@article {pmid31605831,
year = {2019},
author = {Yang, Y and Pan, J and Zhou, Z and Wu, J and Liu, Y and Lin, JG and Hong, Y and Li, X and Li, M and Gu, JD},
title = {Complex microbial nitrogen-cycling networks in three distinct anammox-inoculated wastewater treatment systems.},
journal = {Water research},
volume = {168},
number = {},
pages = {115142},
doi = {10.1016/j.watres.2019.115142},
pmid = {31605831},
issn = {1879-2448},
abstract = {Microbial nitrogen removal mediated by anaerobic ammonium oxidation (anammox) are cost-effective, yet it is time-consuming to accumulate the slow-growing anammox bacteria in conventional wastewater treatment plants (WWTPs). Inoculation of anammox enriched pellets is an effective way to establish anammox and achieve shortcut nitrogen removal in full-scale WWTPs. However, little is known about the complex microbial nitrogen-cycling networks in these anammox-inoculated WWTPs. Here, we applied metagenomic and metatranscriptomic tools to study the microbial nitrogen removal in three conventional WWTPs, which have been inoculated exogenous anammox pellets, representing partial-nitrification anammox (PNA) and nitrification-denitrification nitrogen removal processes. In the PNA system of Bali (BL), ammonia was partially oxidized by ammonia-oxidizing bacteria (AOB) Nitrosomonas and the oxidized nitrite and the remaining ammonium were directly converted to N2 by anammox bacteria Ca. Brocadia and Ca. Kuenenia. In the nitrification-denitrification system of Wenshan (WS), ammonia-oxidizing archaea (AOA) Thaumarchaeota unexpectedly dominated the nitrifying community in the presence of AOB Nitrosomonas. Meanwhile, the biomass yield of Ca. Brocadia was likely inhibited by the high biodegradable organic compound input and limited by substrate competitions from AOA, AOB, complete ammonia oxidizers (comammox) Nitrospira, nitrite-oxidizing bacteria (NOB) Nitrospira, and heterotrophic denitrifiers. Unexpectedly, comammox Nitrospira was the predominant nitrifier in the presence of AOB Nitrosomonas in the organic carbon-rich nitrification-denitrification system of Linkou (LK). These results clearly showed that distinct active groups were working in concert for an effective nitrogen removal in different WWTPs. This study confirmed the feasibility of anammox application in ammonium-rich systems by direct inoculation of the exogenous anammox pellets and improved our understanding of microbial nitrogen cycling in anammox-driven conventional WWTPs from both physiochemical and omics perspectives.},
}

@article {pmid31605691,
year = {2019},
author = {Dubinsky, V and Reshef, L and Bar, N and Keizer, D and Golan, N and Rabinowitz, K and Godny, L and Yadgar, K and Zonensain, K and Tulchinsky, H and Gophna, U and Dotan, I},
title = {Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.10.001},
pmid = {31605691},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis.

METHODS: We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center in Israel. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent acute pouchitis (n=6), chronic pouchitis and Crohn's-like disease of the pouch (n=27), normal pouch from patient with ulcerative colitis (n=10), and normal pouch from patient with familial adenomatous polyposis (n=6). Fecal samples (n=234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by human intestinal epithelial cells HT-29.

RESULTS: Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics. However, 89% of those who completed a 4-weeks course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae but also beneficial species such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to non-related antibiotics including extended-spectrum beta-lactamases.

CONCLUSIONS: The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.},
}

@article {pmid31605240,
year = {2019},
author = {Kayser, BD and Prifti, E and Lhomme, M and Belda, E and Dao, MC and Aron-Wisnewsky, J and , and Kontush, A and Zucker, JD and Rizkalla, SW and Dugail, I and Clément, K},
title = {Elevated serum ceramides are linked with obesity-associated gut dysbiosis and impaired glucose metabolism.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {15},
number = {11},
pages = {140},
doi = {10.1007/s11306-019-1596-0},
pmid = {31605240},
issn = {1573-3890},
support = {ANR MICRO-Obes//Agence Nationale de la Recherche/ ; HEALTH-F4-2012-305312//Seventh Framework Program/ ; 634413//Horizon 2020/ ; Albert Renold//European Foundation for the Study of Diabetes/ ; },
abstract = {INTRODUCTION: Low gut microbiome richness is associated with dyslipidemia and insulin resistance, and ceramides and other sphingolipids are implicated in the development of diabetes.

OBJECTIVES: Determine whether circulating sphingolipids, particularly ceramides, are associated with alterations in the gut microbiome among obese patients with increased diabetes risk.

METHODS: This was a cross-sectional and longitudinal retrospective analysis of a dietary/weight loss intervention. Fasted serum was collected from 49 participants (41 women) and analyzed by HPLC-MS/MS to quantify 45 sphingolipids. Shotgun metagenomic sequencing of stool was performed to profile the gut microbiome.

RESULTS: Confirming the link to deteriorated glucose homeostasis, serum ceramides were positively correlated with fasting glucose, but inversely correlated with fasting and OGTT-derived measures of insulin sensitivity and β-cell function. Significant associations with gut dysbiosis were demonstrated, with SM and ceramides being inversely correlated with gene richness. Ceramides with fatty acid chain lengths of 20-24 carbons were the most associated with low richness. Diet-induced weight loss, which improved gene richness, decreased most sphingolipids. Thirty-one MGS, mostly corresponding to unidentified bacteria species, were inversely correlated with ceramides, including a number of Bifidobacterium and Methanobrevibacter smithii. Higher ceramide levels were also associated with increased metagenomic modules for lipopolysaccharide synthesis and flagellan synthesis, two pathogen-associated molecular patterns, and decreased enrichment of genes involved in methanogenesis and bile acid metabolism.

CONCLUSION: This study identifies an association between gut microbiota richness, ceramides, and diabetes risk in overweight/obese humans, and suggests that the gut microbiota may contribute to dysregulation of lipid metabolism in metabolic disorders.},
}

@article {pmid31602443,
year = {2019},
author = {Li, Q and Chen, H and Zhang, M and Wu, T and Liu, R},
title = {Altered short chain fatty acid profiles induced by dietary fiber intervention regulate AMPK levels and intestinal homeostasis.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/c9fo01465a},
pmid = {31602443},
issn = {2042-650X},
abstract = {The objective of this study was to investigate the effects of dietary intervention on intestinal microbiota-mediated change in short chain fatty acid (SCFA) profile and intestinal homeostasis. Sequencing of the 16S rDNA of gut bacteria, metagenomics, intestinal epithelial transcriptomics, and metabonomics were conducted. Results showed that the dietary interventions altered the microbiota composition of cecal digesta, microbiota-mediated metabolism, and the gene expression profile in intestinal epithelial cells. Compared with red meat-diet-fed mice, fiber-diet-fed mice presented a shift in the gut microbiome toward increased production of butanoate, which was accompanied by up-regulation of microbiota- and AMP-activated protein kinase (AMPK)-dependent gene expression and decrease in serum concentrations of trimethylamine N-oxide (TMAO), triglyceride (TG) and glucose (GLU). The results suggested a new regulatory mechanism via which butanoate and AMPK activation contributed to intestinal integrity and homeostasis by affecting metabolism, intestinal barrier function and transporter expression.},
}

@article {pmid31601060,
year = {2019},
author = {Reddy, KE and Kim, HR and Jeong, JY and So, KM and Lee, S and Ji, SY and Kim, M and Lee, HJ and Lee, S and Kim, KH and Kim, M},
title = {Impact of breed on the fecal microbiome of dogs under the same dietary condition.},
journal = {Journal of microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.4014/jmb.1906.06048},
pmid = {31601060},
issn = {1738-8872},
abstract = {The gut microbiome influences the health and well-being of dogs. However, little is known about the impact of breed on the fecal microbiome composition in dogs. Therefore, we aimed to investigate the differences in the fecal microbiome in three breeds of dog fed and housed under the same conditions, namely eight Maltese (8.0 ± 0.1 years), eight Miniature Schnauzer (8.0 ± 0.0 years), and nine Poodle dogs (8.0 ± 0.0 years). Fresh fecal samples were collected from the dogs and used to extract metagenomic DNA. The composition of the fecal microbiome was evaluated by 16S rRNA gene amplicon sequencing on the MiSeq platform. A total of 840,501 sequences were obtained from the 25 fecal samples and classified as Firmicutes (32.3-97.3% of the total sequences), Bacteroidetes (0.1-62.6%), Actinobacteria (0.2-14.7%), Fusobacteria (0.0-5.7%), and Proteobacteria (0.0-5.1%). The relative abundance of Firmicutes was significantly lower in the Maltese dog breed than that in the other two breeds, while that of Fusobacteria was significantly higher in the Maltese than in the Miniature Schnauzer breed. At the genus level, the relative abundance of Streptococcus, Fusobacterium, Turicibacter, Succinivibrio, and Anaerobiospirillum differed significantly among the three dog breeds. These genera had no correlation with age, diet, sex, body weight, vaccination history, or parasite protection history. Within a breed, some of these genera had a correlation with at least one blood chemistry value. This study indicates that the composition of the fecal microbiome in dogs is affected by breed.},
}

@article {pmid31600863,
year = {2019},
author = {Li, Y and Tremblay, J and Bainard, LD and Cade-Menun, B and Hamel, C},
title = {Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14824},
pmid = {31600863},
issn = {1462-2920},
abstract = {Soil microorganisms play a critical role in the biosphere, and the influence of cropland fertilization on the evolution of soil as a living entity is being actively documented. In this study, we used a shotgun metagenomics approach to globally expose the effects of 50-year N and P fertilization of wheat on soil microbial community structure and function, and their potential involvement in overall N cycling. Nitrogen (N) fertilization increased alpha diversity in archaea and fungi while reducing it in bacteria. Beta diversity of archaea, bacteria, and fungi, as well as soil function, were also mainly driven by N fertilization. The abundance of archaea was negatively impacted by N fertilization while bacterial and fungal abundance was increased. The responses of N-metabolism-related genes to fertilization differed in archaea, bacteria, and fungi. All archaeal N metabolic processes were decreased by N fertilization, while denitrification, assimilatory nitrate reduction and organic-N metabolism were highly increased by N fertilization in bacteria. Nitrate assimilation was the main contribution of fungi to N cycling. Thaumarchaeota and Halobacteria in archaea; Actinobacteria, alpha-, beta-, gamma-, and delta Proteobacteria in bacteria; and Sordariomycetes in fungi participated dominantly and widely in soil N metabolic processes. This article is protected by copyright. All rights reserved.},
}

@article {pmid31600862,
year = {2019},
author = {Martín-Cabello, G and Terrón-González, L and Ferrer, M and Santero, E},
title = {Identification of a complete dibenzothiophene biodesulfurization operon and its regulator by functional metagenomics.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14823},
pmid = {31600862},
issn = {1462-2920},
abstract = {Functional screening for aromatic oxygenases ring of an oil contaminated soil metagenome identified 25 different clones bearing monooxygenases coding genes. One fosmid bore an operon containing 4 tightly linked genes coding for a complete dibenzothiophene biodesulfurization pathway, which included the predicted monooxygenases DszC and DszA, the desulfinase DszB, and an FMN-oxidoreductase designated DszE. The dszEABC operon provided E. coli with the ability to use dibenzothiophene as the only sulfur source. Transcription of the operon is driven from a σN -dependent promoter and regulated by an activator that was designated dszR. DszR has been purified and characterized in vitro, and shown to be a constitutively activeσN -dependent activator of the group IV, which binds to two contiguous sequences located upstream of the promoter. The dsz promoter, and dszE and dszR genes have apparently been recruited from an aliphatic sulfonate biodegradation pathway. If transcribed from a heterologous upstream promoter, the σN -dependent promoter region functions as an 'insulator' that prevents translation of dszE,, by binding with its ribosome binding site. Translational coupling, in turn, prevents translation of the downstream dszABC genes. The silencer combined with translational coupling thus represent an effective way of preventing expression of operons when spuriously transcribed from upstream promoters. This article is protected by copyright. All rights reserved.},
}

@article {pmid31600845,
year = {2019},
author = {Zeng, Y and Chen, S and Fu, Y and Wu, W and Chen, T and Chen, J and Yang, B and Ou, Q},
title = {Gut microbiota dysbiosis in patients with hepatitis B virus-induced chronic liver disease covering chronic hepatitis, liver cirrhosis and hepatocellular carcinoma.},
journal = {Journal of viral hepatitis},
volume = {},
number = {},
pages = {},
doi = {10.1111/jvh.13216},
pmid = {31600845},
issn = {1365-2893},
abstract = {The information regarding the effect of hepatitis B virus (HBV) infection on gut microbiota and the relationship between gut microbiota dysbiosis and hepatitis B virus-induced chronic liver disease (HBVCLD) is limited. In this study, we aimed at characterizing the gut microbiota composition in the three different stages of hepatitis B virus-induced chronic liver disease patients and healthy individuals. Fecal samples and clinical data were collected from HBVCLD patients and healthy individuals. The 16S rDNA gene amplification products were sequenced. Bioinformatic analysis including alpha-diversity, PICRUSt, etc. was performed. A total of 19 phyla, 43 classes, 72 orders, 126 families, and 225 genera were detected. The beta-diversity showed a separate clustering of healthy controls and HBVCLD patients covering chronic hepatitis (CHB), liver cirrhosis (LC), and hepatocellular carcinoma (HCC); and gut microbiota of healthy controls were more consistent, whereas those of CHB, LC and HCC varied substantially. The abundance of Firmicutes was lower, and Bacteroidetes was higher in patients with CHB, LC, and HCC than in healthy controls. Predicted metagenomics of microbial communities showed an increase in glycan biosynthesis and metabolism-related genes and lipid metabolism-related genes in HBVCLD than in healthy individuals. Our study suggested that HBVCLD is associated with gut dysbiosis, with characteristics including, a gain in potential bacteria and a loss in potential beneficial bacteria or genes. Further study of CHB, LC, and HCC based on microbiota may provide a novel insight into the pathogenesis of HBVCLD as well as a novel treatment strategy.},
}

@article {pmid31600627,
year = {2019},
author = {Roshanzadeh, A and Kang, H and You, SH and Park, J and Khoa, ND and Lee, DH and Kim, GJ and Kim, ES},
title = {Real-time monitoring of NADPH levels in living mammalian cells using fluorescence-enhancing protein bound to NADPHs.},
journal = {Biosensors & bioelectronics},
volume = {146},
number = {},
pages = {111753},
doi = {10.1016/j.bios.2019.111753},
pmid = {31600627},
issn = {1873-4235},
abstract = {Nicotinamide adenine nucleotide phosphate (NADPH) has been known to be involved in the multiple pathways of cell metabolism. However, conventional quantification assays for NADPH have required breaking down the cell membranes of around one million cells per assay, and monitoring NADPH flux in living cells has been limited by a few available tools. Here, we visualized NADPH levels in human cervical cancer cells HeLa using metagenome-derived blue fluorescent protein (mBFP), which specifically binds to NADPH and enhances the intrinsic fluorescence of NADPH up to 10-fold when imaged by two-photon microscopy to reduce photodamage. Adding an oxidizing agent such as diamide to HeLa cells that expressed mBFP led to an immediate decrease of intracellular NADPH depending on glucose availability in culture media. Furthermore, inhibiting glucose-6-phosphate dehydrogenase (G6PD) in the pentose phosphate pathway with dehydroandrosterone (DHEA) and knockdown of G6PD transcripts gradually decreased NADPH when diamide was added to living cells. These results demonstrate that introducing a bacterial mBFP gene into mammalian cells is a straightforward approach to monitoring intracellular NADPH flux in real time at the single-cell level. Moreover, this strategy can be expanded to tracking the spatio-temporal changes in NADPH even in single-cell organelles such as mitochondria and chloroplasts, which will allow us to more precisely assess the efficacy of biochemically or biophysically metabolic perturbations in animal and plant cells.},
}

@article {pmid31600503,
year = {2019},
author = {Shkoporov, AN and Clooney, AG and Sutton, TDS and Ryan, FJ and Daly, KM and Nolan, JA and McDonnell, SA and Khokhlova, EV and Draper, LA and Forde, A and Guerin, E and Velayudhan, V and Ross, RP and Hill, C},
title = {The Human Gut Virome Is Highly Diverse, Stable, and Individual Specific.},
journal = {Cell host & microbe},
volume = {26},
number = {4},
pages = {527-541.e5},
doi = {10.1016/j.chom.2019.09.009},
pmid = {31600503},
issn = {1934-6069},
abstract = {The human gut contains a vast array of viruses, mostly bacteriophages. The majority remain uncharacterized, and their roles in shaping the gut microbiome and in impacting on human health remain poorly understood. We performed longitudinal metagenomic analysis of fecal viruses in healthy adults that reveal high temporal stability, individual specificity, and correlation with the bacterial microbiome. Using a database-independent approach that uses most of the sequencing data, we uncovered the existence of a stable, numerically predominant individual-specific persistent personal virome. Clustering of viral genomes and de novo taxonomic annotation identified several groups of crAss-like and Microviridae bacteriophages as the most stable colonizers of the human gut. CRISPR-based host prediction highlighted connections between these stable viral communities and highly predominant gut bacterial taxa such as Bacteroides, Prevotella, and Faecalibacterium. This study provides insights into the structure of the human gut virome and serves as an important baseline for hypothesis-driven research.},
}

@article {pmid31600207,
year = {2019},
author = {Hendriksen, RS and Lukjancenko, O and Munk, P and Hjelmsø, MH and Verani, JR and Ng'eno, E and Bigogo, G and Kiplangat, S and Oumar, T and Bergmark, L and Röder, T and Neatherlin, JC and Clayton, O and Hald, T and Karlsmose, S and Pamp, SJ and Fields, B and Montgomery, JM and Aarestrup, FM},
title = {Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0222531},
doi = {10.1371/journal.pone.0222531},
pmid = {31600207},
issn = {1932-6203},
abstract = {BACKGROUND: Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.

METHOD: We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance.

RESULTS: A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time.

