs, MJ and Brandt, BW and Rozema, FR and Blijlevens, NMA and Zaura, E},
title = {Microbial changes in relation to oral mucositis in autologous hematopoietic stem cell transplantation recipients.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16929},
doi = {10.1038/s41598-019-53073-w},
pmid = {31729407},
issn = {2045-2322},
support = {ACTA 2014-6829//KWF Kankerbestrijding (Dutch Cancer Society)/ ; ACTA 2014-6829//KWF Kankerbestrijding (Dutch Cancer Society)/ ; },
abstract = {The aim of this prospective, two center study was to investigate the dynamics of the microbial changes in relation to the development of ulcerative oral mucositis in autologous SCT (autoSCT) recipients. Fifty-one patients were diagnosed with multiple myeloma and treated with high-dose melphalan followed by autoSCT. They were evaluated before, three times weekly during hospitalization, and three months after autoSCT. At each time point an oral rinse was collected and the presence or absence of ulcerative oral mucositis (UOM) was scored (WHO scale). Oral microbiome was determined by using 16S rRNA amplicon sequencing and fungal load by qPCR. Twenty patients (39%) developed UOM. The oral microbiome changed significantly after autoSCT and returned to pre-autoSCT composition after three months. However, changes in microbial diversity and similarity were more pronounced and rapid in patients who developed UOM compared to patients who did not. Already before autoSCT, different taxa discriminated between the 2 groups, suggesting microbially-driven risk factors. Samples with high fungal load (>0.1%) had a significantly different microbial profile from samples without fungi. In conclusion, autoSCT induced significant and reversible changes in the oral microbiome, while patients who did not develop ulcerative oral mucositis had a more resilient microbial ecosystem.},
}

@article {pmid31729390,
year = {2019},
author = {Medvedeva, S and Liu, Y and Koonin, EV and Severinov, K and Prangishvili, D and Krupovic, M},
title = {Virus-borne mini-CRISPR arrays are involved in interviral conflicts.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {5204},
doi = {10.1038/s41467-019-13205-2},
pmid = {31729390},
issn = {2041-1723},
support = {ANR-17-CE15-0005-01//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {CRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome-all spacers contained in a microbiome-associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1-2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation.},
}

@article {pmid31729183,
year = {2019},
author = {Manasson, J and Wallach, DS and Guggino, G and Stapylton, M and Badri, MH and Solomon, G and Reddy, SM and Coras, R and Aksenov, AA and Jones, DR and Girija, PV and Neimann, AL and Heguy, A and Segal, LN and Dorrestein, PC and Bonneau, R and Guma, M and Ciccia, F and Ubeda, C and Clemente, JC and Scher, JU},
title = {IL-17 Inhibition in Spondyloarthritis Associates with Subclinical Gut Microbiome Perturbations and a Distinctive IL-25-Driven Intestinal Inflammation.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.41169},
pmid = {31729183},
issn = {2326-5205},
abstract = {OBJECTIVE: To characterize the ecological effects of biologic therapies on the gut bacterial and fungal microbiome of psoriatic arthritis (PsA)/spondyloarthritis (SpA) patients.

METHODS: Fecal samples from PsA/SpA patients pre- and post-treatment with tumor necrosis factor inhibitors (TNFi; n=15) or an anti-interleukin (IL)-17A monoclonal antibody inhibitor (IL-17i; n=14) underwent sequencing (16S, ITS and shotgun metagenomics) and computational microbiome analysis. Fecal levels of fatty acid metabolites and cytokines/proteins implicated in PsA/SpA pathogenesis or intestinal inflammation were correlated with sequence data. Additionally, ileal biopsies obtained from SpA patients who developed clinically overt Crohn's disease (CD) after treatment with IL-17i (n=5) were analyzed for expression of IL-23/Th-17 related cytokines, IL-25/IL-17E-producing cells and type-2 innate lymphoid cells (ILC2s).

RESULTS: There were significant shifts in abundance of specific taxa after treatment with IL-17i compared to TNFi, particularly Clostridiales (p=0.016) and Candida albicans (p=0.041). These subclinical alterations correlated with changes in bacterial community co-occurrence, metabolic pathways, IL-23/Th17-related cytokines and various fatty acids. Ileal biopsies showed that clinically overt CD was associated with expansion of IL-25/IL-17E-producing tuft cells and ILC2s (p<0.05) compared to pre-IL-17i treatment levels.

CONCLUSION: In a subgroup of SpA patients, the initiation of IL-17A blockade correlated with features of subclinical gut inflammation and intestinal dysbiosis of certain bacterial and fungal taxa, most notably C. albicans. Further, IL-17i-related CD was associated with overexpression of IL-25/IL-17E-producing tuft cells and ILC2s. These results may help to explain the potential link between inhibition of a specific IL-17 pathway and the (sub)clinical gut inflammation observed in SpA.},
}

@article {pmid31728652,
year = {2019},
author = {Mardanova, A and Lutfullin, M and Hadieva, G and Akosah, Y and Pudova, D and Kabanov, D and Shagimardanova, E and Vankov, P and Vologin, S and Gogoleva, N and Stasevski, Z and Sharipova, M},
title = {Structure and variation of root-associated microbiomes of potato grown in alfisol.},
journal = {World journal of microbiology & biotechnology},
volume = {35},
number = {12},
pages = {181},
pmid = {31728652},
issn = {1573-0972},
support = {16-16-04062//Российский Фонд Фундаментальных Исследований (РФФИ)/ ; АААА-А18-118031390148-1//Basic scientific researchof the Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Root-associated fungi and bacteria play a pivotal role in the plant-soil ecosystem by influencing both plant growth and immunity. The aim of this study was to unravel the biodiversity of the bacterial and fungal rhizosphere (RS) and rhizoplane (RP) microbiota of Zhukovskij rannij potato (Solanum tuberosum L.) cultivar growing in the Alfisol of Tatarstan, Russia. To assess the structure and diversity of microbial communities, we employed the 16S rRNA and internal transcribed spacer gene library technique. Overall, sequence analysis showed the presence of 3982 bacterial and 188 fungal operational taxonomic units (OTUs) in the RP, and 6018 bacterial and 320 fungal OTUs for in the RS. Comparison between microbial community structures in the RS and RP showed significant differences between these compartments. Biodiversity was higher in the RS than in the RP. Although members of Proteobacteria (RS-59.1 ± 4.9%; RP-54.5 ± 9.2%), Bacteroidetes (RS-23.19 ± 10.2%; RP-34.52 ± 10.4%) and Actinobacteria (RS-11.55 ± 4.9%; RP-7.7 ± 5.1%) were the three most dominant phyla, accounting for 94-98% of all bacterial taxa in both compartments, notable variations were observed in the primary dominance of classes and genera in RS and RP samples. In addition, our results demonstrated that the potato rhizoplane was significantly enriched with the genera Flavobacterium, Pseudomonas, Acinetobacter and other potentially beneficial bacteria. The fungal community was predominantly inhabited by members of the Ascomycota phylum (RS-81.4 ± 8.1%; RP-81.7 ± 5.7%), among which the genera Fusarium (RS-10.34 ± 3.41%; RP-9.96 ± 4.79%), Monographella (RS-7.66 ± 4.43%; RP-9.91 ± 5.87%), Verticillium (RS-4.6 ± 1.43%; RP-8.27 ± 3.63%) and Chaetomium (RS-4.95 ± 2.07%; RP-8.33 ± 4.93%) were particularly abundant. Interestingly, potato rhizoplane was significantly enriched with potentially useful fungal genera, such as Mortierella and Metacordiceps. A comparative analysis revealed that the abundance of Fusarium (a cosmopolitan plant pathogen) varied significantly depending on rotation variants, indicating a possible control of phytopathogenic fungi via management-induced shifts through crop rotational methods. Analysis of the core microbiome of bacterial and fungal community structure showed that the formation of bacterial microbiota in the rhizosphere and rhizoplane is dependent on the host plant.},
}

