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Bibliography on: Metagenomics

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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About:  RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE

RJR: Recommended Bibliography 26 Jun 2019 at 01:30 Created: 

Metagenomics

While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.

Created with PubMed® Query: metagenomic OR metagenomics OR metagenome NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)

RevDate: 2019-06-24

Ge YL, Zhu XY, Hu K, et al (2019)

Positive Serum Beta-D-glucan by G Test and Aspergillus Fumigatus Sputum Culture Mimic Invasive Pulmonary Aspergillosis in a Pulmonary Nocardia Patient: a Case Report and Literature Review.

Clinical laboratory, 65(6):.

BACKGROUND: Invasive pulmonary aspergillosis and nocardia overlap in clinical and radiological presentations, so differentiating between nocardia and invasive pulmonary aspergillosis is confusing. Though sputum culture could distinguish between nocardia and aspergillus fumigatus, but for the ultimate diagnosis, sputum culture provided limited help. Here we report a case of a patient with positive G test and aspergillus fumigatus sputum culture mimic invasive pulmonary aspergillosis ultimately diagnosed as nocardia through bronchoalveolar lavage culture combined metagenomic next-generation sequencing (NGS).

METHODS: Bronchoalveolar lavage culture combined metagenomic NGS for infectious diseases were performed for diagnosis.

RESULTS: Bronchoalveolar lavage culture combined metagenomic next-generation sequencing showed Nocardia Gelsenkirchen.

CONCLUSIONS: Positive G test and sputum culture were not specific, while bronchoalveolar lavage culture and NGS gave more information for a differential diagnosis between nocardia and aspergillus fumigatus.

RevDate: 2019-06-24

Shen-Gunther J, Cai H, Zhang H, et al (2019)

Abundance of HPV L1 Intra-Genotype Variants With Capsid Epitopic Modifications Found Within Low- and High-Grade Pap Smears With Potential Implications for Vaccinology.

Frontiers in genetics, 10:489.

Background: The aim of this study was to explore the Human Papillomavirus (HPV) genotype composition and intra-genotype variants within individual samples of low- and high-grade cervical cytology by deep sequencing. Clinical, cytological, sequencing, and functional/structural data were forged into an integrated variant profiling pipeline for the detection of potentially vaccine-resistant genotypes or variants. Methods: Low- and high-grade intraepithelial lesion (LSIL and HSIL) cytology samples with +HPV were subjected to amplicon (L1 gene fragment) sequencing by dideoxy (Sanger) and deep methods. Taxonomic, abundance, diversity, and phylogenetic analyses were conducted to determine HPV genotypes/sub-lineages, relative abundance, species diversity and phylogenetic distances within and between samples. Variant detection and functional analysis of translated L1 amino acid sequences determined structural variations of interest. Results: Pure and mixed HPV infections were common among LSIL (n = 6) and HSIL (n = 6) samples. Taxonomic profiling revealed loss of species richness and gain of dominance by carcinogenic genotypes in HSIL samples. Phylogenetic analysis showed excellent correlation between HPV-type specific genetic distances and carcinogenic potential. For combined LSIL/HSIL samples (n = 12), 11 HPV genotypes and 417 mutations were detected: 375 single-nucleotide variants (SNV), 29 insertion/deletion (indel), 12 multi-nucleotide variants (MNV), and 1 replacement variant. The proportion of nonsynonymous mutations was lower for HSIL (0.38) than for LSIL samples (0.51) (p < 0.05). HPV variant analysis pinpointed nucleotide-level mutations and amino acid-level structural modifications. Conclusion: HPV L1 intra-host and intra-genotype variants are abundant in LSIL and HSIL samples with potential functional/structural consequences. An integrated multi-omics approach to variant analysis may provide a sensitive and practical means of detecting changes in HPV evolution and dynamics within individuals or populations.

RevDate: 2019-06-24

Zhang C, Yang M, AC Ericsson (2019)

Antimicrobial Peptides: Potential Application in Liver Cancer.

Frontiers in microbiology, 10:1257.

The physicochemical properties of antimicrobial peptides (AMPs) including size, net charge, amphipathic structure, hydrophobicity, and mode-of-action together determine their broad-spectrum activities against bacteria, fungi, protozoa, and viruses. Recent studies show that some AMPs have both antimicrobial and anticancer activities, suggesting a new strategy for cancer therapy. Hepatocellular carcinoma (HCC), the primary liver cancer, is a leading cause of cancer mortality worldwide, and lacks effective treatment. Anticancer peptides (ACPs) derived from AMPs or natural resources could be applied to combat HCC directly or as a synergistic treatment. However, the number of known ACPs is low compared to the number of antibacterial and antifungal peptides, and very few of them can be applied clinically for HCC treatment. In this review, we first summarize recent studies related to ACPs for HCC, followed by a description of potential modes-of-action including direct killing, anti-inflammation, immune modulation, and enhanced wound healing. We then describe the structures of AMPs and methods to design and modify these peptides to improve their anticancer efficacy. Finally, we explore the potential application of ACPs as vaccines or nanoparticles for HCC treatment. Overall, ACPs display several attractive properties as therapeutic agents, including broad-spectrum anticancer activity, ease-of-design and modification, and low production costs. As this is an emerging and novel area of cancer therapy, additional studies are needed to identify existing candidate AMPs with ACP activity, and assess their anticancer activity and specificity, and immunomodulatory effects, using in vitro, in silico, and in vivo approaches.

RevDate: 2019-06-24

Pinnell LJ, JW Turner (2019)

Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment.

Frontiers in microbiology, 10:1252.

Plastic is incredibly abundant in marine environments but little is known about its effects on benthic microbiota and biogeochemical cycling. This study reports the shotgun metagenomic sequencing of biofilms fouling plastic and bioplastic microcosms staged at the sediment-water interface of a coastal lagoon. Community composition analysis revealed that plastic biofilms were indistinguishable in comparison to a ceramic biofilm control. By contrast, bioplastic biofilms were distinct and dominated by sulfate-reducing microorganisms (SRM). Analysis of bioplastic gene pools revealed the enrichment of esterases, depolymerases, adenylyl sulfate reductases (aprBA), and dissimilatory sulfite reductases (dsrAB). The nearly 20-fold enrichment of a phylogenetically diverse polyhydroxybutyrate (PHB) depolymerase suggests this gene was distributed across a mixed microbial assemblage. The metagenomic reconstruction of genomes identified novel species of Desulfovibrio, Desulfobacteraceae, and Desulfobulbaceae among the abundant SRM, and these genomes contained genes integral to both bioplastic degradation and sulfate reduction. Findings indicate that bioplastic promoted a rapid and significant shift in benthic microbial diversity and gene pools, selecting for microbes that participate in bioplastic degradation and sulfate reduction. If plastic pollution is traded for bioplastic pollution and sedimentary inputs are large, the microbial response could unintentionally affect benthic biogeochemical activities through the stimulation of sulfate reducers.

RevDate: 2019-06-23

Kan J, Cheng J, Xu L, et al (2019)

The combination of wheat peptides and fucoidan protects against chronic superficial gastritis and alters gut microbiota: a double-blinded, placebo-controlled study.

European journal of nutrition pii:10.1007/s00394-019-02020-6 [Epub ahead of print].

PURPOSE: Chronic gastritis is observed in almost half world population. Traditional medications against chronic gastritis might produce adverse effects, so alternative nutritional strategies are needed to prevent the aggravation of gastric mucosal damage. The aim of this study is to evaluate the protective effect of the combination of wheat peptides and fucoidan (WPF) on adults diagnosed with chronic superficial gastritis in a randomized, double-blind, placebo-controlled clinical trial.

METHODS: Participants were randomized to receive WPF (N = 53) or placebo (N = 53) once daily for 45 days. Pathological grading of gastric mucosal damage was scored using gastroscopy. Fecal samples were collected for the determination of calprotectin, short chain fatty acids (SCFA) levels and metagenomics analysis. Questionnaires for self-reported gastrointestinal discomforts, life quality and food frequency were collected throughout the study.

RESULTS: WPF intervention reduced gastric mucosal damage in 70% subjects (P < 0.001). Significantly less stomach pain (P < 0.001), belching (P = 0.028), bloating (P < 0.001), acid reflux (P < 0.001), loss of appetite (P = 0.021), increased food intake (P = 0.020), and promoted life quality (P = 0.014) were reported in the WPF group. WPF intervention significantly decreased fecal calprotectin level (P = 0.003) while slightly increased fecal SCFAs level (P = 0.092). In addition, we found altered microbiota composition post-intervention with increased Bifidobacterium pseudocatenulatum (P = 0.032), Eubacterium siraeum (P = 0.036), Bacteroides intestinalis (P = 0.024) and decreased Prevotella copri (P = 0.055).

CONCLUSIONS: WPF intervention could be utilized as a nutritional alternative to mitigate the progression of chronic gastritis. Furthermore, WPF played an important role in altering gut microbial profile and SCFA production, which might benefit the lower gastrointestinal tract.

RevDate: 2019-06-23

Souza FFC, Rissi DV, Pedrosa FO, et al (2019)

Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest.

The Science of the total environment, 688:83-86 pii:S0048-9697(19)32791-3 [Epub ahead of print].

Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.

RevDate: 2019-06-23

Culbreath K, Melanson S, Gale J, et al (2019)

Validation and Retrospective Clinical Evaluation of a Quantitative 16S rRNA Gene Metagenomic Sequencing Assay for Bacterial Pathogen Detection in Body Fluids.

The Journal of molecular diagnostics : JMD pii:S1525-1578(18)30499-9 [Epub ahead of print].

Next-generation sequencing-based 16S rRNA gene metagenomic sequencing (16S MG) technology has tremendous potential for improving diagnosis of bacterial infections given its quantitative capability and culture-independent approach. We validated and utilized a quantitative 16S MG assay to identify and quantify bacterial species in clinical samples from a wide spectrum of infections including meningitis, septic arthritis, brain abscess, intra-abdominal abscess, soft tissue abscess, and pneumonia. Twenty clinical samples were tested and 16S MG identified a total of 34 species, compared to 22 species and three descriptive findings identified by culture. 16S MG results matched culture results in 75% (15/20) of the samples but detected at least one more species in five samples, including one culture-negative CSF that was found to contain Streptococcus intermedius. Shotgun metagenomic sequencing verified the presence of all additional species. The 16S MG assay is highly sensitive with a limit of detection of 10 to 100 CFU/mL. Other performance characteristics including linearity, precision, and specificity all met the requirement for a clinical test. This assay showed the advantages of accurate identification and quantification of bacteria in culture-negative and polymicrobial infections for which conventional microbiology methods are limited. It also showed promises to serve unmet clinical needs for solving difficult infectious diseases cases.

RevDate: 2019-06-23

Ammini P, Vijayan J, Krishna AV, et al (2019)

Dominance of Wolbachia sp. in the deep-sea sediment bacterial metataxonomic sequencing analysis in the Bay of Bengal, Indian Ocean.

Genomics pii:S0888-7543(18)30676-1 [Epub ahead of print].

The Bay of Bengal, located in the north-eastern part of the Indian Ocean is world's largest bay occupying an area of ~8,39,000 mile2. The variability in bacterial community structure and function in sediment ecosystems of the Bay of Bengal is examined by Illumina high-throughput metagenomic sequencing. Of five metataxonomics data sets presented, two (SD1 and SD2) were from stations close to the shore and three (SD4, SD5, and SD6) were from the deep-sea (~3000 m depth). Phylum Proteobacteria (90.27 to 92.52%) dominated the deep-sea samples, whereas phylum Firmicutes (65.35 to 90.98%) dominated the coastal samples. Comparative analysis showed that coastal and deep-sea sediments showed distinct microbial communities. Wolbachia species, belonging to class Alphaproteobacteria was the most dominant species in the deep-sea sediments. The gene functions of bacterial communities were predicted for deep-sea and coastal sediment ecosystems. The results indicated that deep-sea sediment bacterial communities were involved in metabolic activities like dehalogenation and sulphide oxidation.

RevDate: 2019-06-23

Kim HE, Lee JJ, Lee MJ, et al (2019)

Analysis of microbiome in raw chicken meat from butcher shops and packaged products in South Korea to detect the potential risk of foodborne illness.

Food research international (Ottawa, Ont.), 122:517-527.

Chicken meat is one of the most widely consumed meats worldwide. The microbiota on the whole body of chicken is a potential source of foodborne pathogens that can be transmitted to humans during the preparation of raw meat. However, to date, there have been no studies comparing the microbiota of packaged chicken products and those of raw chicken carcasses from butcher shops, although such information could be useful for identifying sources of contamination in cases of food poisoning. We addressed this in the present study by analyzing the microbiota of 80 chicken meat samples collected from various butcher shops and processing plants in South Korea with the Illumina MiSeq system based on the 16S rRNA gene sequence. The bacterial amounts in chicken samples were estimated by quantitative real-time PCR. Although different microbial members were present in unpackaged meat from butcher shops as compared to those in packaged products from commercial sources, seasonal differences (sample obtained in January vs. July) in microbiota were more significant even in the packaged products from the same company. We also investigated the influence of contaminated foodborne pathogen on the indigenous microbiota (64 chicken samples) by artificially inoculated with Salmonella enterica serotype Virchow on chicken carcasses under various conditions, and carrying out 16S rRNA gene and whole metagenome sequencing. The amount of contaminated Salmonella in chicken meat samples was the highest and lowest in samples stored at 27 °C and 4 °C after washing, respectively. Additionally, the relative abundance of virulence genes was detected lower in samples stored at 4 °C after washing in both butcher shop and commercial samples. These results could be useful for reducing the risk of foodborne illness caused by cross-contamination during the preparation of chicken meat.

RevDate: 2019-06-23

Ticinesi A, Nouvenne A, T Meschi (2019)

Gut microbiome and kidney stone disease: not just an Oxalobacter story.

Kidney international, 96(1):25-27.

Intestinal regulation of oxalate absorption is a complex mechanism, not exclusively reliant on the oxalate-degrading anaerobe Oxalobacter formigenes. Using metagenomics, Miller et al. were able to describe a network of bacterial taxa co-occurring with Oxalobacter formigenes in fecal samples from non-stone forming controls and less represented in stone formers. These findings may help to illuminate why previous intervention studies with probiotics have failed to reduce the risk of hyperoxaluria, opening new possibilities for future research.

RevDate: 2019-06-24
CmpDate: 2019-06-24

Lorenzi AS, Chia MA, Lopes FAC, et al (2019)

Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology.

Journal of microbiology (Seoul, Korea), 57(6):450-460.

Next-generation DNA sequencing technology was applied to generate molecular data from semiarid reservoirs during well-defined seasons. Target sequences of 16S-23S rRNA ITS and cpcBA-IGS were used to reveal the taxonomic groups of cyanobacteria present in the samples, and genes coding for cyanotoxins such as microcystins (mcyE), saxitoxins (sxtA), and cylindrospermopsins (cyrJ) were investigated. The presence of saxitoxins in the environmental samples was evaluated using ELISA kit. Taxonomic analyses of high-throughput DNA sequencing data showed the dominance of the genus Microcystis in Mundaú reservoir. Furthermore, it was the most abundant genus in the dry season in Ingazeira reservoir. In the rainy season, 16S-23S rRNA ITS analysis revealed that Cylindrospermopsis raciborskii comprised 46.8% of the cyanobacterial community in Ingazeira reservoir, while the cpcBAIGS region revealed that C. raciborskii (31.8%) was the most abundant taxon followed by Sphaerospermopsis aphanizomenoides (17.3%) and Planktothrix zahidii (16.6%). Despite the presence of other potential toxin-producing genera, the detected sxtA gene belonged to C. raciborskii, while the mcyE gene belonged to Microcystis in both reservoirs. The detected mcyE gene had good correlation with MC content, while the amplification of the sxtA gene was related to the presence of STX. The cyrJ gene was not detected in these samples. Using DNA analyses, our results showed that the cyanobacterial composition of Mundaú reservoir was similar in successive dry seasons, and it varied between seasons in Ingazeira reservoir. In addition, our data suggest that some biases of analysis influenced the cyanobacterial communities seen in the NGS output of Ingazeira reservoir.

RevDate: 2019-06-24
CmpDate: 2019-06-24

Bird JT, Tague ED, Zinke L, et al (2019)

Uncultured Microbial Phyla Suggest Mechanisms for Multi-Thousand-Year Subsistence in Baltic Sea Sediments.

mBio, 10(2): pii:mBio.02376-18.

Energy-starved microbes in deep marine sediments subsist at near-zero growth for thousands of years, yet the mechanisms for their subsistence are unknown because no model strains have been cultivated from most of these groups. We investigated Baltic Sea sediments with single-cell genomics, metabolomics, metatranscriptomics, and enzyme assays to identify possible subsistence mechanisms employed by uncultured Atribacteria, Aminicenantes, Actinobacteria group OPB41, Aerophobetes, Chloroflexi, Deltaproteobacteria, Desulfatiglans, Bathyarchaeota, and Euryarchaeota marine group II lineages. Some functions appeared to be shared by multiple lineages, such as trehalose production and NAD+-consuming deacetylation, both of which have been shown to increase cellular life spans in other organisms by stabilizing proteins and nucleic acids, respectively. Other possible subsistence mechanisms differed between lineages, possibly providing them different physiological niches. Enzyme assays and transcripts suggested that Atribacteria and Actinobacteria group OPB41 catabolized sugars, whereas Aminicenantes and Atribacteria catabolized peptides. Metabolite and transcript data suggested that Atribacteria utilized allantoin, possibly as an energetic substrate or chemical protectant, and also possessed energy-efficient sodium pumps. Atribacteria single-cell amplified genomes (SAGs) recruited transcripts for full pathways for the production of all 20 canonical amino acids, and the gene for amino acid exporter YddG was one of their most highly transcribed genes, suggesting that they may benefit from metabolic interdependence with other cells. Subsistence of uncultured phyla in deep subsurface sediments may occur through shared strategies of using chemical protectants for biomolecular stabilization, but also by differentiating into physiological niches and metabolic interdependencies.IMPORTANCE Much of life on Earth exists in a very slow-growing state, with microbes from deeply buried marine sediments representing an extreme example. These environments are like natural laboratories that have run multi-thousand-year experiments that are impossible to perform in a laboratory. We borrowed some techniques that are commonly used in laboratory experiments and applied them to these natural samples to make hypotheses about how these microbes subsist for so long at low activity. We found that some methods for stabilizing proteins and nucleic acids might be used by many members of the community. We also found evidence for niche differentiation strategies, and possibly cross-feeding, suggesting that even though they are barely growing, complex ecological interactions continue to occur over ultralong timescales.

RevDate: 2019-06-24
CmpDate: 2019-06-24

Aleti G, Baker JL, Tang X, et al (2019)

Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease.

mBio, 10(2): pii:mBio.00321-19.