CONCLUSION: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.},
}

@article {pmid31599546,
year = {2019},
author = {Tassoni, L and Zamperin, G and Schiavon, E and Vendramin, V and Cavicchio, L and Mion, M and Tonon, FT and Monne, I and Beato, MS},
title = {First whole genome characterization of porcine astrovirus detected in swine faeces in Italy.},
journal = {Veterinaria italiana},
volume = {55},
number = {3},
pages = {221-229},
doi = {10.12834/VetIt.1873.9956.1},
pmid = {31599546},
issn = {1828-1427},
abstract = {Porcine astroviruses (PoAstV) are found in the gastrointestinal tract of healthy and diseased pigs worldwide. However, their role in causing enteric disease in pigs and other animals has not been elucidated. In the present report, we describe for the first time in Italy, the identification and genetic characterization, through whole genome sequencing, of a PoAstV2 in pigs in Northeast Italy in 2015. This instance is the first detection of PoAstV2 in pigs in Italy. The phylogenetic analysis of the complete ORF2 segment highlights the high similarity of this virus to those circulating that same year in Japan. There are very few full astrovirus genomes available, and the present data represent an important contribution towards a better understanding of the characteristics and evolution of these viruses.},
}

@article {pmid31598844,
year = {2019},
author = {Shi, N and Yang, G and Wang, P and Wang, Y and Yu, D and Huang, B},
title = {Complete genome sequence of a novel partitivirus from the entomogenous fungus Beauveria bassiana in China.},
journal = {Archives of virology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00705-019-04428-1},
pmid = {31598844},
issn = {1432-8798},
support = {31772226//National Natural Science Foundation of China/ ; 31471821//National Natural Science Foundation of China/ ; 30770008//National Natural Science Foundation of China/ ; },
abstract = {In this study, we report a novel double-stranded RNA (dsRNA) virus, Beauveria bassiana partitivirus 3 (BbPV-3), derived from the entomogenous fungus Beauveria bassiana isolate RCEF5853 from China. The genome of BbPV-3, whose sequence was determined by metagenomic sequencing, RT-PCR, and RACE cloning, comprises two dsRNA genome segments that are 1,856 and 1,719 bp long. The first segment contains a single ORF (ORF-1) encoding a 584-amino-acid-long protein (66.05 kDa) with a conserved RNA-dependent RNA polymerase (RdRp) motif. The second segment also has a single ORF (ORF-2) encoding a 500-amino-acid-long coat protein (CP) (55.9 kDa). The CP and RdRp sequences showed highest identity of 43.4% and 60.2%, respectively, to those of Colletotrichum eremochloae partitivirus 1. Phylogenetic analysis of the RdRp domain of the polyprotein revealed that BbPV-3 grouped together with the members of the genus Epsilonpartitivirus. Hence, we proposed that Beauveria bassiana partitivirus 3 is a novel member of the proposed genus Epsilonpartitivirus.},
}

@article {pmid31597769,
year = {2019},
author = {Ma, Y and Marais, A and Lefebvre, M and Theil, S and Svanella-Dumas, L and Faure, C and Candresse, T},
title = {Phytovirome Analysis of Wild Plant Populations: Comparison of Double-Stranded RNA and Virion-Associated Nucleic Acid Metagenomic Approaches.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {},
doi = {10.1128/JVI.01462-19},
pmid = {31597769},
issn = {1098-5514},
abstract = {Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components of ecosystems, there is a need to explore the diversity and richness of the viruses associated with plant populations and to understand the drivers shaping their diversity in space and time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) and Virion-associated nucleic acids (VANA), have been used and compared here for the description of the virome of complex plant pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. A novel bioinformatics strategy was used to assess viral richness not only at family level but also by determining Operational Taxonomic Units (OTU) following the clustering of conserved viral domains. A large viral diversity, dominated by novel dsRNA viruses was detected in all sites while a large between sites variability limited the ability to draw clear conclusion on the impact of cultivation. A trend for a higher diversity of dsRNA viruses was nevertheless detected in unmanaged sites (118 vs 77 unique OTUs). The dsRNA-based approach consistently revealed a broader and more comprehensive diversity for RNA viruses than the VANA approach, whatever the assessment criterion. In addition, dissimilarity analyses indicated both approaches to be largely reproducible, but not necessarily convergent. These findings illustrate features of phytoviromes in various ecosystems and a novel strategy for precise virus richness estimation. These results allow to reason methodological choices in phytovirome studies and, likely in other viromes study where RNA viruses are the focal taxa.IMPORTANCE There are today significant knowledge gaps on phytovirus populations and on the drivers impacting them, but also on the comparative performance methodological approaches for their study. We used and compared two viral sequences enrichment approaches, double-stranded RNAs (dsRNA) and virion-associated nucleic acids (VANA) for phytovirome description in complex pools representative of the most prevalent plant species in unmanaged and cultivated ecosystems. Viral richness was assessed by determining Operational Taxonomic Units (OTU) following the clustering of conserved viral domains. There is some limited evidence of an impact of cultivation on viral populations. These results provide data allowing to reason the methodological choices in virome studies. For researchers primarily interested in RNA viruses, the dsRNA approach is advised because it consistently provided a more comprehensive description of the analysed phytoviromes, but it understandably underrepresented DNA viruses and bacteriophages.},
}

@article {pmid31597568,
year = {2019},
author = {Peters, BA and Wilson, M and Moran, U and Pavlick, A and Izsak, A and Wechter, T and Weber, JS and Osman, I and Ahn, J},
title = {Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients.},
journal = {Genome medicine},
volume = {11},
number = {1},
pages = {61},
doi = {10.1186/s13073-019-0672-4},
pmid = {31597568},
issn = {1756-994X},
support = {P50CA225450/CA/NCI NIH HHS/United States ; P30CA016087/CA/NCI NIH HHS/United States ; R01CA164964/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Recent evidence suggests that immunotherapy efficacy in melanoma is modulated by gut microbiota. Few studies have examined this phenomenon in humans, and none have incorporated metatranscriptomics, important for determining expression of metagenomic functions in the microbial community.

METHODS: In melanoma patients undergoing immunotherapy, gut microbiome was characterized in pre-treatment stool using 16S rRNA gene and shotgun metagenome sequencing (n = 27). Transcriptional expression of metagenomic pathways was confirmed with metatranscriptome sequencing in a subset of 17. We examined associations of taxa and metagenomic pathways with progression-free survival (PFS) using 500 × 10-fold cross-validated elastic-net penalized Cox regression.

RESULTS: Higher microbial community richness was associated with longer PFS in 16S and shotgun data (p < 0.05). Clustering based on overall microbiome composition divided patients into three groups with differing PFS; the low-risk group had 99% lower risk of progression than the high-risk group at any time during follow-up (p = 0.002). Among the species selected in regression, abundance of Bacteroides ovatus, Bacteroides dorei, Bacteroides massiliensis, Ruminococcus gnavus, and Blautia producta were related to shorter PFS, and Faecalibacterium prausnitzii, Coprococcus eutactus, Prevotella stercorea, Streptococcus sanguinis, Streptococcus anginosus, and Lachnospiraceae bacterium 3 1 46FAA to longer PFS. Metagenomic functions related to PFS that had correlated metatranscriptomic expression included risk-associated pathways of L-rhamnose degradation, guanosine nucleotide biosynthesis, and B vitamin biosynthesis.

CONCLUSIONS: This work adds to the growing evidence that gut microbiota are related to immunotherapy outcomes, and identifies, for the first time, transcriptionally expressed metagenomic pathways related to PFS. Further research is warranted on microbial therapeutic targets to improve immunotherapy outcomes.},
}

@article {pmid31597472,
year = {2019},
author = {Dreisbach, C and Prescott, S and Alhusen, J},
title = {Influence of Maternal Prepregnancy Obesity and Excessive Gestational Weight Gain on Maternal and Child Gastrointestinal Microbiome Composition: A Systematic Review.},
journal = {Biological research for nursing},
volume = {},
number = {},
pages = {1099800419880615},
doi = {10.1177/1099800419880615},
pmid = {31597472},
issn = {1552-4175},
abstract = {BACKGROUND: Maternal obesity is a well-known risk factor for significant obstetric and neonatal complications. The influence of the gastrointestinal microbiome in the setting of maternal obesity during pregnancy is less understood. The purpose of this systematic review is to synthesize the literature on the relationships between maternal obesity and excessive gestational weight gain (EGWG) and the composition of maternal and child gastrointestinal microbiomes.

METHOD: We searched CINHAL, OVID Medline, Web of Science, and PubMed for relevant literature using medical subject heading terms related to obesity, pregnancy, and the gastrointestinal microbiome. We assessed 249 articles for potential inclusion using the preferred reporting items for systematic review and meta-analyses framework and deemed 11 articles as relevant for this review.

RESULTS: Maternal obesity was associated with significant microbial changes in both maternal and infant fecal microbiome biospecimens including increases in Bacteroidetes, Firmicutes, and the Actinobacteria phyla and decreases in Bifidobacteria. However, inconsistencies in uniform taxonomic results across all studies mean that evidence of specific microbial associations with obesity and EGWG is inconclusive.

CONCLUSION: Our findings suggest that both maternal and child gastrointestinal microbiome composition is altered in the setting of maternal obesity and EGWG during pregnancy. Future microbiome studies should concentrate on the investigation of metagenomic sequencing to elucidate microbial function rather than solely taxonomic composition. More diverse populations of mothers should be sampled to address health disparities and adverse outcomes of underrepresented populations. Finally, analytic pipelines should be standardized across studies to aid in reproducibility.},
}

@article {pmid31482204,
year = {2019},
author = {Chatterjee, A and Kondabagil, K},
title = {Giant viral genomic signatures in the previously reported gut metagenomes of pre-school children in rural India.},
journal = {Archives of virology},
volume = {164},
number = {11},
pages = {2819-2822},
doi = {10.1007/s00705-019-04387-7},
pmid = {31482204},
issn = {1432-8798},
mesh = {Bacteriophages/*genetics ; Child, Preschool ; Drug Resistance, Microbial/genetics ; Enterobacter/genetics ; Escherichia/virology ; Gastrointestinal Microbiome/*genetics ; Genome, Viral/*genetics ; Giant Viruses/*genetics/isolation & purification ; Humans ; India ; Interspersed Repetitive Sequences/genetics ; Metagenome/*genetics ; Salmonella/virology ; Shigella/virology ; },
abstract = {A recent study by Ghosh et al. compared the gut microbiomes of 20 preschool children from India and found an association between the gut microbiome and the nutritional status of the child. Here, we explored these metagenomes for the presence of genomic signatures of prokaryotic and eukaryotic viruses. Several of the viral signatures found in all 20 metagenomes belonged to giant viruses (GVs). In addition, we found hits for bacteriophages to several major human pathogens, including Shigella, Salmonella, Escherichia, and Enterobacter. Concurrently, we also detected several antibiotic resistance genes (ARGs) in the metagenomes. All of the ARGs detected in this study (beta-lactam, macrolide, metronidazole, and tetracycline) are associated with mobile genetic elements (MGEs) and have been reported to cause high levels of resistance to their respective antibiotics. Despite recent reports of giant viruses and their genomic signatures in gut microbiota, their role in human physiology remains poorly understood. The effect of cooccurrence of ARGs and GVs in the gut needs further investigation.},
}

Bacteriophages/*genetics
Child, Preschool
Drug Resistance, Microbial/genetics
Enterobacter/genetics
Escherichia/virology
Gastrointestinal Microbiome/*genetics
Genome, Viral/*genetics
Giant Viruses/*genetics/isolation & purification
Humans
India
Interspersed Repetitive Sequences/genetics
Metagenome/*genetics
Salmonella/virology
Shigella/virology

@article {pmid29898804,
year = {2018},
author = {Misic, AM and Miedel, EL and Brice, AK and Cole, S and Zhang, GF and Dyer, CD and Secreto, A and Smith, AL and Danet-Desnoyers, G and Beiting, DP},
title = {Culture-independent Profiling of the Fecal Microbiome to Identify Microbial Species Associated with a Diarrheal Outbreak in Immunocompromised Mice.},
journal = {Comparative medicine},
volume = {68},
number = {4},
pages = {261-268},
pmid = {29898804},
issn = {1532-0820},
mesh = {Animals ; Diarrhea/epidemiology/*microbiology ; Disease Outbreaks ; Feces/*microbiology ; Genetic Variation ; Immunocompromised Host ; Metagenomics ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Microbiota/*genetics ; RNA, Ribosomal, 16S/chemistry ; Sequence Analysis, RNA ; Whole Genome Sequencing ; },
abstract = {Immunocompromised mice are used frequently in biomedical research, in part because they accommodate the engraftment and study of primary human cells within a mouse model; however, these animals are susceptible to opportunistic infections and require special husbandry considerations. In 2015, an outbreak marked by high morbidity but low mortality swept through a colony of immunocompromised mice; this outbreak rapidly affected 75% of the colony and ultimately required complete depopulation of the barrier suite. Conventional microbiologic and molecular diagnostics were unsuccessful in determining the cause; therefore, we explored culture-independent methods to broadly profile the microbial community in the feces of affected animals. This approach identified 4 bacterial taxa- Candidatus Arthromitus, Clostridium celatum, Clostridiales bacterium VE202-01, and Bifidobacterium pseudolongum strain PV8-2- that were significantly enriched in the affected mice. Based on these results, specific changes were made to the animal husbandry procedures for immunocompromised mice. This case report highlights the utility of culture-independent methods in laboratory animal diagnostics.},
}

Animals
Diarrhea/epidemiology/*microbiology
Disease Outbreaks
Feces/*microbiology
Genetic Variation
Immunocompromised Host
Metagenomics
Mice
Mice, Inbred NOD
Mice, SCID
Microbiota/*genetics
RNA, Ribosomal, 16S/chemistry
Sequence Analysis, RNA
Whole Genome Sequencing

@article {pmid29872090,
year = {2018},
author = {Paul, F and Otte, J and Schmitt, I and Dal Grande, F},
title = {Comparing Sanger sequencing and high-throughput metabarcoding for inferring photobiont diversity in lichens.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {8624},
pmid = {29872090},
issn = {2045-2322},
mesh = {Ascomycota/growth & development ; Chlorophyta/*classification/*genetics/growth & development ; DNA Barcoding, Taxonomic/*methods ; High-Throughput Nucleotide Sequencing/*methods ; Lichens/*growth & development ; Metagenomics/*methods ; Sequence Analysis, DNA/*methods ; Symbiosis ; },
abstract = {The implementation of HTS (high-throughput sequencing) approaches is rapidly changing our understanding of the lichen symbiosis, by uncovering high bacterial and fungal diversity, which is often host-specific. Recently, HTS methods revealed the presence of multiple photobionts inside a single thallus in several lichen species. This differs from Sanger technology, which typically yields a single, unambiguous algal sequence per individual. Here we compared HTS and Sanger methods for estimating the diversity of green algal symbionts within lichen thalli using 240 lichen individuals belonging to two species of lichen-forming fungi. According to HTS data, Sanger technology consistently yielded the most abundant photobiont sequence in the sample. However, if the second most abundant photobiont exceeded 30% of the total HTS reads in a sample, Sanger sequencing generally failed. Our results suggest that most lichen individuals in the two analyzed species, Lasallia hispanica and L. pustulata, indeed contain a single, predominant green algal photobiont. We conclude that Sanger sequencing is a valid approach to detect the dominant photobionts in lichen individuals and populations. We discuss which research areas in lichen ecology and evolution will continue to benefit from Sanger sequencing, and which areas will profit from HTS approaches to assessing symbiont diversity.},
}

Ascomycota/growth & development
Chlorophyta/*classification/*genetics/growth & development
DNA Barcoding, Taxonomic/*methods
High-Throughput Nucleotide Sequencing/*methods
Lichens/*growth & development
Metagenomics/*methods
Sequence Analysis, DNA/*methods
Symbiosis

@article {pmid29725134,
year = {2018},
author = {ElNaker, NA and Elektorowicz, M and Naddeo, V and Hasan, SW and Yousef, AF},
title = {Assessment of Microbial Community Structure and Function in Serially Passaged Wastewater Electro-Bioreactor Sludge: An Approach to Enhance Sludge Settleability.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {7013},
pmid = {29725134},
issn = {2045-2322},
mesh = {Bacteria/classification/genetics ; Biological Oxygen Demand Analysis ; Bioreactors/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Phosphorus/analysis ; Phylogeny ; Serial Passage ; Sewage/*microbiology ; Water Purification/*methods ; },
abstract = {Several studies have been carried out to understand bulking phenomena and the importance of environmental factors on sludge settling characteristics. The main objective of this study was to carry out functional characterization of microbial community structure of wastewater electro-bioreactor sludge as it undergoes serial passaging in the presence or absence of a current density over 15 days. Illumina MiSeq sequencing and QIIME were used to assess sludge microbial community shifts over time. (α) and (β) diversity analysis were conducted to assess the microbial diversity in electro-bioreactors. A phylogeny-based weighted UniFrac distance analysis was used to compare between bacterial communities while BIO-ENV trend and Spearman's rank correlation analysis were performed to investigate how reactor operational parameters correlated with bacterial community diversity. Results showed that the removal efficiency of soluble chemical oxygen demand (sCOD) ranged from 91-97%, while phosphorous (PO43--P) removal was approximately 99%. Phylogenetic analysis revealed stark differences in the development of sludge microbial communities in the control and treatment reactor. There was no mention of any studies aimed at characterizing functional microbial communities under electric field and the results communicated here are the first, to our knowledge, that address this gap in the literature.},
}

Bacteria/classification/genetics
Biological Oxygen Demand Analysis
Bioreactors/*microbiology
High-Throughput Nucleotide Sequencing
Metagenomics
*Microbiota
Phosphorus/analysis
Phylogeny
Serial Passage
Sewage/*microbiology
Water Purification/*methods

@article {pmid29725059,
year = {2018},
author = {Dittmer, J and Bouchon, D},
title = {Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {6998},
pmid = {29725059},
issn = {2045-2322},
mesh = {Animal Structures/*microbiology ; Animals ; Bacteria/classification/genetics ; Isopoda/*microbiology ; Metagenomics ; Microbial Interactions ; *Microbiota ; Wolbachia/*growth & development ; },
abstract = {Wolbachia are widespread heritable endosymbionts of arthropods notorious for their profound effects on host fitness as well as for providing protection against viruses and eukaryotic parasites, indicating that they can interact with other microorganisms sharing the same host environment. Using the terrestrial isopod crustacean Armadillidium vulgare, its highly diverse microbiota (>200 bacterial genera) and its three feminizing Wolbachia strains (wVulC, wVulM, wVulP) as a model system, the present study demonstrates that Wolbachia can even influence the composition of a diverse bacterial community under both laboratory and natural conditions. While host origin is the major determinant of the taxonomic composition of the microbiota in A. vulgare, Wolbachia infection affected both the presence and, more importantly, the abundance of many bacterial taxa within each host population, possibly due to competitive interactions. Moreover, different Wolbachia strains had different impacts on microbiota composition. As such, infection with wVulC affected a higher number of taxa than infection with wVulM, possibly due to intrinsic differences in virulence and titer between these two strains. In conclusion, this study shows that heritable endosymbionts such as Wolbachia can act as biotic factors shaping the microbiota of arthropods, with as yet unknown consequences on host fitness.},
}

Animal Structures/*microbiology
Animals
Bacteria/classification/genetics
Isopoda/*microbiology
Metagenomics
Microbial Interactions
*Microbiota
Wolbachia/*growth & development

@article {pmid31597208,
year = {2019},
author = {Berman, HL and McLaren, MR and Callahan, BJ},
title = {Understanding and Interpreting Community Sequencing Measurements of the Vaginal Microbiome.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.15978},
pmid = {31597208},
issn = {1471-0528},
abstract = {Community-wide high throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: 1) amplicon sequencing, 2) shotgun metagenomic sequencing, and 3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome.},
}

@article {pmid31596250,
year = {2019},
author = {Kaufman, JH and Elkins, CA and Davis, M and Weis, AM and Huang, BC and Mammel, MK and Patel, IR and Beck, KL and Edlund, S and Chambliss, D and Douglas, J and Bianco, S and Kunitomi, M and Weimer, BC},
title = {Insular Microbiogeography: Three Pathogens as Exemplars.},
journal = {Current issues in molecular biology},
volume = {36},
number = {},
pages = {89-108},
doi = {10.21775/cimb.036.089},
pmid = {31596250},
issn = {1467-3045},
abstract = {Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.},
}

@article {pmid31595646,
year = {2019},
author = {Strazzulli, A and Cobucci-Ponzano, B and Iacono, R and Giglio, R and Maurelli, L and Curci, N and Schiano-di-Cola, C and Santangelo, A and Contursi, P and Lombard, V and Henrissat, B and Lauro, FM and Fontes, CMGA and Moracci, M},
title = {Discovery of hyperstable carbohydrate-active enzymes through metagenomics of extreme environments.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.15080},
pmid = {31595646},
issn = {1742-4658},
abstract = {The enzymes from hyperthermophilic microorganisms populating volcanic sites represent interesting cases of protein adaptation and biotransformations under conditions where conventional enzymes quickly denature. The difficulties in cultivating extremophiles severely limit access to this class of biocatalysts. To circumvent this problem, we embarked on the exploration of the biodiversity of the solfatara Pisciarelli, Agnano (Naples, Italy) to discover hyperthermophilic carbohydrate-active enzymes (CAZymes) and to characterize the entire set of such enzymes in this environment (CAZome). Here we report the results of the metagenomic analysis of two mud/water pools that greatly differ in both temperature and pH (T=85°C and pH 5.5; T=92°C and pH 1.5, for Pool1 and Pool2, respectively). DNA deep sequencing and following in-silico analysis led to 14,934 and 17,652 complete ORFs in Pool1 and Pool2, respectively. They exclusively belonged to archaeal cells and viruses with great genera variance within the phylum Crenarcheaota, which reflected the difference in temperature and pH of the two Pools. Surprisingly, 30% and 62% of all of the reads obtained from Pool1 and 2, respectively, had no match in nucleotide databanks. Genes associated with carbohydrate metabolism were 15% and 16% of the total in the two Pools, with 278 and 308 putative CAZymes in Pool1 and 2, corresponding to ~2.0% of all ORFs. Biochemical characterization of two CAZymes of a previously unknown archaeon revealed a novel subfamily GH5_19 β-mannanase/β-1,3-glucanase whose hemicellulose specificity correlates with the vegetation surrounding the sampling site, and a novel NAD+ dependent GH109 with a previously unreported β-N-acetylglucosaminide/β-glucoside specificity.},
}