@article {pmid31728586,
year = {2019},
author = {Li, T and Tian, D and Zhu, Z and Jin, W and Wu, S and Li, H},
title = {The gut microbiota: a new perspective on the toxicity of malachite green (MG).},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-019-10214-5},
pmid = {31728586},
issn = {1432-0614},
support = {LY18E090010//Zhejiang Provincial Natural Science Foundation of China/ ; LY19D060006//Zhejiang Provincial Natural Science Foundation of China/ ; lzujbky-2018-68//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Gut microbiome critically contributes to host health status. Thus, investigating the relationship between the gut microbiome and toxic chemicals is a hot topic in toxicology research. Exposure to malachite green (MG) has been linked to various health disorders. Thus, exploring the gut microbiota changes in response to MG would provide a new perspective on the toxicity effects of this chemical substance. MG exposure resulted in the significantly lower alpha diversity (Mann-Whitney U test, z = - 6.83, p = 0.00) but higher beta diversity (Mann-Whitney U test, z = - 1.98, p = 0.04) of gut microbiota, and significantly decreased ecosystem stability (alpha and beta variability; Mann-Whitney U test, all p < 0.05) of gut microbial communities. Gut bacterial networks showed that the interactions became more complex and stronger after MG exposure, which could decrease the stability of the network. Changes in gut microbiota composition were mainly reflected in the enrichment of opportunistic bacteria (i.e., Aeromonas and Vibrio) and the depression of fermentative bacteria (i.e., Bacteroides and Paludibacter). MG exposure leads to a significantly increased gut permeability (lipopolysaccharide-binding protein; Mann-Whitney U test, z = - 6.92, p = 0.00), which could reduce the host selective pressures on particular bacterial species (such as members in Aeromonas and Vibrio). This result was further supported by the weakened importance of a deterministic microbial assembly after MG exposure. All these findings indicated that MG exposed fishes might have more possibilities to be infected, as demonstrated by the enrichment of opportunistic pathogenic bacteria, high-level immune responses, and increased gut permeability. These findings greatly improve our understanding of the toxicity effects of MG.},
}

@article {pmid31728526,
year = {2019},
author = {Corrêa, FB and Saraiva, JP and Stadler, PF and da Rocha, UN},
title = {TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkz994},
pmid = {31728526},
issn = {1362-4962},
abstract = {Microbiome studies focused on the genetic potential of microbial communities (metagenomics) became standard within microbial ecology. MG-RAST and the Sequence Read Archive (SRA), the two main metagenome repositories, contain over 202 858 public available metagenomes and this number has increased exponentially. However, mining databases can be challenging due to misannotated, misleading and decentralized data. The main goal of TerrestrialMetagenomeDB is to make it easier for scientists to find terrestrial metagenomes of interest that could be compared with novel datasets in meta-analyses. We defined terrestrial metagenomes as those that do not belong to marine environments. Further, we curated the database using text mining to assign potential descriptive keywords that better contextualize environmental aspects of terrestrial metagenomes, such as biomes and materials. TerrestrialMetagenomeDB release 1.0 includes 15 022 terrestrial metagenomes from SRA and MG-RAST. Together, the downloadable data amounts to 68 Tbp. In total, 199 terrestrial terms were divided into 14 categories. These metagenomes span 83 countries, 30 biomes and 7 main source materials. The TerrestrialMetagenomeDB is publicly available at https://webapp.ufz.de/tmdb.},
}

@article {pmid31728495,
year = {2019},
author = {Hemler, EC and Hu, FB},
title = {Plant-Based Diets for Personal, Population, and Planetary Health.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {10},
number = {Supplement_4},
pages = {S275-S283},
doi = {10.1093/advances/nmy117},
pmid = {31728495},
issn = {2156-5376},
abstract = {Worldwide, the burden of morbidity and mortality from diet-related chronic diseases is increasing, driven by poor diet quality and overconsumption of calories. At the same time, the global food production system is draining our planet's resources, jeopardizing the environment and future food security. Personal, population, and planetary health are closely intertwined and will all continue to be vulnerable to these threats unless action is taken. Fortunately, shifting current global dietary patterns towards high-quality, plant-based diets could alleviate these health and environmental burdens. Compared with typical Western diets with high amounts of animal products, healthy plant-based diets are not only more sustainable, but have also been associated with lower risk of chronic diseases such as obesity, type 2 diabetes, cardiovascular disease, and some cancers. For personalized disease management and prevention, precision nutrition has the potential to offer more effective approaches tailored to individual characteristics such as the genome, metabolome, and microbiome. However, this area of research is in the early stages and is not yet ready for widespread clinical use. Therefore, it must not overshadow public health nutrition strategies, which have the power to improve health and sustainability on a larger scale. If widely implemented, interventions and policy changes that shift the globe towards healthy plant-based dietary patterns could be instrumental in ensuring future personal, population, and planetary health.},
}