Small molecules are the primary communication media of the microbial world. Recent bioinformatic studies, exploring the biosynthetic gene clusters (BGCs) which produce many small molecules, have highlighted the incredible biochemical potential of the signaling molecules encoded by the human microbiome. Thus far, most research efforts have focused on understanding the social language of the gut microbiome, leaving crucial signaling molecules produced by oral bacteria and their connection to health versus disease in need of investigation. In this study, a total of 4,915 BGCs were identified across 461 genomes representing a broad taxonomic diversity of oral bacteria. Sequence similarity networking provided a putative product class for more than 100 unclassified novel BGCs. The newly identified BGCs were cross-referenced against 254 metagenomes and metatranscriptomes derived from individuals either with good oral health or with dental caries or periodontitis. This analysis revealed 2,473 BGCs, which were differentially represented across the oral microbiomes associated with health versus disease. Coabundance network analysis identified numerous inverse correlations between BGCs and specific oral taxa. These correlations were present in healthy individuals but greatly reduced in individuals with dental caries, which may suggest a defect in colonization resistance. Finally, corroborating mass spectrometry identified several compounds with homology to products of the predicted BGC classes. Together, these findings greatly expand the number of known biosynthetic pathways present in the oral microbiome and provide an atlas for experimental characterization of these abundant, yet poorly understood, molecules and socio-chemical relationships, which impact the development of caries and periodontitis, two of the world's most common chronic diseases.IMPORTANCE The healthy oral microbiome is symbiotic with the human host, importantly providing colonization resistance against potential pathogens. Dental caries and periodontitis are two of the world's most common and costly chronic infectious diseases and are caused by a localized dysbiosis of the oral microbiome. Bacterially produced small molecules, often encoded by BGCs, are the primary communication media of bacterial communities and play a crucial, yet largely unknown, role in the transition from health to dysbiosis. This study provides a comprehensive mapping of the BGC repertoire of the human oral microbiome and identifies major differences in health compared to disease. Furthermore, BGC representation and expression is linked to the abundance of particular oral bacterial taxa in health versus dental caries and periodontitis. Overall, this study provides a significant insight into the chemical communication network of the healthy oral microbiome and how it devolves in the case of two prominent diseases.

RevDate: 2019-06-24
CmpDate: 2019-06-24

Ferraro Petrillo U, Roscigno G, Cattaneo G, et al (2018)

Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms.

Bioinformatics (Oxford, England), 34(11):1826-1833.

Motivation: Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in the realm of genome assembly. However, they are so specialized to this domain that they do not extend easily to the computation of informational and linguistic indices, concurrently on sets of genomes.

Results: Following the well-established approach in many disciplines, and with a growing success also in bioinformatics, to resort to MapReduce and Hadoop to deal with 'Big Data' problems, we present KCH, the first set of MapReduce algorithms able to perform concurrently informational and linguistic analysis of large collections of genomic sequences on a Hadoop cluster. The benchmarking of KCH that we provide indicates that it is quite effective and versatile. It is also competitive with respect to the parallel and distributed algorithms highly specialized to k-mer statistics collection for genome assembly problems. In conclusion, KCH is a much needed addition to the growing number of algorithms and tools that use MapReduce for bioinformatics core applications.

The software, including instructions for running it over Amazon AWS, as well as the datasets are available at http://www.di-srv.unisa.it/KCH.

Contact: umberto.ferraro@uniroma1.it.

Supplementary information: Supplementary data are available at Bioinformatics online.

RevDate: 2019-06-21

Assié A, BS Samuel (2019)

The Devil Is in the Microbial Genetic Details.

Molecular cell, 74(6):1108-1109.

The work of Zeevi et al. (2019) in a recent issue of Nature shows that variations in gene content and organization between different strains of the same microbial species are widespread in the human gut microbiota and could be linked to many measures of health.

RevDate: 2019-06-21

Sontheimer EJ (2019)

X-Tracting a New CRISPR-Cas Genome-Editing Platform from Metagenomic Data Sets.

The CRISPR journal, 2:148-150.

RevDate: 2019-06-21

Poutsiaka D, Stern L, Riquelme V, et al (2019)

Impact of Body Mass Index (BMI) on the Effect of a Lactobacillus Rhamnosus GG (LGG)/Bifidobacterium Animalis Subspecies Lactis BB-12 (BB-12) Combination on Gut Microbiota (P20-023-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.P20-023-19.

Objectives: This exploratory study builds upon an earlier study of probiotic supplementation1 to assess the effects of a probiotic combination (P) of LGG and BB-12 on human gut microbiota composition and function, and to uncover an association with BMI.

Methods: Healthy subjects ingested P for 21 days (n = 18, P group) or did not (n = 7, C group).Fecal samples obtained at baseline (D_0) and after 21 days of supplementation (D_21) underwent 16S ribosomal RNA gene and shotgun metagenomics sequencing to characterize the bacterial and archaeal communities to the genus/species level and identify functional community genes.

Results: Following P ingestion, no global differences in microbiota community structure or relative gene abundance were detected. In targeted analyses, the abundances of LGG and BB-12 in the P group at D_21 increased in a statistically significant manner as the BMI decreased (Spearman correlation, P = 0.04 and P = 0.01, respectively). The relative abundance of LGG but not BB-12 appeared increased in P subjects at D_21 with BMI < 25 compared to BMI > 25 (P = 0.09). P group subjects with BMI < 25 demonstrated trends toward or statistically significant increases in the relative abundances of 5 genes involved with flagellar structure (KEGG orthologs K02422, P = 0.04; K03406, P = 0.06; K02407, P = 0.08; K02397, P = 0.08; K02396, P = 0.09) at D_21 compared to those with BMI > 25. No such differences were observed for the C group nor were there differences in relative gene abundance at D_0 in the P group with BMI < 25 vs BMI > 25.

Conclusions: We observed no global changes in the fecal microbial community structure or function with P ingestion in this sample of healthy persons. However, we did observe patterns suggestive of a potential link between BMI and the response of the gut microbiota to P. Although our results are based on a small number of subjects, they are in line with previous findings related to LGG supplementation and the expression of flagellar genes2. We agree with other recent reports that future studies would benefit from a detailed examination of the transcriptome, proteome and/or metabolome to better understand the potential impact of probiotics on the gut microbiota, and the mechanism of the effect of BMI.

Funding Sources: Pfizer Inc.

RevDate: 2019-06-21

Yeung OY, Ng YF, Chiou J, et al (2019)

A Pilot Study to Determine the Gut Microbiota of Hong Kong Infants Fed with Breast-milk And/or Infant Formula (P11-101-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz048.P11-101-19.

Objectives: Gut microbiome in newborn infants affect their gut health and future development. The major nutrient sources for infants aged 2-4 months are breast-milk or infant formula, hence it is worth investigating whether exclusively breastfed or infant formula-fed does affect the early development of the gut microbiota communities. Metagenomics has been applied to analyse the infant fecal samples in the United State and some European countries, however, similar studies were limited in Asia and especially Hong Kong.

Methods: Three groups of infants aged 2-4 months which were exclusively breastfed (BF), exclusively infant formula-fed (IF) or mix-fed with breast-milk and infant formula (MF) were recruited. Genomic DNA from the fecal sample and breast-milk was extracted and subjected to 16S rRNA next-generation sequencing to understand the gut microbiota profile, the difference of microbiota diversity and community abundance in these three feeding groups. The sequencing results were processed using pipelines Mothur and Qiime2.

Results: Overall the breast-milk showed higher alpha-diversity than the fecal samples. The 3 predominant Phyla were Proteobacteria, Firmicutes and Bacteroidetes within the fecal samples from all feeding patterns while the 3 dominant Phyla were Firmicutes, Proteobacteria and Actinobacteria in the breastmilk. Higher abundance of the well-known immune-modulating Genera Bifidobacterium and Lactobacillus were found in the fecal samples of BF and MF groups than the IF group whereas IF group harboured highest abundance of Genus Clostridium among 3 fecal groups. A PCoA based on unweighted UniFrac distance showed that the microbiota from the breastmilk clustered and distinctly separated from those of fecal samples. Moreover, the microbiota of MF subjects were close to BF subjects from the PCoA analysis.

Conclusions: Our preliminary results suggested that partial feeding with breast-milk could still maintain the major gut community composition as in the BF group. Feeding pattern affect the gut microbiota in Hong Kong infants aged 2-4 month and probiotic genera Bifidobacterium and Lactobacillus were found in the breast-milk, and fecal samples of BF and MF groups.

Funding Sources: Health and Medical Research Fund, Food and Health Bureau, The Government of the Hong Kong Special Administrative Region.

RevDate: 2019-06-21

Johnson A, Vangay P, D Knights (2019)

Dietary Patterns Correspond with Microbiome Composition (FS07-02-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.FS07-02-19.

Objectives: Previous studies have defined dietary patterns for comparison with microbiome features using factor analysis from food frequency questionnaires. In this study, we applied a new tree-based method to directly define dietary patterns from 24-hour food records. We aimed to determine if these patterns corresponded with microbial features.

Methods: Daily fecal samples and daily 24-hour food records (ASA24-2016) were collected from 32 healthy adults over 17 days. Dietary patterns were derived using all reported foods for each subject. Foods were arranged into a tree structure using USDA food groups. Tree-based weighted Unifrac food distances (QIIME 1.9.1) were used for principal coordinate analysis to define five dietary patterns. Each pattern was named after its most influential food groups. Average microbiome composition was determined from metagenomic sequencing. Dietary patterns were compared with subjects' average microbiome composition using correlation analysis. Spearman correlations were corrected for multiple comparisons within each taxonomy level. Constrained redundancy analysis (RDA) was used to determine the explanatory power of dietary patterns.

Results: Four of the five most discriminatory dietary patterns (DPs) were associated with microbial taxa (A). DP1 was positively correlated with an unclassified family in the order Burkholderiales and negatively correlated with the species Lachnospiraceae bacterium TF01-11. DP3, DP4, DP5 were most representative of a western diet. DP3 was negatively correlated with family Pasteurellaceae. DP4 was positively correlated with family Erysipelotrichaceae and negatively correlated with family Sutterellaceae. DP5 was positively correlated with members of class Bacteroidia including two specific Bacteroides speciesHMSC073E02 and HMSC067B03. Constrained RDA using the five dietary patterns revealed a gradient of Phylum Bacteroidetes along an axis driven by DP3, DP4, and DP5 (B).

Conclusions: The dietary patterns derived using our tree-based method reveal relationships between diet microbial taxa. In agreement with previous studies, our tree-based patterns show that the western diet corresponds to increased Bacteroidetes, demonstrating the utility of this method.

Funding Sources: Funding for this study was provided by General Mills.

RevDate: 2019-06-21

Casaburi G, Karav S, Frese S, et al (2019)

Gut Barrier Function Is Improved in Infants Colonized by Bifidobacterium Longum Subsp. Infantis EVC001 (FS04-05-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz048.FS04-05-19.

Objectives: The gut epithelium is single-celled barrier that employs many different mechanisms that together provide the first line of defense to physically separate the gut epithelium from our gut microbiome. Notably, the epithelial barrier is protected by a mucin layer providing a physical barrier limiting pathogen access to the epithelial monolayer. We sought to assess how changes in the gut microbiome resulting from colonization by a single strain of Bifidobacterium longum subsp. infantis EVC001 could alter gut barrier function.

Methods: Fecal samples from this trial were assessed for: (1) endotoxin (lipopolysaccharide) concentration; (2) functional contributions to the gut microbiome by shotgun metagenome sequencing; and (3) fecal glycan profiles by mass spectrometry to assess gut epithelial barrier integrity via breakdown of colonic mucin glycoproteins.

Results: Colonization with Bifidobacterium, including B. infantis EVC001, showed a significant four-fold reduction in fecal endoxtoxin levels and reductions in fecal inflammatory markers (P < 0.05). Shotgun metagenomics identified LPS-producing Enterobacteriaceae as the most significant contributor of virulence factors in the infant gut metagenome. These bacteria (primarily E. coli and Klebsiella spp.) were also significantly correlated with both mucolytic bacteria (e.g., Bacteroides) and the signatures of mucin breakdown, as assessed by mass spectrometric quantification of colonic mucin-derived glycans. Five different colonic-mucin specific glycans (3_1_1_0, 2_1_2_0, 2_1_1_1, 2_1_1_0, and 1_1_0_1) were significantly associated with microbiome composition (P < 0.05). Overall mucin glycans were inversely correlated with Bifidobacteriaceae abundance (Spearman's rho -0.66, FDR-corrected P value 0.04).

Conclusions: Complex interactions between the degradation of gut barrier function (e.g., mucin), the production of pro-inflammatory endotoxins, and the risk of infection by these bacteria coming in close contact with the gut epithelium suggest that B. infantis EVC001 can play a role in reducing these combined risks for neonates.

Funding Sources: This work was funded by Evolve Biosystems, Inc.

RevDate: 2019-06-21

Berry S, Valdes A, Davies R, et al (2019)

Predicting Personal Metabolic Responses to Food Using Multi-omics Machine Learning in over 1000 Twins and Singletons from the UK and US: The PREDICT I Study (OR31-01-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz037.OR31-01-19.

Objectives: Glycemic, insulinemic and lipemic postprandial responses are multi-factorial and contribute to diabetes, obesity and cardiovascular disease. The aim of the PREDICT I study is to assess the genetic, metabolic, metagenomic, and meal-context contribution to postprandial responses, integrating the metabolic burden and gut microbiome to predict individual responses to food using a machine learning algorithm.

Methods: A multi-center dietary intervention study of 1000 individuals from the UK (unrelated, identical and non-identical twins) and 100 unrelated individuals from the US, assessed postprandial (0-6 h) metabolic responses to sequential mixed-nutrient dietary challenges in the clinic. Baseline data included metabolomics, genomics, gut metagenomics and DXA body composition. Glycemic responses to 5 duplicate isocaloric meals of different macronutrient content and self-selected meals (>100,000), were tested at home using a continuous glucose monitor (CGM). Interim analysis of the genetic contributions was performed in 110 identical and 25 non-identical twin pairs.

Results: Inter-individual variability in postprandial metabolic responses (glucose, insulin and triacylglycerol (TG)) was high in the clinic setting: incremental area under the curve IQR (median) was; glucose (0-2 h) 2.09 (1.95) mmol/L.h, insulin (0-2 h) 47.0 (67.6) mIU/L.h and TG (0-6 h) 2.34 (2.38) mmol/L.h. The unadjusted genetic contribution for the glucose, insulin and TG responses were 54%, 29% and 27% respectively. A predictive algorithm was developed and interim analyses, using at home CGM data, found that 46% of overall variation in glycemic responses could be predicted from meal content, meal context and individual baseline characteristics excluding genetic and microbiome factors. Only 29% of variation could be explained by the macronutrient content of the meal.

Conclusions: This is the most comprehensive postprandial study performed to date. The large and modifiable variation in metabolic responses to identical meals in healthy people explains why 'one size fits all' nutritional guidelines are problematic. By collecting information on glucose responses to >100,000 meals we will have excellent power to use machine learning to optimise and predict individual responses to foods.

Funding Sources: NIHR, Wellcome Trust, Zoe Global Ltd.

RevDate: 2019-06-21

Konen O, Peters K, P Tsuji (2019)

A Metagenomic Analysis of the Equine Gut Microbiome with and Without Probiotic Supplementation (P09-006-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz033.P09-006-19.

Objectives: The goal of this study is to compare the microbiome of domesticated horses with and without probiotic supplementation.

Methods: Our University's Institutional Animal Care and Use Committee has granted an exemption, as the horses were not housed on campus and there was no experimental manipulation to the horses' feeding implemented. Fecal matter from six privately owned horses maintained on their standard grazing diet were collected. Three of the six horses received a probiotic supplement, SmartDigest, for several years prior to beginning the project. Supplementation ceased for one month, and samples were again obtained. The other three horses never received probiotics. Bacterial DNA was isolated from all fecal samples, the 16S rRNA gene amplified, tagged with index primers, and subsequently sequenced using the Illumina MiSeq.

Results: Dominant groups from non-supplemented horses residing on the same property included the phyla bacteriodetes, firmicutes, proteobacteria, and verrucomicrobia. Interestingly, Sphingobacterium bambusae was identified in all three horses, even though this species has previously been isolated from the soil of bamboo plantations. Currently, samples from horses with probiotics are being analyzed. We are also employing qPCR analysis to validate the NextGen data, and to further investigate relative abundance of specific bacterial groups relevant to equine intestinal health.

Conclusions: Preliminary NextGen sequence analysis of the relative abundance of bacterial phyla suggests that, as expected, the horses residing on the same property and thus receiving the same diet possess a similar intestinal microbiome composition. Similarities between horses persist down to the genus level, and are now being compared to samples from horses on a probiotic-supplemented diet.

Funding Sources: Financial support was provided by Towson University's Fisher College of Science and Mathematics, and Jess and Mildred Fisher Endowed Chair funds to P. Tsuji.

RevDate: 2019-06-21

Kan J, J Du (2019)

The Combination of Wheat Peptides and Fucoidan Protects Against Chronic Superficial Gastritis and Regulates Gut Microbiota: A Double-blinded, Placebo-controlled Study (P06-104-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz031.P06-104-19.

Objectives: Chronic gastritis is observed in almost half world population. Traditional medications against chronic gastritis might produce adverse effects, so alternative nutritional strategies are needed to prevent the aggravation of gastric mucosal damage. The aim of this study is to evaluate the protective effect of the combination of wheat peptides and fucoidan (WPF) on adults diagnosed with chronic superficial gastritis in a randomized, double-blind, placebo-controlled clinical trial.

Methods: Participants were randomized to receive WPF (N = 53) or placebo (N = 53) once daily for 45 days. The pathological grading of gastric mucosal damage was scored using gastroscopy. The fecal samples were collected for the determination of calprotectin, short-chain fatty acids (SCFA) levels and metagenomics analysis. The questionnaires for self-reported gastrointestinal discomforts, life quality and food frequency were collected throughout the study.

Results: WPF intervention reduced gastric mucosal damage of subjects (P < 0.001). Significantly less stomach pain (P < 0.001), belching (P = 0.028), bloating (P < 0.001), acid reflux (P < 0.001), loss of appetite (P = 0.021), increased food intake (P = 0.020), and promoted life quality (P = 0.014) were reported in the WPF group. WPF intervention significantly decreased fecal calprotectin level (P = 0.003) while slightly increased fecal SCFAs level (P = 0.092). Mechanistically, we found a shifted microbiota profile post-intervention with significantly increased bifidobacterium pseudocatenulatum (P = 0.032), eubacterium siraeum (P = 0.036), bacteroides intestinalis (P = 0.024) and decreased prevotella copri (P = 0.055).

Conclusions: In conclusion, WPF intervention could be utilized as a nutritional alternative to reverse the progression of chronic gastritis. Furthermore, WPF played an important role in the regulation of gut microbiota and SCFA production, which might benefit the lower gastrointestinal tract.

Funding Sources: Nutrilite Health Institute funded this research.

RevDate: 2019-06-21

Islam T, Koboziev I, Scoggin S, et al (2019)

Protective Effects of Curcumin in High Fat Diet (HFD)-Induced Obesity Include Anti-Inflammatory Effects in Adipose Tissue and Changes in Gut Microbiome (P06-075-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz031.P06-075-19.

Objectives: Curcumin, a traditionally used spice in Asia has several health-protecting effects. However, its role on gut microbiota and obesity-associated inflammation is still poorly understood. The objective of this study was to determine whether the protective effects of curcumin in high fat diet (HFD)-induced obesity are mediated by reduced white adipose tissue (WAT) inflammation and changes in gut bacteria.

Methods: Male B6 mice were fed a HFD (45% kcal fat) or HFD supplemented with 0.4% (w/w) curcumin (HFC) for thirteen weeks. Body weight, adiposity, glucose and, insulin tolerances, and serum triglycerides, insulin, leptin, resistin levels were measured. Gut microbiome composition was determined by 16S RNA metagenomics sequencing. Expression of inflammation-related genes in WAT was measured by qRT-PCR. Macrophage contents in WAT were evaluated by galectin-3 immunohistochemical staining.