@article {pmid31594929,
year = {2019},
author = {Hua, ZS and Wang, YL and Evans, PN and Qu, YN and Goh, KM and Rao, YZ and Qi, YL and Li, YX and Huang, MJ and Jiao, JY and Chen, YT and Mao, YP and Shu, WS and Hozzein, W and Hedlund, BP and Tyson, GW and Zhang, T and Li, WJ},
title = {Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4574},
doi = {10.1038/s41467-019-12574-y},
pmid = {31594929},
issn = {2041-1723},
support = {U1201233//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31370154//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2015FY110100//Chinese Ministry of Science and Technology | Department of S and T for Social Development (Department of S&T for Social Development)/ ; },
abstract = {Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.},
}

@article {pmid31594828,
year = {2019},
author = {Sakowski, E and Uritskiy, G and Cooper, R and Gomes, M and McLaren, MR and Meisel, JS and Mickol, RL and Mintz, CD and Mongodin, EF and Pop, M and Rahman, MA and Sanchez, A and Timp, W and Vela, JD and Wolz, CM and Zackular, JP and Chopyk, J and Commichaux, S and Davis, M and Dluzen, D and Ganesan, SM and Haruna, M and Nasko, D and Regan, MJ and Sarria, S and Shah, N and Stacy, B and Taylor, D and DiRuggiero, J and Preheim, SP},
title = {Current State of and Future Opportunities for Prediction in Microbiome Research: Report from the Mid-Atlantic Microbiome Meet-up in Baltimore on 9 January 2019.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
doi = {10.1128/mSystems.00392-19},
pmid = {31594828},
issn = {2379-5077},
abstract = {Accurate predictions across multiple fields of microbiome research have far-reaching benefits to society, but there are few widely accepted quantitative tools to make accurate predictions about microbial communities and their functions. More discussion is needed about the current state of microbiome analysis and the tools required to overcome the hurdles preventing development and implementation of predictive analyses. We summarize the ideas generated by participants of the Mid-Atlantic Microbiome Meet-up in January 2019. While it was clear from the presentations that most fields have advanced beyond simple associative and descriptive analyses, most fields lack essential elements needed for the development and application of accurate microbiome predictions. Participants stressed the need for standardization, reproducibility, and accessibility of quantitative tools as key to advancing predictions in microbiome analysis. We highlight hurdles that participants identified and propose directions for future efforts that will advance the use of prediction in microbiome research.},
}

@article {pmid31594827,
year = {2019},
author = {Shan, K and Qu, H and Zhou, K and Wang, L and Zhu, C and Chen, H and Gu, Z and Cui, J and Fu, G and Li, J and Chen, H and Wang, R and Qi, Y and Chen, W and Chen, YQ},
title = {Distinct Gut Microbiota Induced by Different Fat-to-Sugar-Ratio High-Energy Diets Share Similar Pro-obesity Genetic and Metabolite Profiles in Prediabetic Mice.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
doi = {10.1128/mSystems.00219-19},
pmid = {31594827},
issn = {2379-5077},
abstract = {Gut microbiota play important roles in host metabolism, especially in diabetes. However, why different diets lead to similar diabetic states despite being associated with different microbiota is not clear. Mice were fed two high-energy diets (HED) with the same energy density but different fat-to-sugar ratios to determine the associations between the microbiota and early-stage metabolic syndrome. The two diets resulted in different microbiota but similar diabetic states. Interestingly, the microbial gene profiles were not significantly different, and many common metabolites were identified, including l-aspartic acid, cholestan-3-ol (5β, 3α), and campesterol, which have been associated with lipogenesis and inflammation. Our study suggests that different metabolic-syndrome-inducing diets may result in different microbiota but similar microbiomes and metabolomes. This suggests that the metagenome and metabolome are crucial for the prognosis and pathogenesis of obesity and metabolic syndrome.IMPORTANCE Various types of diet can lead to type 2 diabetes. The gut microbiota in type 2 diabetic patients are also different. So, two questions arise: whether there are any commonalities between gut microbiota induced by different pro-obese diets and whether these commonalities lead to disease. Here we found that high-energy diets with two different fat-to-sugar ratios can both cause obesity and prediabetes but enrich different gut microbiota. Still, these different gut microbiota have similar genetic and metabolite compositions. The microbial metabolites in common between the diets modulate lipid accumulation and macrophage inflammation in vivo and in vitro This work suggests that studies that only use 16S rRNA amplicon sequencing to determine how the microbes respond to diet and associate with diabetic state are missing vital information.},
}

@article {pmid31592756,
year = {2019},
author = {Millán-Aguiñaga, N and Soldatou, S and Brozio, S and Munnoch, JT and Howe, J and Hoskisson, PA and Duncan, KR},
title = {Awakening ancient polar Actinobacteria: diversity, evolution and specialized metabolite potential.},
journal = {Microbiology (Reading, England)},
volume = {},
number = {},
pages = {},
doi = {10.1099/mic.0.000845},
pmid = {31592756},
issn = {1465-2080},
abstract = {Polar and subpolar ecosystems are highly vulnerable to global climate change with consequences for biodiversity and community composition. Bacteria are directly impacted by future environmental change and it is therefore essential to have a better understanding of microbial communities in fluctuating ecosystems. Exploration of Polar environments, specifically sediments, represents an exciting opportunity to uncover bacterial and chemical diversity and link this to ecosystem and evolutionary parameters. In terms of specialized metabolite production, the bacterial order Actinomycetales, within the phylum Actinobacteria are unsurpassed, producing 10 000 specialized metabolites accounting for over 45 % of all bioactive microbial metabolites. A selective isolation approach focused on spore-forming Actinobacteria of 12 sediment cores from the Antarctic and sub-Arctic generated a culture collection of 50 strains. This consisted of 39 strains belonging to rare Actinomycetales genera including Microbacterium, Rhodococcus and Pseudonocardia. This study used a combination of nanopore sequencing and molecular networking to explore the community composition, culturable bacterial diversity, evolutionary relatedness and specialized metabolite potential of these strains. Metagenomic analyses using MinION sequencing was able to detect the phylum Actinobacteria across polar sediment cores at an average of 13 % of the total bacterial reads. The resulting molecular network consisted of 1652 parent ions and the lack of known metabolite identification supports the argument that Polar bacteria are likely to produce previously unreported chemistry.},
}

@article {pmid31592688,
year = {2019},
author = {Colman, DR and Lindsay, MR and Amenabar, MJ and Boyd, ES},
title = {The Intersection of Geology, Geochemistry, and Microbiology in Continental Hydrothermal Systems.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1089/ast.2018.2016},
pmid = {31592688},
issn = {1557-8070},
abstract = {Decompressional boiling of ascending hydrothermal waters and separation into a vapor (gas) and a liquid phase drive extensive variation in the geochemical composition of hot spring waters. Yet little is known of how the process of phase separation influences the distribution of microbial metabolisms in springs. Here, we determined the variation in protein coding genes in 51 metagenomes from chemosynthetic hot spring communities that span geochemical gradients in Yellowstone National Park. The 51 metagenomes could be divided into 5 distinct groups that correspond to low and high temperatures and acidic and circumneutral/alkaline springs. A fifth group primarily comprised metagenomes from springs with moderate acidity and that are influenced by elevated volcanic gas input. Protein homologs putatively involved in the oxidation of sulfur compounds, a process that leads to acidification of spring waters, in addition to those involved in the reduction of sulfur compounds were enriched in metagenomes from acidic springs sourced by vapor phase gases. Metagenomes from springs with evidence for elevated volcanic gas input were enriched in protein homologs putatively involved in oxidation of those gases, including hydrogen and methane. Finally, metagenomes from circumneutral/alkaline springs sourced by liquid phase waters were enriched in protein homologs putatively involved in heterotrophy and respiration of oxidized nitrogen compounds and oxygen. These results indicate that the geological process of phase separation shapes the ecology of thermophilic communities through its influence on the availability of nutrients in the form of gases, solutes, and minerals. Microbial acidification of hot spring waters further influences the kinetic and thermodynamic stabilities of nutrients and their bioavailability. These data therefore provide an important framework to understand how geological processes have shaped the evolutionary history of chemosynthetic thermophiles and how these organisms, in turn, have shaped their geochemical environments.},
}

@article {pmid31592568,
year = {2019},
author = {Zhang, HC and Zhang, QR and Ai, JW and Cui, P and Wu, HL and Zhang, WH and Wang, T},
title = {The role of bone marrow metagenomics next-generation sequencing to differential diagnosis among visceral leishmaniasis, histoplasmosis, and talaromycosis marneffei.},
journal = {International journal of laboratory hematology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijlh.13103},
pmid = {31592568},
issn = {1751-553X},
support = {SHDC12017104//New and Advanced Technology Project 155 of Shanghai Municipal Hospital: Application of next-generation sequencing technique 156 Ain precise diagnosis of infectious diseases/ ; },
}

@article {pmid31591719,
year = {2019},
author = {Breton, S and Jouhet, J and Guyet, U and Gros, V and Pittera, J and Demory, D and Partensky, F and Doré, H and Ratin, M and Maréchal, E and Nguyen, NA and Garczarek, L and Six, C},
title = {Unveiling membrane thermoregulation strategies in marine picocyanobacteria.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.16239},
pmid = {31591719},
issn = {1469-8137},
abstract = {The wide latitudinal distribution of marine Synechococcus cyanobacteria partly relies on the differentiation of lineages adapted to distinct thermal environments. Membranes are highly thermosensitive cell components and the ability to modulate their fluidity can be critical for the fitness of an ecotype in a particular thermal niche. We compared the thermophysiology of Synechococcus strains representative of major temperature ecotypes in the field. We measured growth, photosynthetic capacities and membrane lipidome variations. We carried out a metagenomic analysis of stations of the Tara Oceans expedition to describe the latitudinal distribution of the lipid desaturase genes in the oceans. All strains maintained efficient photosynthetic capacities over their different temperature growth ranges. Subpolar and cold temperate strains showed enhanced capacities of lipid monodesaturation at low temperature thanks to an additional, poorly regiospecific Δ9-desaturase. In contrast, tropical and warm temperate strains displayed moderate monodesaturation capacities but high proportions of double unsaturations in response to cold, thanks to regiospecific Δ12-desaturases. The desaturase genes displayed specific distributions directly related to latitudinal variations in ocean surface temperature. This study highlights the critical importance of membrane fluidity modulation by desaturases in the adaptive strategies of Synechococcus cyanobacteria during the colonization of novel thermal niches.},
}

@article {pmid31591239,
year = {2019},
author = {},
title = {Correction for Sotoudeh et al., Effects of the peer metagenomic environment on smoking behavior.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {},
number = {},
pages = {},
doi = {10.1073/pnas.1916279116},
pmid = {31591239},
issn = {1091-6490},
}

@article {pmid31589561,
year = {2019},
author = {Salah, M and Azab, M and Ramadan, A and Hanora, A},
title = {New Insights on Obesity and Diabetes from Gut Microbiome Alterations in Egyptian Adults.},
journal = {Omics : a journal of integrative biology},
volume = {23},
number = {10},
pages = {477-485},
doi = {10.1089/omi.2019.0063},
pmid = {31589561},
issn = {1557-8100},
abstract = {Obesity and diabetes are reaching epidemic levels globally. Metagenomics and microbiome science have recently emerged as new tools for studying common complex human diseases. We report in this study notable differences in gut microbiome in adult patients with obesity and diabetes in Egypt. The experimental design was based on comparisons of four study groups: (1) Controls (C) with a normal body mass index, without obesity or diabetes, (2) Obese adults (O) without diabetes, (3) adults with diabetes (D) who are not obese, and (4) Adults who are both obese and diabetic (OD). In a total study sample of 60 participants, we sequenced the 16S ribosomal RNA (rRNA) gene using the Illumina MiSeq platform. Alpha diversity analysis revealed greater diversity in bacterial communities of (D) than controls. Phylum-level analysis identified a trend for overrepresentation of Bacteroidetes (p < 0.07) in (O) and (D) than controls. The ratio of Firmicutes/Bacteroidetes (F/B) displayed a remarkable increase in (OD) than controls. At genus level, Faecalibacterium (p < 0.05) and Akkermansia (p < 0.001) distinguished (O) from controls, while Fusobacterium (p < 0.001) and Bacteroides (p < 0.001) was significantly more abundant in (OD) compared with D. Surprisingly, isoquinoline, quinone and ubiquinone alkaloid biosynthesis were overrepresented in controls compared with other three study groups. Presumably, the latter observation might potentially suggest an antihyperglycemic activity of the gut microbiota. In conclusion, the health state of the adults in our study defined the composition of the gut microbiota. Moreover, obesity and diabetes were associated with remarkably enriched populations of Firmicutes and Bacteroidetes. The abundance of Fusobacterium is worth further research and exploration as a candidate biomarker for prediabetes especially in obese individuals. The potential antihyperglycemic activity of the gut microbiota is also noteworthy for future studies in other world populations.},
}

@article {pmid31589310,
year = {2019},
author = {Ye, L and Das, P and Li, P and Ji, B and Nielsen, J},
title = {Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiz159},
pmid = {31589310},
issn = {1574-6941},
abstract = {Infants experience a dramatic change in their food in the first year after birth when they shift from breast milk to solid food. This results in a large change in presence of indigestible polysaccharides, a primary energy resource of gut microbes. How the gut microbiota adapts to this dietary shift has not been well examined. Here by using metagenomics data, we studied carbohydrate-active enzymes (CAZymes) of gut microbiota, which are essential enzymes catalyzing the breakdown of polysaccharides, during this dietary shift. We developed a new approach to categorize CAZyme families by food intake and found CAZyme families associated with milk or solid food. We also found CAZymes with most abundance in 12 months infants are not associated with solid food or milk, but may be related to modulating carbohydrates in the mucus. Additionally, the abundance of gut CAZymes were found to be affected by many other factors, including delivery modes and life style in adults. Taken together, our findings provide novel insights into the dynamic change of gut CAZymes in early human life and provide potential markers for food interference or gut microbiota restoration.},
}

@article {pmid31589186,
year = {2019},
author = {Takhar, JS and Doan, TA and Gonzales, JA},
title = {Primary vitreoretinal lymphoma: empowering our clinical suspicion.},
journal = {Current opinion in ophthalmology},
volume = {30},
number = {6},
pages = {491-499},
doi = {10.1097/ICU.0000000000000620},
pmid = {31589186},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: Vitreoretinal lymphoma (VRL) is well known as a masquerade syndrome. However, delays in diagnosis are common particularly because of the small volume of tissue that is used for investigative studies. We outline the current diagnostic tests available to clinicians and provide a glimpse of possible future novel diagnostics.

RECENT FINDINGS: The use of spectral domain ocular coherence tomography to identify subretinal lesions has proven to be a reliable ally to clinicians. Nevertheless, the diagnostic gold standard remains cytology, which requires a skilled pathologist. Molecular tests, including MYD88 polymerase chain reaction testing has further refined our diagnostic capabilities. Metagenomic deep sequencing is a newer molecular test that offers the ability to identify any mutation associated with lymphoma development and may offer more sensitive testing in the future.

SUMMARY: Clinicians have developed a strong acumen for suspecting VRL based upon clinical features, which can further be supported by a variety of imaging modalities. Delays in diagnosis continue to occur particularly because of the small volume of ocular fluid available for testing and because current tests offer a biased approach in terms of limited scope of detecting a specific mutation or cytopathologic feature(s). Newer molecular techniques feature an expanded scope of detecting any mutation associated with lymphomatous development.},
}

@article {pmid31589025,
year = {2019},
author = {Huang, ZS and Wei, Z and Xiao, XL and Tang, MR and Li, BL and Ming, S and Cheng, XL},
title = {Biooxidation of Elemental Mercury into Mercury Sulfide and Humic Acid Bound Mercury by Sulfate Reduction for Hg0 Removal in Flue Gas.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.9b04029},
pmid = {31589025},
issn = {1520-5851},
abstract = {Bioconversion of elemental mercury (Hg0) into immobile, non-toxic and less bioavailable species is of vital environmental significance. Here, we investigated bioconversion of Hg0 in a sulfate-reducing membrane biofilm reactor (MBfR). MBfR achieved effective Hg0 removal by sulfate bio-reduction.16 S rDNA sequencing and metagenomic sequencing revealed that diverse groups of mercury-oxidizing/sulfate-reducing bacteria (Desulfobulbus, Desulfuromonas, Desulfomicrobium and etc.) utilized Hg0 as initial electron donor and sulfate as terminal electron acceptor to form the overall redox, these microorganisms could couple mercury bio-oxidation to sulfate bio-reduction. Analysis on mercury speciation in biofilm by sequential extraction processes (SEPs) and inductively coupled mass spectrometry (ICP-MS) and mercury temperature programmed desorption (Hg-TPD) showed that mercury sulfide (HgS) and humic acid bound mercury (HA-Hg) were two major products of Hg0 bio-oxidation. With HgS and HA-Hg comprehensively characterized by X-ray diffraction (XRD), excitation-emission matrix spectra (EEM), scanning electron microscopy-energy disperse spectroscopy (SEM-EDS), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR), it was proposed that biologically oxidized mercury (Hg2+) further reacted with biogenic sulfides to form cubically crystallized metacinnbar (β-HgS) extracellular particles. Hg2+ was also complexed with functional groups -SH, -OH, -NH- and -COO- in humic acids from extracellular polymeric substances (EPS) to form HA-Hg. HA-Hg may further react with biogenic sulfides to form HgS. Bioconversion of Hg0 into HgS was therefore achieved and can be a feasible biotechnique for flue gas demercuration.},
}

@article {pmid31588624,
year = {2019},
author = {Zhao, F and Zhou, G and Liu, X and Song, S and Xu, X and Hooiveld, G and Müller, M and Liu, L and Kristiansen, K and Li, C},
title = {Dietary Protein Sources Differentially Affect the Growth of Akkermansia muciniphila and Maintenance of the Gut Mucus Barrier in Mice.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e1900589},
doi = {10.1002/mnfr.201900589},
pmid = {31588624},
issn = {1613-4133},
abstract = {SCOPE: The gut microbiota plays an essential role in linking diet to host health. The specific role of different dietary proteins on the gut microbiota and health is less understood. Here we investigated the impact of proteins derived from chicken and soy on the gut microbiota and host gut barrier in C57BL/6 mice.

METHODS AND RESULTS: Specific-pathogen-free and germ-free mice were assigned to either a chicken or a soy protein-based diet for 4 weeks. Compared with a chicken protein-based diet, intake of a soy protein-based diet reduced the abundance of A. muciniphila and the number of goblet cells, lowered the level of Muc2 mRNA, and decreased the thickness of the mucus layer in the colon of specific-pathogen-free mice. In germ-free mice colonization with A. muciniphila combined with intake of a chicken protein-based diet resulted in a higher expression of the Muc2 mRNA in colon, and surprisingly, an increased potential for oxidative phosphorylation in A. muciniphila compared with colonized mice fed a soy protein-based diet.