@article {pmid31728100,
year = {2019},
author = {Migacz-Gruszka, K and Branicki, W and Obtulowicz, A and Pirowska, M and Gruszka, K and Wojas-Pelc, A},
title = {What's New in the Pathophysiology of Alopecia Areata? The Possible Contribution of Skin and Gut Microbiome in the Pathogenesis of Alopecia - Big Opportunities, Big Challenges, and Novel Perspectives.},
journal = {International journal of trichology},
volume = {11},
number = {5},
pages = {185-188},
pmid = {31728100},
issn = {0974-7753},
abstract = {The term "microbiome" defines the collective genome of all commensal, symbiotic, and pathogenic microbes living in the human body. The composition of microbiota in the gut and skin is influenced by many factors such as the stage of life, nutrition, lifestyle, and gender. In the past few years, several scientific papers have demonstrated an implication of microbiota in many immune-mediated diseases, for example, diabetes, ulcerative colitis, and multiple sclerosis. The alterations in the proportion of gut microbiota have emerged as potential immunomodulators with the capacity to induce physiologic as well as pathologic immune responses against the human body, causing inflammation and destruction of tissues or organs. The microbiota influences the differentiation of adaptive immune cells not only in the gut but also in the skin. Alopecia areata (AA) is a dermatologic disorder which causes hair loss in most cases resistant to treatment. There are some clinical and experimental evidences indicating that AA is the demonstration of autoimmune attack against hair follicles. The factors that may implicate such an autoimmunity in AA still remain unknown. Despite more and more evidences demonstrate that human microbiome plays a key role in human health and diseases, to the best of our knowledge, no study has been conducted to analyze an implication of microbiome in the pathogenesis of AA. Undoubtedly, there is a need to performing a study which might explain the involvement of gut and skin microbiota in the unclear pathogenesis of AA and lead to alternative treatment options for numerous patients suffering from current treatment limitations.},
}

@article {pmid31727980,
year = {2019},
author = {Kim, HJ and Kim, JJ and Myeong, NR and Kim, T and Kim, D and An, S and Kim, H and Park, T and Jang, SI and Yeon, JH and Kwack, I and Sul, WJ},
title = {Segregation of age-related skin microbiome characteristics by functionality.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16748},
doi = {10.1038/s41598-019-53266-3},
pmid = {31727980},
issn = {2045-2322},
support = {2016R1A6A3A11933991//National Research Foundation of Korea (NRF)/ ; 2019R1C1C1009360//National Research Foundation of Korea (NRF)/ ; },
abstract = {Although physiological changes are the most evident indicators of skin aging by alteration of the skin's structure and function, we question whether skin aging is also affected by the structure and assembly process of the skin microbiome. We analysed the skin microbiomes of 73 healthy Chinese women in two age groups (25-35 years old and 56-63 years old) using 16S rRNA gene amplicon sequencing; the overall microbiome structure was significantly different between the two age groups. An analysis using ecological theory to evaluate the process of microbial community assembly processes revealed that the microbiomes of the older group were formed under a greater influence of the niche-based process, with the network of microbes being more collapsed than that of the younger group. Inferred metagenomic functional pathways associated with replication and repair were relatively more predominant in the younger group whereas, among the various metabolism-related pathways, those associated with biodegradation were more predominant in the older group. Interestingly, we found two segregated sub-typing patterns in the younger group which were also observed in the skin microbiomes of young Chinese women living in four other cities in China. The results of our study highlights candidate microbes and functional pathways that are important for future research into preventing skin aging and which could lead to a comprehensive understanding of age-related skin microbiome characteristics.},
}

@article {pmid31727963,
year = {2019},
author = {Watson, EJ and Giles, J and Scherer, BL and Blatchford, P},
title = {Human faecal collection methods demonstrate a bias in microbiome composition by cell wall structure.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16831},
doi = {10.1038/s41598-019-53183-5},
pmid = {31727963},
issn = {2045-2322},
abstract = {Clinical trial faecal collections present challenges through geographical spread and inexperienced participants. Collection techniques have been developed and tested to overcome these challenges, but previous studies investigating these techniques have demonstrated a highly variable capacity for sample preservation. Furthermore, these studies typically only examine either preservation of genetic content or metabolites, not both. This study investigated the Stool Nucleic Acid Collection and Preservation Tube (Norgen BioTek Corp) for the preservation of both microbial DNA and microbial organic acid metabolites in human faecal samples when compared to frozen samples. Twenty six healthy adult participants were instructed to collect a bowel movement, subsample into collection tubes and immediately transfer the remaining bulk to -20 °C storage. Resulting organic acid concentrations remained comparable across methods when the preservation tubes were used correctly. The 16S rRNA gene sequencing data revealed twenty significantly different bacterial genera between the two collection methods. Ten Gram-negative genera were more abundant in the collection tubes, and ten Gram-positive genera were more abundant in the fresh frozen samples. This study has illustrated that faecal collection methods bias the microbial community profile according to Gram status and this should be considered when designing studies that collect and store human faecal samples.},
}

@article {pmid31727954,
year = {2019},
author = {Liu, HH and Lin, YC and Chung, CS and Liu, K and Chang, YH and Yang, CH and Chen, Y and Ni, YH and Chang, PF},
title = {Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16836},
doi = {10.1038/s41598-019-53173-7},
pmid = {31727954},
issn = {2045-2322},
support = {105-2628B-400-001-MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; FEMH-2015-C-023//Far Eastern Memorial Hospital (FEMH)/ ; FEMH-2017-C-035//Far Eastern Memorial Hospital (FEMH)/ ; },
abstract = {Bowel microbiota is a "metaorgan" of metabolisms on which quantitative readouts must be performed before interventions can be introduced and evaluated. The study of the effects of probiotic Clostridium butyricum MIYAIRI 588 (CBM588) on intestine transplantees indicated an increased percentage of the "other glycan degradation" pathway in 16S-rRNA-inferred metagenomes. To verify the prediction, a scoring system of carbohydrate metabolisms derived from shotgun metagenomes was developed using hidden Markov models. A significant correlation (R = 0.9, p < 0.015) between both modalities was demonstrated. An independent validation revealed a strong complementarity (R = -0.97, p < 0.002) between the scores and the abundance of "glycogen degradation" in bacteria communities. On applying the system to bacteria genomes, CBM588 had only 1 match and ranked higher than the other 8 bacteria evaluated. The gram-stain properties were significantly correlated to the scores (p < 5 × 10-4). The distributions of the scored protein domains indicated that CBM588 had a considerably higher (p < 10-5) proportion of carbohydrate-binding modules than other bacteria, which suggested the superior ability of CBM588 to access carbohydrates as a metabolic driver to the bowel microbiome. These results demonstrated the use of integrated counts of protein domains as a feasible readout for metabolic potential within bacteria genomes and human metagenomes.},
}