Results: Pro-inflammatory transcription factor nuclear factor NF-kappa-B p65 subunit (p65) and toll-like receptor-4 (TLR-4) gene expression was downregulated in HFC group compared to HFD mice. Furthermore, curcumin reduced total macrophage infiltration in WAT in HFC mice compared to HFD group. Expression of both M1 (CD80, CD38) and M2 (Arginase-1) associated genes was decreased. The relative abundance of bacteria representing the Clostridium genus, which contains numerous short-chain fatty acid (SCFA) producing species, was increased by the curcumin supplement.

Conclusions: Curcumin exerts protective effects in dietary obesity, in part through downregulation of adipose tissue inflammation which may be due to the production of SCFA and, possibly other curcumin metabolites by gut microflora.

Funding Sources: Startup funds and Come N Go award from the College of Human Sciences at Texas Tech University.

RevDate: 2019-06-21

Antony J, Iyer J, Guthrie N, et al (2019)

The Supremacy of Aggregated N-of-1 Trials for Evidence-based Nutrition Studies (P06-096-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz031.P06-096-19.

Objectives: Design of aggregated N-of-1 trials with the intent of identifying individuals' unique response to probiotics by studying each individual directly. Consideration of their biochemical uniqueness will ensure sufficient data are collected on each individual to make unequivocal claims on their responses to probiotics.

Methods: In the aggregate N-of-1 trial design, measurements taken will encompass multivariate outcomes including monitoring weight, microbiome species abundance in total fecal DNA for quantitative metagenomics to evaluate microbial gene richness and quantification of short chain fatty acids; influence of probiotics on mood, cognition, depression and sleep may be measured using wireless devices.

Results: A pragmatic analysis approach will provide information beyond significant differences in outcomes from baseline, as well, identifying variation around outcomes for the individual. Decreasing variation over time would suggest a more stable state for a particular outcome. Data from a series of sophisticated N-of-1 studies will, therefore, provide a scientifically sound basis for the creation of a global index detailing the relationship between a nutritional response and genetic features, biochemical, behavioural and exposure levels. Physicians and health care providers can leverage this data to decide on how to manage a patient's condition, while nutraceutical companies can make more specific claims for their products.

Conclusions: N-of-1 trials are a logical extension to clinical practice as physicians deal with patients as individuals with unique characteristics and treatment algorithms in a traditional clinical care setting using patient outcomes to decide if the intervention worked. N-of-1 trials and aggregated N-of-1 trials help identify factors that influence responses to nutrition that may be shared among individuals. Results from N-of-1 trials may be effectively used in Augmented Randomized double-blind Clinical Trial design to identify responders with a goal in formulating successful probiotic interventions.

Funding Sources: KGK Science Inc.

RevDate: 2019-06-21

Young W, Carco C, Mullaney J, et al (2019)

The Microbiome in Functional Gastrointestinal Disorders Is Characterized by Bacteria and Genes Involved in Carbohydrate and Bile Acid Metabolism (OR23-01-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.OR23-01-19.

Objectives: Irritable Bowel Syndrome (IBS) is a functional gastrointestinal (GI) disorder featuring chronic or recurrent abdominal discomfort, usually with changes in GI habit. To improve our understanding of links between the microbiome and IBS, and how these links can be manipulated through diet, we undertook shotgun metagenomic sequencing of fecal samples from a case-control study.

Methods: Fecal samples from 172 individuals were analyzed by shotgun sequencing using the Illumina NextSeq platform. Of these, 77 were classified as controls, 16 were constipation-predominant IBS (IBS-C), 39 were diarrhea-predominant IBS (IBS-D), 29 were diagnosed with functional constipation (FC), and 11 had functional diarrhea (FD). Taxonomic classifications were determined using Metaxa2 and the SILVA 128 database. Gene functions were assigned by alignment of sequences against a protein reference database using DIAMOND. Mean relative abundance of bacterial taxa and functional genes were compared using permutation ANOVA. Ethical approval was obtained from the University of Otago Human Ethics Committee (Health) (Reference H16/094).

Results: Bacterial genera that discriminated case-controls (P < 0.05) from those with constipation (IBS-C + FC) and diarrhea (IBS-D + FD) included Megasphaera (increased in those with constipation), Blautia (increased in those with diarrhea), and Bilophila (increased in both constipation and diarrhea groups). Megasphaera and Blautia include bacteria that are bile-resistant and produce butyrate, possessing a wide range of Carbohydrate-Active enzymes. Bilophila are sulfite-reducing bacteria that are able to utilize bile-acids. Associated with these taxonomic differences, a wide range of genes involved in carbohydrate, energy, and amino acid metabolism differed significantly (P < 0.05), including some involved in taurine and glycine metabolism. Bile acids are conjugated with taurine or glycine in the liver, and these amino acids are removed by the action of members of the GI microbiota.

Conclusions: Results from our study suggest carbohydrate and bile acid metabolism by the GI microbiome may be important distinguishing characteristics in functional GI disorders.

Funding Sources: Funded by the New Zealand National Science Challenge High-Value Nutrition program.

RevDate: 2019-06-21

Cheng R, F He (2019)

Impacts of Ceftriaxone Exposure During Pregnancy on Maternal Gut and Placental Microbiota and Its Influence on Maternal and Offspring Immunity in Mice (OR01-04-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.OR01-04-19.

Objectives: This study aimed to investigate whether antibiotic exposure during pregnancy could alter maternal gut and placental microbiota, and consequently affect the immunity of both mother and offspring.

Methods: Pregnant BALB/c mice (n = 24) were gavaged with ceftriaxone from gestation day 13 to delivery. Both dams and pups were then sacrificed immediately after delivery. Spleen, placental, and fecal samples were collected from the tested dams, and blood samples were collected from both the dams and their pups. The microbiota in the feces and placenta of the dams were comprehensively analyzed using16S rRNA sequencing. Furthermore, viable bacteria in the placentas of dams were also isolated by plate cultivation then taxonomically identified in detail by clone sequencing. Serum cytokines collected from dams and pups were quantitatively profiled using Luminex.

Results: The maternal spleen index was significantly lower and the offspring serum interleukin-6 (IL-6) levels were significantly higher in ceftriaxone-treated mice compared with the control group. The diversity of maternal fecal microbiota was significantly lower in ceftriaxone-treated mice. The relative abundance of Bacteriodetes was significantly lower, while the relative abundance of Tenericutes was significantly higher in ceftriaxone-treated mothers. However, no significant differences in placental microbiota communities or metagenomic activity were found between the control group and the ceftriaxone-treated mice.

Conclusions: These results indicated that ceftriaxone exposure in pregnancy could dramatically alter maternal intestinal microbiota, which affected the immunity of the mothers and their offspring, characteristically by enhanced pro-inflammatory responses. The results from the present study also indicated that the placenta might harbor its own microbes, which may not be affected by environmental factors, such as oral administration of ceftriaxone during pregnancy. Further studies should be focused on the role of these microbes in the health of the fetus and infants.

Funding Sources: This work was supported by the National Natural Science Foundation of China (Grant number 81372982).

RevDate: 2019-06-21

Roy N, Fraser K, Young W, et al (2019)

The COMFORT Cohort: Identifying Biomarkers Relevant to Functional Gastrointestinal Disorders (P20-039-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.P20-039-19.

Objectives: The links between food, gastrointestinal (GI) function and comfort, and mental well-being are at the forefront of nutritional research. Irritable Bowel Syndrome (IBS) is a functional GI disorder and the combination of detailed patient reported outcomes (PROs) combined with omic data could better define these disorders.

Methods: The Christchurch COMFORT cohort is a case-control study: 337 participants with functional GI disorders (functional constipation FC, functional diarrhoea FD, IBS constipation IBS-C, IBS diarrhoea IBS-D) and asymptomatic controls. Demographics, symptom scores, psychological scores and dietary intake were recorded using the 'Modified Hunter New England' (Rome IV diagnostic criteria questionnaires; Medical History Questions; Hospital Anxiety and Depression Scale, HADS). Demographics included Structured Assessment of Gastrointestinal Symptoms (SAGIS); and Diet Diary and Live Symptoms Score (FAST) along with PRO Measurement Information System (PROMIS). Biological samples collected for an untargeted LCMS analysis of plasma and shot-gun metagenome analysis of faecal DNA. Ethical approval was obtained from the University of Otago Human Ethics Committee (H16/094).

Results: Symptom questionnaires were able to cluster 287 subjects into: IBS (42%), functional disorders (18%) and healthy controls (40%). Within IBS, 46% were IBS-D, 23% were IBS-C and 31% were IBS-M. Severity scores were higher for all IBS cases with PROMIS-GI scales. A higher score of health worry was reported in IBS-C than other IBS subtypes. HADS anxiety and depression scales were higher in IBS cases (vs. healthy controls). The FAST diary symptoms correlated with PROMIS GI scales (exception for constipation). Metabolomic analyses detected differential plasma metabolites and pathways (bile acids, lipids, specific amino acids) affected between IBS-C + FC vs IBS-D + FD, healthy vs IBS-D and healthy vs IBS-C. Metagenomics suggests that carbohydrate, methane, and sulfur metabolism may be important in IBS.

Conclusions: These data will allow us to apply a systems biology approach to identify key pathways and correlate them with the questionnaire data to better understand functional GI disorders.

Funding Sources: Funded by the NZ National Science Challenge High-Value Nutrition programme.

RevDate: 2019-06-21

Fraser K, Young W, McNabb W, et al (2019)

Lipid and Metabolite Profiles in Human Plasma and Associations with the Microbiome and Functional Gastrointestinal Disorders (P20-033-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.P20-033-19.

Objectives: Metabolomic profiling of plasma provides a biochemical fingerprint of the circulating metabolites from the host and microbiome, and may assist with understanding mechanisms underlying functional gastrointestinal (GI) disorders such as Irritable Bowel Syndrome (IBS). In a case-control study, we aimed to identify microbial and host factors in plasma to provide mechanistic insights into functional GI disorders and increase the predictability of phenotypes for use in nutrition intervention studies.

Methods: Plasma samples from 246 individuals with functional GI disorders (cases) or asymptomatic (controls), consisting of 93 healthy controls, 54 with functional constipation (C) or IBS-C, 60 with functional diarrhoea (D) or IBS-D, and 39 diagnosed as IBS-mixed or awaiting diagnosis. Plasma was subjected to biphasic extraction and global metabolite profiling was performed using three separate untargeted liquid chromatography high resolution mass spectrometry analysis (LC-MS) methods (polar, semi-polar and non-polar chromatography).

Results: Plasma metabolomic profiles differed considerably between the IBS phenotypes and those of the control subjects. Multivariate partial least squares discriminant analysis of 428 annotated lipid species highlighted significant differences (P < 0.001) between IBS-C and healthy control subjects. Univariate analysis revealed significant differences in the concentrations of 48 lipid species (P < 0.05) between the two groups, including elevated concentrations of many sphingolipids and phospholipids in the IBS-C group. Biochemical network analysis also revealed major perturbations in amino acid, bile acid and lipid metabolism, and highlighted key metabolic pathways included microbial related pathways.

Conclusions: Perturbations of plasma lipid concentrations in the IBS subjects suggest changes may occur with both host and microbial lipid metabolism. Future efforts to investigate these links will utilize a systems biology approach integrating metabolomic and fecal metagenomic datasets to further identify key pathways and biomarkers that characterize functional GI disorders and how nutrition can improve GI health and function.

Funding Sources: Funded by the New Zealand National Science Challenge High-Value Nutrition program.

RevDate: 2019-06-21

Spector T, Berry S, Valdes A, et al (2019)

Integrating Metagenomic Information into Personalized Nutrition Tools: The PREDICT I Study (P20-005-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.P20-005-19.

Objectives: The existence of a link between the intestinal microbiome and diet is well established. The demonstration that the microbiome information increases the prediction accuracy of postprandial blood glucose levels (Zeevi et al, 2015) is opening intriguing perspectives for developing personalized nutrition tools. However, reproducibly inferring the diet-induced microbiome changes and stratifying individual responses to dietary interventions based on the microbiome remain open challenges. The PREDICT I study aims to develop: (i) a protocol for gut microbiome sampling and analysis for large-scale nutritional studies and (ii) a microbiome-based machine learning integrative component for predictive personalized nutrition tools.

Methods: We performed three metagenomic investigations to; (i) identify the best combination for stool collection, sample storage, DNA extraction, and sequencing (n = 45); (ii) develop and validate the computational pipeline on an exploratory dietary interventional cohort (n = 1000); (iii) apply the validated pipeline on an independent validation cohort (n = 100). The generated total dataset (>8x10^12 sequenced bases) was analyzed with existing and newly developed computational tools and integrated with the metagenomic profiles of >10,000 samples processed from public repositories.

Results: Our resulting validated protocol involves a minimally time-demanding procedure for at-home sample collection, sample storage in a preservation buffer, and DNA extraction with a recently commercialized kit (Qiagen). Metagenomic sequencing proved substantially more accurate than 16S rRNA sequencing and was able to perfectly capture subject-specific strain-level features with longitudinal sampling. This method was also able to stratify by pre-intervention habitual dietary regimes. Our prediction algorithm showed that embedding the microbiome features in a 50-dimension space was sufficient to improve the prediction performance of postprandial blood glucose levels.

Conclusions: We present the largest investigation to date on the reproducible connections between the gut microbiome and dietary interventions. Further we describe our methods and results in using the microbiome as a component of a precise integrated postprandial blood glucose and blood lipid level predictor.

Funding Sources: Zoe Global Limited, National Institute for Health Research (NIHR), Wellcome Trust.

RevDate: 2019-06-21

Berry S, Valdes A, Davies R, et al (2019)

Large Inter-individual Variation in Postprandial Lipemia Following a Mixed Meal in over 1000 Twins and Singletons from the UK and US: The PREDICT I Study (OR19-06-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz046.OR19-06-19.

Objectives: Postprandial lipemia is an important risk factor for cardiovascular disease, independent of fasting levels, and is influenced by multiple factors including; environmental, genetic, metabolic, metagenomic and the meal-context. Postprandial lipemic responses may therefore differ between individuals, however previously this has only been studied in limited numbers. The PREDICT I study is the largest study to date to measure inter-individual variability in postprandial lipemic responses using a standardized test meal model.

Methods: A multi-center postprandial study of 1000 individuals from the UK (unrelated, identical and non-identical twins) and 100 unrelated individuals from US, assessed postprandial (hourly 0-6h) lipemic responses to sequential mixed-nutrient dietary challenges (50g fat and 85g carbohydrate at 0h; 22g fat and 71g carbohydrate at 4h) in a clinical setting. Inter-individual variability in postprandial triacylglycerol (TG) responses was measured for incremental area under the curve (iAUC), Cmax, Tmax and increase above fasting at 5h (mean peak concentration time-point).

Results: Analysis showed high inter-individual variability in postprandial lipemic responses (Figures 1-3) in the tightly controlled clinic setting (interim analysis of n = 537); IQR (median) was; iAUC (0-6h) 2.34 (2.38) mmol/L.h; Cmax 1.32 (2.02) mmol/L; Tmax 30.0 (300) min; and increase above fasting at 5h 0.92 (0.95). TG variation was higher in the non-fasting versus the fasting state; fasting TG concentration IQR (median); 0.57 (0.91) mmol/L.

Conclusions: The large variation in the magnitude and pattern of lipemic responses to identical meals in healthy people demonstrates the limitations of using the group mean and the importance of individualized dietary approaches. Ongoing exploration in PREDICT I of the determinants of postprandial lipemic responses considering environmental, genetic, metagenomic and microbiome variables will significantly advance our ability to predict an individual's postprandial response.

Funding Sources: NIHR, Wellcome Trust, Zoe Global Ltd.

RevDate: 2019-06-21

Shinn L, Li Y, Zhu R, et al (2019)

Applying Machine-Learning to Human Gastrointestinal Microbial Species to Predict Dietary Intake (P20-040-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.P20-040-19.

Objectives: To better understand host-microbe interactions, a more computationally intensive, multivariate, machine learning approach must be utilized. Accordingly, we aimed to identify biomarkers with high predictive accuracy for dietary intake.

Methods: Data were aggregated from five randomized, controlled, feeding studies in adults (n = 199) that provided avocados, almonds, broccoli, walnuts, or whole grain oats and whole grain barley. Fecal samples were collected during treatment and control periods for each study for DNA extraction. Subsequently, the 16S rRNA gene (V4 region) was amplified and sequenced. Sequence data were analyzed using DADA2 and QIIME2. Marginal screening using the Kruskal-Wallis test was performed on all species-level taxa to examine the differences between each of the 6 treatment groups and respective control groups. The top 20 species from each diet were selected and pooled together for multiclass classification using random forest. The resultant bacterial species were further decreased in a stepwise fashion and iteratively analyzed with the variable importance generated from random forest to determine a compact feature set with a minor loss of accuracy in the prediction of food consumed.

Result: When all six foods were analyzed together using the top 20 species of each diet, oats and barley were frequently confused for each other, with 44% and 47% classification error, respectively, and the overall model accuracy was 66%. Collapsing oats and barley into one category, whole grains, reduced the classification error of the whole grain category to 6% and improved the overall model accuracy to 73%. Refitting the random forest with the top 30, 20, and 10 important species resulted in correct identification of the 5 foods (avocados, almonds, broccoli, walnuts, and whole grains) 75%, 74%, and 70% of the time, respectively.

Conclusions: These results reveal promise in accurately predicting foods consumed using bacterial species as biomarkers. Ongoing analyses include incorporation of metagenomic and metabolomic data into the models to improve predictive accuracy and utilize the multi-omics dataset to predict health status. Long-term, these approaches may inform diet-microbiota-tailored recommendations.

Funding Sources: This research was funded by The Foundation for Food and Agriculture Research, USDA, Hass Avocado Board, and USDA National Institute of Food and Agriculture, Hatch project 1009249.

RevDate: 2019-06-21

Solano-Aguilar G, Shao J, Urban J, et al (2019)

Dietary Patterns Differentially Affect Microbiome Composition and Function in a Porcine Model of Obesity-related Metabolic Disorder (OR23-04-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz040.OR23-04-19.

Objectives: To determine the impact of two isocaloric diets containing (38% ,15% and 47% energy from fat, protein and carbohydrate, respectively): Western diet (WD) rich in saturated fat, refined carbohydrate, low in fiber and high in cholesterol, and a heart healthy diet (HHD) rich in unsaturated fat, unrefined carbohydrate, fruits/vegetables, high in fiber and low in cholesterol, on the composition and function of the gut microbiome.

Methods: Thirty-Ossabaw pigs were fed WD or HHD diets with half within each group therapeutically treated with statin (atorvastatin [Lipitor]). The fecal microbiome was analyzed one and six months after dietary intervention by 16S rRNA sequencing and metagenomic function was empirically inferred.

Results: Genus diversity was transiently affected with a reduced Shannon Diversity index one month after feeding the WD or HHD (FDR P < 0.05) with no change between groups at 6 months. Bacterial communities were clustered and separated by diet independent of gender and separated by treatment with statin in the HHD only. Verrucomicrobiaceae (Akkermansia) and Methanobacteriales (Methanobrevibacter) were increased in pigs as early as one month after feeding the HHD, as was Clostridiales and Bifidobacterium (associated with optimal intestinal health). There was an enrichment of Proteobacteria (Succinivibrionaceae, Desulfovibrionaceae) in pigs fed the WD. Additional members of the Firmicutes phylum were detected. Diet-dependent associations (all P < 0.05) were identified between Lachnospiraceae members and early host dyslipidemia, inflammation, and atheromatous lesions in the left anterior descending proximal (LAD) and LAD/Left circumflex (LCX) bifurcation six months post-intervention.