CONCLUSION: These findings suggest possible mutually beneficial interactions between the growth and function of A. muciniphila and host mucus barrier in response to intake of a chicken protein-based diet contrasting the intake of a soy protein-based diet. This article is protected by copyright. All rights reserved.},
}

@article {pmid31588388,
year = {2019},
author = {Khalid, NA and Rajandas, H and Parimannan, S and Croft, LJ and Loke, S and Chong, CS and Bruce, NC and Yahya, A},
title = {Insights into microbial community structure and diversity in oil palm waste compost.},
journal = {3 Biotech},
volume = {9},
number = {10},
pages = {364},
doi = {10.1007/s13205-019-1892-4},
pmid = {31588388},
issn = {2190-572X},
abstract = {Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.},
}

@article {pmid31587913,
year = {2019},
author = {Galvão, KN and Bicalho, RC and Jeon, SJ},
title = {Symposium review: The uterine microbiome associated with the development of uterine disease in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2019-17106},
pmid = {31587913},
issn = {1525-3198},
abstract = {Until 2010, our knowledge of the uterine microbiome in cows that developed uterine disease relied almost exclusively on culture-dependent studies and mostly included cows with clinical endometritis (i.e., with purulent uterine discharge). Those studies consistently found a strong positive correlation between Trueperella pyogenes and clinical endometritis, whereas other pathogens such as Escherichia coli, Fusobacterium necrophorum, Prevotella melaninogenica, and Bacteroides spp. were also commonly cocultured. In contrast, Streptococcus spp., Staphylococcus spp., and Bacillus spp. were usually isolated from healthy cows. Starting in 2010, culture-independent studies using PCR explored the microbiome of cows with metritis and clinical endometritis, and observed that E. coli was a pioneer pathogen that predisposed cows to infection with F. necrophorum, which was strongly associated with metritis, and to infection with T. pyogenes, which was strongly associated with clinical endometritis. Starting in 2011, culture-independent studies using metagenomic sequencing expanded our knowledge of the uterine microbiome. It has been shown that cows have bacteria in the uterus even before calving, they have an established uterine microbiome within 20 min of calving, and that the microbiome structure is identical between cows that develop metritis and healthy cows until 2 d postpartum, after which the bacterial structure of cows that developed metritis deviates in favor of greater relative abundance of Bacteroidetes and Fusobacteria and lesser relative abundance of Proteobacteria and Tenericutes. The shift in the uterine microbiome in cows that develop metritis is characterized by a loss of heterogeneity and a decrease in bacterial richness. At the genus level, Bacteroides, Porphyromonas, and Fusobacterium have the strongest association with metritis. At the species level, we observed that Bacteroides pyogenes, Porphyromonas levii, and Helcococcus ovis were potential emerging uterine pathogens. Finally, we have shown that the hematogenous route is a viable route of uterine infection with uterine pathogens. Herein, we propose that metritis is associated with a dysbiosis of the uterine microbiota characterized by decreased richness, and an increase in Bacteroidetes and Fusobacteria, particularly Bacteroides, Porphyromonas, and Fusobacterium.},
}

@article {pmid31587641,
year = {2019},
author = {Keeling, PJ},
title = {Combining morphology, behaviour and genomics to understand the evolution and ecology of microbial eukaryotes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190085},
doi = {10.1098/rstb.2019.0085},
pmid = {31587641},
issn = {1471-2970},
abstract = {Microbial eukaryotes (protists) are structurally, developmentally and behaviourally more complex than their prokaryotic cousins. This complexity makes it more difficult to translate genomic and metagenomic data into accurate functional inferences about systems ranging all the way from molecular and cellular levels to global ecological networks. This problem can be traced back to the advent of the cytoskeleton and endomembrane systems at the origin of eukaryotes, which endowed them with a range of complex structures and behaviours that still largely dominate how they evolve and interact within microbial communities. But unlike the diverse metabolic properties that evolved within prokaryotes, the structural and behavioural characteristics that strongly define how protists function in the environment cannot readily be inferred from genomic data, since there is generally no simple correlation between a gene and a discrete activity or function. A deeper understanding of protists at both cellular and ecological levels, therefore, requires not only high-throughput genomics but also linking such data to direct observations of natural history and cell biology. This is challenging since these observations typically require cultivation, which is lacking for most protists. Potential remedies with current technology include developing a more phylogenetically diverse range of model systems to better represent the diversity, as well as combining high-throughput, single-cell genomics with microscopic documentation of the subject cells to link sequence with structure and behaviour. This article is part of a discussion meeting issue 'Single cell ecology'.},
}

@article {pmid31587640,
year = {2019},
author = {Santoro, AE and Kellom, M and Laperriere, SM},
title = {Contributions of single-cell genomics to our understanding of planktonic marine archaea.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190096},
doi = {10.1098/rstb.2019.0096},
pmid = {31587640},
issn = {1471-2970},
abstract = {Single-cell genomics has transformed many fields of biology, marine microbiology included. Here, we consider the impact of single-cell genomics on a specific group of marine microbes-the planktonic marine archaea. Despite single-cell enabled discoveries of novel metabolic function in the marine thaumarchaea, population-level investigations are hindered by an overall lower than expected recovery of thaumarchaea in single-cell studies. Metagenome-assembled genomes have so far been a more useful method for accessing genome-resolved insights into the Marine Group II euryarchaea. Future progress in the application of single-cell genomics to archaeal biology in the ocean would benefit from more targeted sorting approaches, and a more systematic investigation of potential biases against archaea in single-cell workflows including cell lysis, genome amplification and genome screening. This article is part of a discussion meeting issue 'Single cell ecology'.},
}

@article {pmid31587639,
year = {2019},
author = {Needham, DM and Poirier, C and Hehenberger, E and Jiménez, V and Swalwell, JE and Santoro, AE and Worden, AZ},
title = {Targeted metagenomic recovery of four divergent viruses reveals shared and distinctive characteristics of giant viruses of marine eukaryotes.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {374},
number = {1786},
pages = {20190086},
doi = {10.1098/rstb.2019.0086},
pmid = {31587639},
issn = {1471-2970},
abstract = {Giant viruses have remarkable genomic repertoires-blurring the line with cellular life-and act as top-down controls of eukaryotic plankton. However, to date only six cultured giant virus genomes are available from the pelagic ocean. We used at-sea flow cytometry with staining and sorting designed to target wild predatory eukaryotes, followed by DNA sequencing and assembly, to recover novel giant viruses from the Pacific Ocean. We retrieved four 'PacV' partial genomes that range from 421 to 1605 Kb, with 13 contigs on average, including the largest marine viral genomic assembly reported to date. Phylogenetic analyses indicate that three of the new viruses span a clade with deep-branching members of giant Mimiviridae, incorporating the Cafeteria roenbergensis virus, the uncultivated terrestrial Faunusvirus, one PacV from a choanoflagellate and two PacV with unclear hosts. The fourth virus, oPacV-421, is phylogenetically related to viruses that infect haptophyte algae. About half the predicted proteins in each PacV have no matches in NCBI nr (e-value < 10-5), totalling 1735 previously unknown proteins; the closest affiliations of the other proteins were evenly distributed across eukaryotes, prokaryotes and viruses of eukaryotes. The PacVs encode many translational proteins and two encode eukaryotic-like proteins from the Rh family of the ammonium transporter superfamily, likely influencing the uptake of nitrogen during infection. cPacV-1605 encodes a microbial viral rhodopsin (VirR) and the biosynthesis pathway for the required chromophore, the second finding of a choanoflagellate-associated virus that encodes these genes. In co-collected metatranscriptomes, 85% of cPacV-1605 genes were expressed, with capsids, heat shock proteins and proteases among the most highly expressed. Based on orthologue presence-absence patterns across the PacVs and other eukaryotic viruses, we posit the observed viral groupings are connected to host lifestyles as heterotrophs or phototrophs. This article is part of a discussion meeting issue 'Single cell ecology'.},
}

@article {pmid31580397,
year = {2019},
author = {Ma, A and Sun, M and McDermaid, A and Liu, B and Ma, Q},
title = {MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btz696},
pmid = {31580397},
issn = {1367-4811},
}

@article {pmid29803476,
year = {2018},
author = {González-Escobar, JL and Grajales-Lagunes, A and Smoliński, A and Chagolla-López, A and De Léon-Rodríguez, A and Barba de la Rosa, AP},
title = {Microbiota of edible Liometopum apiculatum ant larvae reveals potential functions related to their nutritional value.},
journal = {Food research international (Ottawa, Ont.)},
volume = {109},
number = {},
pages = {497-505},
doi = {10.1016/j.foodres.2018.04.049},
pmid = {29803476},
issn = {1873-7145},
mesh = {Animals ; Ants/*microbiology ; Bacteria/classification/genetics/*isolation & purification ; Female ; Food Analysis/methods ; Host-Pathogen Interactions ; Larva/microbiology ; Male ; Metagenomics ; *Microbiota ; *Nutritive Value ; Ribotyping ; Symbiosis ; },
abstract = {Edible insects, due to their high nutritive value, are currently considered as a potential renewable source for food and feed production. Liometopum apiculatum ants are widely distributed in arid and semi-arid ecosystems and their larvae (escamoles) are considered as a delicacy, however the microbial importance in L. apiculatum nutritional ecology is unknown. The aim of this research was to characterize the microorganisms associated with both L. apiculatum larvae and the reproductive adult ants using the 16S rRNA gene sequencing and culturomics approaches. The obligate endosymbionts were also investigated through microscopic analysis. The most abundant Phylum identified by sequencing in the larvae was Firmicutes while in adult ants was Proteobacteria. Interestingly, the culturomics results showed 15 genera corresponding to the bacteria identified by sequencing analysis. Particularly, it was observed a large population of nitrogen-fixing bacteria, which could be linked with the high protein content in escamoles. Endosymbionts were detected in bacteoriocytes, these bacteria are related with vitamins and essential amino acids biosynthesis, and both compounds contributing to the high nutritional value of escamoles. This is the first report of the microorganisms present in the escamolera ant ensuring their safety as food and opening new areas of nutritional ecological and food processing.},
}

Animals
Ants/*microbiology
Bacteria/classification/genetics/*isolation & purification
Female
Food Analysis/methods
Host-Pathogen Interactions
Larva/microbiology
Male
Metagenomics
*Microbiota
*Nutritive Value
Ribotyping
Symbiosis

@article {pmid29651010,
year = {2018},
author = {Ndou, SP and Tun, HM and Kiarie, E and Walsh, MC and Khafipour, E and Nyachoti, CM},
title = {Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta- and mucosa-associated microbiota in pigs.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {5880},
pmid = {29651010},
issn = {2045-2322},
mesh = {Animals ; *Avena ; Bile Acids and Salts/biosynthesis/genetics ; Dietary Fiber/administration & dosage ; *Dietary Supplements ; Digestion/drug effects/physiology ; *Flax ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/*drug effects/growth & development ; Intestines/drug effects/microbiology ; Metagenome/drug effects/genetics ; Swine/growth & development ; },
abstract = {The establishment of a healthy gastrointestinal milieu may not only offer an opportunity to reduce swine production costs but could also open the way for a lifetime of human health improvement. This study investigates the effects of feeding soluble fibre from flaxseed meal-containing diet (FM) and insoluble fibre from oat hulls-containing diet (OH) on histomorphological characteristics, digesta- and mucosa-associated microbiota and their associations with metabolites in pig intestines. In comparison with the control (CON) and OH diets, the consumption of FM increased (P < 0.001) the jejunal villi height (VH) and the ratio of VH to crypt depths. The PERMANOVA analyses showed distinct (P < 0.05) microbial communities in ileal digesta and mucosa, and caecal mucosa in CON and FM-diets fed pigs compared to the OH diet-fed pigs. The predicted functional metagenomes indicated that amino acids and butanoate metabolism, lysine degradation, bile acids biosynthesis, and apoptosis were selectively enhanced at more than 2.2 log-folds in intestinal microbiota of pigs fed the FM diet. Taken together, flaxseed meal and oat hulls supplementation in growing pigs' diets altered the gastrointestinal development, as well as the composition and function of microbial communities, depending on the intestinal segment and physicochemical property of the dietary fibre source.},
}

Animals
*Avena
Bile Acids and Salts/biosynthesis/genetics
Dietary Fiber/administration & dosage
*Dietary Supplements
Digestion/drug effects/physiology
*Flax
Gastrointestinal Microbiome/drug effects
Gastrointestinal Tract/*drug effects/growth & development
Intestines/drug effects/microbiology
Metagenome/drug effects/genetics
Swine/growth & development

@article {pmid29593315,
year = {2018},
author = {Sun, T and Wang, XQ and Zhao, ZL and Yu, SH and Yang, P and Chen, XM},
title = {A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {5324},
pmid = {29593315},
issn = {2045-2322},
mesh = {Animals ; DNA, Ribosomal Spacer ; Female ; *Fungi/classification/genetics ; Hemiptera/*microbiology ; *Host-Pathogen Interactions ; Metagenome ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S ; },
abstract = {The Chinese white wax scale insect (Ericerus pela) is an economically valuable species with an important role in wax production. Recently, in a greenhouse in Kunming, we identified a genus of fungus that infects and kills E. pela females. This study sought to perform the molecular detection of entomopathogens and analyze the changes in the host microbiota after entomopathogen infection. We used library construction, high-throughput sequencing and real-time quantitative polymerase chain reaction (RT-qPCR) to identify the fungi infecting adult E. pela, to understand the changes in the host organism, and to determine the distribution of the entomopathogens. Cladosporium langeronii and C. sphaerospermum were the main pathogenic species that infected the E. pela females, and they were most prevalent in the dorsal cuticle. In vivo, after infection, the proportion of Cladosporium clearly increased. The infection had little influence on the fungal community but had a strong influence on the bacterial community. After infection, Arsenophonus was dominant, and numerous bacterial genera disappeared. However, Rickettsia, instead of Arsenophonus, became dominant in the Cladosporium-infected individuals that had also been infected with Rickettsia. We identified the species that infected E. pela females and determined the influence of infection on the host microorganisms.},
}

Animals
DNA, Ribosomal Spacer
Female
*Fungi/classification/genetics
Hemiptera/*microbiology
*Host-Pathogen Interactions
Metagenome
Metagenomics/methods
*Microbiota
RNA, Ribosomal, 16S

@article {pmid29593299,
year = {2018},
author = {Wang, X and Wang, Z and Jiang, P and He, Y and Mu, Y and Lv, X and Zhuang, L},
title = {Bacterial diversity and community structure in the rhizosphere of four Ferula species.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {5345},
pmid = {29593299},
issn = {2045-2322},
mesh = {*Bacteria/classification ; *Biodiversity ; Ferula/*microbiology ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {The medicinal value of the Ferula L. has been recognized for more than a thousand years. Wild stocks of Ferula have declined dramatically because high economic value has led to overharvesting. The objective of this study was to compare the rhizosphere microbial community of four Ferula species [F. syreitschikowii K.-Pol., F. gracilis (Ledeb.) Ledeb., F. ferulaeoides (Steud.) Korov., and F. lehmannii Boiss.] in the northern part of Xinjiang, China. The 16S rRNA sequences of rhizosphere bacteria were obtained with an Illumina paired-end sequence platform. Analysis was conducted to determine the richness and diversity of the rhizosphere bacterial communities. Two-way ANOVA indicated that plant species and soil depth had no significant effect on the alpha diversity of rhizobacteria. Linear discriminant analysis effect size showed that F. lehmannii followed by F. ferulaeoides had the most biomarkers and the highest taxon level, F. syreitschikowii and F. gracilis the least, while F. syreitschikowii and F. gracilis had the least property. This trend is consistent with reports that the medicinal value of F. lehmannii and F. ferulaeoides is greater than that of F. gracilis and F. syreitschikowii. The results of this study provide information that could be used for the commercial cultivation of Ferula spp.},
}

*Bacteria/classification
*Biodiversity
Ferula/*microbiology
Metagenome
Metagenomics/methods
*Microbiota
Phylogeny
Plant Roots/microbiology
RNA, Ribosomal, 16S/genetics
*Rhizosphere
Soil/chemistry
*Soil Microbiology

@article {pmid31586453,
year = {2019},
author = {Cox, SR and Lindsay, JO and Fromentin, S and Stagg, AJ and McCarthy, NE and Galleron, N and Ibraim, SB and Roume, H and Levenez, F and Pons, N and Maziers, N and Lomer, MC and Ehrlich, SD and Irving, PM and Whelan, K},
title = {Effects of Low-FODMAP Diet on Symptoms, Fecal Microbiome, and Markers of Inflammation in Patients With Quiescent Inflammatory Bowel Disease in a Randomized Trial.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.09.024},
pmid = {31586453},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: There is limited evidence that a diet low in fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) reduces gut symptoms in quiescent inflammatory bowel disease (IBD). We performed a randomized, controlled trial to investigate the effects of a low-FODMAP diet on persistent gut symptoms, the intestinal microbiome, and circulating markers of inflammation in patients with quiescent IBD.

METHODS: We performed a single-blind trial of 52 patients with quiescent Crohn's disease or ulcerative colitis and persistent gut symptoms at 2 large gastroenterology clinics in the United Kingdom. Patients were randomly assigned to groups that followed a diet low in FODMAPs (n=27) or a control diet (n=25), with dietary advice, for 4 weeks. Gut symptoms and health-related quality of life were measured using validated questionnaires. Stool and blood samples were collected at baseline and end of trial. We assessed fecal microbiome composition and function using shotgun metagenomic sequencing and phenotypes of T cells in blood using flow cytometry.

RESULTS: A higher proportion of patients reported adequate relief of gut symptoms following the low-FODMAP diet (14/27, 52%) than the control diet (4/25, 16%, P=.007). Patients had a greater reduction in irritable bowel syndrome severity scores following the low-FODMAP diet (mean reduction of 67; standard error, 78) than the control diet (mean reduction of 34; standard error, 50), although this difference was not statistically significant (P=.075). Following the low-FODMAP diet, patients had higher health-related quality of life scores (81.9±1.2) than patients on the control diet (78.3±1.2, P=.042). A targeted analysis revealed that in stool samples collected at the end of the study period, patients on the low-FODMAP diet had significantly lower abundance of Bifidobacterium adolescentis, B longum, and Faecalibacterium prausnitzii than patients on control diet. However, microbiome diversity and markers of inflammation did not differ significantly between groups.

CONCLUSIONS: In a trial of the low-FODMAP diet vs a control diet in patients with quiescent IBD, we found no significant difference after 4 weeks in change in irritable bowel syndrome severity scores, but significant improvements in specific symptom scores and numbers reporting adequate symptom relief. The low-FODMAP diet reduced fecal abundance of microbes believed to regulate the immune response, compared with the control diet, but had no significant effect on markers of inflammation. We conclude that a 4-week diet low in FODMAPs is safe and effective for managing persistent gut symptoms in patients with quiescent IBD. www.isrctn.com no: ISRCTN17061468.},
}

@article {pmid31585992,
year = {2019},
author = {Peña-Gonzalez, A and Soto-Girón, MJ and Smith, S and Sistrunk, J and Montero, L and Páez, M and Ortega, E and Hatt, JK and Cevallos, W and Trueba, G and Levy, K and Konstantinidis, KT},
title = {Metagenomic signatures of gut infection caused by different Escherichia coli pathotypes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01820-19},
pmid = {31585992},
issn = {1098-5336},
abstract = {Escherichia coli is a leading contributor to infectious diarrhea and child mortality worldwide but it remains unknown how alterations in the gut microbiome vary for distinct E. coli pathotypes and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. Towards addressing these issues, we devised a novel approach that combined traditional, isolate-based and molecular biology techniques with metagenomics analysis of stool samples and epidemiological data. Application of this pipeline to children enrolled in a case-control study of diarrhea in Ecuador showed that, in about half of the cases where an E. coli pathotype was detected by culture and PCR, E. coli was likely not the causative agent based on metagenomic-derived low relative abundance, level of clonality and/or virulence gene content. Our results also showed that diffuse adherent E. coli (DAEC), a pathotype that is generally underrepresented in previous studies of diarrhea and thus, thought to not be highly virulent, caused several small-scale diarrheal outbreaks across a rural to urban gradient in Ecuador. DAEC infections were uniquely accompanied by co-elution of high amounts of human DNA and conferred significant shifts in the gut microbiome composition relative to controls or infections caused by other E. coli pathotypes. Our study shows that diarrheal infections can be efficiently diagnosed for their etiological agent and categorized based on their effects on the gut microbiome using metagenomic tools, which opens new possibilities for diagnostics and treatment.ImportanceE. coli infectious diarrhea is an important contributor to child mortality worldwide. However, diagnosing and thus, treating E. coli infections remains challenging due to technical and other reasons associated with the limitations of the traditional culture-based techniques and the requirement to apply Koch's postulates. In this study, we integrated traditional microbiology techniques with metagenomics and epidemiology data in order to identify cases of diarrhea where E. coli was most likely the causative disease agent and evaluate specific signatures in the disease-state gut microbiome that distinguish between DAEC, ETEC and EPEC E. coli pathotypes. Therefore, our methodology and results should be highly relevant for diagnosing and treating diarrheal infections, and have important applications in public health.},
}

@article {pmid31585652,
year = {2019},
author = {Wang, B and Wang, XL},
title = {Species diversity of fecal microbial flora in Canis lupus familiaris infected with canine parvovirus.},
journal = {Veterinary microbiology},
volume = {237},
number = {},
pages = {108390},
doi = {10.1016/j.vetmic.2019.108390},
pmid = {31585652},
issn = {1873-2542},
abstract = {Parvovirosis is a highly contagious disease in dogs, often causing acute hemorrhagic enteritis and altering the intestinal microflora. In this study, real-time PCR was used to detect the viral copy numbers in dogs diagnosed with the disease. Hematological and hemobiochemical parameters were also determined. The species and abundances of the fecal microbial flora in both sick and healthy dogs were determined and compared via metagenomic sequencing. The viral copy numbers in the sick dogs were infected with little difference in the positive samples. The blood coagulation time was significantly shorter and the number of white blood cells was significantly greater in the sick dogs. The serum calcium content was slightly increased and the phosphorus content was reduced in the sick dogs. The LDH and CK activities were significantly elevated in the sick dogs. Metagenomic sequencing and analysis revealed relatively more Escherichia, Lachnoclostridium, gnavus group (Ruminococcus), and uncultured_bacterium_f_lachnospiraceae in the infected dogs, whereas the abundance of Collinsella was relatively reduced. Alloprevotella and Sutterella were absent among the fecal microorganisms of the infected dogs. The relative abundances of Romboutsia, Erysipelatoclostridium, Anaerotruncus, and Blautia were significantly increased in the infected dogs. Functional analysis of the metagenomes of the samples indicated a significant enrichment of the 'replication, recombination and repair', 'nucleotide transport and metabolism', 'transcription', and 'defense metabolism' functions in the fecal microbial flora of the infected dogs. In summary, this study provides a scientific theoretical basis for preventing and controlling diarrhea caused by the canine parvovirus.},
}