@article {pmid31727922,
year = {2019},
author = {Half, E and Keren, N and Reshef, L and Dorfman, T and Lachter, I and Kluger, Y and Reshef, N and Knobler, H and Maor, Y and Stein, A and Konikoff, FM and Gophna, U},
title = {Fecal microbiome signatures of pancreatic cancer patients.},
journal = {Scientific reports},
volume = {9},
number = {1},
pages = {16801},
doi = {10.1038/s41598-019-53041-4},
pmid = {31727922},
issn = {2045-2322},
abstract = {Pancreatic cancer (PC) is a leading cause of cancer-related death in developed countries, and since most patients have incurable disease at the time of diagnosis, developing a screening method for early detection is of high priority. Due to its metabolic importance, alterations in pancreatic functions may affect the composition of the gut microbiota, potentially yielding biomarkers for PC. However, the usefulness of these biomarkers may be limited if they are specific for advanced stages of disease, which may involve comorbidities such as biliary obstruction or diabetes. In this study we analyzed the fecal microbiota of 30 patients with pancreatic adenocarcinoma, 6 patients with pre-cancerous lesions, 13 healthy subjects and 16 with non-alcoholic fatty liver disease, using amplicon sequencing of the bacterial 16S rRNA gene. Fourteen bacterial features discriminated between PC and controls, and several were shared with findings from a recent Chinese cohort. A Random Forest model based on the microbiota classified PC and control samples with an AUC of 82.5%. However, inter-subject variability was high, and only a small part of the PC-associated microbial signals were also observed in patients with pre-cancerous pancreatic lesions, implying that microbiome-based early detection of such lesions will be challenging.},
}

@article {pmid31727837,
year = {2019},
author = {Gil-Cruz, C and Perez-Shibayama, C and De Martin, A and Ronchi, F and van der Borght, K and Niederer, R and Onder, L and Lütge, M and Novkovic, M and Nindl, V and Ramos, G and Arnoldini, M and Slack, EMC and Boivin-Jahns, V and Jahns, R and Wyss, M and Mooser, C and Lambrecht, BN and Maeder, MT and Rickli, H and Flatz, L and Eriksson, U and Geuking, MB and McCoy, KD and Ludewig, B},
title = {Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy.},
journal = {Science (New York, N.Y.)},
volume = {366},
number = {6467},
pages = {881-886},
doi = {10.1126/science.aav3487},
pmid = {31727837},
issn = {1095-9203},
support = {/SNSF_/Swiss National Science Foundation/Switzerland ; },
abstract = {Myocarditis can develop into inflammatory cardiomyopathy through chronic stimulation of myosin heavy chain 6-specific T helper (TH)1 and TH17 cells. However, mechanisms governing the cardiotoxicity programming of heart-specific T cells have remained elusive. Using a mouse model of spontaneous autoimmune myocarditis, we show that progression of myocarditis to lethal heart disease depends on cardiac myosin-specific TH17 cells imprinted in the intestine by a commensal Bacteroides species peptide mimic. Both the successful prevention of lethal disease in mice by antibiotic therapy and the significantly elevated Bacteroides-specific CD4+ T cell and B cell responses observed in human myocarditis patients suggest that mimic peptides from commensal bacteria can promote inflammatory cardiomyopathy in genetically susceptible individuals. The ability to restrain cardiotoxic T cells through manipulation of the microbiome thereby transforms inflammatory cardiomyopathy into a targetable disease.},
}

@article {pmid31727626,
year = {2019},
author = {Moiseev, S and Rameev, V and Karovaikina, E and Lysenko Kozlovskaya, L},
title = {Gut microbiome in rheumatic diseases.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1136/annrheumdis-2019-216560},
pmid = {31727626},
issn = {1468-2060},
}

@article {pmid31726559,
year = {2019},
author = {Liu, D and Mariman, R and Gerlofs-Nijland, ME and Boere, JF and Folkerts, G and Cassee, FR and Pinelli, E},
title = {Microbiome composition of airborne particulate matter from livestock farms and their effect on innate immune receptors and cells.},
journal = {The Science of the total environment},
volume = {688},
number = {},
pages = {1298-1307},
doi = {10.1016/j.scitotenv.2019.06.217},
pmid = {31726559},
issn = {1879-1026},
abstract = {Patients with respiratory diseases in rural areas have been reported to have enhanced responsiveness to ambient particulate matter (PM). In addition to the physical and chemical components, ambient PM can contain microorganisms or parts thereof, referred here as BioPM, that can also contribute to the adverse health effects. This study aimed to characterize the microbial composition of BioPM originating from livestock, and to investigate whether these BioPM can trigger the activation of innate receptors and cells. Coarse (PM2.5-10 μm) and fine (PM<2.5 μm) BioPM samples were collected from indoor chicken, pig and goat farms using the versatile aerosol concentration enrichment system (VACES) connected to a Biosampler. The fungal and bacterial communities were assessed with an amplicon based approach using Next Generation Sequencing (NGS). In parallel, HEK-Blue cells expressing different pattern recognition receptors (Toll like receptors (TLR) 2, 3, 4, 5, 7, 8, 9 and NOD 1, 2) and a human monocytic cell line (MM6) were exposed to BioPM samples from these sites. Distinct airborne microbiota profiles associated with the corresponding animal farm were observed. Moreover, the various BioPM contained mainly ligands for TLR2 and TLR4 resulting in a concentration-dependent increase of pro-inflammatory cytokine secreted by MM6 cells. In addition, we show for the first time that only the pig-derived BioPM induced TLR5 activation. These findings suggest that animal farm specific BioPM trigger distinct inflammatory responses, which may contribute to airway diseases in humans.},
}

@article {pmid31726393,
year = {2019},
author = {Paranjape, K and Bédard, É and Whyte, LG and Ronholm, J and Prévost, M and Faucher, SP},
title = {Presence of Legionella spp. in cooling towers: the role of microbial diversity, Pseudomonas, and continuous chlorine application.},
journal = {Water research},
volume = {169},
number = {},
pages = {115252},
doi = {10.1016/j.watres.2019.115252},
pmid = {31726393},
issn = {1879-2448},
abstract = {Legionnaires' disease (LD) is a severe pneumonia caused by several species of the genus Legionella, most frequently by Legionella pneumophila. Cooling towers are the most common source for large community-associated outbreaks. Colonization, survival, and proliferation of L. pneumophila in cooling towers are necessary for outbreaks to occur. These steps are affected by the chemical and physical parameters of the cooling tower environment. We hypothesize that the bacterial community residing in the cooling tower could also affect the presence of L. pneumophila. A 16S rRNA gene targeted amplicon sequencing approach was used to study the bacterial community of cooling towers and its relationship with the Legionella spp. and L. pneumophila communities. The results indicated that the water source shaped the bacterial community of cooling towers. Several taxa were enriched and positively correlated with Legionella spp. and L. pneumophila. In contrast, Pseudomonas showed a strong negative correlation with Legionella spp. and several other genera. Most importantly, continuous chlorine application reduced microbial diversity and promoted the presence of Pseudomonas creating a non-permissive environment for Legionella spp. This suggests that disinfection strategies as well as the resident microbial population influences the ability of Legionella spp. to colonize cooling towers.},
}