Conclusions: These data document for the first time a distinctive bacterial profile in Ossabaw pigs with a diet-induced dyslipidemia and early stage atherosclerosis. Taken together these results represent a new model to examine mechanistic pathways of dietary patterns and/or drug interactions and its effect on modulating microbiome in developing atherosclerosis.

Funding Sources: USDA project 8040-51530-056-00 and Inter Agency USDA Agreement 588-1950-9-001 between BHNRC and Jean Mayer USDA-HNRCA.

RevDate: 2019-06-21

Shafizadeh T, Frese S, G Casaburi (2019)

Maximizing Nutrient Availability for the Breastfed Infant Through Colonization with B. Infantis EVC001 (FS04-04-19).

Current developments in nutrition, 3(Suppl 1): pii:nzz048.FS04-04-19.

Objectives: Human breastmilk contains complete nutrient composition required for the developing infant, including human milk oligosaccharides (HMO). These complex carbohydrates are indigestible by the infant alone, and require digestion by gut microbes, namely Bifidobacterium longum subsp. infantis (B. infantis). However, decades of C-section delivery, formula feeding and increasing exposure to antibiotics have contributed the loss of this critical infant-associated gut bacterium in developed countries. Therefore, restoring B. infantis to the infant gut was hypothesized to improve the nutritional utilization of human breastmilk in healthy term infants.

Methods: In an open trial, healthy, exclusively breastfed term infants were fed 1.8 × 1010 CFU B. infantis EVC001 daily from day 7-27 postnatal (n = 34; EVC001-fed), or breastmilk alone (n = 32; control group). Fecal samples, milk samples, and weekly self-reported data were collected and analyzed for infant gut microbiome composition and function, human milk oligosaccharide composition, and fecal metabolites. 16S rRNA sequencing and shotgun metagenome sequencing provided characterization of microbial communities from birth through 60 days postnatal.

Results: Infants fed B. infantis EVC001 were uniformly colonized with this organism at 1011 CFU/g feces, while infants in the control group had a median total Bifidobacterium level below 10^5 CFU/g feces, despite exclusive breastfeeding. Mass spectrometry of fecal samples from B. infantis EVC001-fed infants showed that the resulting microbial community produced higher concentrations of lactate and acetate and lower excretion of HMO, while control infants showed significantly lower ability to capture and utilize these carbohydrates from human milk. Importantly, HMO content of breastmilk was not significantly different between groups and no difference was found in the gut microbiome of infants based on secretor status of mothers (presence or absence of 2'FL in breastmilk). Further, these changes were associated with reductions in taxa that have been associated with negative health outcomes including colic, asthma, eczema and allergy.

Conclusions: Overall, colonization with B. infantis is observed to be an effective way to restore maximal function of the infant gut microbiome to improve nutrient availability in the breastfed infant.

Funding Sources: This study was funded by Evolve BioSystems, Inc.

RevDate: 2019-06-21

Schumacker ST, Chidester CAM, Enke RA, et al (2019)

RNA sequencing dataset characterizing transcriptomic responses to dietary changes in Caenorhabditis elegans.

Data in brief, 25:104006 pii:104006.

Transcriptome analysis using next generation sequencing (NGS) technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. The nematode Caenorhabditis elegans (C. elegans) is a well-established genetic system used for analyzing a number of biological processes. C. elegans are a bacteria-eating soil nematode, and changes in bacterial diet have been shown to cause a number of physiological and molecular changes. Here we used Illumina RNA sequencing (RNA-seq) analysis to characterize the mRNA transcriptome of mixed C. elegans populations fed differing strains of bacteria to further understand dietary changes at the molecular level. Raw FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA) and have been assigned BioProject accession PRJNA412551.

RevDate: 2019-06-21

Banhos Danneskiold-Samsøe N, Sonne SB, Larsen JM, et al (2019)

Overexpression of cyclooxygenase-2 in adipocytes reduces fat accumulation in inguinal white adipose tissue and hepatic steatosis in high-fat fed mice.

Scientific reports, 9(1):8979 pii:10.1038/s41598-019-45062-w.

Cyclooxygenases are known as important regulators of metabolism and immune processes via conversion of C20 fatty acids into various regulatory lipid mediators, and cyclooxygenase activity has been implicated in browning of white adipose tissues. We generated transgenic (TG) C57BL/6 mice expressing the Ptgs2 gene encoding cyclooxygenase-2 (COX-2) in mature adipocytes. TG mice fed a high-fat diet displayed marginally lower weight gain with less hepatic steatosis and a slight improvement in insulin sensitivity, but no difference in glucose tolerance. Compared to littermate wildtype mice, TG mice selectively reduced inguinal white adipose tissue (iWAT) mass and fat cell size, whereas the epididymal (eWAT) fat depot remained unchanged. The changes in iWAT were accompanied by increased levels of specific COX-derived lipid mediators and increased mRNA levels of interleukin-33, interleukin-4 and arginase-1, but not increased expression of uncoupling protein 1 or increased energy expenditure. Epididymal WAT (eWAT) in TG mice exhibited few changes except from increased infiltration with eosinophils. Our findings suggest a role for COX-2-derived lipid mediators from adipocytes in mediating type 2 immunity cues in subcutaneous WAT associated with decreased hepatic steatosis, but with no accompanying induction of browning and increased energy expenditure.

RevDate: 2019-06-21

Yadav D, Dutta A, SS Mande (2019)

OTUX: V-region specific OTU database for improved 16S rRNA OTU picking and efficient cross-study taxonomic comparison of microbiomes.

DNA research : an international journal for rapid publication of reports on genes and genomes, 26(2):147-156.

Many microbiome studies employ reference-based operational taxonomic unit (OTU)-picking methods, which in general, rely on databases cataloguing reference OTUs identified through clustering full-length 16S rRNA genes. Given that the rate of accumulation of mutations are not uniform throughout the length of a 16S rRNA gene across different taxonomic clades, results of OTU identification or taxonomic classification obtained using 'short-read' sequence queries (as generated by next-generation sequencing platforms) can be inconsistent and of suboptimal accuracy. De novo OTU clustering results too can significantly vary depending upon the hypervariable region (V-region) targeted for sequencing. As a consequence, comparison of microbiomes profiled in different scientific studies becomes difficult and often poses a challenge in analysing new findings in context of prior knowledge. The OTUX approach of reference-based OTU-picking proposes to overcome these limitations by using 'customized' OTU reference databases, which can cater to different sets of short-read sequences corresponding to different 16S V-regions. The results obtained with OTUX-approach (which are in terms of OTUX-OTU identifiers) can also be 'mapped back' or represented in terms of other OTU database identifiers/taxonomy, e.g. Greengenes, thus allowing for easy cross-study comparisons. Validation with simulated datasets indicates more efficient, accurate, and consistent taxonomic classifications obtained using OTUX-approach, as compared with conventional methods.

RevDate: 2019-06-21
CmpDate: 2019-06-21

Purcell RV, Visnovska M, Biggs PJ, et al (2017)

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer.

Scientific reports, 7(1):11590.

Colorectal cancer (CRC) is a heterogeneous disease and recent advances in subtype classification have successfully stratified the disease using molecular profiling. The contribution of bacterial species to CRC development is increasingly acknowledged, and here, we sought to analyse CRC microbiomes and relate them to tumour consensus molecular subtypes (CMS), in order to better understand the relationship between bacterial species and the molecular mechanisms associated with CRC subtypes. We classified 34 tumours into CRC subtypes using RNA-sequencing derived gene expression and determined relative abundances of bacterial taxonomic groups using 16S rRNA amplicon metabarcoding. 16S rRNA analysis showed enrichment of Fusobacteria and Bacteroidetes, and decreased levels of Firmicutes and Proteobacteria in CMS1. A more detailed analysis of bacterial taxa using non-human RNA-sequencing reads uncovered distinct bacterial communities associated with each molecular subtype. The most highly enriched species associated with CMS1 included Fusobacterium hwasookii and Porphyromonas gingivalis. CMS2 was enriched for Selenomas and Prevotella species, while CMS3 had few significant associations. Targeted quantitative PCR validated these findings and also showed an enrichment of Fusobacterium nucleatum, Parvimonas micra and Peptostreptococcus stomatis in CMS1. In this study, we have successfully associated individual bacterial species to CRC subtypes for the first time.

RevDate: 2019-06-21
CmpDate: 2019-06-21

Potter C, Freeman C, Golyshin PN, et al (2017)

Subtle shifts in microbial communities occur alongside the release of carbon induced by drought and rewetting in contrasting peatland ecosystems.

Scientific reports, 7(1):11314.

Peat represents a globally significant pool of sequestered carbon. However, peatland carbon stocks are highly threatened by anthropogenic climate change, including drought, which leads to a large release of carbon dioxide. Although the enzymatic mechanisms underlying drought-driven carbon release are well documented, the effect of drought on peatland microbial communities has been little studied. Here, we carried out a replicated and controlled drought manipulation using intact peat 'mesocosm cores' taken from bog and fen habitats, and used a combination of community fingerprinting and sequencing of marker genes to identify community changes associated with drought. Community composition varied with habitat and depth. Moreover, community differences between mesocosm cores were stronger than the effect of the drought treatment, emphasising the importance of replication in microbial marker gene studies. While the effect of drought on the overall composition of prokaryotic and eukaryotic communities was weak, a subset of the microbial community did change in relative abundance, especially in the fen habitat at 5 cm depth. 'Drought-responsive' OTUs were disproportionately drawn from the phyla Bacteroidetes and Proteobacteria. Collectively, the data provide insights into the microbial community changes occurring alongside drought-driven carbon release from peatlands, and suggest a number of novel avenues for future research.

RevDate: 2019-06-21
CmpDate: 2019-06-21

Wu X, Zhang H, Chen J, et al (2017)

Analysis and comparison of the wolf microbiome under different environmental factors using three different data of Next Generation Sequencing.

Scientific reports, 7(1):11332.

Next Generation Sequencing has been widely used to characterize the prevalence of fecal bacteria in many different species. In this study, we attempted to employ a low-cost and high-throughput sequencing model to discern information pertaining to the wolf microbiota. It is hoped that this model will allow researchers to elucidate potential protective factors in relation to endangered wolf species. We propose three high-throughput sequencing models to reveal information pertaining to the micro-ecology of the wolf. Our analyses advised that, among the three models, more than 100,000 sequences are more appropriate to retrieve the communities' richness and diversity of micro-ecology. In addition, the top five wolf microbiome OTUs (99%) were members of the following five phyla: Bacteroidetes, Fusobacteria, Firmicutes, Proteobacteria, and Actinobacteria. While Alloprevotella, Clostridium_sensu_stricto_1, Anaerobiospirillum, Faecalibactreium and Streptococcus were shared by all samples, their relative abundances were differentially represented between domestic dogs and other wolves. Our findings suggest that altitude, human interference, age, and climate all contribute towards the micro-ecology of the wolf. Specifically, we observed that genera Succinivibrio and Turicibacter are significantly related to altitude and human interference (including hunting practices).

RevDate: 2019-06-20

Tian H, Hu Y, Xu X, et al (2019)

Enhanced wastewater treatment with high o-aminophenol concentration by two-stage MABR and its biodegradation mechanism.

Bioresource technology, 289:121649 pii:S0960-8524(19)30879-X [Epub ahead of print].

A two-stage bench-scale membrane-aerated biofilm reactor (MABR) was developed to treat wastewater containing high o-aminophenol (OAP) content. Long-term process showed that MABR-1 can achieve the removal rates of 17.6 g OAP/m2 d and 29.4 g COD/m2 d. MABR-2 can effectively perform more than 90% TN removal with the addition of external glucose. Pseudomonas and Nitrosomonas were the key functional genera in MABR-1 and MABR-2, respectively. Functional genes related to OAP degradation, including amnA,B,D, dmpC,H, mhpD,E,F, and bphH,I,J, were detected, and the involved enzymes were predicted. The OAP-degrading species and functional contribution analysis indicated that OAP can be metabolized by a single Pseudomonas or by the synergistic effects of bacteria, mainly including Cupriavidus, Thauera, unclassified Sphingomonadaceae, Lysobacter, and Azotobacter or by the cooperation of all the bacteria above. These diversified patterns guaranteed the high efficiency for OAP removal in MABR when treating wastewater with high OAP concentration.

RevDate: 2019-06-20

Trifi H, Najjari A, Achouak W, et al (2019)

Metataxonomics of Tunisian phosphogypsum based on five bioinformatics pipelines: Insights for bioremediation.

Genomics pii:S0888-7543(19)30022-9 [Epub ahead of print].

Phosphogypsum (PG) is an acidic by-product from the phosphate fertilizer industry and it is characterized by a low nutrient availability and the presence of radionuclides and heavy metals which pose a serious problem in its management. Here, we have applied Illumina MiSeq sequencing technology and five bioinformatics pipelines to explore the phylogenetic communities in Tunisian PG. Taking One Codex as a reference method, we present the results of 16S-rDNA-gene-based metataxonomics abundances with four other alternative bioinformatics pipelines (MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST), mothur, MICrobial Community Analysis (MICCA) and Quantitative Insights into Microbial Ecology (QIIME)), when analyzing the Tunisian PG. Importantly, based on 16S rDNA datasets, the functional capabilities of microbial communities of PG were deciphered. They suggested the presence of PG autochthonous bacteria recoverable into (1) removal of radioactive elements and toxic heavy metals (2) promotion of plant growth (3) oxidation and (4) reduction of sulfate.

RevDate: 2019-06-20

Fang Z, Tan J, Wu S, et al (2019)

PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning.

GigaScience, 8(6):.

BACKGROUND: Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods that can simultaneously identify phages and plasmids in metagenomic data, and the existing tools identifying either phages or plasmids have not yet presented satisfactory performance.

FINDINGS: We present PPR-Meta, a 3-class classifier that allows simultaneous identification of both phage and plasmid fragments from metagenomic assemblies. PPR-Meta consists of several modules for predicting sequences of different lengths. Using deep learning, a novel network architecture, referred to as the Bi-path Convolutional Neural Network, is designed to improve the performance for short fragments. PPR-Meta demonstrates much better performance than currently available similar tools individually for phage or plasmid identification, while testing on both artificial contigs and real metagenomic data. PPR-Meta is freely available via http://cqb.pku.edu.cn/ZhuLab/PPR_Meta or https://github.com/zhenchengfang/PPR-Meta.

CONCLUSIONS: To the best of our knowledge, PPR-Meta is the first tool that can simultaneously identify phage and plasmid fragments efficiently and reliably. The software is optimized and can be easily run on a local PC by non-computer professionals. We developed PPR-Meta to promote the research on mobile genetic elements and horizontal gene transfer.

RevDate: 2019-06-20

Ramesh A, Nakielny S, Hsu J, et al (2019)

Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda.

PloS one, 14(6):e0218318 pii:PONE-D-18-35569.

Febrile illness is a major burden in African children, and non-malarial causes of fever are uncertain. In this retrospective exploratory study, we used metagenomic next-generation sequencing (mNGS) to evaluate serum, nasopharyngeal, and stool specimens from 94 children (aged 2-54 months) with febrile illness admitted to Tororo District Hospital, Uganda. The most common microbes identified were Plasmodium falciparum (51.1% of samples) and parvovirus B19 (4.4%) from serum; human rhinoviruses A and C (40%), respiratory syncytial virus (10%), and human herpesvirus 5 (10%) from nasopharyngeal swabs; and rotavirus A (50% of those with diarrhea) from stool. We also report the near complete genome of a highly divergent orthobunyavirus, tentatively named Nyangole virus, identified from the serum of a child diagnosed with malaria and pneumonia, a Bwamba orthobunyavirus in the nasopharynx of a child with rash and sepsis, and the genomes of two novel human rhinovirus C species. In this retrospective exploratory study, mNGS identified multiple potential pathogens, including 3 new viral species, associated with fever in Ugandan children.

RevDate: 2019-06-20

Knudsen C, Neyrinck AM, Lanthier N, et al (2019)

Microbiota and nonalcoholic fatty liver disease: promising prospects for clinical interventions?.

Current opinion in clinical nutrition and metabolic care [Epub ahead of print].

PURPOSE OF REVIEW: Nonalcoholic fatty liver disease (NAFLD) is becoming the most important cause of chronic liver disease in Western countries but no pharmacological therapy is currently available. Growing evidence suggests that the microbiota plays a role in the occurrence and evolution of this disease, namely through the production of bioactive metabolites.

RECENT FINDINGS: Omics technologies (metagenomic, metabolomic, and phenomic data) allow providing a robust prediction of steatosis. More than just correlations, causative effects of certain bacterial metabolites have been evidenced in vitro and in rodent models. Butyrate has been shown to be a potent metabolic and inflammatory modulator in the liver. Several aromatic amino-acids such as phenylacetic acid, imidazole propionate, and 3-(4-hydroxyphenyl)lactate have been identified as potential inducers of steatosis and hepatic inflammation, whereas indolic compounds (indole and indole-3-acetate) seem to preserve liver integrity. Current clinical trials aim at evaluating the efficacy of novel approaches (functional foods, prebiotic and probiotics, and fecal microbial transplants).

SUMMARY: The microbiota brings new hopes in the management of nonalcoholic fatty liver diseases, including nonalcoholic steatohepatitis. Adequate intervention studies in targeted patients are needed to unravel the relevance of such approaches in the management of those liver diseases.

RevDate: 2019-06-20

Myer PR (2019)

Bovine Genome-Microbiome Interactions: Metagenomic Frontier for the Selection of Efficient Productivity in Cattle Systems.

mSystems, 4(3): pii:4/3/e00103-19.

The mutualistic, commensal, and parasitic microorganisms that reside in the rumen and lower gastrointestinal tract of cattle and other ruminants exert enormous influence over animal physiology and performance. Because these microbial communities are critical for host nutrient utilization and contribute to the metabolic capacity of the rumen, past research has aimed to define host-microbe symbioses in cattle by examining the rumen and lower gut microbiomes with respect to production phenotypes, such as feed efficiency. However, as the field of bovine gut microbial ecology progresses, multidisciplinary approaches must be employed, combining host genomics and other omics-based techniques to understand the complex host-microbe network. In this perspective, I discuss the direction of the field of bovine gut microbial ecology with regard to feed efficiency and explore how the grand challenge of such research will be to maintain host-efficient gut microbiomes in cattle production through manipulations of genome-microbiome interactions.

RevDate: 2019-06-20

Liu X, Yang QF, Gan N, et al (2019)

[Oral microbiological diversity in patients with salivary adenoid cystic carcinoma].

Hua xi kou qiang yi xue za zhi = Huaxi kouqiang yixue zazhi = West China journal of stomatology, 37(3):304-308.

OBJECTIVE: The aim of this study was to identify the differences in microbial diversity and community in patients with salivary adenoid cystic carcinoma (SACC).

METHODS: Saliva was collected from 13 patients with SACC confirmed by histopathological diagnosis and 10 healthy control subjects. Total metagenomic DNA was extracted. The DNA amplicons of the V3-V4 hypervariable regions of the 16S rRNA gene were generated and subjected to high-throughput sequencing. Microbial diversity and community structure were analyzed with Mothur software.