@article {pmid31585382,
year = {2019},
author = {Wang, HG and Huang, H and Liu, RL and Mao, YP and Biswal, BK and Chen, GH and Wu, D},
title = {Investigation on polyphosphate accumulation in the sulfur transformation-centric EBPR (SEBPR) process for treatment of high-temperature saline wastewater.},
journal = {Water research},
volume = {167},
number = {},
pages = {115138},
doi = {10.1016/j.watres.2019.115138},
pmid = {31585382},
issn = {1879-2448},
abstract = {This study investigated the polyphosphates accumulation rate in a novel sulfur transformation-centric enhanced biological phosphorus removal (SEBPR) process. The SEBPR system was continuously operated over 120 days in a sequencing batch reactor (SBR) that alternated between the anaerobic mode and the anoxic mode of operation (temperature: 30 °C and salinity: 6000 mg/L Cl-). In addition to the SBR, batch experiments were carried out to test the effect of two different sulfate concentrations on the system performance and sulfur-phosphorus transformations. The key intercellular polymers of polyphosphates and polysulfur (poly-S) were identified by employing advanced microscopes. Metagenomic analysis was performed to characterize the diversity of microbes and their functions enriched in the SEBPR system. Finally, several molecular techniques including flow cytometry cell sorting and 16S DNA high-throughput sequencing were applied to identify the phosphorus-accumulating organisms (PAOs). The amounts of P release and P uptake in the SEBPR increased gradually to nearly 18 ± 6.4 mg P/L and 26.5 ± 6.7 mg P/L respectively, yielding a net P removal efficiency of 84 ± 25%. Batch tests indicated no polyhydroxyalkanate (PHA) synthesis, but P uptake was observed and it was correlated with the intracellular poly-S consumption, suggesting that the poly-S could act as an intracellular energy source for P uptake and polyphosphates formation. Moreover, CLSM and TEM micrographs clearly showed the presence of intercellular polyphosphates and poly-S respectively. Metagenomic analysis revealed that Proteobacteria (36.5%), Bacteroidetes (23.3%), Thermotogae (7.1%), Chloroflexi (4.5%) and Firmicutes (2.3%) were the dominant phyla in Bacteria. The conventional PAO of Candidatus Accumulibacter was found at a low abundance of 0.32% only; and an uncultured genus close to Rhodobacteraceae at the family level is speculated to be the putative sulfur PAO (SPAO). Finally, this research suggests that poly-S considerably impacts on polyphosphates accumulation in the SEBPR system when no PHAs are formed.},
}

@article {pmid31585122,
year = {2019},
author = {Gu, S and Zaidi, S and Hassan, MI and Mohammad, T and Malta, TM and Noushmehr, H and Nguyen, B and Crandall, KA and Srivastav, J and Obias, V and Lin, P and Nguyen, BN and Yao, M and Yao, R and King, CH and Mazumder, R and Mishra, B and Rao, S and Mishra, L},
title = {Mutated CEACAMs Disrupt Transforming Growth Factor beta Signaling and Alter the Intestinal Microbiome to Promote Colorectal Carcinogenesis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2019.09.023},
pmid = {31585122},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: We studied interactions among proteins of the carcinoembryonic antigen related cell adhesion molecule (CEACAM) family, which interact with microbes, and transforming growth factor beta (TGFB) signaling pathway, which is often altered in colorectal cancer cells. We investigated mechanisms by which CEACAM proteins inhibit TGFB signaling and alter the intestinal microbiome to promote colorectal carcinogenesis.

METHODS: We collected data on DNA sequences, mRNA expression levels, and patient survival times from 456 colorectal adenocarcinoma cases, and a separate set of 594 samples of colorectal adenocarcinomas, in the Cancer Genome Atlas. We performed shotgun metagenomic sequencing analyses of feces from wild-type mice and mice with defects in TGFB signaling (Sptbn1+/- and Smad4+/-/Sptbn1+/-) to identify changes in microbiota composition before development of colon tumors. Proteins were knocked down in SW480 and HCT116 colorectal cancer cell lines, which were analyzed by immunoblotting and in proliferation and colony formation assays.

RESULTS: In colorectal adenocarcinomas, high expression levels of genes encoding CEACAM proteins, especially CEACAM5, were associated with reduced survival times of patients. There was an inverse correlation between expression of CEACAM genes and expression of TGFB pathway genes (TGFBR1, TGFBR2, and SMAD3). In colorectal adenocarcinomas, we also found an inverse correlation between expression of genes in the TGFB signaling pathway and genes that regulate stem cell features of cells. We found mutations encoding L640I and A643T in the B3 domain of human CEACAM5 in colorectal adenocarcinomas; structural studies indicated that these mutations would alter the interaction between CEACAM5 and TGFBR1. Overexpression of these mutants in SW480 and HCT116 colorectal cancer cell lines increased their anchorage-independent proliferation and inhibited TGFB signaling to a greater extent than overexpression of wild-type CEACAM5, indicating that they are gain of function mutations. Compared with feces from wild-type mice, feces from mice with defects in TGFB signaling had increased abundance of bacterial species that have been associated with the development of colon tumors, including Clostridium septicum, and decreased amounts of beneficial bacteria such as Bacteroides vulgatus and Parabacteroides distasonis.

CONCLUSION: We found expression of CEACAMs and genes that regulate stem cell features of cells to be increased in colorectal adenocarcinomas and inversely correlated with expression of TGFB pathway genes. We found colorectal adenocarcinomas to express mutant forms of CEACAM5 that inhibit TGFB signaling and increase proliferation and colony formation. We propose that CEACAM proteins disrupt TGFB signaling, which alters the composition of the intestinal microbiome to promote colorectal carcinogenesis.},
}

@article {pmid31584168,
year = {2020},
author = {Browne, PD and Kot, W and Jørgensen, TS and Hansen, LH},
title = {The Mobilome: Metagenomic Analysis of Circular Plasmids, Viruses, and Other Extrachromosomal Elements.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2075},
number = {},
pages = {253-264},
doi = {10.1007/978-1-4939-9877-7_18},
pmid = {31584168},
issn = {1940-6029},
abstract = {Isolation, sequencing, and analysis of circular genetic elements bring new insights to mobile genetic elements related to microbial ecology. One method used to study circular plasmids, viruses, and other elements is called the mobilome method. The mobilome method presented here is an unamplified mobilome approach allowing fast isolation of circular DNA elements from a variety of samples followed by directly building unamplified Illumina-compatible sequencing libraries using enzymatic tagging and fragmentation. Several methods for bioinformatic analysis of mobilome data are also suggested.},
}

@article {pmid31583848,
year = {2019},
author = {Kang, H and Park, B and Bolo, NR and Pathiraja, D and Park, S and Cha, M and Choi, IG and Chang, IS},
title = {Gene-Centric Metagenome Analysis Reveals Gene Clusters for Carbon Monoxide Conversion and Validates Isolation of a Clostridial Acetogen for C2 Chemical Production.},
journal = {Biotechnology journal},
volume = {14},
number = {10},
pages = {e1970083},
doi = {10.1002/biot.201970083},
pmid = {31583848},
issn = {1860-7314},
}

@article {pmid31582752,
year = {2019},
author = {Visconti, A and Le Roy, CI and Rosa, F and Rossi, N and Martin, TC and Mohney, RP and Li, W and de Rinaldis, E and Bell, JT and Venter, JC and Nelson, KE and Spector, TD and Falchi, M},
title = {Interplay between the human gut microbiome and host metabolism.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4505},
doi = {10.1038/s41467-019-12476-z},
pmid = {31582752},
issn = {2041-1723},
abstract = {The human gut is inhabited by a complex and metabolically active microbial ecosystem. While many studies focused on the effect of individual microbial taxa on human health, their overall metabolic potential has been under-explored. Using whole-metagenome shotgun sequencing data in 1,004 twins, we first observed that unrelated subjects share, on average, almost double the number of metabolic pathways (82%) than species (43%). Then, using 673 blood and 713 faecal metabolites, we found metabolic pathways to be associated with 34% of blood and 95% of faecal metabolites, with over 18,000 significant associations, while species showed less than 3,000 associations. Finally, we estimated that the microbiome was involved in a dialogue between 71% of faecal, and 15% of blood, metabolites. This study underlines the importance of studying the microbial metabolic potential rather than focusing purely on taxonomy to find therapeutic and diagnostic targets, and provides a unique resource describing the interplay between the microbiome and the systemic and faecal metabolic environments.},
}

@article {pmid31582724,
year = {2019},
author = {Yang, J and McDowell, A and Kim, EK and Seo, H and Lee, WH and Moon, CM and Kym, SM and Lee, DH and Park, YS and Jee, YK and Kim, YK},
title = {Development of a colorectal cancer diagnostic model and dietary risk assessment through gut microbiome analysis.},
journal = {Experimental & molecular medicine},
volume = {51},
number = {10},
pages = {117},
doi = {10.1038/s12276-019-0313-4},
pmid = {31582724},
issn = {2092-6413},
support = {NRF-2016M3A9B6901516//National Research Foundation of Korea (NRF)/ ; NRF-2017M3A9F3047497//National Research Foundation of Korea (NRF)/ ; H17C1996//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; },
abstract = {Colorectal cancer (CRC) is the third most common form of cancer and poses a critical public health threat due to the global spread of westernized diets high in meat, cholesterol, and fat. Although the link between diet and colorectal cancer has been well established, the mediating role of the gut microbiota remains elusive. In this study, we sought to elucidate the connection between the gut microbiota, diet, and CRC through metagenomic analysis of bacteria isolated from the stool of CRC (n = 89) and healthy (n = 161) subjects. This analysis yielded a dozen genera that were significantly altered in CRC patients, including increased Bacteroides, Fusobacterium, Dorea, and Porphyromonas prevalence and diminished Pseudomonas, Prevotella, Acinetobacter, and Catenibacterium carriage. Based on these altered genera, we developed two novel CRC diagnostic models through stepwise selection and a simplified model using two increased and two decreased genera. As both models yielded strong AUC values above 0.8, the simplified model was applied to assess diet-based CRC risk in mice. Mice fed a westernized high-fat diet (HFD) showed greater CRC risk than mice fed a regular chow diet. Furthermore, we found that nonglutinous rice, glutinous rice, and sorghum consumption reduced CRC risk in HFD-fed mice. Collectively, these findings support the critical mediating role of the gut microbiota in diet-induced CRC risk as well as the potential of dietary grain intake to reduce microbiota-associated CRC risk. Further study is required to validate the diagnostic prediction models developed in this study as well as the preventive potential of grain consumption to reduce CRC risk.},
}

@article {pmid31582523,
year = {2019},
author = {Sugimoto, Y and Camacho, FR and Wang, S and Chankhamjon, P and Odabas, A and Biswas, A and Jeffrey, PD and Donia, MS},
title = {A metagenomic strategy for harnessing the chemical repertoire of the human microbiome.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1126/science.aax9176},
pmid = {31582523},
issn = {1095-9203},
abstract = {Remarkable progress has been made in determining the effects of the microbiome on human physiology and disease, but the underlying molecules and mechanisms governing these effects remain largely unexplored. Here, we combine a new computational algorithm with synthetic biology to access biologically active small molecules encoded directly in human microbiome-derived metagenomic sequencing data. We discover that members of a clinically used class of molecules are widely encoded in the human microbiome, and that they exert potent antibacterial activities against neighboring microbes, implying a possible role in niche competition and host defense. Our approach paves the way toward a systematic unveiling of the chemical repertoire encoded by the human microbiome and provides a generalizable platform for discovering molecular mediators of microbiome-host and microbiome-microbiome interactions.},
}

@article {pmid31582460,
year = {2019},
author = {Damashek, J and Edwardson, CF and Tolar, BB and Gifford, SM and Moran, MA and Hollibaugh, JT},
title = {Coastal Ocean Metagenomes and Curated Metagenome-Assembled Genomes from Marsh Landing, Sapelo Island (Georgia, USA).},
journal = {Microbiology resource announcements},
volume = {8},
number = {40},
pages = {},
doi = {10.1128/MRA.00934-19},
pmid = {31582460},
issn = {2576-098X},
abstract = {Microbes play a dominant role in the biogeochemistry of coastal waters, which receive organic matter from diverse sources. We present metagenomes and 45 metagenome-assembled genomes (MAGs) from Sapelo Island, Georgia, to further understand coastal microbial populations. Notably, four MAGs are archaea, with two Thaumarchaeota and two marine group II Euryarchaeota.},
}

@article {pmid31582454,
year = {2019},
author = {Fetters, AM and Cantalupo, PG and Ashman, TL and Pipas, JM},
title = {Coding-Complete Genome Sequence of a Pollen-Associated Virus Belonging to the Secoviridae Family Recovered from a Japanese Apricot (Prunus mume) Metagenome Data Set.},
journal = {Microbiology resource announcements},
volume = {8},
number = {40},
pages = {},
doi = {10.1128/MRA.00881-19},
pmid = {31582454},
issn = {2576-098X},
abstract = {We report the coding-complete genome sequence of Japanese apricot pollen-associated secovirus 1 (JAPSV1), a virus belonging to the Secoviridae family, recovered from Japanese apricot (Prunus mume) pollen that is closely related to Peach leaf pitting-associated virus (PLPAV). This discovery adds to the number of known pollen-associated viruses.},
}

@article {pmid31581946,
year = {2019},
author = {Parrello, B and Butler, R and Chlenski, P and Olson, R and Overbeek, J and Pusch, GD and Vonstein, V and Overbeek, R},
title = {A machine learning-based service for estimating quality of genomes using PATRIC.},
journal = {BMC bioinformatics},
volume = {20},
number = {1},
pages = {486},
doi = {10.1186/s12859-019-3068-y},
pmid = {31581946},
issn = {1471-2105},
abstract = {BACKGROUND: Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains over 220,000 genomes, and current metagenomic technology supports assemblies of many draft-quality genomes from a single sample, most of which will be novel.

DESCRIPTION: We have added two quality assessment tools to the PATRIC annotation pipeline. EvalCon uses supervised machine learning to calculate an annotation consistency score. EvalG implements a variant of the CheckM algorithm to estimate contamination and completeness of an annotated genome.We report on the performance of these tools and the potential utility of the consistency score. Additionally, we provide contamination, completeness, and consistency measures for all genomes in PATRIC and in a recent set of metagenomic assemblies.

CONCLUSION: EvalG and EvalCon facilitate the rapid quality control and exploration of PATRIC-annotated draft genomes.},
}

@article {pmid31581714,
year = {2019},
author = {Ghaju Shrestha, R and Sherchan, SP and Kitajima, M and Tanaka, Y and Gerba, CP and Haramoto, E},
title = {Reduction of Arcobacter at Two Conventional Wastewater Treatment Plants in Southern Arizona, USA.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/pathogens8040175},
pmid = {31581714},
issn = {2076-0817},
abstract = {This study aimed to identify the bacterial community in two wastewater treatment plants (WWTPs) and to determine the occurrence and reduction of Arcobacter, along with virulence genes (ciaB and pldA). A total of 48 samples (24 influent and 24 effluent) were collected at two WWTPs in southern Arizona in the United States, monthly from August 2011 to July 2012. Bacterial DNA extract was utilized for 16S rRNA metagenomic sequencing. Quantification of Arcobacter 16S rRNA gene was conducted using a recently developed SYBR Green-based quantitative PCR assay. Among 847 genera identified, 113 (13%) were identified as potentially pathogenic bacteria. Arcobacter 16S rRNA gene was detected in all influent samples and ten (83%) and nine (75%) effluent samples at each plant, respectively. Log reduction ratios of Arcobacter 16S rRNA gene in Plant A and Plant B were 1.7 ± 0.9 (n = 10) and 2.3 ± 1.5 (n = 9), respectively. The ciaB gene was detected by quantitative PCR in eleven (92%) and twelve (100%) of 12 influent samples from Plant A and Plant B, respectively, while the pldA gene was detected in eight (67%) and six (50%) influent samples from Plant A and Plant B, respectively. The prevalence of potentially pathogenic bacteria in WWTP effluent indicated the need for disinfection before discharge into the environment.},
}

@article {pmid31581560,
year = {2019},
author = {Cai, P and Ning, Z and Zhang, N and Zhang, M and Guo, C and Niu, M and Shi, J},
title = {Insights into Biodegradation Related Metabolism in an Abnormally Low Dissolved Inorganic Carbon (DIC) Petroleum-Contaminated Aquifer by Metagenomics Analysis.},
journal = {Microorganisms},
volume = {7},
number = {10},
pages = {},
doi = {10.3390/microorganisms7100412},
pmid = {31581560},
issn = {2076-2607},
support = {2018YFC1803302//National Key R&D Program of China/ ; 41602261//National Natural Science Foundation of China/ ; 2018ZX07109-001-04//Major Science and Technology Project of Water Pollution control and management in China/ ; },
abstract = {In petroleum-contaminated aquifers, biodegradation is always associated with various types of microbial metabolism. It can be classified as autotrophic (such as methanogenic and other carbon fixation) and heterotrophic (such as nitrate/sulfate reduction and hydrocarbon consumption) metabolism. For each metabolic type, there are several key genes encoding the reaction enzymes, which can be identified by metagenomics analysis. Based on this principle, in an abnormally low dissolved inorganic carbon (DIC) petroleum-contaminated aquifer in North China, nine groundwater samples were collected along the groundwater flow, and metagenomics analysis was used to discover biodegradation related metabolism by key genes. The major new finding is that autotrophic metabolism was revealed, and, more usefully, we attempt to explain the reasons for abnormally low DIC. The results show that the methanogenesis gene, Mcr, was undetected but more carbon fixation genes than nitrate reduction and sulfate genes were found. This suggests that there may be a considerable number of autotrophic microorganisms that cause the phenomenon of low concentration of dissolved inorganic carbon in contaminated areas. The metagenomics data also revealed that most heterotrophic, sulfate, and nitrate reduction genes in the aquifer were assimilatory sulfate and dissimilatory nitrate reduction genes. Although there was limited dissolved oxygen, aerobic degrading genes AlkB and Cdo were more abundant than anaerobic degrading genes AssA and BssA. The metagenomics information can enrich our microorganic knowledge about petroleum-contaminated aquifers and provide basic data for further bioremediation.},
}

@article {pmid31581216,
year = {2019},
author = {Caza, F and Joly de Boissel, PG and Villemur, R and Betoulle, S and St-Pierre, Y},
title = {Liquid biopsies for omics-based analysis in sentinel mussels.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0223525},
doi = {10.1371/journal.pone.0223525},
pmid = {31581216},
issn = {1932-6203},
abstract = {Liquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transcriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in mussels to assess the quality of aquatic ecosystems.},
}