@article {pmid31726030,
year = {2019},
author = {Fehlner-Peach, H and Magnabosco, C and Raghavan, V and Scher, JU and Tett, A and Cox, LM and Gottsegen, C and Watters, A and Wiltshire-Gordon, JD and Segata, N and Bonneau, R and Littman, DR},
title = {Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.},
journal = {Cell host & microbe},
volume = {26},
number = {5},
pages = {680-690.e5},
doi = {10.1016/j.chom.2019.10.013},
pmid = {31726030},
issn = {1934-6069},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; TL1 TR001447/TR/NCATS NIH HHS/United States ; T32 CA009161/CA/NCI NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; UL1 RR029893/RR/NCRR NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; /ERC_/European Research Council/International ; },
abstract = {Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.},
}

@article {pmid31726026,
year = {2019},
author = {Moskowitz, JE and Devkota, S},
title = {Determinants of Microbial Antibiotic Susceptibility: The Commensal Gut Microbiota Perspective.},
journal = {Cell host & microbe},
volume = {26},
number = {5},
pages = {574-576},
doi = {10.1016/j.chom.2019.10.019},
pmid = {31726026},
issn = {1934-6069},
mesh = {Anti-Bacterial Agents ; Diet ; *Gastrointestinal Microbiome ; *Microbiota ; Symbiosis ; },
abstract = {Ng et al. (2019) unravel the complex factors that shape commensal gut microbiota susceptibility and resilience to antibiotics. These findings depict the microbiota's malleable dynamics resulting from compositional changes, environmental variability, and dietary shifts, further informing potential strategies to mitigate incomplete microbiome recovery accompanying antibiotic treatment.},
}

Anti-Bacterial Agents
Diet
*Gastrointestinal Microbiome
*Microbiota
Symbiosis

@article {pmid31726014,
year = {2019},
author = {Wu, L and Yang, B and Li, M and Chen, J and Xiao, Z and Wu, H and Tong, Q and Luo, X and Lin, W},
title = {Modification of Rhizosphere Bacterial Community Structure and Functional Potentials to Control Pseudostellaria heterophylla Replant Disease.},
journal = {Plant disease},
volume = {},
number = {},
pages = {PDIS04190833RE},
doi = {10.1094/PDIS-04-19-0833-RE},
pmid = {31726014},
issn = {0191-2917},
abstract = {Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.},
}

@article {pmid31725875,
year = {2019},
author = {Hellmann, J and Andersen, H and Fei, L and Linn, A and Bezold, R and Lake, K and Jackson, K and Meyer, D and Dirksing, K and Bonkowski, E and Ollberding, NJ and Haslam, DB and Denson, L},
title = {Microbial Shifts and Shorter Time to Bowel Resection Surgery Associated with C. difficile in Pediatric Crohn's Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izz263},
pmid = {31725875},
issn = {1536-4844},
abstract = {BACKGROUND: Clostridioides difficile infection and colonization are common in pediatric Crohn's disease (CD). Our aims were to test the relationship between C. difficile positivity and bowel resection surgery and to characterize microbial shifts associated with C. difficile carriage and surgery.

METHODS: A retrospective single-center study of 75 pediatric CD patients tested for association between C. difficile carriage and bowel resection surgery. A prospective single-center study of 70 CD patients utilized C. difficile testing and shotgun metagenomic sequencing of fecal samples to define microbiota variation stratified by C. difficile carriage or history of surgery.

RESULTS: The rate of bowel resection surgery increased from 21% in those without C. difficile to 67% in those with (P = 0.003). From a Kaplan-Meier survival model, the hazard ratio for time to first surgery was 4.4 (95% CI, 1.2-16.2; P = 0.00) in patients with positive C. difficile testing in the first year after diagnosis. Multivariable logistic regression analysis confirmed this association (odds ratio 16.2; 95% CI, 2.2-120; P = 0.006). Larger differences in microbial abundance and metabolic pathways were observed in patients with prior surgery than in those with C. difficile carriage. Depletion of Alistipes and Ruminococcus species and reduction in methionine biosynthesis were noted in patients with both C. difficile carriage and past surgery.

CONCLUSIONS: A positive C. difficile test during the first year after diagnosis is associated with decreased time to first bowel resection surgery in pediatric Crohn's disease. Depletion of beneficial commensals and methionine biosynthesis in patients with C. difficile carriage may contribute to increased risk for surgery.},
}

@article {pmid31725757,
year = {2019},
author = {Andrews, T and Neher, DA and Weicht, TR and Barlow, JW},
title = {Mammary microbiome of lactating organic dairy cows varies by time, tissue site, and infection status.},
journal = {PloS one},
volume = {14},
number = {11},
pages = {e0225001},
doi = {10.1371/journal.pone.0225001},
pmid = {31725757},
issn = {1932-6203},
abstract = {Infections of the cow udder leading to mastitis and reducing milk quality are a critical challenge facing all dairy farmers. Mastitis may be linked to the ecological disruption of an endogenous mammary microbial community, suggesting an ecosystems approach to management and prevention of this disease. The teat end skin represents a first point of host contact with mastitis pathogens and may offer an opportunity for microbially mediated resistance to infection, yet we know little about the microbial community of teat end skin or its potential interaction with the microbial community of intramammary milk of organic dairy cattle. High-throughput sequencing of marker genes for bacterial and fungal communities was used to characterize the skin and milk microbiome of cows with both a healthy and infected gland (i.e., udder quarter) and to assess the sharing of microbial DNA between these tissue habitat sites. The mammary microbiome varied among cows, through time, and between skin and milk. Microbiomes of milk from healthy and infected quarters reflected a diverse group of microbial DNA sequences, though milk had far fewer operational taxonomic units (OTUs) than skin. Milk microbiomes of infected quarters were generally more variable than healthy quarters and were frequently dominated by a single OTU; teat end skin microbiomes were relatively similar between healthy and infected quarters. Commonly occurring genera that were shared between skin and milk of infected glands included Staphylococcus spp. bacteria and Debaryomyces spp. fungi. Commonly occurring genera that were shared between skin and milk of healthy glands included bacteria SMB53 (Clostridiaceae) and Penicillium spp. fungi. Results support an ecological interpretation of the mammary gland and the notion that mastitis can be described as a dysbiosis, an imbalance of the healthy mammary gland microbiome.},
}

@article {pmid31725012,
year = {2019},
author = {Goraya, N and Wesson, DE},
title = {Novel dietary and pharmacologic approaches for acid-base modulation to preserve kidney function and manage uremia.},
journal = {Current opinion in nephrology and hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/MNH.0000000000000568},
pmid = {31725012},
issn = {1473-6543},
abstract = {PURPOSE OF REVIEW: We review mechanisms for chronic kidney disease (CKD) progression that might be addressed with nonpharmacologic and novel pharmacologic interventions as strategies by which to slow or even prevent CKD progression.