RESULTS: A total of 16 genera of dominant bacteria in the SACC group were found, including Streptococcus (36.68%), Neisseria (8.55%), Prevotella_7 (7.53%), and Veillonella (6.37%), whereas 15 dominant bacteria in the control group were found, including Streptococcus (18.41%), Neisseria (18.20%), Prevotella_7 (8.89%), Porphyromonas (6.20%), Fusobacterium (5.86%) and Veillonella (5.82%). The statistically different phyla between the two groups were Firmicutes, Proteobacteria and Fusobacterium (P<0.05). The statistically different genera between the two groups were Streptococcus, Neisseria and Porphyromonas (P<0.05), and Capnocytophaga was only detected in patients with SACC.

CONCLUSIONS: Significant differences were observed in the oral microorganisms between the two groups.

RevDate: 2019-06-20

Castillo Villamizar GA, Funkner K, Nacke H, et al (2019)

Functional Metagenomics Reveals a New Catalytic Domain, the Metallo-β-Lactamase Superfamily Domain, Associated with Phytase Activity.

mSphere, 4(3): pii:4/3/e00167-19.

Inositol-6-phosphate, also known as phytic acid, is a phosphorus source that plays several important roles in the phosphorus cycle and in cell metabolism. The known characterized enzymes responsible for its degradation, the phytases, are mostly derived from cultured individual microorganisms. The catalytic signatures of phytases are restricted to the molecular domains of four protein superfamilies: histidine phosphatases, protein tyrosine phosphatases, the purple acid phosphatases and the β-propeller phosphatases. During function-based screening of previously generated forest soil metagenomic libraries for Escherichia coli clones conferring phytase activity, two positive clones harboring the plasmids pLP05 and pLP12 were detected. Analysis of the insert sequences revealed the absence of classic phosphatase/phytase signatures of the proteins deduced from the putative genes, but the genes mblp01 (pLP05) and mblp02 (pLP12) encoded putative metallo-β-lactamases (MBLs). Several MBL representatives are promiscuous proteins with phosphoesterase activity, but phytase activity was previously not reported. Both mblp01 and mblp02 were subcloned, expressed, and analyzed. Mblp01 and Mblp02 are members of the lactamase B2 family. Protein modeling showed that the closest structural homologue of both proteins was ZipD of E. coli Mblp01 and Mblp02 showed activity toward the majority of the tested phosphorylated substrates, including phytate. The maximal enzyme activities were recorded for Mblp01 at 50°C under acidic conditions and for Mblp02 at 35°C and a neutral pH. In the presence of Cu2+ or SDS, the activities of Mblp01 and Mblp02 were strongly inhibited. Analyses of the minimal inhibitory concentrations of several β-lactam antibiotics revealed that recombinant E. coli cells carrying mblp01 or mblp02 showed reduced sensitivity toward β-lactam antibiotics.IMPORTANCE Phytic acid is a phosphorus storage molecule in many plant tissues, a source of phosphorus alternative to phosphate rocks, but it can also be a problematic antinutrient. In comparison to other phosphorus sources, phytic acid exhibits reduced bioavailability. Additionally, it influences functions of secondary messengers and acts as antioxidant in tumor growth prevention. The enzymatic capability to process phytate has been reported for a limited number of protein families. This might be due to the almost exclusive use of proteins derived from individual microorganisms to analyze phytase activity. With such a restriction, the study of the complexity and diversity of the phytases remains incomplete. By using metagenome-derived samples, this study demonstrates the existence of phytase activity in one of the most promiscuous superfamilies, the metallo-β-lactamases. Our results increase the general knowledge on phytase diversity in environmental samples and could provide new avenues for the study and engineering of new biocatalysts.

RevDate: 2019-06-20

Nguyen AT, Nguyen HTT, Le NNT, et al (2019)

Viruses in Vietnamese patients presenting with community acquired sepsis of unknown cause.

Journal of clinical microbiology pii:JCM.00386-19 [Epub ahead of print].

Community-acquired (CA) sepsis is a major public-health problem worldwide. Yet, the etiology remains unknown in >50% of the patients. Here, we applied metagenomic next-generation sequencing (mNGS) to characterize the human virome in 492 clinical samples (384 sera) from 386 patients (213 adults and 173 children) presenting with CA sepsis recruited from 6 hospitals across Vietnam between 2013 and 2015. Specific monoplex PCRs were subsequently used to confirm the presence of viral sequences detected by mNGS. We found sequences related to 47 viral species belonging to 21 families in 358/386 (93%) of patients, including viruses known to cause human infections. After PCR confirmation, human viruses were found in 52 of 386 patients (13.4%), with picornavirus (enteroviruses (n=14), rhinovirus (n=5) and parechovirus (n=2)), hepatitis B virus (n=10), cytomegalovirus (n=9), Epstein-Barr virus (n=5) and rotavirus A (n=3) being the most common viruses detected. Recently discovered viruses were also found (gemycircularvirus (n=5), WU-polyomavirus, saffold virus, salivirus, cyclovirus-VN and human pegivirus 2 (HPgV2) (1 each), adding to the growing literature about the geographic distribution of these novel viruses. Notably, sequences related to numerous viruses not previously reported in human tissues were also detected. To summarize, we identified 21 viral species known to be infectious to humans in 52/386 (13.4%) patients presenting with CA sepsis of unknown cause. The study, however, cannot directly impute sepsis causation involving the viruses identified. The results highlight the fact that it remains a challenge to establish the causative agents in CA sepsis patients, especially in tropical settings like Vietnam.

RevDate: 2019-06-20

Lo C, R Marculescu (2019)

MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks.

BMC bioinformatics, 20(Suppl 12):314 pii:10.1186/s12859-019-2833-2.

BACKGROUND: Microbiome profiles in the human body and environment niches have become publicly available due to recent advances in high-throughput sequencing technologies. Indeed, recent studies have already identified different microbiome profiles in healthy and sick individuals for a variety of diseases; this suggests that the microbiome profile can be used as a diagnostic tool in identifying the disease states of an individual. However, the high-dimensional nature of metagenomic data poses a significant challenge to existing machine learning models. Consequently, to enable personalized treatments, an efficient framework that can accurately and robustly differentiate between healthy and sick microbiome profiles is needed.

RESULTS: In this paper, we propose MetaNN (i.e., classification of host phenotypes from Metagenomic data using Neural Networks), a neural network framework which utilizes a new data augmentation technique to mitigate the effects of data over-fitting.

CONCLUSIONS: We show that MetaNN outperforms existing state-of-the-art models in terms of classification accuracy for both synthetic and real metagenomic data. These results pave the way towards developing personalized treatments for microbiome related diseases.

RevDate: 2019-06-20
CmpDate: 2019-06-20

Easton AV, Quiñones M, Vujkovic-Cvijin I, et al (2019)

The Impact of Anthelmintic Treatment on Human Gut Microbiota Based on Cross-Sectional and Pre- and Postdeworming Comparisons in Western Kenya.

mBio, 10(2): pii:mBio.00519-19.

Murine studies suggest that the presence of some species of intestinal helminths is associated with changes in host microbiota composition and diversity. However, studies in humans have produced varied conclusions, and the impact appears to vary widely depending on the helminth species present. To demonstrate how molecular approaches to the human gut microbiome can provide insights into the complex interplay among disparate organisms, DNA was extracted from cryopreserved stools collected from residents of 5 rural Kenyan villages prior to and 3 weeks and 3 months following albendazole (ALB) therapy. Samples were analyzed by quantitative PCR (qPCR) for the presence of 8 species of intestinal parasites and by MiSeq 16S rRNA gene sequencing. Based on pretreatment results, the presence of neither Ascaris lumbricoides nor Necator americanus infection significantly altered the overall diversity of the microbiota in comparison with age-matched controls. Following ALB therapy and clearance of soil-transmitted helminths (STH), there were significant increases in the proportion of the microbiota made up by Clostridiales (P = 0.0002; average fold change, 0.57) and reductions in the proportion made up by Enterobacteriales (P = 0.0004; average fold change, -0.58). There was a significant posttreatment decrease in Chao1 richness, even among individuals who were uninfected pretreatment, suggesting that antimicrobial effects must be considered in any posttreatment setting. Nevertheless, the helminth-associated changes in Clostridiales and Enterobacteriales suggest that clearance of STH, and of N. americanus in particular, alters the gut microbiota.IMPORTANCE The gut microbiome is an important factor in human health. It is affected by what we eat, what medicines we take, and what infections we acquire. In turn, it affects the way we absorb nutrients and whether we have excessive intestinal inflammation. Intestinal worms may have an important impact on the composition of the gut microbiome. Without a complete understanding of the impact of mass deworming programs on the microbiome, it is impossible to accurately calculate the cost-effectiveness of such public health interventions and to guard against any possible deleterious side effects. Our research examines this question in a "real-world" setting, using a longitudinal cohort, in which individuals with and without worm infections are treated with deworming medication and followed up at both three weeks and three months posttreatment. We quantify the impact of roundworms and hookworms on gut microbial composition, suggesting that the impact is small, but that treatment of hookworm infection results in significant changes. This work points to the need for follow-up studies to further examine the impact of hookworm on the gut microbiota and determine the health consequences of the observed changes.

RevDate: 2019-06-20
CmpDate: 2019-06-20

Kleinjans L, Veening-Griffioen DH, Wehkamp T, et al (2019)

Mice co-administrated with partially hydrolysed whey proteins and prebiotic fibre mixtures show allergen-specific tolerance and a modulated gut microbiota.

Beneficial microbes, 10(2):165-178.

Non-breastfed infants at-risk of allergy are recommended to use a hydrolysed formula before the age of 6 months. The addition of prebiotics to this formula may reduce the allergy development in these infants, but clinical evidence is still inconclusive. This study evaluates (1) whether the exposure duration to different prebiotics alongside a partially hydrolysed whey protein (pHP) influences its' effectiveness to prevent allergy development and (2) whether the gut microbiota plays a role in this process. Mice orally sensitised with whey and/or cholera toxin were orally treated for six days before sensitization with phosphate buffered saline, whey or pHP to potentially induce tolerance. Two groups received an oligosaccharide diet only from day -7 until -2 (GFshort and GFAshort) whereas two other groups received their diets from day -15 until 37 (GFlong and GFAlong). On day 35, mice underwent an intradermal whey challenge, and the acute allergic skin response, shock score, and body temperatures were measured. At day 37, mice received whey orally and serum mouse mast cell protease-1, SLPI and whey-specific antibodies were assessed. Faecal samples were taken at day -15, -8 and 34. Feeding mice pHP alone during tolerance induction did not reduce ear swelling. The tolerance inducing mechanisms seem to vary according to the oligosaccharide-composition. GFshort, GFlong, and GFAlong reduced the allergic skin response, whereas GFAshort was not potent enough. However, in the treatment groups, the dominant Lactobacillus species decreased, being replaced by Bacteroidales family S24-7 members. In addition, the relative abundance of Prevotella was significantly higher in the GFlong, GFAshort and GFAlong groups. Co-administration of oligosaccharides and pHP can induce immunological tolerance in mice, although tolerance induction was strongest in the animals that were fed oligosaccharides during the entire protocol. Some microbial changes coincided with tolerance induction, however, a specific mechanism could not be determined based on these data.

RevDate: 2019-06-19

Gill T, Brooks SR, Rosenbaum JT, et al (2019)

Novel Inter-omic Analysis Reveals Relationships Between Diverse Gut Microbiota and Host Immune Dysregulation in HLA-B27-Induced Experimental Spondyloarthritis.

Arthritis & rheumatology (Hoboken, N.J.) [Epub ahead of print].

OBJECTIVE: To define inflammation-related host-microbe interactions in experimental spondyloarthritis using novel inter-omic approaches.

METHODS: The relative frequency of gut microbes was determined by 16S rRNA gene sequencing, and gene expression by RNA-seq of host tissue. HLA-B27/human β2 -microglobulin transgenic (HLA-B27 TG) and wild type (WT) rats from Dark Agouti, Lewis, and Fischer backgrounds were used. Inter-omic analyses using Cytoscape were employed to identify relevant relationships. PICRUSt was used to predict microbial functions based on known metagenomic profiles.

RESULTS: Inter-omic analysis revealed several gut microbes microbes strongly associated with dysregulated cytokines driving inflammatory response pathways (e.g. IL-23, IL-17, IL-1, IFN-γ, TNF). Many microbes were uniquely associated with inflammation in Lewis or Fischer rats, and one was relevant on both backgrounds. Several microbes strongly correlated with immune dysregulation were not differentially abundant in HLA-B27 TG compared to WT controls. Multi-omic network analysis revealed non-overlapping clusters of microbes in Lewis and Fischer rats that were strongly linked to overlapping dysregulated immune/inflammatory genes. Prevotella, Clostridiales, and Blautia were important in Lewis rats, while Akkermansia muciniphila and members of the Lachnospiraceae family dominated in Fischer animals. Inflammation-associated metabolic pathway perturbation (e.g. butanoate, propanoate, LPS, and steroid biosynthesis) was also predicted from both backgrounds.

CONCLUSIONS: Inter-omic and network anaylsis of gut microbes and the host immune response in experimental SpA provides an unprecedented view of organisms strongly linked to dysregulated IL-23, IL-17, IL-1, IFN-γ, and TNF pathways. Functional similarities between these organisms may explain why different genetic backgrounds exhibit common patterns of immune dysregulation, possibly through perturbation of similar metabolic pathways. These results highlight the power of linking analyses of gut microbiota with the host immune response to gain insights into role of dysbiotic microbes in SpA beyond taxonomic profiling. This article is protected by copyright. All rights reserved.

RevDate: 2019-06-19

Shockey AC, Dabney J, CS Pepperell (2019)

Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria.

Frontiers in genetics, 10:477.

Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.

RevDate: 2019-06-19

Zhang H, Wang Q, Liu S, et al (2019)

Genomic and Metagenomic Insights Into the Microbial Community in the Regenerating Intestine of the Sea Cucumber Apostichopus japonicus.

Frontiers in microbiology, 10:1165.

Host-intestine microbiota interactions have been widely studied in aquatic animals, but these interactions in the intestine regeneration process of the sea cucumber Apostichopus japonicus have been rarely investigated. To understand how intestine regeneration impacts the developing intestinal microbiome composition and function, we performed a case study to characterize the intestinal microbial composition and functional genes of A. japonicus during intestine regeneration stages. High-throughput 16S rRNA gene sequencing revealed significantly different intestine microbiota compositions in different regeneration stages. The phylogenetic diversity and composition of the intestinal microbiota changed significantly in the early regeneration stage and tended to recover in the end stage. During the regeneration process, the abundance of Bacteroidetes and Rhodobacterales increased significantly. A network analysis revealed that Rhodobacteraceae and Flavobacteriaceae may function as keystone taxa in the intestinal microbial community of A. japonicus during intestine regeneration. Metagenomic analyses of representative samples revealed that the microbiomes of regenerating intestines were enriched in genes facilitating cell proliferation, digestion and immunity. The increased abundance of Bacteroidetes elevated the enrichment of genes associated with carbohydrate utilization. Some functional features in the subsystem category changed in a pattern that was consistent with the changing pattern of microbiota composition during intestine regeneration. Our results revealed that seemingly regular alterations in the intestinal microbiome composition and function are associated with intestine regeneration stages. Intestinal microbiota can increase the abundance of beneficial bacterial members and upregulate related functional genes to adapt to intestine regeneration and reconstruct a stable community structure. This study provides a new insight into the mechanism of the host-microbiota interaction response to organ regeneration.

RevDate: 2019-06-19

Cuevas-Caballé C, Riutort M, M Álvarez-Presas (2019)

Diet assessment of two land planarian species using high-throughput sequencing data.

Scientific reports, 9(1):8679 pii:10.1038/s41598-019-44952-3.

Geoplanidae (Platyhelminthes: Tricladida) feed on soil invertebrates. Observations of their predatory behavior in nature are scarce, and most of the information has been obtained from food preference experiments. Although these experiments are based on a wide variety of prey, this catalog is often far from being representative of the fauna present in the natural habitat of planarians. As some geoplanid species have recently become invasive, obtaining accurate knowledge about their feeding habits is crucial for the development of plans to control and prevent their expansion. Using high throughput sequencing data, we perform a metagenomic analysis to identify the in situ diet of two endemic and codistributed species of geoplanids from the Brazilian Atlantic Forest: Imbira marcusi and Cephaloflexa bergi. We have tested four different methods of taxonomic assignment and find that phylogenetic-based assignment methods outperform those based on similarity. The results show that the diet of I. marcusi is restricted to earthworms, whereas C. bergi preys on spiders, harvestmen, woodlice, grasshoppers, Hymenoptera, Lepidoptera and possibly other geoplanids. Furthermore, both species change their feeding habits among the different sample locations. In conclusion, the integration of metagenomics with phylogenetics should be considered when establishing studies on the feeding habits of invertebrates.

RevDate: 2019-06-19

Shi Z, Yin H, Van Nostrand JD, et al (2019)

Functional Gene Array-Based Ultrasensitive and Quantitative Detection of Microbial Populations in Complex Communities.

mSystems, 4(4): pii:4/4/e00296-19.

While functional gene arrays (FGAs) have greatly expanded our understanding of complex microbial systems, specificity, sensitivity, and quantitation challenges remain. We developed a new generation of FGA, GeoChip 5.0, using the Agilent platform. Two formats were created, a smaller format (GeoChip 5.0S), primarily covering carbon-, nitrogen-, sulfur-, and phosphorus-cycling genes and others providing ecological services, and a larger format (GeoChip 5.0M) containing the functional categories involved in biogeochemical cycling of C, N, S, and P and various metals, stress response, microbial defense, electron transport, plant growth promotion, virulence, gyrB, and fungus-, protozoan-, and virus-specific genes. GeoChip 5.0M contains 161,961 oligonucleotide probes covering >365,000 genes of 1,447 gene families from broad, functionally divergent taxonomic groups, including bacteria (2,721 genera), archaea (101 genera), fungi (297 genera), protists (219 genera), and viruses (167 genera), mainly phages. Computational and experimental evaluation indicated that designed probes were highly specific and could detect as little as 0.05 ng of pure culture DNAs within a background of 1 μg community DNA (equivalent to 0.005% of the population). Additionally, strong quantitative linear relationships were observed between signal intensity and amount of pure genomic (∼99% of probes detected; r > 0.9) or soil (∼97%; r > 0.9) DNAs. Application of the GeoChip to a contaminated groundwater microbial community indicated that environmental contaminants (primarily heavy metals) had significant impacts on the biodiversity of the communities. This is the most comprehensive FGA to date, capable of directly linking microbial genes/populations to ecosystem functions.IMPORTANCE The rapid development of metagenomic technologies, including microarrays, over the past decade has greatly expanded our understanding of complex microbial systems. However, because of the ever-expanding number of novel microbial sequences discovered each year, developing a microarray that is representative of real microbial communities, is specific and sensitive, and provides quantitative information remains a challenge. The newly developed GeoChip 5.0 is the most comprehensive microarray available to date for examining the functional capabilities of microbial communities important to biogeochemistry, ecology, environmental sciences, and human health. The GeoChip 5 is highly specific, sensitive, and quantitative based on both computational and experimental assays. Use of the array on a contaminated groundwater sample provided novel insights on the impacts of environmental contaminants on groundwater microbial communities.