@article {pmid31581036,
year = {2019},
author = {Blázquez-Pallí, N and Rosell, M and Varias, J and Bosch, M and Soler, A and Vicent, T and Marco-Urrea, E},
title = {Integrative isotopic and molecular approach for the diagnosis and implementation of an efficient in-situ enhanced biological reductive dechlorination of chlorinated ethenes.},
journal = {Water research},
volume = {167},
number = {},
pages = {115106},
doi = {10.1016/j.watres.2019.115106},
pmid = {31581036},
issn = {1879-2448},
abstract = {Based on the previously observed intrinsic bioremediation potential of a site originally contaminated with perchloroethene (PCE), field-derived lactate-amended microcosms were performed to test different lactate isomers and concentrations, and find clearer isotopic and molecular parameters proving the feasibility of an in-situ enhanced reductive dechlorination (ERD) from PCE-to-ethene (ETH). According to these laboratory results, which confirmed the presence of Dehalococcoides sp. and the vcrA gene, an in-situ ERD pilot test consisting of a single injection of lactate in a monitoring well was performed and monitored for 190 days. The parameters used to follow the performance of the ERD comprised the analysis of i) hydrochemistry, including redox potential (Eh), and the concentrations of redox sensitive species, chlorinated ethenes (CEs), lactate, and acetate; ii) stable isotope composition of carbon of CEs, and sulphur and oxygen of sulphate; and iii) 16S rRNA gene sequencing from groundwater samples. Thus, it was proved that the injection of lactate promoted sulphate-reducing conditions, with the subsequent decrease in Eh, which allowed for the full reductive dechlorination of PCE to ETH in the injection well. The biodegradation of CEs was also confirmed by the enrichment in 13C and carbon isotopic mass balances. The metagenomic results evidenced the shift in the composition of the microbial population towards the predominance of fermentative bacteria. Given the success of the in-situ pilot test, a full-scale ERD with lactate was then implemented at the site. After one year of treatment, PCE and trichloroethene were mostly depleted, whereas vinyl chloride (VC) and ETH were the predominant metabolites. Most importantly, the shift of the carbon isotopic mass balances towards more positive values confirmed the complete reductive dechlorination, including the VC-to-ETH reaction step. The combination of techniques used here provides complementary lines of evidence for the diagnosis of the intrinsic biodegradation potential of a polluted site, but also to monitor the progress, identify potential difficulties, and evaluate the success of ERD at the field scale.},
}

@article {pmid31581017,
year = {2019},
author = {Franzetti, A and Gandolfi, I and Bestetti, G and Padoa Schioppa, E and Canedoli, C and Brambilla, D and Cappelletti, D and Sebastiani, B and Federici, E and Papacchini, M and Ambrosini, R},
title = {Plant-microorganisms interaction promotes removal of air pollutants in Milan (Italy) urban area.},
journal = {Journal of hazardous materials},
volume = {384},
number = {},
pages = {121021},
doi = {10.1016/j.jhazmat.2019.121021},
pmid = {31581017},
issn = {1873-3336},
abstract = {Plants and phyllosphere microorganisms may effectively contribute to reducing air pollution in cities through the adsorption and biodegradation of pollutants onto leaves. In this work, during all seasons, we sampled atmospheric particulate matter (PM10) and leaves of southern magnolia Magnolia grandiflora and deodar cedar Cedrus deodara, two evergreen plant species widespread in the urban area of Milan where the study was carried out. We then quantified Polycyclic Aromatic Hydrocarbons (PAHs) both in PM10 and on leaves and used sequencing of 16S rRNA gene, shotgun metagenomics and qPCR analyses to investigate the microbial communities hosted by the sampled leaves. Taxonomic and functional profiles of epiphytic bacterial communities differed between host plant species and seasons and the microbial communities on leaves harboured genes involved in the degradation of hydrocarbons. Evidence collected in this work also suggested that the abundance of hydrocarbon-degrading microorganisms on evergreen leaves increased with the concentration of hydrocarbons when atmospheric pollutants were deposited at high concentration on leaves, and that the biodegradation on the phyllosphere can contribute to the removal of PAHs from the urban air.},
}

@article {pmid31577814,
year = {2019},
author = {Vijayvargiya, P and Jeraldo, PR and Thoendel, MJ and Greenwood-Quaintance, KE and Esquer Garrigos, Z and Sohail, MR and Chia, N and Pritt, BS and Patel, R},
title = {Application of metagenomic shotgun sequencing to detect vector-borne pathogens in clinical blood samples.},
journal = {PloS one},
volume = {14},
number = {10},
pages = {e0222915},
doi = {10.1371/journal.pone.0222915},
pmid = {31577814},
issn = {1932-6203},
abstract = {BACKGROUND: Vector-borne pathogens are a significant public health concern worldwide. Infections with these pathogens, some of which are emerging, are likely under-recognized due to the lack of widely-available laboratory tests. There is an urgent need for further advancement in diagnostic modalities to detect new and known vector-borne pathogens. We evaluated the utility of metagenomic shotgun sequencing (MGS) as a pathogen agnostic approach for detecting vector-borne pathogens from human blood samples.

METHODS: Residual whole blood samples from patients with known infection with Babesia microti, Borrelia hermsii, Plasmodium falciparum, Mansonella perstans, Anaplasma phagocytophilum or Ehrlichia chaffeensis were studied. Samples underwent DNA extraction, removal of human DNA, whole genome amplification, and paired-end library preparation, followed by sequencing on Illumina HiSeq 2500. Bioinformatic analysis was performed using the Livermore Metagenomics Analysis Toolkit (LMAT), Metagenomic Phylogenetic Analysis (MetaPhlAn2), Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) and Kraken 2.

RESULTS: Eight samples were included in the study (2 samples each for P. falciparum and A. phagocytophilum). An average of 27.5 million read pairs was generated per sample (range, 18.3-38.8 million) prior to removal of human reads. At least one of the analytic tools was able to detect four of six organisms at the genus level, and the organism present in five of eight specimens at the species level. Mansonella and Ehrlichia species were not detected by any of the tools; however, mitochondrial cytochrome c oxidase subunit I amino acid sequence analysis suggested the presence of M. perstans genetic material.

CONCLUSIONS: MGS is a promising tool with the potential to evolve as a non-hypothesis driven diagnostic test to detect vector-borne pathogens, including protozoa and helminths.},
}

@article {pmid31576623,
year = {2019},
author = {Maltecca, C and Bergamaschi, M and Tiezzi, F},
title = {The interaction between microbiome and pig efficiency: A review.},
journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie},
volume = {},
number = {},
pages = {},
doi = {10.1111/jbg.12443},
pmid = {31576623},
issn = {1439-0388},
support = {(NPB 16-020)//National Pork Board/ ; },
abstract = {The existence of genetic control over the abundance of particular taxa and the link of these to energy balance and growth has been documented in model organisms and humans as well as several livestock species. Preliminary evidence of the same mechanisms is currently under investigation in pigs. Future research should expand these results and elicit the extent of genetic control of the gut microbiome population in swine and its relationship with growth efficiency. The quest for a more efficient pig at the interface between the host and its metagenome rests on the central hypothesis that the gut microbiome is an essential component of the variability of growth in all living organisms. Swine do not escape this general rule, and the identification of the significance of the interaction between host and its gut microbiota in the growth process could be a game-changer in the achievement of sustainable and efficient lean meat production. Standard sampling protocols, sequencing techniques, bioinformatic pipelines and methods of analysis will be paramount for the portability of results across experiments and populations. Likewise, characterizing and accounting for temporal and spatial variability will be a necessary step if microbiome is to be utilized routinely as an aid to selection.},
}

@article {pmid31576454,
year = {2019},
author = {Alibrahim, A and Al-Gharabally, D and Mahmoud, H and Dittrich, M},
title = {Proto-dolomite formation in microbial consortia dominated by Halomonas strains.},
journal = {Extremophiles : life under extreme conditions},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00792-019-01135-2},
pmid = {31576454},
issn = {1433-4909},
support = {PR17-12SL-10//Kuwait Foundation for the Advancement of Sciences/ ; },
abstract = {Microbes can be found in hypersaline environments forming diverse populations with complex ecological interactions. Microbes in such environments were found to be involved in the formation of minerals including dolomite, a mineral of economic importance and whose origin has been long-debated. Various reports on in vitro experiments using pure cultures provided evidence for the microbial role in dolomite formation. However, culturing experiments have been limited in scope and do not fully address the possible interactions of the naturally occurring microbial communities; consequently, the ability of microbes as a community to form dolomite has been investigated in this study. Our experiments focused on examining the microbial composition by culturing aerobic heterotrophs from the top hypersaline sediments of Al-Khiran sabkha in Kuwait, a modern dolomite-forming environment. The objectives of this study were to assess the ability of two microbial consortia to form dolomite using enrichment culture experiments, mineralogy, and metagenomics. Proto-dolomite was formed by a microbial community dominated by Halomonas strains whereby degradation of the extracellular polymeric substances (EPS) was observed and the pH changed from 7.00 to 8.58. Conversely, proto-dolomite was not observed within a microbial community dominated by Clostridiisalibacter in which EPS continuously accumulated and the pH slightly changed from 7.00 to 7.29.},
}

@article {pmid31576426,
year = {2019},
author = {Long, Y and Jiang, J and Hu, X and Zhou, J and Hu, J and Zhou, S},
title = {Actinobacterial community in Shuanghe Cave using culture-dependent and -independent approaches.},
journal = {World journal of microbiology & biotechnology},
volume = {35},
number = {10},
pages = {153},
doi = {10.1007/s11274-019-2713-y},
pmid = {31576426},
issn = {1573-0972},
support = {2016YFC0400702//National Key R&D Program of China/ ; },
abstract = {Karst caves, considering to be the "arks" of biodiversity, often contain high levels of endemism. In the present study, the actinobacterial community in Shuanghe Cave, the longest cave in Asia, was analyzed for the first-time using culture-dependent and -independent (16S rRNA amplicon sequencing) approaches. The amplicon sequencing analysis revealed a broad taxonomic diversity in Shuanghe Cave, including 19 phyla (predominantly Actinobacteria) and 264 different genera. While the culture-dependent method got the unrepresentative but supplemental result, a total of 239 actinomycetes were isolated and were identified to seven genera based on culture features and 16S rRNA tests. Among the three habitats (soil, rock soil, and bat guano), the dominant phyla did not differ significantly, while the dominant genus community varied among different habitats, and the richness in soil and rock soil samples was higher than that in bat guano. Furthermore, 16 isolate strains showed antimicrobial activity, especially, the strain S142 (Streptomyces badius) and S761 (Actinoplanes friuliensis) exhibited the most promising activity against various pathogens. Overall, this work showed the abundant bacterial diversity and the antimicrobial potential of the isolates from the Shuanghe Cave.},
}

@article {pmid31575762,
year = {2019},
author = {Brewer, TE and Aronson, EL and Arogyaswamy, K and Billings, SA and Botthoff, JK and Campbell, AN and Dove, NC and Fairbanks, D and Gallery, RE and Hart, SC and Kaye, J and King, G and Logan, G and Lohse, KA and Maltz, MR and Mayorga, E and O'Neill, C and Owens, SM and Packman, A and Pett-Ridge, J and Plante, AF and Richter, DD and Silver, WL and Yang, WH and Fierer, N},
title = {Ecological and Genomic Attributes of Novel Bacterial Taxa That Thrive in Subsurface Soil Horizons.},
journal = {mBio},
volume = {10},
number = {5},
pages = {},
doi = {10.1128/mBio.01318-19},
pmid = {31575762},
issn = {2150-7511},
abstract = {While most bacterial and archaeal taxa living in surface soils remain undescribed, this problem is exacerbated in deeper soils, owing to the unique oligotrophic conditions found in the subsurface. Additionally, previous studies of soil microbiomes have focused almost exclusively on surface soils, even though the microbes living in deeper soils also play critical roles in a wide range of biogeochemical processes. We examined soils collected from 20 distinct profiles across the United States to characterize the bacterial and archaeal communities that live in subsurface soils and to determine whether there are consistent changes in soil microbial communities with depth across a wide range of soil and environmental conditions. We found that bacterial and archaeal diversity generally decreased with depth, as did the degree of similarity of microbial communities to those found in surface horizons. We observed five phyla that consistently increased in relative abundance with depth across our soil profiles: Chloroflexi, Nitrospirae, Euryarchaeota, and candidate phyla GAL15 and Dormibacteraeota (formerly AD3). Leveraging the unusually high abundance of Dormibacteraeota at depth, we assembled genomes representative of this candidate phylum and identified traits that are likely to be beneficial in low-nutrient environments, including the synthesis and storage of carbohydrates, the potential to use carbon monoxide (CO) as a supplemental energy source, and the ability to form spores. Together these attributes likely allow members of the candidate phylum Dormibacteraeota to flourish in deeper soils and provide insight into the survival and growth strategies employed by the microbes that thrive in oligotrophic soil environments.IMPORTANCE Soil profiles are rarely homogeneous. Resource availability and microbial abundances typically decrease with soil depth, but microbes found in deeper horizons are still important components of terrestrial ecosystems. By studying 20 soil profiles across the United States, we documented consistent changes in soil bacterial and archaeal communities with depth. Deeper soils harbored communities distinct from those of the more commonly studied surface horizons. Most notably, we found that the candidate phylum Dormibacteraeota (formerly AD3) was often dominant in subsurface soils, and we used genomes from uncultivated members of this group to identify why these taxa are able to thrive in such resource-limited environments. Simply digging deeper into soil can reveal a surprising number of novel microbes with unique adaptations to oligotrophic subsurface conditions.},
}

@article {pmid31575666,
year = {2019},
author = {Zhang, X and Johnston, ER and Wang, Y and Yu, Q and Tian, D and Wang, Z and Zhang, Y and Gong, D and Luo, C and Liu, W and Yang, J and Han, X},
title = {Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes.},
journal = {mSystems},
volume = {4},
number = {5},
pages = {},
doi = {10.1128/mSystems.00374-19},
pmid = {31575666},
issn = {2379-5077},
abstract = {It is a central ecological goal to explore the effects of global change factors on soil microbial communities. The vast functional gene repertoire of soil microbial communities is composed of both core and accessory genes, which may be governed by distinct drivers. This intuitive hypothesis, however, remains largely unexplored. We conducted a 5-year nitrogen and water addition experiment in the Eurasian steppe and quantified microbial gene diversity via shotgun metagenomics. Nitrogen addition led to an 11-fold increase in the abundance (based on quantitative PCR [qPCR]) of ammonia-oxidizing bacteria, which have mainly core community genes and few accessory community genes. Thus, nitrogen addition substantially increased the relative abundance of many core genes at the whole-community level. Water addition stimulated both plant diversity and microbial respiration; however, increased carbon/energy resources from plants did not counteract increased respiration, so soil carbon/energy resources became more limited. Thus, water addition selected for microorganisms with genes responsible for degrading recalcitrant soil organic matter. Accordingly, many other microorganisms without these genes (but likely with other accessory community genes due to relatively stable average microbial genome size) were selected against, leading to the decrease in the diversity of accessory community genes. In summary, nitrogen addition primarily affected core community genes through nitrogen-cycling processes, and water addition primarily regulated accessory community genes through carbon-cycling processes. Although both gene components may significantly respond as the intensity of nitrogen/water addition increases, our results demonstrated how these common global change factors distinctly impact each component.IMPORTANCE Our results demonstrated increased ecosystem nitrogen and water content as the primary drivers of the core and accessory components of soil microbial community functional diversity, respectively. Our findings suggested that more attention should be paid to certain components of community functional diversity under specific global change conditions. Our findings also indicated that microbial communities have adapted to nitrogen addition by strengthening the function of ammonia oxidization to deplete the excess nitrogen, thus maintaining ecosystem homeostasis. Because community gene richness is primarily determined by the presence/absence of accessory community genes, our findings further implied that strategies such as maintaining the amount of soil organic matter could be adopted to effectively improve the functional gene diversity of soil microbial communities subject to global change factors.},
}

@article {pmid31575055,
year = {2019},
author = {Di Martino, B and Di Profio, F and Melegari, I and Marsilio, F},
title = {Feline Virome-A Review of Novel Enteric Viruses Detected in Cats.},
journal = {Viruses},
volume = {11},
number = {10},
pages = {},
doi = {10.3390/v11100908},
pmid = {31575055},
issn = {1999-4915},
abstract = {Recent advances in the diagnostic and metagenomic investigations of the feline enteric environment have allowed the identification of several novel viruses that have been associated with gastroenteritis in cats. In the last few years, noroviruses, kobuviruses, and novel parvoviruses have been repetitively detected in diarrheic cats as alone or in mixed infections with other pathogens, raising a number of questions, with particular regards to their pathogenic attitude and clinical impact. In the present article, the current available literature on novel potential feline enteric viruses is reviewed, providing a meaningful update on the etiology, epidemiologic, pathogenetic, clinical, and diagnostic aspects of the infections caused by these pathogens.},
}

@article {pmid31575004,
year = {2019},
author = {Needle, DB and Gibson, R and Hollingshead, NA and Sidor, IF and Marra, NJ and Rothenheber, D and Thachil, AJ and Stanhope, BJ and Stevens, BA and Ellis, JC and Spanswick, S and Murray, M and Goodman, LB},
title = {Atypical Dermatophytosis in 12 North American Porcupines (Erethizon dorsatum) from the Northeastern United States 2010-2017.},
journal = {Pathogens (Basel, Switzerland)},
volume = {8},
number = {4},
pages = {},
doi = {10.3390/pathogens8040171},
pmid = {31575004},
issn = {2076-0817},
support = {U18FD006448//U.S. Food and Drug Administration/ ; U18FD005144//U.S. Food and Drug Administration/ ; },
abstract = {Twelve wild North American porcupines (Erethizon dorsatum) out of a total of 44 of this species examined in an 8-year period were diagnosed with dermatopathies while being cared for at two wildlife rehabilitation clinics. Biopsy and necropsy were performed on seven and five animals, respectively. Atypical dermatophytosis was diagnosed in all cases. Lesions consisted of diffuse severe epidermal hyperkeratosis and mild hyperplasia with mild lymphoplasmacytic dermatitis and no folliculitis. Dermatophytes were noted histologically as hyphae and spores in hair shafts, and follicular and epidermal keratin. Trichophyton sp. was grown in 5/6 animals where culture was performed, with a molecular diagnosis of Arthroderma benhamiae/Trichophyton mentagrophytes in these five cases. Metagenomic analysis of formalin-fixed paraffin-embedded tissue samples from three cases identified fungi from 17 orders in phyla Basidiomycota and Ascomycota. Alteration of therapy from ketaconazole, which was unsuccessful in four out of five early cases, to terbinafine or nitraconazole led to the resolution of disease and recovery to release in four subsequent animals. In all, six animals were euthanized or died due to dermatopathy, no cases resolved spontaneously, and six cases were resolved with therapy. The work we present demonstrates an atypical lesion and anatomical distribution due to dermatophytosis in a series of free-ranging wild porcupines and the successful development of novel techniques for extracting and sequencing nucleic acids from fungus in archival formalin-fixed paraffin-embedded animal tissue.},
}

@article {pmid31574349,
year = {2019},
author = {Chen, H and Bai, X and Li, Y and Jing, L and Chen, R and Teng, Y},
title = {Source identification of antibiotic resistance genes in a peri-urban river using novel crAssphage marker genes and metagenomic signatures.},
journal = {Water research},
volume = {167},
number = {},
pages = {115098},
doi = {10.1016/j.watres.2019.115098},
pmid = {31574349},
issn = {1879-2448},
abstract = {Antimicrobial resistance is a growing public health concern, and environment is regarded as an important reservoir and dissemination route for antibiotic resistance genes (ARGs). To prevent and control ARG pollution, it is essential to correctly disentangle source-sink relationship of ARGs in the environment. However, accurately apportioning sources of ARGs is still a big challenge due to the complex interaction of multiple sources and contaminants in the environment with changing dynamics. In this study, we addressed this problem and focused on identifying the potential sources of ARGs in a peri-urban river by jointly utilizing two novel microbial source tracking methods. To attain the objective, sediment/water samples were collected from the peri-urban river and four ARG-associated ecotypes including effluents of sewage treatment plants (STPs), STP influent, chicken manures and pig manures. The high-throughput profilings of ARGs and microbial taxa in the river sediments and the four ecotypes were comprehensively characterized in combination of shotgun sequencing and metagenomic assembly analysis. CrAssphage, a recently-discovered DNA bacteriophage, was employed to track the impact of human fecal pollution on ARGs in the river sediments. Further, SourceTracker, a machine-learning classification tool, was used for quantifying the contributions of potential sources to ARGs in the river sediments based on the metagenomic signatures of ARGs and microbial taxa. In total, 888 ARG subtypes belonging to 29 ARG types were detected across all samples, including mcr-1 and a range of carbapenemases types. Statistical analyses suggested different ecotypes generally had distinct profiles of both ARGs and microbial taxa, while the ARG compositions were significantly correlated with the microbial community. Source tracking with crAssphage showed the presence of ARGs in the river sediments might be largely impacted by the extent of human fecal pollution, which was also confirmed by the analyses of SourceTracker that the discharge from STPs was the largest contributor of ARGs (81.6-92.1%) and microbes (49.3-68.1%) in the river sediments. Results of the study can help us to better understand the characterization of ARGs in the peri-urban ecosystem and to design effective prevention and control strategies for reducing ARG dissemination.},
}