RECENT FINDINGS: Evolving data support the contribution of the broad spectrum of disorders of acid (H) accumulation, which we refer to as 'H stress', to CKD progression. Recent studies support that amelioration of H stress, including spectra of H accumulation that are insufficient to cause metabolic acidosis, is kidney-protective. In addition, gut-derived toxins appear to contribute to CKD progression and to the well described increased cardiovascular disease (CVD) risk in patients with CKD. Dietary and novel pharmacologic interventions hold promise as strategies to slow CKD progression through reducing levels of these gut-derived toxins. In addition, oxidative stress appears to mediate CKD progression and contributing factors like diet and cigarette smoking can exacerbate oxidative stress. Dietary changes and smoking cessation hold promise to favorably affect CKD progression by reducing kidney oxidative stress.

SUMMARY: The urgent need to add to the traditional armamentarium of blood pressure control and antiangiotensin II pharmacologic therapy for kidney protection has led to investigations into additional kidney-protective strategies. Acid stress, a disordered gut microbiome, and oxidative stress each appear to contribute to CKD progression and can be potentially addressed by nonpharmacologic and novel pharmacologic interventions.},
}

@article {pmid31725010,
year = {2019},
author = {Caggiano, G and Cosola, C and Di Leo, V and Gesualdo, M and Gesualdo, L},
title = {Microbiome modulation to correct uremic toxins and to preserve kidney functions.},
journal = {Current opinion in nephrology and hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/MNH.0000000000000565},
pmid = {31725010},
issn = {1473-6543},
abstract = {PURPOSE OF REVIEW: The association between dysbiosis and CKD is well established. This review focuses on the current understanding of microbiome, in normal individuals and CKD patients, in order to hypothesize how to correct uremic toxins levels and preserve the renal function and reduce associated comorbidities. Here we discuss our current opinion on microbiome modulation in order to manage the CKD-associated dysbiosis.

RECENT FINDINGS: Emerging evidence confirms the role of gut microbiome in the progression of CKD. In this scenario, the need is felt to set up multifaceted approaches for dysbiosis management. Among many strategies able to improve gut wellness, a crucial approach is represented by the functional nutrition. At the same time, drug-based treatments show significant results in microbiome modulation. Furthermore, we examine here the potentialities of fecal microbiome transplantation (FMT) in CKD, an approach currently applied in Clostridium difficile infection.

SUMMARY: The gut microbiome plays a pivotal role in the pathophysiology of CKD. The vicious cycle triggered by kidney function decline leads to gut dysbiosis. Considering the gut microbiome as a therapeutic target in CKD, multiple approaches aimed at its modulation should be envisioned to preserve kidney function. Dietary interventions and pharmacological strategies are able to improve microbiome dysbiosis, oxidative stress and fibrosis. Additionally, FMT could represent a promising novel therapy in the management of CKD-associated dysbiosis.},
}

@article {pmid31724973,
year = {2019},
author = {Favazzo, LJ and Hendesi, H and Villani, DA and Soniwala, S and Dar, QA and Schott, EM and Gill, SR and Zuscik, MJ},
title = {The gut microbiome-joint connection: implications in osteoarthritis.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000000681},
pmid = {31724973},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: Osteoarthritis is a debilitating disease leading to joint degeneration, inflammation, pain, and disability. Despite efforts to develop a disease modifying treatment, the only accepted and available clinical approaches involve palliation. Although many factors contribute to the development of osteoarthritis, the gut microbiome has recently emerged as an important pathogenic factor in osteoarthritis initiation and progression. This review examines the literature to date regarding the link between the gut microbiome and osteoarthritis.

RECENT FINDINGS: Studies showing correlations between serum levels of bacterial metabolites and joint degeneration were the first links connecting a dysbiosis of the gut microbiome with osteoarthritis. Further investigations have demonstrated that microbial community shifts induced by antibiotics, a germ-free environment or high-fat are important underlying factors in joint homeostasis and osteoarthritis. It follows that strategies to manipulate the microbiome have demonstrated efficacy in mitigating joint degeneration in osteoarthritis. Moreover, we have observed that dietary supplementation with nutraceuticals that are joint protective may exert their influence via shifts in the gut microbiome.

SUMMARY: Although role of the microbiome in osteoarthritis is an area of intense study, no clear mechanism of action has been determined. Increased understanding of how the two factors interact may provide mechanistic insight into osteoarthritis and lead to disease modifying treatments.},
}

@article {pmid31724526,
year = {2019},
author = {Kalala, G and Kambashi, B and Taminiau, B and Schroyen, M and Everaert, N and Beckers, Y and Richel, A and Njeumen, P and Pachikian, B and Neyrinck, AM and Hiel, S and Rodriguez, J and Fall, PA and Daube, G and Thissen, JP and Delzenne, NM and Bindelle, J},
title = {In vitro approach to evaluate the fermentation pattern of inulin-rich food in obese individuals.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-19},
doi = {10.1017/S0007114519002915},
pmid = {31724526},
issn = {1475-2662},
abstract = {Alterations of the gut microbiome have been associated with obesity and metabolic disorders. The gut microbiota can be influenced by the intake of dietary fibres with prebiotic properties, such as inulin-type fructans. This study tested the hypothesis that obese individuals subjected for 12 weeks to a inulin-enriched versus inulin-poor diet have differential faecal fermentation patterns. The fermentation of cellulose and inulin hydrolysates, of six different inulin-rich and inulin-poor vegetables of both groups was analysed in vitro on faecal inocula. The results showed that the microbiota from obese patients who received fructan-rich diet for three weeks produce more gas and total short-chain fatty acid (SCFA) compared to the microbiota taken of the same individuals before the treatment. Obese individuals fed with a low-fructan diet produce less gas and less SCFA compared to the treated group. This study highlighted profound changes in microbiota fermentation capacity obtained by prebiotic intervention in obese individuals, which favors the production of specific bioactive metabolites.},
}

@article {pmid31723804,
year = {2019},
author = {Vinchi, F},
title = {Thrombosis Prevention: Let's Drug the Microbiome!.},
journal = {HemaSphere},
volume = {3},
number = {1},
pages = {e165},
pmid = {31723804},
issn = {2572-9241},
}

@article {pmid31722729,
year = {2019},
author = {Kawulok, J and Kawulok, M and Deorowicz, S},
title = {Environmental metagenome classification for constructing a microbiome fingerprint.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {20},
doi = {10.1186/s13062-019-0251-z},
pmid = {31722729},
issn = {1745-6150},
abstract = {BACKGROUND: Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.