RevDate: 2019-06-18

Tapadia-Maheshwari S, Pore S, Engineer A, et al (2019)

Illustration of the microbial community selected by optimized process and nutritional parameters resulting in enhanced biomethanation of rice straw without thermo-chemical pretreatment.

Bioresource technology, 289:121639 pii:S0960-8524(19)30869-7 [Epub ahead of print].

Effects of different process and nutritional parameters on microbial community structure and function were investigated to enhance the biomethanation of rice straw without any thermochemical pre-treatment. The study was performed in a mesophilic anaerobic digester with cattle dung slurry as inoculum. The highest methane yield of 274 ml g-1 volatile solids was obtained from particulate rice straw (1 mm size, 7.5% solids loading rate) at 37 °C, pH-7, when supplemented with urea (carbon: nitrogen ratio, 25:1) and zinc as trace element (100 µM) at 21 days hydraulic retention time. The optimization of conditions selected Clostridium, Bacteroides, and Ruminococcus as dominant hydrolytic bacteria and Methanosarcina as the methanogen. Analysis of metagenome and metatranscriptome revealed wide array of bacterial lignocellulolytic enzymes that efficiently hydrolyzed the rice straw. The methane yield was >80% of the theoretical yield, making this green process a sustainable choice for efficient extraction of energy from rice straw.

RevDate: 2019-06-18

Langelier C, Graves M, Kalantar K, et al (2019)

Microbiome and Antimicrobial Resistance Gene Dynamics in International Travelers.

Emerging infectious diseases, 25(7):1380-1383.

We used metagenomic next-generation sequencing to longitudinally assess the gut microbiota and antimicrobial resistomes of international travelers to clarify global exchange of resistant organisms. Travel resulted in an increase in antimicrobial resistance genes and a greater proportion of Escherichia species within gut microbial communities without impacting diversity.

RevDate: 2019-06-18

Van Regenmortel MHV (2019)

Solving the species problem in viral taxonomy: recommendations on non-Latinized binomial species names and on abandoning attempts to assign metagenomic viral sequences to species taxa.

Archives of virology pii:10.1007/s00705-019-04320-y [Epub ahead of print].

Properties useful for defining virus species are phenotypic properties of viruses that can be altered by a few mutations. Such properties include the natural host range, cell and tissue tropism, symptomatology, pathogenicity and mode of transmission. All these properties are not necessarily present in identical form in all the members of a species; therefore, a virus species is a polythetic class of viruses defined by a variable combination of several properties rather than by a single conserved property present in all the members of the species. This review will discuss current controversies about what virus species actually are as well as which names should be given to them. It will be emphasized that most species-defining properties are so-called relational properties that arise because viruses necessarily interact with biological partners such as vectors, hosts and immune systems. Although these relational properties are of utmost importance to laboratory and clinical virologists, they remain unknown if only the viral genome is available and the relational partners of the virus have not yet been identified. Since the International Committee on Taxonomy of Viruses (ICTV) in 2013 ratified a new definition of virus species, which no longer accepts that species are polythetic classes but instead are monophyletic groups, the implications of this new definition for viral taxonomy and nomenclature will be analyzed. In my private capacity, I also make the following recommendations regarding current debates on proposed new names for virus species as well as on the feasibility of assigning viral sequences found in metagenomic databases to individual species taxa in the current ICTV classification. 1) The ICTV should abandon the current rule that the names of virus species (for instance Measles virus) should differ from the virus name (measles virus) only by typography. 2) Non-Latinized binomial species names based on familiar virus and genus names should become the norm. This would obviate the need to create about 5000 hard-to-memorize Latinized species names. 3) Virus species are defined not by the intrinsic properties of virions and viral genomes but by the relational properties of viruses that arise from their interactions with host and vector partners. Since the hosts and vectors associated with nearly all viral sequences found in metagenomic databases are unknown, the phenotypic properties of the putative viruses also remain unknown, and these viral sequences cannot be allocated to established species in the ICTV classification.

RevDate: 2019-06-18

Ghadikolaei KK, Sangachini ED, Vahdatirad V, et al (2019)

An extreme halophilic xylanase from camel rumen metagenome with elevated catalytic activity in high salt concentrations.

AMB Express, 9(1):86 pii:10.1186/s13568-019-0809-2.

An extreme halophilic xylanase, designated as XylCMS, was characterized by cloning and expression of the encoding gene from a camel rumen metagenome. XylCMS proved to be a GH11 xylanase with high identity to a hypothetical glycosyl hydrolase from Ruminococcus flavefaciens. XylCMS with a molecular weight of about 47 kDa showed maximum activity at pH 6 and 55 °C. The enzyme activity was significantly stimulated by NaCl in 1-5 M concentrations. Interestingly, the optimum temperature was not influenced by NaCl but the Kcat of the enzyme was enhanced by 2.7-folds at 37 °C and 1.2-folds at 55 °C. The Km value was decreased with NaCl by 4.3-folds at 37 °C and 3.7-folds at 55 °C resulting in a significant increase in catalytic efficiency (Kcat/Km) by 11.5-folds at 37 °C and 4.4-folds at 55 °C. Thermodynamic analysis indicated that the activation energy (Ea) and enthalpy (∆H) of the reaction were decreased with NaCl by 2.4 and threefold, respectively. From the observations and the results of fluorescence spectroscopy, it was concluded that NaCl at high concentrations improves both the flexibility and substrate affinity of XylCMS that are crucial for catalytic activity by influencing substrate binding, product release and the energy barriers of the reaction. XylCMS as an extreme halophilic xylanase with stimulated activity in artificial seawater and low water activity conditions has potentials for application in industrial biotechnology.

RevDate: 2019-06-18

Olson CA, Dominguez SR, Miller S, et al (2019)

Gastroenteritis, Hepatitis, Encephalopathy, and Human Herpesvirus 6 Detection in an Immunocompetent Child: Benefits and Risks of Syndromic Multiplex Molecular Panel Testing.

The Journal of pediatrics pii:S0022-3476(19)30541-4 [Epub ahead of print].

An immunocompetent toddler came to medication attention with gastroenteritis, complicated by encephalopathy and hepatitis. Multiplexed testing using a polymerase chain reaction meningitis panel was positive for human herpesvirus 6 (HHV-6). Clinical correlation, quantitative HHV-6 polymerase chain reaction, and metagenomic next-generation sequencing supported a likely diagnosis of primary HHV-6B infection.

RevDate: 2019-06-18

Liu S, Qin P, J Wang (2019)

High-Fat Diet Alters the Intestinal Microbiota in Streptozotocin-Induced Type 2 Diabetic Mice.

Microorganisms, 7(6): pii:microorganisms7060176.

Intestinal microbiota is closely associated with various metabolic diseases such as type 2 diabetes (T2D), and microbiota is definitely affected by diet. However, more work is required to gain detailed information about gut metagenome and their associated impact with diet in T2D patients. We used a streptozotocin-high-fat diet (HFD) to induce a T2D mouse model and investigated the effect of standard chow diet and HFD on the composition and function of gut microbiota. We found that a HFD could worsen the diabetes status compared with a standard diet. 16S rRNA gene sequencing revealed that a HFD caused a large disturbance to the microbial structure and was linked to an increased ratio of Firmicutes to Bacteroidetes. A HFD increased the bacteria of the Ruminococcaceae and Erysipelotrichaceae family and decreased the bacteria of S24-7 and Rikenellaceae. Meanwhile, a HFD decreased the abundance of Parabacteroidesdistasonis and Eubacteriumdolichum, both of which have previously been reported to alleviate obesity and metabolic dysfunctions. Moreover, PICRUSt-predicted KEGG pathways related to membrane transport, lipid metabolism, and xenobiotics biodegradation and metabolism were significantly elevated in HFD-fed T2D mice. Our results provide insights into dietary and nutritional approaches for improving host metabolism and ameliorating T2D.

RevDate: 2019-06-18

Garrido-Sanz D, Redondo-Nieto M, Guirado M, et al (2019)

Metagenomic Insights into the Bacterial Functions of a Diesel-Degrading Consortium for the Rhizoremediation of Diesel-Polluted Soil.

Genes, 10(6): pii:genes10060456.

Diesel is a complex pollutant composed of a mixture of aliphatic and aromatic hydrocarbons. Because of this complexity, diesel bioremediation requires multiple microorganisms, which harbor the catabolic pathways to degrade the mixture. By enrichment cultivation of rhizospheric soil from a diesel-polluted site, we have isolated a bacterial consortium that can grow aerobically with diesel and different alkanes and polycyclic aromatic hydrocarbons (PAHs) as the sole carbon and energy source. Microbiome diversity analyses based on 16S rRNA gene showed that the diesel-degrading consortium consists of 76 amplicon sequence variants (ASVs) and it is dominated by Pseudomonas, Aquabacterium, Chryseobacterium, and Sphingomonadaceae. Changes in microbiome composition were observed when growing on specific hydrocarbons, reflecting that different populations degrade different hydrocarbons. Shotgun metagenome sequence analysis of the consortium growing on diesel has identified redundant genes encoding enzymes implicated in the initial oxidation of alkanes (AlkB, LadA, CYP450) and a variety of hydroxylating and ring-cleavage dioxygenases involved in aromatic and polyaromatic hydrocarbon degradation. The phylogenetic assignment of these enzymes to specific genera allowed us to model the role of specific populations in the diesel-degrading consortium. Rhizoremediation of diesel-polluted soil microcosms using the consortium, resulted in an important enhancement in the reduction of total petroleum hydrocarbons (TPHs), making it suited for rhizoremediation applications.

RevDate: 2019-06-18

Thompson LR, Haroon MF, Shibl AA, et al (2019)

Red Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes.

Applied and environmental microbiology, 85(13): pii:AEM.00369-19.

Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this "microbial seed bank" hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, and II) and 5 Prochlorococcus (ecotype HLII) samples from the Red Sea and combined them with globally sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically cryptic Prochlorococcus ecotypes LLII and LLIII. Compared with reference genomes, 1% of Prochlorococcus and 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they are functional. Searching Tara Oceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence/absence of OGs.IMPORTANCE Studies have shown that as we sequence seawater from a selected environment deeper and deeper, we approach finding every bacterial taxon known for the ocean as a whole. However, such studies have focused on taxonomic marker genes rather than on whole genomes, raising the possibility that the lack of endemism results from the method of investigation. We took a geographically isolated water body, the Red Sea, and sequenced single cells from it. We compared those single-cell genomes to available genomes from around the ocean and to ocean-spanning metagenomes. We showed that gene ortholog groups found in Red Sea genomes but not in other genomes are nevertheless common across global ocean metagenomes. These results suggest that Baas Becking's hypothesis "everything is everywhere, but the environment selects" also applies to gene ortholog groups. This widely dispersed functional diversity may give oceanic microbial communities the functional capacity to respond rapidly to changing conditions.

RevDate: 2019-06-17

Mahmood A, Shama S, Ni H, et al (2019)

Viral Metagenomics Revealed a Novel Cardiovirus in Feces of Wild Rats.

BACKGROUND/AIMS: Cardiovirus is a genus of viruses belonging to the family Picornaviridae. Here, we used viral metagenomic techniques to detect the viral nucleic acid in the fecal samples from wild rats in Zhenjiang city in China.

METHOD: Fecal samples were collected from 20 wild rats and pooled into four sample pools and then subjected to libraries construction which were then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline.

RESULTS: A novel cardiovirus from feces of a wild rat was identified, named amzj-2018, of which the complete genome was acquired. Phylogenetic analysis based on the complete amino acid sequence of polyprotein revealed that amzj-2018 formed a separate branch located between clusters of Saffold virus and Rat Theilovirus 1 (RTV-1). Phylogenetic analysis based on different regions of the polyproteins, including P1, P2, P3, and P2+P3, respectively, showed discordant trees, where the tree based on P3 region indicated that amzj-2018 clustered separately between Theiler's murine encephalomyelitis virus and RTV-1.

CONCLUSION: The complete genome of a cardiovirus was determined from the feces of wild rats which belonged to a novel type of cardiovirus based on phylogenetic analysis. Whether it is associated with disease needs further investigation.

RevDate: 2019-06-17

Kirisits MJ, Emelko MB, AJ Pinto (2019)

Applying biotechnology for drinking water biofiltration: advancing science and practice.

Current opinion in biotechnology, 57:197-204 pii:S0958-1669(18)30129-0 [Epub ahead of print].

Drinking water biofiltration processes have evolved over time, moving from unintentional to deliberate, with careful filter media selection, nutrient and trace metal supplementation, oxidant amendment, and bioaugmentation of key microorganisms, to achieve improvements in water quality. Biofiltration is on the precipice of a revolution that aims to customize the microbial community for targeted functional outcomes. These outcomes might be to enhance or introduce target functional activity for contaminant removal, to avoid hydraulic challenges, or to shape beneficially the downstream microbial community. Moving from the foundational molecular techniques that are commonly applied to biofiltration processes, such as amplicon sequencing and quantitative, real-time polymerase chain reaction, the biofiltration revolution will be facilitated by modern biotechnological tools, including metagenomics, metatranscriptomics, and metaproteomics. The application of such tools will provide a rich knowledge base of microbial community structure/function data under various water quality and operational conditions, where this information will be utilized to select biofilter conditions that promote the enrichment and maintenance of microorganisms with the desired functions.

RevDate: 2019-06-17

Parente E, De Filippis F, Ercolini D, et al (2019)

Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database.

International journal of food microbiology, 305:108249 pii:S0168-1605(19)30169-2 [Epub ahead of print].

We present a new version of FoodMicrobionet, a database for the exploration of food bacterial communities. The database, available as an app built with the Shiny package of R, includes data from 44 studies and 2234 samples (food or food environment), covering dairy, meat, fruit and vegetables, cereal based and ready-to-eat foods. The interactive interface allows exploration of data, access to external resources (on line versions of the studies, sequence data on SRA, taxonomic databases), filtering samples on the basis of a number of criteria, aggregation of samples and bacterial taxa and export of data in a variety of formats. FoodMicrobionet is the largest collection of data on food bacterial communities and, due to the structure of sample metadata, largely derived from the European Food Safety Agency FoodEx2 classification, makes comparison and re-analysis of data from published and unpublished studies easy. Data exported from FoodMicrobionet can be readily used for graphical and statistical meta-analyses using open-source software (Gephi, Cytoscape, CoNet, and R packages and apps, such as phyloseq and Shiny-Phyloseq) thus providing scientists, risk assessors and industry with a wealth of information on the structure of food biomes.

RevDate: 2019-06-17

Guss JD, Taylor E, Rouse Z, et al (2019)

The microbial metagenome and bone tissue composition in mice with microbiome-induced reductions in bone strength.

Bone pii:S8756-3282(19)30242-X [Epub ahead of print].

The genetic components of microbial species that inhabit the body are known collectively as the microbiome. Modifications to the microbiome have been implicated in disease processes throughout the body and have recently been shown to influence bone. Prior work has associated changes in the microbial taxonomy (phyla, class, species, etc.) in the gut with bone phenotypes but has provided limited information regarding mechanisms. With the goal of achieving a more mechanistic understanding of the effects of the microbiome on bone, we perform a metagenomic analysis of the gut microbiome that provides information on the functional capacity of the microbes (all microbial genes present) rather than only characterizing the microbial taxa. Male C57Bl/6 mice were subjected to disruption of the gut microbiota (ΔMicrobiome) using oral antibiotics (from 4 to 16 weeks of age) or remained untreated (n = 6-7/group). Disruption of the gut microbiome in this manner has been shown to lead to reductions in tissue mechanical properties and whole bone strength in adulthood with only minor changes in bone geometry and density. ΔMicrobiome led to modifications in the abundance of microbial genes responsible for the synthesis of the bacterial cell wall and capsule; bacterially synthesized carbohydrates; and bacterially synthesized vitamins (B and K) (p < 0.01). Follow up analysis focused on vitamin K, a factor that has previously been associated with bone health. The vitamin K content of the cecum, liver and kidneys was primarily microbe-derived forms of vitamin K (menaquinones) and was decreased by 32-66% in ∆Microbiome mice compared to untreated animals (p < 0.01). Bone mineral crystallinity determined using Raman spectroscopy was decreased in ∆Microbiome mice (p = 0.01). This study illustrates the use of metagenomic analysis to link the microbiome to bone phenotypes and provides preliminary findings implicating microbially synthesized vitamin-K as a regulator of bone matrix quality.

RevDate: 2019-06-17

Martí JM (2019)

Correction: Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.

PLoS computational biology, 15(6):e1007131 pii:PCOMPBIOL-D-19-00859.

[This corrects the article DOI: 10.1371/journal.pcbi.1006967.].

RevDate: 2019-06-17

Duchatelet S, Join-Lambert O, Delage M, et al (2019)

Remission of chronic acne fulminans and severe hidradenitis suppurativa with targeted antibiotherapy.

JAAD case reports, 5(6):525-528 pii:S2352-5126(19)30135-3.

RevDate: 2019-06-17

Yao R, Xu L, Lu G, et al (2019)

Evaluation of the Function of Wild Animal Gut Microbiomes Using Next-Generation Sequencing and Bioinformatics and its Relevance to Animal Conservation.

Evolutionary bioinformatics online, 15:1176934319848438 pii:10.1177_1176934319848438.

The relationship between animal conservation and the animal gut microbiome is a hot topic in current microbial ecology research. Our group has recently revealed that the occurrence of diverse combinations of gut microbial compositions and functions (metagenomics) in Père David's deer (Elaphurus davidianus) populations is likely to lead to increased evolutionary potential and resilience in response to environmental changes. Thus, considering the effects of diet on the gut microbiome and the importance of a stable gut microbial community to host health, we suggest that a transitional buffer period (with feeding on a regular diet and a diet from the translocation habitat) is needed before animal translocation. When the gut microbiome enters into relatively stable stages and adapts to the new diet from the translocation site, the time is suitable for translocation. Long-term monitoring of the gut microbiomes of translocated animals (by collecting fresh feces and carrying out next-generation sequencing) is still necessary after their translocation.

RevDate: 2019-06-17

Mojarro A, Hachey J, Bailey R, et al (2019)

Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection.

Astrobiology [Epub ahead of print].

Recent studies regarding the origins of life and Mars-Earth meteorite transfer simulations suggest that biological informational polymers, such as nucleic acids (DNA and RNA), have the potential to provide unambiguous evidence of life on Mars. To this end, we are developing a metagenomics-based life-detection instrument which integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG). Our goal is to isolate and sequence nucleic acids from extant or preserved life on Mars in order to determine if a particular genetic sequence (1) is distantly related to life on Earth, indicating a shared ancestry due to lithological exchange, or (2) is unrelated to life on Earth, suggesting a convergent origins of life on Mars. In this study, we validate prior work on nucleic acid extraction from cells deposited in Mars analog soils down to microbial concentrations (i.e., 104 cells in 50 mg of soil) observed in the driest and coldest regions on Earth. In addition, we report low-input nanopore sequencing results from 2 pg of purified Bacillus subtilis spore DNA simulating ideal extraction yields equivalent to 1 ppb life-detection sensitivity. We achieve this by employing carrier sequencing, a method of sequencing sub-nanogram DNA in the background of a genomic carrier. After filtering of carrier, low-quality, and low-complexity reads we detected 5 B. subtilis reads, 18 contamination reads (including Homo sapiens), and 6 high-quality noise reads believed to be sequencing artifacts.

RevDate: 2019-06-17
CmpDate: 2019-06-17

Feye KM, SC Ricke (2019)

Establishment of a Standardized 16S rDNA Library Preparation to Enable Analysis of Microbiome in Poultry Processing Using Illumina MiSeq Platform.