@article {pmid31573126,
year = {2019},
author = {Galambos, D and Anderson, RE and Reveillaud, J and Huber, JA},
title = {Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.14806},
pmid = {31573126},
issn = {1462-2920},
abstract = {The structure and function of microbial communities inhabiting the subseafloor near hydrothermal systems are influenced by fluid geochemistry, geologic setting, and fluid flux between vent sites, as well as biological interactions. Here we used genome-resolved metagenomics and metatranscriptomics to examine patterns of gene abundance and expression and assess potential niche differentiation in microbial communities in venting fluids from hydrothermal vent sites at the Mid-Cayman Rise. We observed similar patterns in gene and transcript abundance between two geochemically distinct vent fields at the community level, but found that each vent site harbors a distinct microbial community with differing transcript abundances for individual microbial populations. Through an analysis of metabolic pathways in 64 metagenome-assembled genomes (MAGs), we show that MAG transcript abundance can be tied to differences in metabolic pathways and to potential metabolic interactions between microbial populations, allowing for niche-partitioning and divergence in both population distribution and activity. Our results illustrate that most microbial populations have a restricted distribution within the seafloor, and that the activity of those microbial populations is tied to both genome content and abiotic factors. This article is protected by copyright. All rights reserved.},
}

@article {pmid31572686,
year = {2019},
author = {Genton, L and Mareschal, J and Charretier, Y and Lazarevic, V and Bindels, LB and Schrenzel, J},
title = {Targeting the Gut Microbiota to Treat Cachexia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {305},
doi = {10.3389/fcimb.2019.00305},
pmid = {31572686},
issn = {2235-2988},
abstract = {Cachexia occurs in many chronic diseases and is associated with increased morbidity and mortality. It is treated by nutritional support but often with limited effectiveness, leading to the search of other therapeutic strategies. The modulation of gut microbiota, whether through pro-, pre-, syn- or antibiotics or fecal transplantation, is attracting ever-growing interest in the field of obesity, but could also be an interesting and innovative alternative for treating cachexia. This article reviews the evidence linking the features of malnutrition, as defined by the Global Leadership Initiative on Malnutrition [low body mass index (BMI), unintentional body weight loss, low muscle mass, low appetite, and systemic inflammation] and the gut microbiota in human adults with cachexia-associated diseases, and shows the limitations of the present research in that field with suggestions for future directions.},
}

@article {pmid31571125,
year = {2019},
author = {Oh, HN and Park, D and Seong, HJ and Kim, D and Sul, WJ},
title = {Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {57},
number = {10},
pages = {865-873},
doi = {10.1007/s12275-019-9217-1},
pmid = {31571125},
issn = {1976-3794},
abstract = {Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil's metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.},
}

@article {pmid29738088,
year = {2018},
author = {Faure, D and Simon, JC and Heulin, T},
title = {Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems.},
journal = {The New phytologist},
volume = {218},
number = {4},
pages = {1321-1324},
doi = {10.1111/nph.15199},
pmid = {29738088},
issn = {1469-8137},
mesh = {*Biological Evolution ; *Ecosystem ; Genomics ; *Host Microbial Interactions/genetics ; Metagenome ; Research Personnel ; },
}

*Biological Evolution
*Ecosystem
Genomics
*Host Microbial Interactions/genetics
Metagenome
Research Personnel

@article {pmid29636512,
year = {2018},
author = {Pechal, JL and Schmidt, CJ and Jordan, HR and Benbow, ME},
title = {A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {5724},
pmid = {29636512},
issn = {2045-2322},
mesh = {*Autopsy ; Computational Biology/methods ; Cross-Sectional Studies ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Time Factors ; },
abstract = {The microbiome plays many roles in human health, often through the exclusive lens of clinical interest. The inevitable end point for all living hosts, death, has its own altered microbiome configurations. However, little is understood about the ecology and changes of microbial communities after death, or their potential utility for understanding the health condition of the recently living. Here we reveal distinct postmortem microbiomes of human hosts from a large-scale survey of death cases representing a predominantly urban population, and demonstrated these microbiomes reflected antemortem health conditions within 24-48 hours of death. Our results characterized microbial community structure and predicted function from 188 cases representing a cross-section of an industrial-urban population. We found strong niche differentiation of anatomic habitat and microbial community turnover based on topographical distribution. Microbial community stability was documented up to two days after death. Additionally, we observed a positive relationship between cell motility and time since host death. Interestingly, we discovered evidence that microbial biodiversity is a predictor of antemortem host health condition (e.g., heart disease). These findings improve the understanding of postmortem host microbiota dynamics, and provide a robust dataset to test the postmortem microbiome as a tool for assessing health conditions in living populations.},
}

*Autopsy
Computational Biology/methods
Cross-Sectional Studies
Humans
Metagenome
Metagenomics/methods
*Microbiota
Time Factors

@article {pmid29604236,
year = {2018},
author = {Chen, KH and Liao, HL and Arnold, AE and Bonito, G and Lutzoni, F},
title = {RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi.},
journal = {The New phytologist},
volume = {218},
number = {4},
pages = {1597-1611},
doi = {10.1111/nph.15092},
pmid = {29604236},
issn = {1469-8137},
mesh = {Bryophyta/genetics/*microbiology ; Endophytes/physiology ; Fungi/*genetics ; Metagenome ; RNA, Fungal/genetics/*metabolism ; RNA, Ribosomal/metabolism ; Transcription, Genetic ; Transcriptome/genetics ; },
abstract = {Diverse plant-associated fungi are thought to have symbiotrophic and saprotrophic states because they can be isolated from both dead and living plant tissues. However, such tissues often are separated in time and space, and fungal activity at various stages of plant senescence is rarely assessed directly in fungal community studies. We used fungal ribosomal RNA metatranscriptomics to detect active fungal communities across a natural senescence gradient within wild-collected gametophytes of Dicranum scoparium (Bryophyta) to understand the distribution of active fungal communities in adjacent living, senescing and dead tissues. Ascomycota were active in all tissues across the senescence gradient. By contrast, Basidiomycota were prevalent and active in senescing and dead tissues. Several fungi were detected as active in living and dead tissues, suggesting their capacity for multi-trophy. Differences in community assembly detected by metatranscriptomics were echoed by amplicon sequencing of cDNA and compared to culture-based inferences and observation of fungal fruit bodies in the field. The combination of amplicon sequencing of cDNA and metatranscriptomics is promising for studying symbiotic systems with complex microbial diversity, allowing for the simultaneous detection of their presence and activity.},
}

Bryophyta/genetics/*microbiology
Endophytes/physiology
Fungi/*genetics
Metagenome
RNA, Fungal/genetics/*metabolism
RNA, Ribosomal/metabolism
Transcription, Genetic
Transcriptome/genetics

@article {pmid31568677,
year = {2019},
author = {Feng, Y and Duan, Y and Xu, Z and Lyu, N and Liu, F and Liang, S and Zhu, B},
title = {An examination of data from the American Gut Project reveals that the dominance of the genus Bifidobacterium is associated with the diversity and robustness of the gut microbiota.},
journal = {MicrobiologyOpen},
volume = {},
number = {},
pages = {e939},
doi = {10.1002/mbo3.939},
pmid = {31568677},
issn = {2045-8827},
support = {2015CB554200//National Basic Research Program of China/ ; 31601081//National Natural Science Foundation of China/ ; 5174037//Beijing Municipal Natural Science Foundation/ ; },
abstract = {Bifidobacterium and Lactobacillus are beneficial for human health, and many strains of these two genera are widely used as probiotics. We used two large datasets published by the American Gut Project (AGP) and a gut metagenomic dataset (NBT) to analyze the relationship between these two genera and the community structure of the gut microbiota. The meta-analysis showed that Bifidobacterium, but not Lactobacillus, is among the dominant genera in the human gut microbiota. The relative abundance of Bifidobacterium was elevated when Lactobacillus was present. Moreover, these two genera showed a positive correlation with some butyrate producers among the dominant genera, and both were associated with alpha diversity, beta diversity, and the robustness of the gut microbiota. Additionally, samples harboring Bifidobacterium present but no Lactobacillus showed higher alpha diversity and were more robust than those only carrying Lactobacillus. Further comparisons with other genera validated the important role of Bifidobacterium in the gut microbiota robustness. Multivariate analysis of 11,744 samples from the AGP dataset suggested Bifidobacterium to be associated with demographic features, lifestyle, and disease. In summary, Bifidobacterium members, which are promoted by dairy and whole-grain consumption, are more important than Lactobacillus in maintaining the diversity and robustness of the gut microbiota.},
}

@article {pmid31568480,
year = {2019},
author = {Gawande, SJ and Anandhan, S and Ingle, A and Roylawar, P and Khandagale, K and Gawai, T and Jacobson, A and Asokan, R and Singh, M},
title = {Microbiome profiling of the onion thrips, Thrips tabaci Lindeman (Thysanoptera: Thripidae).},
journal = {PloS one},
volume = {14},
number = {9},
pages = {e0223281},
doi = {10.1371/journal.pone.0223281},
pmid = {31568480},
issn = {1932-6203},
abstract = {The gut microbial community structure of adult Thrips tabaci collected from 10 different agro-climatically diverse locations of India was characterized by using the Illumina MiSeq platform to amplify the V3 region of the 16S rRNA gene of bacteria present in the sampled insects. Analyses were performed to study the bacterial communities associated with Thrips tabaci in India. The complete bacterial metagenome of T. tabaci was comprised of 1662 OTUs of which 62.25% belong to known and 37.7% of unidentified/unknown bacteria. These OTUs constituted 21 bacterial phyla of 276 identified genera. Phylum Proteobacteria was predominant, followed by Actinobacteria, Firmicutes, Bacteroidetes and Cyanobacteria. Additionally, the occurrence of the reproductive endosymbiont, Wolbachia was detected at two locations (0.56%) of the total known OTUs. There is high variation in diversity and species richness among the different locations. Alpha-diversity metrics indicated the higher gut bacterial diversity at Bangalore and lowest at Rahuri whereas higher bacterial species richness at T. tabaci samples from Imphal and lowest at Jhalawar. Beta diversity analyses comparing bacterial communities between the samples showed distinct differences in bacterial community composition of T. tabaci samples from different locations. This paper also constitutes the first record of detailed bacterial communities associated with T. tabaci. The location-wise variation in microbial metagenome profile of T. tabaci suggests that bacterial diversity might be governed by its population genetic structure, environment and habitat.},
}

@article {pmid31567695,
year = {2019},
author = {Valerio, GS and Lin, CC},
title = {Ocular manifestations of herpes simplex virus.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICU.0000000000000618},
pmid = {31567695},
issn = {1531-7021},
abstract = {PURPOSE OF REVIEW: To review ocular manifestations and complications of herpes simplex virus (HSV) and discuss recent advancements in diagnostic and treatment strategy.

RECENT FINDINGS: In-vivo confocal microscopy has expanded our understanding of corneal nerve degeneration, corneal dendritic cell activity, and changes in biomechanical properties in HSV keratitis. Although currently available only as a research tool, metagenomic deep sequencing has the potential to improve diagnostic accuracy beyond the well established PCR technology, especially in atypical cases. Development of an HSV vaccine has shown some encouraging results in a murine model. New treatment options for neurotrophic cornea offer promise, specifically cenegermin nerve growth factor.

SUMMARY: Ocular herpes simplex infection and its complications continue to cause significant visual burden and decreased quality of life. Familiarity with its clinical features, wider adoption of viral PCR diagnostic technology, and recognition of the need for long-term maintenance medications for recurrent or chronic cases form the basis for effective management. Metagenomic deep sequencing, the development of a herpes vaccine, and cenegermin nerve growth factor offer promise as diagnostic, preventive, and therapeutic options, respectively.},
}

@article {pmid31566729,
year = {2019},
author = {Kusakabe, S and Fukushima, K and Maeda, T and Motooka, D and Nakamura, S and Fujita, J and Yokota, T and Shibayama, H and Oritani, K and Kanakura, Y},
title = {Pre- and post-serial metagenomic analysis of gut microbiota as a prognostic factor in patients undergoing haematopoietic stem cell transplantation.},
journal = {British journal of haematology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjh.16205},
pmid = {31566729},
issn = {1365-2141},
abstract = {The human gut harbours diverse microorganisms, and gut dysbiosis has recently attracted attention because of its possible involvement in various diseases. In particular, the lack of diversity in the gut microbiota has been associated with complications of haematopoietic stem cell transplantation (HSCT), such as infections, acute graft-versus-host disease and relapse of primary disease, which lead to a poor prognosis. However, few studies have serially examined the composition of the intestinal microbiota after HSCT. In this study, we demonstrated, using next-generation sequencing of the bacterial 16S ribosomal RNA gene, combined with uniFrac distance analysis, that the intestinal microbiota of patients undergoing allogeneic HSCT substantially differed from that of healthy controls and recipients of autologous transplants. Faecal samples were obtained daily throughout the clinical course, before and after transplantation. Notably, the proportions of Bifidobacterium and genera categorized as butyrate-producing bacteria were significantly lower in patients with allogeneic HSCT than in healthy controls. Furthermore, among allogeneic transplant recipients, a subgroup with a preserved microbiota composition showed a benign course, whereas patients with a skewed microbiota showed a high frequency of complications and mortality after transplantation. Thus, we conclude that the stability of intestinal microbiota is critically involved in outcomes of HSCT.},
}

@article {pmid31566105,
year = {2019},
author = {Amar, J and Lelouvier, B and Servant, F and Lluch, J and Burcelin, R and Bongard, V and Elbaz, M},
title = {Blood Microbiota Modification After Myocardial Infarction Depends Upon Low-Density Lipoprotein Cholesterol Levels.},
journal = {Journal of the American Heart Association},
volume = {8},
number = {19},
pages = {e011797},
doi = {10.1161/JAHA.118.011797},
pmid = {31566105},
issn = {2047-9980},
abstract = {Background The role of bacteria on the onset of cardiovascular disease has been suggested. Reciprocally, increased intestinal bacterial translocation and bloodstream infection are common comorbidities associated with heart failure and myocardial infarction (MI). In this context, the aim of this study was to analyze the blood microbiome in patients shortly after acute myocardial infarction. Methods and Results We carried out a case control study comparing 103 patients at high cardiovascular risk but free of coronary disease and 99 patients who had an MI. The blood microbiome was analyzed both quantitatively by 16S quantitative polymerase chain reaction and qualitatively by 16S targeted metagenomic sequencing specifically optimized for blood samples. A significant increase in blood bacterial 16S rDNA concentration was observed in patients admitted for MI. This increase in blood bacterial DNA concentration was independent of post-MI left ventricular function and was more marked in patients with low-density lipoprotein cholesterol ≥1 g/L. In addition, differences in the proportion of numerous bacterial taxa in blood were significantly modified with the onset of MI, thus defining a blood microbiota signature of MI. Among the bacterial taxa whose proportions are decreased in patients with MI, at least 6 are known to include species able to metabolize cholesterol. Conclusions These results could provide the basis for the identification of blood microbiome-based biomarkers for the stratification of MI patients. Furthermore, these findings should provide insight into the mechanism underlying the negative correlation reported between low-density lipoprotein cholesterol concentration and the prognosis at the acute onset of MI and mortality. Clinical Trial Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT02405468.},
}

@article {pmid31564944,
year = {2019},
author = {Gibbons, TF and Noe, JC and Patterson, AT and Lenz, BL and Beachkofsky, TM},
title = {Temporal shifts in the collective dermatologic microbiome of military trainees.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {12},
number = {},
pages = {625-637},
doi = {10.2147/CCID.S216993},
pmid = {31564944},
issn = {1178-7015},
abstract = {Background: New military members undergo a highly-regimented 7-week training course during which trainees live and work within the same group of approximately 50 subjects for nearly 24 hours a day. This creates an optimal environment for assessing the impact of communal living on the collective skin microbiome.

Purpose : The objective of this pilot study was to investigate dynamic changes of the skin microbiome in basic military trainees (BMT), in light of the unique environmental influences faced by this population.

Patients and methods: We evaluated collective changes in the skin microbiome of normal healthy adult basic trainees in response to communal living and universal Group A Strep prophylaxis with penicillin over the course of their initial 7-week training course. Samples from 10 flights of trainees were collected by swabbing upon arrival at Lackland AFB for their training (week 0) which is prior to prophylaxis with penicillin, at the 4 week point, and at the conclusion of their 7-week course of basic military training. Three separate high-throughput sequencing platforms and three bioinformatic pipeline analysis tools were utilized to assess the data.

Results : At all three time points we found that the top three bacterial genus identified were Propionibacterium, Staphylococcus, and Corynebacterium. We detected a community membership difference between the initial week 0 samples and the week 4 and 7 samples. A strong inverse correlation between Propionibacterium and Staphylococcus was noted with Propionibacterium being high at week 0 and much lower at weeks 4 and 7; conversely, Staphylococcus was low at week 0 and higher at weeks 4 and 7, this relationship was noted in both the individual and collective specimens.

Conclusion : The collective dermatologic microbiome in the military trainee population examined exhibited a relative increase in Staphylococcus and Corynebacterium abundance coupled with a relative decrease in Propionibacterium abundance in this observational pilot study. Additional studies are needed to further assess the causal impact of communal living and widespread penicillin chemoprophylaxis.},
}

@article {pmid31564708,
year = {2019},
author = {Zheng, A and Yi, H and Li, F and Han, L and Yu, J and Cheng, X and Su, H and Hong, K and Li, J},
title = {Changes in Gut Microbiome Structure and Function of Rats with Isoproterenol-Induced Heart Failure.},
journal = {International heart journal},
volume = {60},
number = {5},
pages = {1176-1183},
doi = {10.1536/ihj.18-194},
pmid = {31564708},
issn = {1349-3299},
abstract = {Recently, the potential role of gut microbiome (GM) in cardiovascular diseases has been revealed. Heart failure (HF) is one of the most prevalent cardiovascular diseases worldwide; however, whether GM dysbiosis participates in the development of HF remains largely unknown. This study aimed to investigate the specific changes in GM composition and function in isoproterenol (ISO)-induced HF in rats.The rats were divided into C (control), 4w-HF (ISO, 2.5 mg/kg/day for 4 weeks, intraperitoneally), and 2w-HF (ISO, 2.5 mg/kg/day for 2 weeks, intraperitoneally) groups. The cardiac structure and function in rats were assessed, and metagenomic analyses were then performed. Compared with the healthy control group, we found that the Shannon diversity index and microbial gene count in the 4w-HF and 2w-HF groups was drastically decreased. High-throughput sequencing showed that the three groups differed in intestinal bacterial community composition. Overgrowth of bacteria, such as Prevotella, was observed in the 4w-HF group, with reduced growth of bacteria, such as Roseburia, Lactobacillus, and Butyrivibrio, associated with healthy status compared with the C group on the genus level. Concomitant with the alteration of GM composition, underrepresentation of health-linked microbial function was observed in both the 4w-HF and 2w-HF groups compared with the C group.Iso-induced HF rats showed a significant decrease in the diversity and richness of the intestinal microbiome, with a downregulation of the key intestinal bacterial groups and overgrowth of bacteria considered to be involved in inflammatory responses as well as a decrease in health-linked microbial function. Our data indicated that altered GM may be a potential player in the pathogenesis and progression of HF.},
}

@article {pmid30208728,
year = {2018},
author = {Myint, H and Kishi, H and Iwahashi, Y and Saburi, W and Koike, S and Kobayashi, Y},
title = {Functional modulation of caecal fermentation and microbiota in rat by feeding bean husk as a dietary fibre supplement.},
journal = {Beneficial microbes},
volume = {9},
number = {6},
pages = {963-974},
doi = {10.3920/BM2017.0174},
pmid = {30208728},
issn = {1876-2891},
mesh = {*Animal Feed ; Animals ; Cecum/*metabolism/*microbiology ; Dietary Fiber/*administration & dosage ; Fermentation/*drug effects ; Gastrointestinal Contents/chemistry ; Gastrointestinal Microbiome/*drug effects ; Metagenomics ; Organic Chemicals/analysis ; Phaseolus ; Prebiotics/*administration & dosage ; Rats, Sprague-Dawley ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; Soybeans ; },
abstract = {A feeding study using rats was conducted to evaluate the utility of lablab bean husk and soya bean husk as sources of potential prebiotic fibre. Twenty 5-week-old Sprague Dawley rats were divided into 4 groups and fed one of the following diets for 3 weeks: purified diet (AIN93 G) containing 5% cellulose (CEL), or the same diet in which cellulose was replaced by corn starch (STA), lablab bean husk (LBH), or soya bean husk (SBH). Rats were sacrificed at 8 weeks of age and caecal digesta were collected. Feed intake, body weight, anatomical parameters, and caecal ammonia level did not differ significantly among diets. Rats on LBH and SBH showed higher concentrations of caecal short-chain fatty acid and lactate than those on CEL. Rats on CEL, SBH, and LBH exhibited lower caecal indole and skatole levels. LBH yielded increased caecal abundance of Akkermansia muciniphila and Oscillibacter relatives, as demonstrated by either qPCR, MiSeq, or clone library analysis. SBH favoured the growth of lactobacilli as assessed by both qPCR and MiSeq, and favoured the growth of bifidobacteria as assessed by MiSeq. In comparison with STA, LBH and SBH yielded lower caecal abundance of bacteria related to Dorea massiliensis, as demonstrated by qPCR, MiSeq, and clone library analysis. Both types of bean husk were found to contain oligosaccharides that might selectively stimulate the growth of beneficial bacteria. Based on these results, the two species of bean husk tested are considered potentially functional for promoting the gut health of monogastric animals.},
}