RESULTS: We report the results of our extensive experimental study to investigate the behavior of our method and its sensitivity to different parameters. In our tests, we have followed the protocol of the MetaSUB Challenge, which allowed us to compare the obtained results with the solutions based on taxonomic and functional classification.

CONCLUSIONS: The results reported in the paper indicate that our method is competitive with those based on taxonomic classification. Importantly, by measuring the similarity at the reads level, we avoid the necessity of using large databases with annotated gene sequences. Hence our main finding is that environmental classification of metagenomic data can be proceeded without using large databases required for taxonomic or functional classification.

REVIEWERS: This article was reviewed by Eran Elhaik, Alexandra Bettina Graf, Chengsheng Zhu, and Andre Kahles.},
}

@article {pmid31722703,
year = {2019},
author = {LaMonte, MJ and Genco, RJ and Buck, MJ and McSkimming, DI and Li, L and Hovey, KM and Andrews, CA and Zheng, W and Sun, Y and Millen, AE and Tsompana, M and Banack, HR and Wactawski-Wende, J},
title = {Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation.},
journal = {BMC oral health},
volume = {19},
number = {1},
pages = {246},
doi = {10.1186/s12903-019-0906-2},
pmid = {31722703},
issn = {1472-6831},
support = {N01WH32122/HL/NHLBI NIH HHS/United States ; DE13505, DE4898, DE022654, and DE024523/DE/NIDCR NIH HHS/United States ; Al125982//National Institute of Allergy and Infectious Diseases/ ; DAMD17-96-1-6319//U.S. Army Medical Department Center and School/ ; },
abstract = {BACKGROUND: The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood.

METHODS: The 16S rRNA gene of subgingival plaque in 1219 women, aged 53-81 years, was sequenced and its taxonomy annotated against the Human Oral Microbiome Database (v.14.5). Composition of the subgingival microbiome was described in terms of centered log(2)-ratio (CLR) transformed OTU values, relative abundance, and prevalence. Correlations between microbiota abundance and age were evelauted using Pearson Product Moment correlations. P-values were corrected for multiple testing using the Bonferroni method.

RESULTS: Of the 267 species identified overall, Veillonella dispar was the most abundant bacteria when described by CLR OTU (mean 8.3) or relative abundance (mean 8.9%); whereas Streptococcus oralis, Veillonella dispar and Veillonella parvula were most prevalent (100%, all) when described as being present at any amount. Linear correlations between age and several CLR OTUs (Pearson r = - 0.18 to 0.18), of which 82 (31%) achieved statistical significance (P < 0.05). The correlations lost significance following Bonferroni correction. Twelve species that differed across age groups (each corrected P < 0.05); 5 (42%) were higher in women ages 50-59 compared to ≥70 (corrected P < 0.05), and 7 (48%) were higher in women 70 years and older.

CONCLUSIONS: We identified associations between several bacterial species and age across the age range of postmenopausal women studied. Understanding the functions of these bacteria could identify intervention targets to enhance oral health in later life.},
}

@article {pmid31722669,
year = {2019},
author = {Sauvage, T and Schmidt, WE and Yoon, HS and Paul, VJ and Fredericq, S},
title = {Promising prospects of nanopore sequencing for algal hologenomics and structural variation discovery.},
journal = {BMC genomics},
volume = {20},
number = {1},
pages = {850},
doi = {10.1186/s12864-019-6248-2},
pmid = {31722669},
issn = {1471-2164},
support = {GIAR 2013&2014//Phycological Society of America/ ; },
abstract = {BACKGROUND: The MinION Access Program (MAP, 2014-2016) allowed selected users to test the prospects of long nanopore reads for diverse organisms and applications through the rapid development of improving chemistries. In 2014, faced with a fragmented Illumina assembly for the chloroplast genome of the green algal holobiont Caulerpa ashmeadii, we applied to the MAP to test the prospects of nanopore reads to investigate such intricacies, as well as further explore the hologenome of this species with native and hybrid approaches.

RESULTS: The chloroplast genome could only be resolved as a circular molecule in nanopore assemblies, which also revealed structural variants (i.e. chloroplast polymorphism or heteroplasmy). Signal and Illumina polishing of nanopore-assembled organelle genomes (chloroplast and mitochondrion) reflected the importance of coverage on final quality and current limitations. In hybrid assembly, our modest nanopore data sets showed encouraging results to improve assembly length, contiguity, repeat content, and binning of the larger nuclear and bacterial genomes. Profiling of the holobiont with nanopore or Illumina data unveiled a dominant Rhodospirillaceae (Alphaproteobacteria) species among six putative endosymbionts. While very fragmented, the cumulative hybrid assembly length of C. ashmeadii's nuclear genome reached 24.4 Mbp, including 2.1 Mbp in repeat, ranging closely with GenomeScope's estimate (> 26.3 Mbp, including 4.8 Mbp in repeat).