Methods in molecular biology (Clifton, N.J.), 1918:213-227.

The standardization of the microbiome sequencing of poultry rinsates is essential for generating comparable microbial composition data among poultry processing facilities if this technology is to be adopted by the industry. Samples must first be acquired, DNA must be extracted, and libraries must be constructed. In order to proceed to library sequencing, the samples should meet quality control standards. Finally, data must be analyzed using computer bioinformatics pipelines. This data can subsequently be incorporated into more advanced computer algorithms for risk assessment. Ultimately, a uniform sequencing pipeline will enable both the government regulatory agencies and the poultry industry to identify potential weaknesses in food safety. This chapter presents the different steps for monitoring the population dynamics of the microbiome in poultry processing using 16S rDNA sequencing.

RevDate: 2019-06-17
CmpDate: 2019-06-17

Libertucci J, VB Young (2019)

The role of the microbiota in infectious diseases.

Nature microbiology, 4(1):35-45.

The human body is colonized by a diverse community of microorganisms collectively referred to as the microbiota. Here, we describe how the human microbiota influences susceptibility to infectious diseases using examples from the respiratory, gastrointestinal and female reproductive tract. We will discuss how interactions between the host, the indigenous microbiota and non-native microorganisms, including bacteria, viruses and fungi, can alter the outcome of infections. This Review Article will highlight the complex mechanisms by which the microbiota mediates colonization resistance, both directly and indirectly, against infectious agents. Strategies for the therapeutic modulation of the microbiota to prevent or treat infectious diseases will be discussed, and we will review potential therapies that directly target the microbiota, including prebiotics, probiotics, synbiotics and faecal microbiota transplantation.

RevDate: 2019-06-16

Wang X, Shen J, Kang J, et al (2019)

Mechanism of oxytetracycline removal by aerobic granular sludge in SBR.

Water research, 161:308-318 pii:S0043-1354(19)30519-6 [Epub ahead of print].

In this study, oxytetracycline (OTC) as a target pollutant in swine wastewater was removed by aerobic granular sludge (AGS). The removal rate of 300 μg/L OTC in aerobic granular sludge sequencing batch reactor (AGSBR) increased to 88.00% in 33 days and maintained stable. The chemical oxygen demand (COD), ammonium nitrogen (NH4+-N) and total phosphorus (TP) in wastewater were also efficiently removed. The removal of OTC mainly depended on the adsorption and biodegradation of AGS, and the biodegradation was increased obviously after AGS adaptation to OTC. The degradation products of OTC were analyzed by mass spectrometry. The analysis of metagenome sequencing revealed that the enzymes, such as glycosyl transferases (GTs), polysaccharide lyases (PLs) and auxiliary activities (AAs), may play an important role in the removal of OTC. The Lefse analysis showed that the Flavobacteriia, Flavobacteriales, Cryomorphaceae and Fluviicola were four kinds of microbes with significant difference in OTC feed reactor, which are considered to be drug-resistant bacteria in AGSBR. Furthermore, the dynamics of microbial community changed significantly at three levels, including the enrichment of drug-resistant microorganisms and the microorganisms that gradually reduced or even disappeared under the pressure of OTC.

RevDate: 2019-06-16

Wang H, Qin X, Mi S, et al (2019)

Contamination of yellow-feathered broiler carcasses: Microbial diversity and succession during processing.

Food microbiology, 83:18-26.

The processing environment of broiler processing plants is a potential major source of bacterial contamination of broiler carcasses. This study investigated the effect of processing water and processing time on the microbial diversity of yellow-feathered broiler carcasses at select stages of slaughter during one commercial processing day using a high-throughput sequencing technique targeting the V3V4 region of the 16S RNA gene. Our results demonstrated that Firmicutes and Proteobacteria were the dominant bacterial phyla of broiler carcasses and processing water in the chiller tank, whereas the processing water in the scalder tank contained a high abundance of Firmicutes and Deinococcus-Thermus. At the genus level, Escherichia-Shigella and Streptococcus were present on broiler carcasses with high abundances after defeathering, but their abundance decreased after washing and chilling. The bacterial community structure was revealed to become more complex at later stages of processing, as indicated by the consistent increase in microbial alpha diversity metrics (Chao 1, Shannoneven and Shannon) throughout the processing stages (p < 0.05). Significantly separate clustering of bacterial communities between scalder tank water and carcasses was revealed by PCoA analysis, indicating the limited effect of scalding water on the bacterial communities of broiler carcasses.

RevDate: 2019-06-16

Soverini M, Turroni S, Biagi E, et al (2019)

HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.

BMC genomics, 20(1):496 pii:10.1186/s12864-019-5883-y.

BACKGROUND: Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.

RESULTS: HumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.

CONCLUSIONS: Although blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.

RevDate: 2019-06-15

Zhao Y, Jiang B, Tang X, et al (2019)

Metagenomic insights into functional traits variation and coupling effects on the anammox community during reactor start-up.

The Science of the total environment, 687:50-60 pii:S0048-9697(19)32551-3 [Epub ahead of print].

Anammox technology is an energy-efficient wastewater treatment process and anammox community structure has gained extensive attention. However, the dynamics of community functional traits are still elusive. Here, we combined the long-term reactor operation and metagenomic, multiple bioinformatic and network analyses to reveal the succession of anammox community and function traits during reactor start-up. We found the cooperation of denitrifiers that affiliated to the phylum Proteobacteria could reduce nitrite to dinitrogen gas. These organisms and genes had higher abundance after the inhibition phase, which could contribute to nitrite consuming and reactor performance recovery. Importantly, the Terrimonas and Anaerolinea organisms had ability of extracellular polymers secretion or aggregate formation. They had the highest abundance at the end of the lag phase, which could benefit for promoting the nitrogen removal rate (NRR). Meanwhile, Terrimonas and Anaerolinea bacteria could cooperate with methanogenic and nitrite-denitrifying methanotrophic organisms based on H2 and CH4, respectively. Since these organisms also had higher abundance after the inhibition phase, their cooperation could prevent anammox bacteria from nitrite inhibiting when the influent nitrite concentration was higher. The analysis of community and function shift is expected to emphasize the importance of functional bacteria in anammox process and provides a potential control strategy for nitrogen-containing wastewater treatment process.

RevDate: 2019-06-15

Supreetha K, Rao SN, Srividya D, et al (2019)

Advances in cloning, structural and bioremediation aspects of nitrile hydratases.

Molecular biology reports pii:10.1007/s11033-019-04811-w [Epub ahead of print].

Nitrile hydratase (NHase) is a prominent enzyme in many microorganisms for its nitrile metabolism. The potentiality in the bioconversion of nitriles to its high-value amides has been extensively used in industries for the production of acrylamide and nicotinamide which are essential chemicals. Enzymologists are still considering NHases for its potential biotechnological applications including biotransformations and bioremediations. But most of the nitrile hydratases have limitations like the low expression, low thermostability and enantioselectivity. Though considerable data has been generated in the area of gene configuration, crystal structure, kinetic mechanism and photoreactivity of NHases, there is a need for constant improvement to develop a robust biocatalyst for bioremediation of toxic nitriles. With these considerations, in the present review, we report advances with the main focus to structure, catalytic mechanism, cloning strategy, gene expression, bioinformatic tools, metagenomics, thermostability and current bioremediation applications of NHases.

RevDate: 2019-06-14

Liu X, Cao L, Zeng J, et al (2019)

Improving the cellobiose-hydrolysis activity and glucose-tolerance of a thermostable β-glucosidase through rational design.

International journal of biological macromolecules pii:S0141-8130(19)31662-9 [Epub ahead of print].

β-Glucosidase is the rate-limiting component of a cellulase-hydrolyzing reaction. Thermostability and glucose-tolerance are two critical criteria of the enzyme, which practically determine its performance in industrial applications. In this study, a thermostable and glucose-tolerant β-glucosidase (named Bgl1317) belonging to the glycoside hydrolase family 1 was acquired from a metagenomic library of Turpan soil through functional screening. Bgl1317 showed excellent thermostability and glucose-tolerance and its crystal structure was subsequently determined at a high resolution. Rational design based on the structure was conducted, producing three beneficial mutations A397R, L188A and A262S. While A397R improved the cellobiose activity by 80%, L188A and A262S increased the IC50 value of glucose from 0.8 to 1.5 M. The residues that may play a role in glucose-tolerance of GH1 β-glucosidases were summarized and the performances of glucose-tolerant β-glucosidases reported in recent years were discussed and compared. This study provides insights into enzymatic properties of Bgl1317 for engineering it into a powerful catalyst and β-glucosidases in general.

RevDate: 2019-06-14

Luiken REC, Van Gompel L, Munk P, et al (2019)

Associations between antimicrobial use and the faecal resistome on broiler farms from nine European countries.

The Journal of antimicrobial chemotherapy pii:5519196 [Epub ahead of print].

OBJECTIVES: To determine associations between farm- and flock-level antimicrobial usage (AMU), farm biosecurity status and the abundance of faecal antimicrobial resistance genes (ARGs) on broiler farms.

METHODS: In the cross-sectional pan-European EFFORT study, conventional broiler farms were visited and faeces, AMU information and biosecurity records were collected. The resistomes of pooled faecal samples were determined by metagenomic analysis for 176 farms. A meta-analysis approach was used to relate total and class-specific ARGs (expressed as fragments per kb reference per million bacterial fragments, FPKM) to AMU (treatment incidence per DDD, TIDDDvet) per country and subsequently across all countries. In a similar way, the association between biosecurity status (Biocheck.UGent) and the resistome was explored.

RESULTS: Sixty-six (38%) flocks did not report group treatments but showed a similar resistome composition and roughly similar ARG levels to antimicrobial-treated flocks. Nevertheless, we found significant positive associations between β-lactam, tetracycline, macrolide and lincosamide, trimethoprim and aminoglycoside antimicrobial flock treatments and ARG clusters conferring resistance to the same class. Similar associations were found with purchased products. In gene-level analysis for β-lactams and macrolides, lincosamides and streptogramins, a significant positive association was found with the most abundant gene clusters blaTEM and erm(B). Little evidence was found for associations with biosecurity.

CONCLUSIONS: The faecal microbiome in European broilers contains a high diversity of ARGs, even in the absence of current antimicrobial selection pressure. Despite this, the relative abundance of genes and the composition of the resistome is positively related to AMU in European broiler farms for several antimicrobial classes.

RevDate: 2019-06-14

Karabudak S, Ari O, Durmaz B, et al (2019)

Analysis of the effect of smoking on the buccal microbiome using next-generation sequencing technology.

Journal of medical microbiology [Epub ahead of print].

PURPOSE: This study aimed to investigate the effect of smoking on the buccal microbiome and to analyse the descriptive ability of each of the seven hypervariable regions in their 16S rRNA genes.

METHODOLOGY: Microbiome compositions of 40 buccal swab samples collected from smokers (n =20) and non-smokers (n =20) were determined using 16S rRNA sequencing. Seven different 16S rRNA hypervariable regions (V2, V3, V4, V6-7, V8 and V9) in each sample were amplified using the Ion Torrent 16S Metagenomics kit and were sequenced on the Ion S5 instrument.

RESULTS: Seven hypervariable regions in the 16S rRNA gene were successfully sequenced for all samples tested. The data obtained with the V2 region was found to be informative but the consensus data generated according to a number of operational taxonomic unit reads gathered from all seven hypervariable regions gave the most accurate result. At the phylum level, no statistically significant difference was found between smokers and non-smokers whereas relative abundances of Veillonella atypica, Streptococcus australis, Prevotella melaninogenica, Prevotella salivae and Rothia mucilaginosa showed significant increases in the smoker group (P-adj=0.05). Alpha diversity results did not show a significant difference between the two groups; however, beta diversity analysis indicated that samples of smoker and non-smoker groups had a tendency to be clustered within themselves.

CONCLUSION: The results of the current study indicate that smoking is a factor influencing buccal microbiome composition. In addition, sequencing of all seven hypervariable regions yielded more accurate results than those with any of the single variable regions.

RevDate: 2019-06-14

Lee S, Kim JY, Yi MH, et al (2019)

Comparative microbiomes of ticks collected from a black rhino and its surrounding environment.

International journal for parasitology. Parasites and wildlife, 9:239-243 pii:S2213-2244(19)30045-8.

'Eliska,' an endangered black rhino (Diceros bicornis), died suddenly in Mkomazi National Park in Tanzania in 2016. Three Amblyomma gemma ticks were collected from Eliska's body, and four ticks were collected from the surrounding field. We conducted 16S rRNA targeted high-throughput sequencing to evaluate the overall composition of bacteria in the ticks' microbiomes and investigate whether the ticks could be the cause of Eliska's death. The ticks collected from Eliska's body and the field were found to differ in their bacterial composition. Bacillus chungangensis and B. pumilus were the most commonly found bacteria in the ticks collected from the field, and B. cereus and Lysinibacillus sphaericus were the most commonly found in the ticks collected from Eliska's body. The abundance was higher in the ticks collected from the field. In contrast, the equity was higher in the ticks collected from Eliska's body. No known pathogenic bacteria that could explain Eliska's sudden death were found in any of the ticks. The differences between the microbiome of ticks collected from Eliska's body and from the field indicate that the microbiome of ticks' changes through the consumption of blood.

RevDate: 2019-06-14

Debédat J, Clément K, J Aron-Wisnewsky (2019)

Gut Microbiota Dysbiosis in Human Obesity: Impact of Bariatric Surgery.

Current obesity reports pii:10.1007/s13679-019-00351-3 [Epub ahead of print].

PURPOSE OF REVIEW: In this review, we summarize what is currently described in terms of gut microbiota (GM) dysbiosis modification post-bariatric surgery (BS) and their link with BS-induced clinical improvement. We also discuss how the major inter-individual variability in terms of GM changes could impact the clinical improvements seen in patients.

RECENT FINDINGS: The persisting increase in severe obesity prevalence has led to the subsequent burst in BS number. Indeed, it is to date the best treatment option to induce major and sustainable weight loss and metabolic improvement in these patients. During obesity, the gut microbiota displays distinctive features such as low microbial gene richness and compositional and functional alterations (termed dysbiosis) which have been associated with low-grade inflammation, increased body weight and fat mass, as well as type-2 diabetes. Interestingly, GM changes post-BS is currently being proposed as one the many mechanism explaining BS beneficial clinical outcomes. BS enables partial rescue of GM dysbiosis observed during obesity. Some of the GM characteristics modified post-BS (composition in terms of bacteria and functions) are linked to BS beneficial outcomes such as weight loss or metabolic improvements. Nevertheless, the changes in GM post-BS display major variability from one patient to the other. As such, further large sample size studies associated with GM transfer studies in animals are still needed to completely decipher the role of GM in the clinical improvements observed post-surgery.

RevDate: 2019-06-14

Chi C, Xue Y, Liu R, et al (2019)

Effects of a formula with a probiotic Bifidobacterium lactis Supplement on the gut microbiota of low birth weight infants.

European journal of nutrition pii:10.1007/s00394-019-02006-4 [Epub ahead of print].

PURPOSE: Low birth weight (LBW) infants have a less diverse gut microbiota, enriched in potential pathogens, which places them at high risk of systemic inflammation diseases. This study aimed to identify the differences in gut bacterial community structure between LBW infants who received probiotics and LBW infants who did not receive probiotics.

METHODS: Forty-one infants were allocated to the non-probiotic group (N group) and 56 infants to the probiotic group (P group), according to whether the formula they received contained a probiotic Bifidobacterium lactis. Gut bacterial composition was identified with sequencing of the 16S rRNA gene in fecal samples collected at 14 days after birth.

RESULTS: There was no significant difference between the alpha diversity of the two groups, while the beta diversity was significantly different (p < 0.05). Our results showed that Bifidobacterium and Lactobacillus (both p < 0.05) were enriched in the P group, while Veillonella, Dolosigranulum and Clostridium sensu stricto 1 (all p < 0.05) were enriched in the N group. Predicted metagenome function analysis revealed enhancement of fatty acids, peroxisome, starch, alanine, tyrosine and peroxisome pathways in the P group, and enhancement of plant pathogen, Salmonella and Helicobacter pylori infection pathways in the N group.

CONCLUSIONS: Probiotic supplement in formula may affect the composition, stability and function of LBW infants' gut microbiota. LBW infants who receive probiotic intervention may benefit from gut microbiota that contains more beneficial bacteria.

RevDate: 2019-06-14

Ma Y, Ma S, Chang L, et al (2019)

Gut microbiota adaptation to high altitude in indigenous animals.

Biochemical and biophysical research communications pii:S0006-291X(19)30961-1 [Epub ahead of print].

Limited is known about role of gut microbiota in the metabolism of high-altitude-living herbivores, and potential co-evolution between gut microbiome and host genome during high altitude adaptation were not fully understood. Here, DNA from faecal samples was used to investigate the gut microbial compositions and diversity in three host species endemic to the high-altitude Tibetan plateau, the Tibetan antelope (Pantholops hodgsonii, T-antelope, 4300 m) and the Tibetan wild ass (Equus kiang, T-ass, 4300 m), and in the Tibetan sheep (Ovis aries, T-sheep) collected from two different altitudes (T-sheep [k], 4300 m and T-sheep [l] 3000 m). Ordinary sheep (O. aries, sheep) from low altitudes (1800 m) were used for comparison. 16S rRNA gene sequencing revealed that the genera Ruminococcus (22.78%), Oscillospira (20.00%), and Clostridium (10.00%) were common taxa in all high-altitude species (T-antelope, T-ass and T-sheep [k]). Ruminococcaceae, Clostridiales, Clostridia, and Firmicutes showed greater enrichment in the T-antelopes' gut microbiota than in the microbiota of lower-altitude sheep (T-sheep [l] and sheep). The T-antelopes' gut microbiota displayed a higher ratio of Firmicutes to Bacteroidetes than lower-altitude sheep (T-sheep [l] and sheep). A functional capacity analysis of the paired-end metagenomics sequences of the gut metagenomes of high-altitude T-antelopes and T-sheep annotated over 80% of the unique genes to metabolism (especially carbohydrate metabolism pathways) and genetic information processing in the Kyoto Encyclopedia of Genes and Genomes database. The gut metagenome of the T-antelope may have co-evolved with the host genomes (e.g. glycolysis and DNA repair). The higher-altitude herbivores tended to have similar gut microbial compositions, with similar functional capacities, suggesting that their gut microbiota could involved in their high-altitude adaptation.

RevDate: 2019-06-14

Smith BJ, Miller RA, Ericsson AC, et al (2019)

Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice.

BMC microbiology, 19(1):130 pii:10.1186/s12866-019-1494-7.

BACKGROUND: Treatment with the α-glucosidase inhibitor acarbose increases median lifespan by approximately 20% in male mice and 5% in females. This longevity extension differs from dietary restriction based on a number of features, including the relatively small effects on weight and the sex-specificity of the lifespan effect. By inhibiting host digestion, acarbose increases the flux of starch to the lower digestive system, resulting in changes to the gut microbiota and their fermentation products. Given the documented health benefits of short-chain fatty acids (SCFAs), the dominant products of starch fermentation by gut bacteria, this secondary effect of acarbose could contribute to increased longevity in mice. To explore this hypothesis, we compared the fecal microbiome of mice treated with acarbose to control mice at three independent study sites.