*Animal Feed
Animals
Cecum/*metabolism/*microbiology
Dietary Fiber/*administration & dosage
Fermentation/*drug effects
Gastrointestinal Contents/chemistry
Gastrointestinal Microbiome/*drug effects
Metagenomics
Organic Chemicals/analysis
Phaseolus
Prebiotics/*administration & dosage
Rats, Sprague-Dawley
Real-Time Polymerase Chain Reaction
Sequence Analysis, DNA
Soybeans

@article {pmid29540790,
year = {2018},
author = {Ushio, M and Murata, K and Sado, T and Nishiumi, I and Takeshita, M and Iwasaki, W and Miya, M},
title = {Demonstration of the potential of environmental DNA as a tool for the detection of avian species.},
journal = {Scientific reports},
volume = {8},
number = {1},
pages = {4493},
pmid = {29540790},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; Birds/*classification/*genetics ; Computational Biology/methods ; *DNA ; DNA Barcoding, Taxonomic ; Metagenomics/methods ; Phylogeny ; },
abstract = {Birds play unique functional roles in the maintenance of ecosystems, such as pollination and seed dispersal, and thus monitoring bird species diversity is a first step towards avoiding undesirable consequences of anthropogenic impacts on bird communities. In the present study, we hypothesized that birds, regardless of their main habitats, must have frequent contact with water and that tissues that contain their DNA that persists in the environment (environmental DNA; eDNA) could be used to detect the presence of avian species. To this end, we applied a set of universal PCR primers (MiBird, a modified version of fish/mammal universal primers) for metabarcoding avian eDNA. We confirmed the versatility of MiBird primers by performing in silico analyses and by amplifying DNAs extracted from bird tissues. Analyses of water samples from zoo cages of birds with known species composition suggested that the use of MiBird primers combined with Illumina MiSeq could successfully detect avian species from water samples. Additionally, analysis of water samples collected from a natural pond detected five avian species common to the sampling areas. The present findings suggest that avian eDNA metabarcoding would be a complementary detection/identification tool in cases where visual census of bird species is difficult.},
}

Animals
Biodiversity
Birds/*classification/*genetics
Computational Biology/methods
*DNA
DNA Barcoding, Taxonomic
Metagenomics/methods
Phylogeny

@article {pmid31563955,
year = {2019},
author = {Weinroth, MD and Martin, JN and Doster, E and Geornaras, I and Parker, JK and Carlson, CR and Metcalf, JL and Morley, PS and Belk, KE},
title = {Investigation of tylosin in feed of feedlot cattle and effects on liver abscess prevalence, and fecal and soil microbiomes and resistomes.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skz306},
pmid = {31563955},
issn = {1525-3163},
abstract = {Liver abscesses in feedlot cattle are detrimental to animal performance and economic return. Tylosin, a macrolide antibiotic, is used to reduce prevalence of liver abscesses, though there is variable efficacy among different groups of cattle. There is an increased importance in better understanding the etiology and pathogenesis of this condition because of growing concern over antibiotic resistance and increased scrutiny regarding use of antibiotics in food animal production. The objective of this study was to compare the microbiomes and antimicrobial resistance genes (resistomes) of feces of feedlot cattle administered or not administered tylosin and in their pen soil in three geographical regions with differing liver abscess prevalences. Cattle (total of 2,256) from three geographical regions were selected for inclusion based on dietary supplementation with tylosin (yes/no). Feces and pen soil samples were collected before harvest, and liver abscesses were identified at harvest. Shotgun and 16S rRNA amplicon sequencing were used to evaluate the soil and feces. Microbiome and resistome composition of feces (as compared by UniFrac distances and Euclidian distances, respectively) did not differ (P > 0.05) among tylosin or no tylosin administered cattle. However, feedlot location was associated with differences (P ≤ 0.05) of resistomes and microbiomes. Using LASSO, a statistical model identified both fecal and soil microbial communities as predictive of liver abscess prevalence in pens. This model explained 75% of the variation in liver abscess prevalence, though a larger sample size would be needed to increase robustness of the model. These data suggest that tylosin exposure does not have a large impact on cattle resistomes or microbiomes; but instead, location of cattle production may be a stronger driver of both the resistome and microbiome composition of feces.},
}

@article {pmid31563940,
year = {2019},
author = {Crawford, E and Kamm, J and Miller, S and Li, LM and Caldera, S and Lyden, A and Yokoe, D and Nichols, A and Tran, NK and Barnard, SE and Conner, PM and Nambiar, A and Zinter, MS and Moayeri, M and Serpa, PH and Prince, BC and Quan, J and Sit, R and Tan, M and Phelps, M and DeRisi, JL and Tato, CM and Langelier, C},
title = {Investigating Transfusion-Related Sepsis using Culture-Independent Metagenomic Sequencing.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciz960},
pmid = {31563940},
issn = {1537-6591},
abstract = {BACKGROUND: Transfusion-related sepsis remains an important hospital infection control challenge. Investigating septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration.

METHODS: In three Gram-negative septic transfusion cases, we performed mNGS of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events.

RESULTS: mNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis, and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture, or that failed to grow due to prior antibiotic administration. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens sharing taxonomic similarity to contaminants commonly found in mNGS library preparations.

CONCLUSIONS: Culture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.},
}

@article {pmid31563779,
year = {2019},
author = {Xie, WY and Zou, X and Liu, DY and Li, Q and Shen, Q and Zhao, FJ},
title = {Dynamics of metal(loid) resistance genes driven by succession of bacterial community during manure composting.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {255},
number = {Pt 2},
pages = {113276},
doi = {10.1016/j.envpol.2019.113276},
pmid = {31563779},
issn = {1873-6424},
abstract = {Metal(loid) resistance genes (MRGs) play important roles in conferring resistance to metal(loid)s in bacterial communities. How MRGs respond to bacterial succession during manure composting remains largely unknown. Metagenomics was used in the present study to investigate the compositional changes of MRGs, their candidate hosts and association with integrons during thermophilic composting of chicken manures. MRGs conferring resistance to 20 metal(loid)s were detected, and their diversity and abundance (normalized to the abundance of 16S rRNA genes) were significantly reduced during composting. MRGs associated with integron were exclusively observed in proteobacterial species. Class 1 integron likely played an important role in maintaining mercury-resistance mer operon genes in composts. Escherichia coli harbored the most abundant MRGs in the original composting material, whereas species of Actinobacteria and Bacilli became more important in carrying MRGs during the late phases. There were significant linear relationships between the relative abundance of some specific bacterial species (E. coli, Actinobacteria species and Enterococcus faecium) and the abundance of MRGs they potentially harbored. The succession of these bacteria contributed to an overall linear regression between the relative abundance of all predicted candidate hosts and the abundance of total MRGs. Our results suggest that the succession of bacterial community was the main driver of MRG dynamics during thermophilic composting.},
}

@article {pmid31563776,
year = {2019},
author = {Torres, GG and Figueroa-Galvis, I and Muñoz-García, A and Polanía, J and Vanegas, J},
title = {Potential bacterial bioindicators of urban pollution in mangroves.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {255},
number = {Pt 2},
pages = {113293},
doi = {10.1016/j.envpol.2019.113293},
pmid = {31563776},
issn = {1873-6424},
abstract = {Despite their ecological and socioeconomic importance, mangroves are among the most threatened tropical environments in the world. In the past two decades, the world's mangrove degradation and loss were estimated to lie between an 35% and >80%. However, appropriate bioindicators for assessing the impact of external factors, and for differentiating polluted from unpolluted areas are still scarce. Here, we determine the physicochemical profiles of the soils of two mangroves, one exposed to and one not exposed to anthropogenic factors. By metagenomic analysis based on 16S rRNA, we generated the bacterial diversity profiles of the soils and estimated their functional profiles. Our results showed that the two examined mangrove forests differed significantly in the physicochemical properties of the soils, especially regarding organic carbon, phosphorus and metal content, as well as in their microbial communities, which was likely caused by anthropogenic pollution. The physicochemical differences between the soils explained 76% of the differential bacterial composition, and 64% depended solely on gradients of phosphorus, metal ions and potassium. We found two genera JL-ETNP-Z39 and TA06 exclusively in polluted and non-polluted mangroves, respectively. Additionally, the polluted mangrove was enriched in Gemmatimonadetes, Cyanobacteria, Chloroflexi, Firmicutes, Acidobacteria, and Nitrospirae. A total of 77 genera were affected by anthropic contamination, of which we propose 33 as bioindicators; 26 enriched, and 7 depleted upon pollution.},
}

@article {pmid31562300,
year = {2019},
author = {Liu, J and Taft, DH and Maldonado-Gomez, MX and Johnson, D and Treiber, ML and Lemay, DG and DePeters, EJ and Mills, DA},
title = {The fecal resistome of dairy cattle is associated with diet during nursing.},
journal = {Nature communications},
volume = {10},
number = {1},
pages = {4406},
doi = {10.1038/s41467-019-12111-x},
pmid = {31562300},
issn = {2041-1723},
abstract = {Antimicrobial resistance is a global public health concern, and livestock play a significant role in selecting for resistance and maintaining such reservoirs. Here we study the succession of dairy cattle resistome during early life using metagenomic sequencing, as well as the relationship between resistome, gut microbiota, and diet. In our dataset, the gut of dairy calves serves as a reservoir of 329 antimicrobial resistance genes (ARGs) presumably conferring resistance to 17 classes of antibiotics, and the abundance of ARGs declines gradually during nursing. ARGs appear to co-occur with antibacterial biocide or metal resistance genes. Colostrum is a potential source of ARGs observed in calves at day 2. The dynamic changes in the resistome are likely a result of gut microbiota assembly, which is closely associated with diet transition in dairy calves. Modifications in the resistome may be possible via early-life dietary interventions to reduce overall antimicrobial resistance.},
}

@article {pmid31562171,
year = {2019},
author = {Inaba, R and Nagoya, M and Kouzuma, A and Watanabe, K},
title = {Metatranscriptomic evidences for magnetite nanoparticle-stimulated acetoclastic methanogenesis under continuous agitation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1128/AEM.01733-19},
pmid = {31562171},
issn = {1098-5336},
abstract = {Conductive nano-materials have been reported to accelerate methanogenesis by promoting direct interspecies electron transfer (DIET), while their effects seem to vary depending on operational conditions. The present study examined effects of magnetite nanoparticles (MNPs) on methanogenesis from acetate by soil-derived anaerobic cultures under continuous agitation. We found that MNPs accelerated methanogenesis in agitated cultures as has been observed previously for static cultures. Metabarcoding of 16S rRNA gene amplicons showed that Methanosarcina substantially increased in the presence of MNPs, while DIET-related Geobacter did not occur. Metagenomic and metatranscriptomic analyses confirmed the predominance of Methanosarcina in MNP-supplemented agitated cultures. In addition, genes coding for acetoclastic methanogenesis but not those for hydrogenotrophic methanogenesis were abundantly expressed in the dominant Methanosarcina in the presence of MNPs. These results suggest that MNPs stimulate acetoclastic methanogenesis under continuous agitation.IMPORTANCE Previous studies have shown that conductive nano particles, such as MNPs, accelerate methanogenesis and suggested that MNPs facilitate DIET between exoelectrogenic bacteria and methanogenic archaea. In these methanogens, electron thus obtained are considered to be used for hydrogenotrophic methanogenesis. However, the present work provides evidence that shows that MNPs accelerate DIET-independent acetoclastic methanogenesis under continuous agitation. Since most of previous studies have examined effects of MNPs in static or weakly agitated methanogenic cultures, results obtained in the present work suggest that hydraulic conditions definitively determine how MNPs accelerate methanogenesis. Besides, the knowledge obtained in this study is useful for engineers operating stirred-tank anaerobic digesters, since we show that MNPs accelerate methanogenesis under continuous agitation.},
}

@article {pmid31561965,
year = {2019},
author = {Jahn, MT and Arkhipova, K and Markert, SM and Stigloher, C and Lachnit, T and Pita, L and Kupczok, A and Ribes, M and Stengel, ST and Rosenstiel, P and Dutilh, BE and Hentschel, U},
title = {A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2019.08.019},
pmid = {31561965},
issn = {1934-6069},
abstract = {Phages are increasingly recognized as important members of host-associated microbiomes, with a vast genomic diversity. The new frontier is to understand how phages may affect higher order processes, such as in the context of host-microbe interactions. Here, we use marine sponges as a model to investigate the interplay between phages, bacterial symbionts, and eukaryotic hosts. Using viral metagenomics, we find that sponges, although massively filtering seawater, harbor species-specific and even individually unique viral signatures that are taxonomically distinct from other environments. We further discover a symbiont phage-encoded ankyrin-domain-containing protein, which is widely spread in phages of many host-associated contexts including human. We confirm in macrophage infection assays that the ankyrin protein (ANKp) modulates the eukaryotic host immune response against bacteria. We predict that the role of ANKp in nature is to facilitate coexistence in the tripartite interplay between phages, symbionts, and sponges and possibly many other host-microbe associations.},
}

@article {pmid31561435,
year = {2019},
author = {Siegwald, L and Caboche, S and Even, G and Viscogliosi, E and Audebert, C and Chabé, M},
title = {The Impact of Bioinformatics Pipelines on Microbiota Studies: Does the Analytical "Microscope" Affect the Biological Interpretation?.},
journal = {Microorganisms},
volume = {7},
number = {10},
pages = {},
doi = {10.3390/microorganisms7100393},
pmid = {31561435},
issn = {2076-2607},
abstract = {Targeted metagenomics is the solution of choice to reveal differential microbial profiles (defined by richness, diversity and composition) as part of case-control studies. It is well documented that each data processing step may have the potential to introduce bias in the results. However, selecting a bioinformatics pipeline to analyze high-throughput sequencing data from A to Z remains one of the critical considerations in a case-control microbiota study design. Consequently, the aim of this study was to assess whether the same biological conclusions regarding human gut microbiota composition and diversity could be reached using different bioinformatics pipelines. In this work, we considered four pipelines (mothur, QIIME, kraken and CLARK) with different versions and databases, and examined their impact on the outcome of metagenetic analysis of Ion Torrent 16S sequencing data. We re-analyzed a case-control study evaluating the impact of the colonization of the intestinal protozoa Blastocystis sp. on the human gut microbial profile. Although most pipelines reported the same trends in this case-control study, we demonstrated how the use of different pipelines affects the biological conclusions that can be drawn. Targeted metagenomics must therefore rather be considered as a profiling tool to obtain a broad sense of the variations of the microbiota, rather than an accurate identification tool.},
}

@article {pmid31561379,
year = {2019},
author = {Paley, EL},
title = {Discovery of Gut Bacteria Specific to Alzheimer's Associated Diseases is a Clue to Understanding Disease Etiology: Meta-Analysis of Population-Based Data on Human Gut Metagenomics and Metabolomics.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {},
doi = {10.3233/JAD-190873},
pmid = {31561379},
issn = {1875-8908},
abstract = {Alzheimer's disease (AD)-associated sequence (ADAS) of cultured fecal bacteria was discovered in human gut targeted screening. This study provides important information to expand our current understanding of the structure/activity relationship of ADAS and putative inhibitors/activators that are potentially involved in ADAS appearance/disappearance. The NCBI database analysis revealed that ADAS presents at a large proportion in American Indian Oklahoman (C&A) with a high prevalence of obesity/diabetes and in colorectal cancer (CRC) patients from the US and China. An Oklahoman non-native group (NNI) showed no ADAS. Comparison of two large US populations reveals that ADAS is more frequent in individuals aged ≥66 and in females. Prevalence and levels of fecal metabolites are altered in the C&A and CRC groups versus controls. Biogenic amines (histamine, tryptamine, tyramine, phenylethylamine, cadaverine, putrescine, agmatine, spermidine) that present in food and are produced by gut microbiota are significantly higher in C&A (e.g., histamine/histidine 95-fold) versus NNI (histamine/histidine 16-fold). The majority of these bio-amines are cytotoxic at concentrations found in food. Inositol phosphate signaling implicated in AD is altered in C&A and CRC. Tryptamine stimulated accumulation of inositol phosphate. The seizure-eliciting tryptamine induced cytoplasmic vacuolization and vesiculation with cell fragmentation. Present additions of ADAS-carriers at different ages including infants led to an ADAS-comprising human sample size of 2,830 from 27 studies from four continents (North America, Australia, Asia, Europe). Levels of food-derived monoamine oxidase inhibitors and anti-bacterial compounds, the potential modulators of ADAS-bacteria growth and biogenic amine production, were altered in C&A versus NNI. ADAS is attributable to potentially modifiable risk factors of AD associated diseases.},
}

@article {pmid31561274,
year = {2019},
author = {Bergner, LM and Orton, RJ and Benavides, JA and Becker, DJ and Tello, C and Biek, R and Streicker, DG},
title = {Demographic and environmental drivers of metagenomic viral diversity in vampire bats.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.15250},
pmid = {31561274},
issn = {1365-294X},
abstract = {Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. We test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities which was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile-biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.},
}

@article {pmid31561205,
year = {2019},
author = {Wu, J and Zhang, PB and Ren, ZQ and Zhou, F and Hu, HH and Zhang, H and Xue, KK and Xu, P and Shao, XQ},
title = {Changes of serum lipopolysaccharide, inflammatory factors, and cecal microbiota in obese rats with type 2 diabetes induced by Roux-en-Y gastric bypass.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {67-68},
number = {},
pages = {110565},
doi = {10.1016/j.nut.2019.110565},
pmid = {31561205},
issn = {1873-1244},
abstract = {OBJECTIVES: Previous studies have shown that Roux-en-Y gastric bypass (RYGB) leads to rapid regression of obesity and type 2 diabetes (T2D). However, the underlying mechanism remains unclear. This study aimed to investigate the effect of RYGB on serum lipopolysaccharide (LPS), interleukin (IL)-1, IL-6, tumor necrosis factor alpha (TNF-α), and cecal microbiota in obese rats with T2D.

METHODS: Obese Sprague-Dawley rats with T2D were randomly divided into RYGB diabetes operation (DO; n = 8), diabetes sham operation (DS; n = 8), and diabetic control (DC; n = 8) groups. Healthy Sprague-Dawley rats were grouped as normal control (NC; n = 8). Fasting plasma glucose and body weight were measured. The levels of peripheral serum LPS, IL-1, IL-6, and TNF-α were measured by enzyme-linked immunosorbent assay. The rats were sacrificed 12 wk after operation. Subsequently, a superior mesenteric venous blood sample was taken to measure serum LPS levels by enzyme-linked immunosorbent assay. The cecal contents of the DO and DS groups were taken to extract metagenomic DNA per the genomic DNA standardization procedure. The V4 region of the 16 S rRNA was sequenced with the Illumina Hiseq sequencing platform to compare the structure and relative abundance of cecal microbiota between the DO and DS groups.

RESULTS: Twelve weeks after operation in the DO group, fasting plasma glucose and body weight showed a significant decrease (P < 0.05). Moreover, the levels of peripheral serum LPS, IL-1, IL-6, and TNF-α were obviously decreased (P < 0.05). A change in the LPS level of superior mesenteric venous blood also revealed a dramatic decrease (P < 0.05). Additionally, RYGB resulted in a shift of cecal microbiota in obese rats with T2D.

CONCLUSIONS: Hypoglycemic effects after RYGB may be associated with improved levels of LPS, IL-1, IL-6, and TNF-α. Changes in the structure of cecal microbiota may also play an important role.},
}