CONCLUSION: Our findings relying on a very modest number of nanopore R9 reads as compared to current output with newer chemistries demonstrate the promising prospects of the technology for the assembly and profiling of an algal hologenome and resolution of structural variation. The discovery of polymorphic 'chlorotypes' in C. ashmeadii, most likely mediated by homing endonucleases and/or retrohoming by reverse transcriptases, represents the first report of chloroplast heteroplasmy in the siphonous green algae. Improving contiguity of C. ashmeadii's nuclear and bacterial genomes will require deeper nanopore sequencing to greatly increase the coverage of these larger genomic compartments.},
}

@article {pmid31722384,
year = {2019},
author = {Landesman, WJ and Mulder, K and Fredericks, LP and Allan, BF},
title = {Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {12},
pages = {},
doi = {10.1093/femsec/fiz167},
pmid = {31722384},
issn = {1574-6941},
abstract = {The tick microbiota may influence the colonization of Ixodes scapularis by Borrelia burgdorferi, the Lyme disease bacterium. Using conserved and pathogen-specific primers we performed a cross-kingdom analysis of bacterial, fungal, protistan and archaeal communities of I. scapularis nymphs (N = 105) collected from southern Vermont, USA. The bacterial community was dominated by a Rickettsia and several environmental taxa commonly reported in I. scapularis, as well as the human pathogens B. burgdorferi and Anaplasma phagocytophilum, agent of human granulocytic anaplasmosis. With the fungal primer set we detected primarily plant- and litter-associated taxa and >18% of sequences were Malassezia, a fungal genus associated with mammalian skin. Two 18S rRNA gene primer sets, intended to target protistan communities, returned mostly Ixodes DNA as well as the wildlife pathogen Babesia odocoilei (7% of samples), a Gregarines species (14%) and a Spirurida nematode (18%). Data from pathogen-specific and conserved primers were consistent in terms of prevalence and identification. We measured B. burgdorferi presence/absence and load and found that bacterial beta diversity varied based on B. burgdorferi presence/absence. Load was weakly associated with bacterial community composition. We identified taxa associated with B. burgdorferi infection that should be evaluated for their role in vector colonization by pathogens.},
}

@article {pmid31722343,
year = {2019},
author = {Flowers, SA and Ward, KM and Clark, CT},
title = {The Gut Microbiome in Bipolar Disorder and Pharmacotherapy Management.},
journal = {Neuropsychobiology},
volume = {},
number = {},
pages = {1-7},
doi = {10.1159/000504496},
pmid = {31722343},
issn = {1423-0224},
abstract = {The gut microbiome is a complex and dynamic community of commensal, symbiotic, and pathogenic microorganisms that exist in a bidirectional relationship with the host. Bacterial functions in the gut play a critical role in healthy host functioning, and its disruption can contribute to many medical conditions. The relationship between gut microbiota and the brain has gained attention in mental health due to the mounting evidence supporting the association of gut bacteria with mood and behavior. Patients with bipolar disorder exhibit an increased frequency of gastrointestinal illnesses such as inflammatory bowel disease, which mechanistically has been linked to microbial community function. While the heterogeneity in microbial communities between individuals might be associated with disease risk, it may also moderate the efficacy or adverse effects associated with the use of medication. The following review highlights published evidence linking the function of gut microbiota both to bipolar disorder risk and to the effect of medications that influence microbiota, inflammation, and mood symptoms.},
}

@article {pmid31722195,
year = {2019},
author = {Hertel, J and Harms, AC and Heinken, A and Baldini, F and Thinnes, CC and Glaab, E and Vasco, DA and Pietzner, M and Stewart, ID and Wareham, NJ and Langenberg, C and Trenkwalder, C and Krüger, R and Hankemeier, T and Fleming, RMT and Mollenhauer, B and Thiele, I},
title = {Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease.},
journal = {Cell reports},
volume = {29},
number = {7},
pages = {1767-1777.e8},
doi = {10.1016/j.celrep.2019.10.035},
pmid = {31722195},
issn = {2211-1247},
abstract = {Parkinson's disease (PD) exhibits systemic effects on the human metabolism, with emerging roles for the gut microbiome. Here, we integrate longitudinal metabolome data from 30 drug-naive, de novo PD patients and 30 matched controls with constraint-based modeling of gut microbial communities derived from an independent, drug-naive PD cohort, and prospective data from the general population. Our key results are (1) longitudinal trajectory of metabolites associated with the interconversion of methionine and cysteine via cystathionine differed between PD patients and controls; (2) dopaminergic medication showed strong lipidomic signatures; (3) taurine-conjugated bile acids correlated with the severity of motor symptoms, while low levels of sulfated taurolithocholate were associated with PD incidence in the general population; and (4) computational modeling predicted changes in sulfur metabolism, driven by A. muciniphila and B. wadsworthia, which is consistent with the changed metabolome. The multi-omics integration reveals PD-specific patterns in microbial-host sulfur co-metabolism that may contribute to PD severity.},
}

@article {pmid31722138,
year = {2019},
author = {Ivashkin, VT and Kashukh, YA},
title = {[Impact of L-carnitine and phosphatidylcholine containing products on the proatherogenic metabolite TMAO production and gut microbiome changes in patients with coronary artery disease].},
journal = {Voprosy pitaniia},
volume = {88},
number = {4},
pages = {25-33},
doi = {10.24411/0042-8833-2019-10038},
pmid = {31722138},
issn = {0042-8833},
abstract = {The aim of the study was to assess the impact of L-carnitine and phosphatidylcholine containing products on the production of the proatherogenic metabolite TMAO and gut microbiome changes in patients with coronary artery disease (CAD). Material and methods. The study consisted of 2 parts. In the first part, a comparison was made between the diet of patients with CAD (n=29) and healthy volunteers (n=30) over the age of 50 with respect to the frequency of intake of L-carnitine and phosphatidylcholine containing products. All participants underwent blood sampling and stool tests to assess the concentration of TMAO and the composition of fecal microflora. The second part of the study was dedicated to assessing the correlation between TMAO blood concentration in patients with CAD (n=89) and the frequency of intake of L-carnitine and phosphatidylcholine containing products. Results and discussion. Patients with CAD comparing to healthy people among the predecessor products of TMAO consumed red meat, dairy products more often, eggs and fish less often. TMAO concentration in patients with CAD was higher than in healthy volunteers (1036.4±748.2 vs 376.5±147.9 ng/ml, p=0.0001). Analysis of fecal microflora in patients with CAD revealed an increase number of bacteria from Verrucomicrobiaceae family (p<0.05) and Enterobacteriaceae family (p<0.05), of the Escherichia/Shigella genera (p<0.05), there was a trend to increased number of Ruminococcus (р=0.065), Clostridium XlV (b) genera (р=0.10). Correlation between TMAO concentration and frequency of red meat, eggs, and dairy products consumption was estimated in patients with CAD (r>0.525, р<0.05). Conclusion. Patients with CAD consume more precursors of TMAO, have higher blood TMAO concentrations compared to healthy volunteers. Fecal microflora of patients with CAD contains a greater number of gut bacteria related to trimethylamine producers compared to healthy volunteers. Reducing the number of L-carnitine and phosphatidylcholine containing products in the diet of patients with CAD may affect the decrease in the proatherogenic metabolite TMAO concentration.},
}