RESULTS: Microbial communities and the concentrations of SCFAs in the feces of mice treated with acarbose were notably different from those of control mice. At all three study sites, the bloom of a single bacterial taxon was the most obvious response to acarbose treatment. The blooming populations were classified to the largely uncultured Bacteroidales family Muribaculaceae and were the same taxonomic unit at two of the three sites. Propionate concentrations in feces were consistently elevated in treated mice, while the concentrations of acetate and butyrate reflected a dependence on study site. Across all samples, Muribaculaceae abundance was strongly correlated with propionate and community composition was an important predictor of SCFA concentrations. Cox proportional hazards regression showed that the fecal concentrations of acetate, butyrate, and propionate were, together, predictive of mouse longevity even while controlling for sex, site, and acarbose.

CONCLUSION: We observed a correlation between fecal SCFAs and lifespan in mice, suggesting a role of the gut microbiota in the longevity-enhancing properties of acarbose. Treatment modulated the taxonomic composition and fermentation products of the gut microbiome, while the site-dependence of the responses illustrate the challenges facing reproducibility and interpretation in microbiome studies. These results motivate future studies exploring manipulation of the gut microbial community and its fermentation products for increased longevity, testing causal roles of SCFAs in the observed effects of acarbose.

RevDate: 2019-06-13

Askri R, Erable B, Neifar M, et al (2019)

Understanding the cumulative effects of salinity, temperature and inoculation size for the design of optimal halothermotolerant bioanodes from hypersaline sediments.

Bioelectrochemistry (Amsterdam, Netherlands), 129:179-188 pii:S1567-5394(19)30188-4 [Epub ahead of print].

The main objective of this study was to understand the interaction between salinity, temperature and inoculum size and how it could lead to the formation of efficient halothermotolerant bioanodes from the Hypersaline Sediment of Chott El Djerid (HSCE). Sixteen experiments on bioanode formation were designed using a Box-Behnken matrix and response surface methodology to understand synchronous interactions. All bioanode formations were conducted on 6 cm2 carbon felt electrodes polarized at -0.1 V/SCE and fed with lactate (5 g/L) at pH 7.0. Optimum levels for salinity, temperature and inoculum size were predicted by NemrodW software as 165 g/L, 45 °C and 20%, respectively, under which conditions maximum current production of 6.98 ± 0.06 A/m2 was experimentally validated. Metagenomic analysis of selected biofilms indicated a relative abundance of the two phyla Proteobacteria (from 85.96 to 89.47%) and Firmicutes (from 61.90 to 68.27%). At species level, enrichment of Psychrobacter aquaticus, Halanaerobium praevalens, Psychrobacter alimentaris, and Marinobacter hydrocarbonoclasticus on carbon-based electrodes was correlated with high current production, high salinity and high temperature. Members of the halothermophilic bacteria pool from HSCE, individually or in consortia, are candidates for designing halothermotolerant bioanodes applicable in the bioelectrochemical treatment of industrial wastewater at high salinity and temperature.

RevDate: 2019-06-13

Álvarez-Díaz DA, Quintero PA, Peláez-Carvajal D, et al (2019)

Novel pan-serotype control RNA for dengue virus typing through real-time reverse transcription-polymerase chain reaction.

Journal of virological methods pii:S0166-0934(19)30052-7 [Epub ahead of print].

Dengue virus (DENV) is the causative agent of one of the most important febrile illnesses worldwide. Four DENV serotypes are responsible for a broad clinical spectrum of the disease. Positive controls are costly and required for the validation of molecular test results of DENV serotyping. In this study, we describe the in silico design of the qDENV-Control plasmid with the target sequences to oligonucleotides and probes widely used for DENV serotyping, and the subsequent production of qDENV Control RNA by T7-driven run-off in vitro transcription. The qDENV Control RNA was successfully used to validate the positive and negative DENV serotyping results, allowing its incorporation in routine in-house protocols for virologic surveillance. This Control RNA allowed the absolute quantification of viral RNA copies from unknown samples as required in several fundamental studies.

RevDate: 2019-06-13

Johnson AJ, Vangay P, Al-Ghalith GA, et al (2019)

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.

Cell host & microbe, 25(6):789-802.e5.

Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and human gut microbiome composition remain unexplored. Here, we used multivariate methods to integrate 24-h food records and fecal shotgun metagenomes from 34 healthy human subjects collected daily over 17 days. Microbiome composition depended on multiple days of dietary history and was more strongly associated with food choices than with conventional nutrient profiles, and daily microbial responses to diet were highly personalized. Data from two subjects consuming only meal replacement beverages suggest that a monotonous diet does not induce microbiome stability in humans, and instead, overall dietary diversity associates with microbiome stability. Our work provides key methodological insights for future diet-microbiome studies and suggests that food-based interventions seeking to modulate the gut microbiota may need to be tailored to the individual microbiome. Trial Registration: ClinicalTrials.gov: NCT03610477.

RevDate: 2019-06-13

Brown E, Dessai U, McGarry S, et al (2019)

Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States.

Foodborne pathogens and disease [Epub ahead of print].

Whole-genome sequencing (WGS) is increasingly used by food regulatory and public health agencies in the United States to facilitate the detection, investigation, and control of foodborne bacterial outbreaks, and food regulatory and other activities in support of food safety. WGS has added a level of precision to the surveillance leading to faster and more efficient decision making in the preparedness and response to foodborne infections. In this review, we report the history of WGS technology at the Centers for Disease Control & Prevention (CDC), the Food and Drug Administration (FDA), and the United States Department of Agriculture's Food Safety and Inspection Service (USDA/FSIS) as it applies to food safety. The basic principle of the method, the analysis, and interpretation of the data are explained as is its major strengths and limitations. We also describe the benefits and possibilities of the WGS technology to the food industry throughout the farm-to-fork continuum and the prospects of metagenomic sequencing applied directly to the sample specimen with or without pre-enrichment culture.

RevDate: 2019-06-13

Bae S, Lyons C, N Onstad (2019)

A culture-dependent and metagenomic approach of household drinking water from the source to point of use in a developing country.

Water research X, 2:100026 pii:100026.

Rural households in developing countries rely on communal water supplies and household water frequently becomes contaminated following its collection, transportation and during its storage. Using culture-dependent and -independent techniques, we examined the changes in microbial water quality between communal tap water and household water storage in a rural area of Cameroon, Africa. The culturable fecal indicator bacteria (FIB) were used to assess the potential health risks associated with different household water storage conditions (e.g., type of container and open vs. closed container) and interventions (e.g., water storage days, cleaned on the last day of use, and hygiene practices). Only the amount of days the water was stored significantly differed (p-value < 0.05), which showed that potential health risks increased when water was stored for more than 3 days. The higher abundance of molecular FIB in biofilm than household water suggested that omnipresent biofilm in household water could potential health risk. The high-throughput sequencing revealed that the most abundant phylum was Proteobacteria, followed by Actinobacteria and Bacteroidetes in both the water and the biofilm samples. Bacterial genera seen in biofilm bacteria, such as Pseudomonas, Acinetobacter and Comamonas. Acinetobacter, Chryseobacterium, Stenotrophomonas and Corynebacterium, were relatively more abundant in the biofilm than in the water. Potential bacterial pathogens including Acinetobacter baumannii, Citrobacter freundii, Stenotrophomonas maltophilia and Haemophilus influenza, were detected in household water and biofilm. The microbial quality might be affected by water-storage time and households repeatedly using the same water storage containers without proper sanitization, triggering microbial regrowth and biofilm formation on water containers. Higher bacterial diversity and potentially pathogenic bacteria found in the biofilm samples of a household water supply are unhealthy for the house's inhabitants. It is important to develop interventions aimed at preventing the formation of these dangerous biofilms in a communal water supply.

RevDate: 2019-06-13

Wang H, Ling Y, Shan T, et al (2019)

Gut virome of mammals and birds reveals high genetic diversity of the family Microviridae.

Virus evolution, 5(1):vez013 pii:vez013.

Nineteen families of phages infecting bacteria or archaea are currently recognized by the International Committee on Taxonomy of Viruses (ICTV). Of these, only two have single-stranded DNA genomes, namely Inoviridae and Microviridae. The distribution, genetic characteristics, and ecological roles of Microviridae remain largely under explored. Here, using viral metagenomics, we investigate the intestinal virome from human and twenty-four species of animals, as well as freshwater samples, containing abundant sequence reads showing similarity to the Microviridae. Eight hundred and sixty complete or near complete Microviridae-related genomes were generated, showing high levels of co-infections and sequence divergence. Sequence comparison and phylogenetic analysis showed that the Microviridae subfamily Gokushovirinae was highly prevalent and that some strains may qualify as new subfamilies. This study significantly augments our knowledge of the genetic diversity, genome evolution, and distribution in animal species of members of the family Microviridae.

RevDate: 2019-06-13

Cook TB, BF Pfleger (2019)

Leveraging synthetic biology for producing bioactive polyketides and non-ribosomal peptides in bacterial heterologous hosts.

MedChemComm, 10(5):668-681 pii:c9md00055k.

Bacteria have historically been a rich source of natural products (e.g. polyketides and non-ribosomal peptides) that possess medically-relevant activities. Despite extensive discovery programs in both industry and academia, a plethora of biosynthetic pathways remain uncharacterized and the corresponding molecular products untested for potential bioactivities. This knowledge gap comes in part from the fact that many putative natural product producers have not been cultured in conventional laboratory settings in which the corresponding products are produced at detectable levels. Next-generation sequencing technologies are further increasing the knowledge gap by obtaining metagenomic sequence information from complex communities where production of the desired compound cannot be isolated in the laboratory. For these reasons, many groups are turning to synthetic biology to produce putative natural products in heterologous hosts. This strategy depends on the ability to heterologously express putative biosynthetic gene clusters and produce relevant quantities of the corresponding products. Actinobacteria remain the most abundant source of natural products and the most promising heterologous hosts for natural product discovery and production. However, researchers are discovering more natural products from other groups of bacteria, such as myxobacteria and cyanobacteria. Therefore, phylogenetically similar heterologous hosts have become promising candidates for synthesizing these novel molecules. The downside of working with these microbes is the lack of well-characterized genetic tools for optimizing expression of gene clusters and product titers. This review examines heterologous expression of natural product gene clusters in terms of the motivations for this research, the traits desired in an ideal host, tools available to the field, and a survey of recent progress.

RevDate: 2019-06-13

Yao Q, Yu K, Liang J, et al (2019)

The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea).

Frontiers in microbiology, 10:1168.

Sea urchins strongly affect reef ecology, and the bacteria associated with their gut digesta have not been well studied in coral reefs. In the current study, we analyze the bacterial composition of five sea urchin species collected from Luhuitou fringing reef, namely Stomopneustes variolaris, Diadema setosum, Echinothrix calamaris, Diadema savignyi, and Tripneustes gratilla, using high-throughput 16S rRNA gene-based pyrosequencing. Propionigenium, Prolixibacter, and Photobacterium were found to be the dominant bacterial genera in all five species. Interestingly, four sea urchin species, including S. variolaris, D. setosum, E. calamaris, and D. savignyi, displayed a higher mean total abundance of the three bacterial genera (69.72 ± 6.49%) than T. gratilla (43.37 ± 13.47%). Diversity analysis indicated that the gut digesta of sea urchin T. gratilla displayed a higher bacterial α-diversity compared with the other four species. PCoA showed that the four groups representing D. setosum, D. savignyi, E. calamaris, and S. variolaris were overlapping, but distant from the group representing T. gratilla. Predictive metagenomics performed by PICRUSt revealed that the abundances of genes involved in amino acid metabolism and metabolism of terpenoid and polyketide were higher in T. gratilla, while those involved in carbohydrate metabolism were higher in the other four sea urchin species. Therefore, our results indicated that the composition, diversity and predictive metabolic profiles of bacteria associated with the gut digesta of T. gratilla were significantly different from those of the other four sea urchin species in Luhuitou fringing reef.

RevDate: 2019-06-13

Poeker SA, Lacroix C, de Wouters T, et al (2019)

Stepwise Development of an in vitro Continuous Fermentation Model for the Murine Caecal Microbiota.

Frontiers in microbiology, 10:1166.

Murine models are valuable tools to study the role of gut microbiota in health or disease. However, murine and human microbiota differ in species composition, so further investigation of the murine gut microbiota is important to gain a better mechanistic understanding. Continuous in vitro fermentation models are powerful tools to investigate microbe-microbe interactions while circumventing animal testing and host confounding factors, but are lacking for murine gut microbiota. We therefore developed a novel continuous fermentation model based on the PolyFermS platform adapted to the murine caecum and inoculated with immobilized caecal microbiota. We followed a stepwise model development approach by adjusting parameters [pH, retention time (RT), growth medium] to reach fermentation metabolite profiles and marker bacterial levels similar to the inoculum. The final model had a stable and inoculum-alike fermentation profile during continuous operation. A lower pH during startup and continuous operation stimulated bacterial fermentation (115 mM short-chain fatty acids at pH 7 to 159 mM at pH 6.5). Adjustments to nutritive medium, a decreased pH and increased RT helped control the in vitro Enterobacteriaceae levels, which often bloom in fermentation models, to 6.6 log gene copies/mL in final model. In parallel, the Lactobacillus, Lachnospiraceae, and Ruminococcaceae levels were better maintained in vitro with concentrations of 8.5 log gene copies/mL, 8.8 log gene copies/mL and 7.5 log gene copies/mL, respectively, in the final model. An independent repetition with final model parameters showed reproducible results in maintaining the inoculum fermentation metabolite profile and its marker bacterial levels. Microbiota community analysis of the final model showed a decreased bacterial diversity and compositional differences compared to caecal inoculum microbiota. Most of the caecal bacterial families were represented in vitro, but taxa of the Muribaculaceae family were not maintained. Functional metagenomics prediction showed conserved metabolic and functional KEGG pathways between in vitro and caecal inoculum microbiota. To conclude, we showed that a rational and stepwise approach allowed us to model in vitro the murine caecal microbiota and functions. Our model is a first step to develop murine microbiota model systems and offers the potential to study microbiota functionality and structure ex vivo.

RevDate: 2019-06-13

Imperato V, Kowalkowski L, Portillo-Estrada M, et al (2019)

Characterisation of the Carpinus betulus L. Phyllomicrobiome in Urban and Forest Areas.

Frontiers in microbiology, 10:1110.

Urban green areas are highly valued by citizens for their contribution to the quality of life in cities. Plants play an important role in mitigating airborne pollutants and are assisted in this role by the metabolic capacities of the millions of microbial cells that colonize leaf surfaces (phyllosphere). Many factors influence phyllosphere microbial community composition and function, but to what extent does airborne pollution in cities impact the composition of microbial communities and their functional degradation genes? Here we describe the characterization of the phyllospheric bacterial communities of Carpinus betulus L. trees (hornbeam) across three locations: the city center of Warsaw (Poland), a forest in a UNESCO World Heritage Site (Białowieża), and a forest in one of the world's oldest operational oil fields (Bóbrka). C. betulus contained higher particulate matter (PM) concentrations, with higher concentrations of palladium and radon in the PM, on leaves in Warsaw than in the forests. Volatile organic compound (VOC) analyses of sampled air revealed higher concentrations of butanone methyl propanal, butylbenzene, and cyclohexane in Bóbrka than Warsaw and Białowieża, while in Warsaw, xylene and toluene were higher. Shotgun microbiome sequencing uncovered a dominance of Gammaproteobacteria (71%), mainly Pseudomonas spp., Actinobacteria, Alpha- and Betaproteobacteria, and Firmicutes. Community composition and function differed significantly between the forests and Warsaw city center. Statistically more hydrocarbon degradation genes were found in Białowieża compared to Warsaw and Bóbrka, and in vitro tests of diesel degradation and plant growth promotion traits of culturable representatives revealed that Białowieża held the highest number of bacteria with plant beneficial properties and degradation genes. This study provides the first detailed insights into the microbiome of C. betulus and sets the stage for developing to a more integrated understanding of phyllosphere microbiota in cities, and their relationships with human health.

RevDate: 2019-06-13

Waldvogel-Abramowski S, Taleb S, Alessandrini M, et al (2019)

Viral Metagenomics of Blood Donors and Blood-Derived Products Using Next-Generation Sequencing.

Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie, 46(2):87-93.

Transfusion-transmitted infections remain a permanent threat in medicine. It keeps the burden of the past, marked by serious infections transmitted by transfusion, and is constantly threatened by emerging viruses. The global rise of immunosuppression among patients undergoing frequent transfusions exacerbates this problem. Over the past decade, criteria for donor selection have become increasingly more stringent. Although routine nucleic acid testing (NAT) for virus-specific detection has become more sensitive, these safety measures are only valuable for a limited number of select viruses. The scientific approach to this is however changing, with the goal of trying to identify infectious agents in donor units as early as possible to mitigate the risk of a clinically relevant infection. To this end, and in addition to an epidemiological surveillance of the general population, researchers are adopting new methods to discover emerging infectious agents, while simultaneously screening for an extended number of viruses in donors. Next-generation sequencing (NGS) offers the opportunity to explore the entire viral landscape in blood donors, the so-called metagenomics, to investigate severe transfusion reactions of unknown etiology. In the not too distant future, one could imagine this platform being used for routine testing of donated blood products.

RevDate: 2019-06-13

Altan E, Dib JC, Gulloso AR, et al (2019)

Effect of geographic isolation on the nasal virome of indigenous children.

Journal of virology pii:JVI.00681-19 [Epub ahead of print].

The influence of living in small remote villages on the diversity of viruses in the nasal mucosa was investigated in three Colombian villages with widely different levels of geographic isolation. Metagenomics was used to characterize viral nucleic acids in nasal swabs from 63 apparently healthy young children. Sequences from human virus members of the families Anelloviridae, Papillomaviridae, Picornaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, and Paramyxoviridae were detected in a decreasing fraction of children. The number of papillomavirus infections detected was greater among Hispanic-speaking children most exposed to outside contacts while anellovirus infections were more common in the isolated indigenous villages. The diversity of the other human viruses detected did not differ between villages. Closely related variants of rhinoviruses A or B were identified in 2 to 4 children from each village reflecting ongoing transmission clusters. Genomes of viruses not currently known to infect humans, including in the family Parvoviridae, Partitiviridae, Dicistroviridae, and Iflaviridae and circular Rep expressing ssDNA genomes (CRESS-DNA) were also detected in nasal swabs possibly reflecting environmental contamination from insect, fungal, or unknown sources. Despite the high level of geographic and cultural isolation, the overall diversity of human viruses in the nasal passages of children was not reduced in highly isolated indigenous villages indicating ongoing exposure to globally circulating viruses.ImportanceExtreme geographic and cultural isolation can still be found in some indigenous South American villages. Such isolation may be expected to limit the introduction of otherwise common and widely distributed viruses. Very small population size may also result in rapid local viral extinction due to lack of sero-negative subjects to maintain transmission chains of rapidly cleared viruses. We compared the viruses in the nasal passage of young children in three villages with increasing level of geographic isolation. We find that isolation did not reduce the overall diversity of viral infections. Multiple infections with nearly identical rhinoviruses could be detected within each villages likely reflecting recent viral introductions and transmission clusters amongst epidemiologically linked members of these very small communities. We conclude that despite their geographic isolation remote indigenous villages show evidence of ongoing exposures to globally circulating viruses.

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RJR Experience and Expertise

Researcher

Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.

Educator

Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.

Administrator

Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.

Technologist

Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.

Publisher

While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.

Speaker

Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.

Facilitator

Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.

Designer

Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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